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EUR 23132 EU-funded collaborative research projects

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FUNDAMENTAL GENOMICS RESEARCH

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A-23132-E

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The sequencing of the human genome and many other genomes heralded a new age in human biology, offering unprecedented opportunities to improve human health and to stimulate industrial and economic activity. The global understanding of the complete function of approximately 22 000 human genes constitutes a major challenge for understanding normal and pathological situations. To tackle this challenge, the European Commission made fundamental genomics research a priority in the Sixth Framework Programme for RTD (FP6) (2002-2006).

The European Commission has allocated approximately 594 million in FP6 to fundamental genomics research activities with the overall aim of fostering the basic understanding of genomic information by developing the knowledge base, tools and resources needed to decipher the function of genes and gene products relevant to human health, and to explore their interactions with each other and with their environment.

The present publication provides a brief description of the goals, expected results, achievements and expected impact of all the projects supported during FP6 in the fundamental genomics priority area in the following scientific sub-areas: the development of tools and technologies for functional genomics; regulation of gene expression; structural genomics and proteomics; comparative genomics and model organisms; population genetics and biobanks; bioinformatics; multidisciplinary fundamental genomics research for understanding basic biological processes in health and disease; and the emerging area of systems biology.

During FP6, the European Commission has supported several systems biology initiatives which paved the way for further developing the genomics and systems biology programme in the Seventh Framework Programme for RTD (FP7) (2007-2013). The introduction provides an overview of the FP6 research policies and the steps taken to strengthen the European Research Area in each of the scientific sub-areas, as well as the FP7 vision in genomics and systems biology collaborative research.

EUROPEAN COMMISSION

Directorate-General for Research Directorate F- Health Unit F.4- Genomics and Systems Biology

Contact: Christina Kyriakopoulou Office CDMA -1/19 B-1049 Brussels Tel. (32-2) 29-59890 Fax.(32-2) 29-60588 E-mail: [email protected]

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mailto:[email protected]

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Directorate-General for Research Life Sciences, Genomics and Biotechnology for Health

EU-funded collaborative research projects

EUROPEAN COMMISSION

EUR 23132 2008

From Fundamental Genomicsto Systems Biology:

UNDERSTANDING THE BOOK OF LIFE

Synopses of EU collaborative research projects funded in FundamentalGenomics under the Sixth Framework Programme for the Thematic Priority

«Life Sciences, genomics and biotechnology for health» FP6 and FP7 research policies in Fundamental Genomics and Systems Biology

edited by Christina Kyriakopoulou


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ISBN 978-92-79-08004-3DOI 10.2777/49314

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Acknowledgements

This publication could have only been accomplished thanks to the essential contribution of the project coordinators and the input of my colleagues in the Health Directorate. Thanks to my colleagues, scientific officers, in the Genomics and Systems Biology unit: Christian Desaintes, Tomasz Dylag, Iiro Eerola, Sasa Jenko, Fred Marcus, Sandra Pinto Marques and Ioana Siska. Thanks to the former colleagues of the fundamental genomics area Henriette Van Eijl, Indridi Benediktsson, Bill Baig and Elena Bordini. My special thanks to Mrs Josefina Enfedaque, scientific officer on health communication activities for her valuable input. Finally, my special gratitude to Patrik Kolar, Bernard Mulligan and Jacques Remacle for their continuous support and valuable guidance.

Christina Kyriakopoulou


http://europa.eu

5

Contact details for the Genomics and Systems Biology unit

European CommissionDirectorate-General for ResearchDirectorate F- HealthUnit F4- Genomics and Systems Biology

Dr Patrik Kolar, Head of Unit ([email protected])Dr Bernard Mulligan, Deputy Head of Unit ([email protected])Dr Jacques Remacle, Scientific officer ([email protected])Dr Christian Desaintes, Scientific officer ([email protected])Dr Tomasz Dylag, Scientific officer ([email protected])Dr Iiro Eerola, Scientific officer ([email protected])Dr Sasa Jenko, Scientific officer ([email protected])Dr Christina Kyriakopoulou, Scientific officer ([email protected])Dr Beatrice Lucaroni, Scientific officer ([email protected])Dr Fred Marcus ([email protected])Dr Sandra Pinto Marques ([email protected])Dr Ioana Siska ([email protected])

Further information:

http://cordis.europa.eu/fp7/health/home_en.htmlhttp://cordis.europa.eu/lifescihealth/genomics/home.htm














http://cordis.europa.eu/fp7/health/home_en.html

http://cordis.europa.eu/lifescihealth/genomics/home.htm


From Fundamental Genomics to Systems Biology: Understanding the Book of Life 7

Foreword Abbreviations Part A Overview of FP6 and FP7 research policies in Fundamental Genomics and Systems Biology Section 1 The importance of Fundamental Genomics research in the European Union’s Framework Programmes for RTD Section 2 Fundamental Genomics programme in FP6: sub-areas and their objectives Section 3 Scientifi c Excellence and impact of European Fundamental Genomics Collaborative Research Section 4 The way forward in FP7: From Fundamental Genomics to Systems Biology Section 5 Content of the present publication Section 6 EC’s fi nancial contribution in Fundamental Genomics & Systems Biology Collaborative Research Section 7 Scientifi c sub-areas supported in the FP6 and FP7 in Fundamental Genomics and Systems Biology

7.1 Tools and technologies for functional genomics 7.1.1 Tools and technologies for gene expression 7.1.2 Tools and technologies for proteomics 7.1.3 Tools and technologies for molecular imaging 7.1.4 Tools and technologies for gene integration and recombination 7.2 Regulation of gene expression 7.2.1 Transcriptional regulation 7.2.2 Epigenetic regulation 7.3 Structural Genomics and Structural Proteomics 7.4 Comparative Genomics and Model organisms 7.4.1 Mouse 7.4.2 Rat 7.4.3 Zebrafi sh 7.4.4 Other models 7.5 Population Genetics and Biobanks 7.6 Bioinformatics 7.7 Multidisciplinary functional genomics approaches to basic biological processes 7.7.1 Biological pathways and intracellular and extracellular signalling 7.7.2 Tissue and organ development, homeostasis and disease 7.7.3 Stem cell biology 7.7.4 RNA biology 7.7.5 Chronobiology 7.7.6 Biology of prokaryotes and other organisms 7.8 Systems Biology

Annexes Basic facts and fi gures for Fundamental Genomics activity area Annex I Funding instruments-schemes in FP6 and FP7 Annex II Development of the specifi c scientifi c topics for calls for proposals in the FP6 Fundamental Genomics programme Annex III European Commission’s strategic workshops in different scientifi c areas of fundamental genomics and systems biology Annex IV Evaluation process in the FP6 and FP7 Fundamental Genomics programme Annex V Evaluation criteria in FP6 and FP7 Annex VI Basic facts and fi gures for Fundamental Genomics activity area in FP6

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From Fundamental Genomics to Systems Biology: Understanding the Book of Life

TABLE OF CONTENTS


8 From Fundamental Genomics to Systems Biology: Understanding the Book of Life From Fundamental Genomics to Systems Biology: Understanding the Book of Life

1. Tools and technologies for functional genomics

1.1 Tools and technologies for gene expression

MolTools 86 Advanced Molecular Tools for Array-Based Analyses of Genomes, Transcriptomes, Proteomes and Cells

REGULATORY GENOMICS 90 Advanced Genomics Instruments, Technology and Methods for Determination of Transcription Factor Binding Specifi cities: Applications for Identifi cation of Genes Predisposing to Colorectal Cancer

Tat machine 92 Functional genomic characterisation of the bacterial Tat complex as a nanomachine for biopharmaceutical production and a target for novel anti-infectives

TransCode 94 Novel Tool for High-Throughput Characterisation of Genomic Elements Regulating Gene Expression in Chordates

EMERALD 96 Empowering the Microarray-Based European Research Area to Take a Lead in Development and Exploitation

Autoscreen 98 Autoscreen for Cell Based High-throughput and High-content Gene Function Analysis and Drug Discovery Screens

TargetHerpes 100 Molecular intervention strategies targeting latent and lytic herpesvirus infections

FGENTCARD 102 Functional GENomic diagnostic Tools for Coronary Artery Disease

MODEST 104 Modular Devices for Ultrahigh-throughput and Small-volume Transfection

1.2 Tools and technologies for proteomics

INTERACTION PROTEOME 108 Functional Proteomics: Towards defi ning the interaction proteome

NEUPROCF 112 Development of New Methodologies for Low Abundance Proteomics: Application to Cystic Fibrosis

CAMP 114 Chemical Genomics by Activity Monitoring of Proteases

ProDac 116 Proteomics Data Collection

MOLECULAR IMAGING 120 Integrated Technologies for In vivo Molecular Imaging

Tips4Cells 124 Scanning Probe Microscopy techniques for real time, high resolution imaging and molecular recognition in functional and structural genomics

COMPUTIS 126 Molecular Imaging in Tissue and Cells by Computer- Assisted Innovative Multimode Mass Spectrometry

1.3 Tools and technologies for molecular imaging

1.4 Tools and technologies for gene integration and recombination

GENINTEG 130 Controlled gene integration: a requisite for genome analysis and gene therapy

PLASTOMICS 132 Mechanisms of transgene integration and expression in crop plant plastids, underpinning a technology for improving human health

TAGIP 134 Targeted Gene Integration in Plants: Vectors, Mechanisms and Applications for Protein Production

MEGATOOLS 136 New tools for Functional Genomics based on homologous recombination induced by double-strand break and specifi c meganucleases

Part B Synopses of projects funded in Fundamental Genomics in FP6


From Fundamental Genomics to Systems Biology: Understanding the Book of Life 9 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

2. Regulation of gene expression

2.1 Transcription regulation

2.2 Epigenetic regulation

TRANS-REG 142 Transcription Complex Dynamics Controlling Specifi c Gene Expression Programmes

X-TRA-NET 144 ChIP-Chip to Decipher Transcription Networks of RXR and Partners

THE EPIGENOME 148 Epigenetic plasticity of the genome

HEROIC 152 High-Throughput Epigenetic Regulatory Organisation in Chromatin

ChILL 156 Chromatin Immuno-linked ligation: A novel generation of biotechnological tools for research and diagnosis

SMARTER 158 Development of small modulators of gene activation and repression by targeting epigenetic regulators

3DGENOME 164 3D Genome Structure and Function

BIOXHIT 166 Bio-Crystallography on a Highly Integrated Technology Platform for European Structural Genomics

3D-EM 170 New Electron Microscopy Approaches for Studying Protein Complexes and Cellular Supramolecular Architecture

GeneFun 174 Prediction of gene function

E-MeP 176 The European Membrane Protein Consortium

FSG-V-RNA 180 Functional and Structural Genomics of Viral RNA

VIZIER 182 Comparative structural genomics on viral enzymes involved in replication

UPMAN 186 Understanding Protein Misfolding and Aggregation by NMR

NDDP 188 NMR Tools for Drug Design Validated on Phosphatases

3D repertoire 190 A Multidisciplinary Approach to Determine the Structures of Protein Complexes in a Model Organism

FESP 194 Forum for European Structural Proteomics

E-MeP-Lab 196 E-MeP-Lab Training events in membrane protein structural biology

HT3DEM 198 High throughput Three-dimensional Electron Microscopy

NMR-Life 200 Focusing NMR on the Machinery of Life

Extend-NMR 202 Extending NMR for Functional and Structural Genomics

IMPS 204 Innovative tools for membrane structural proteomics

SPINE2-COMPLEXES 206 From Receptor to Gene: Structures of Complexes from Signalling Pathways linking Immunology, Neurobiology and Cancer

OptiCryst 210 Optimisation of Protein Crystallisation for European Structural Genomics

TEACH-SG 212 Training and Education in High Volume and High Value Structural Genomics

3. Structural Genomics and Proteomics


10 From Fundamental Genomics to Systems Biology: Understanding the Book of Life From Fundamental Genomics to Systems Biology: Understanding the Book of Life

4. Comparative Genomics and Model organisms

4.1 Mouse

4.2 Rat

4.3 Zebrafi sh

4.4 Other models

5.Population Genetics and Biobanks

EURExpress 218 A European Consortium to Generate a Web-Based Gene Expression Atlas by RNA in situ Hybridisation

MUGEN 222 Integrated Functional Genomics in Mutant Mouse Models as Tools to Investigate the Complexity of Human Immunological Disease

PRIME 226 Priorities for mouse functional genomics research across Europe: integrating and strengthening research in Europe

FLPFLEX 228 A Flexible Toolkit for Controlling Gene Expression in the Mouse

EUCOMM 230 The European Conditional Mouse Mutagenesis Programme

EUMODIC 234 The European Mouse Disease Clinic: A distributed phenotyping resource for studying human disease

CASIMIR 238 Co-ordination And Sustainability of International Mouse Informatics Resources

STAR 242 A SNP and Haplotype Map for the Rat

EURATools 244 European Rat Tools for Functional Genomics

Med-Rat 248 New Tools to Generate Transgenic and Knock-out Mouse and Rat Models

ZF-MODELS 252 Zebrafi sh Models for Human Development and Disease

ZF-TOOLS 256 High-throughput Tools for Biomedical Screens in Zebrafi sh

NemaGENETAG 260 Nematode Gene-Tagging Tools and Resources

TP Plants and Health 262 The European Technology Platform on Plant Genomics and Biotechnology: Plants for healthy lifestyles and for sustainable development

X-OMICS 264 Xenopus Comparative Genomics: Coordinating Integrated and Comparative Functional Genomics for Understanding Normal and Pathologic Development

HUMGERI 270 Human Genomic Research Integration

MolPAGE 272 Molecular Phenotyping to Accelerate Genomic Epidemiology

GenOSept 276 Genetics of Sepsis in Europe

MICROSAT workshop 278 Microsatellites and VNTRs: workshop on bioinformatics, genomics and functionality

EUHEALTHGEN 280 Harnessing the Potential of Human Population Genetics Research to Improve the Quality of the EU Citizen

PHOEBE 282 Promoting harmonisation of epidemiological biobanks in Europe



6. Bioinformatics

7.Functional Genomics approaches for Basic biological processes

7.1 Biological pathways and signalling

EUROSPAN 284 EUROpean Special Populations Research Network: Quantifying and Harnessing Genetic Variation for Gene Discovery

DanuBiobank 286 The Danubian Biobank Initiative — Towards Information-based Medicine

Impacts 288 Archive tissues: improving molecular medicine research and clinical practice

EpiGenChlamydia 290 Contribution of molecular epidemiology and host- pathogen genomics to understand Chlamydia trachomatis disease

BioSapiens 296 A European Network for Integrated Genome Annotation

ATD 300 The Alternate Transcript Diversity Project

EMBRACE 302 A European Model for Bioinformatics Research and Community Education

ENFIN 306 An Experimental Network for Functional Integration

EUROFUNGBASE 310 Strategy to build up and maintain an integrated sustainable European fungal genomic database required for innovative genomics research on , important for biotechnology and human health

MAIN 316 Targeting Cell Migration in Chronic Infl ammation

WOUND 320 A multi-organism functional genomics approach to study signalling pathways in epithelial fusion/wound healing

MitoCheck 322 Regulation of Mitosis by Phosphorylation-

A Combined Functional Genomics, Proteomics and Chemical Biology Approach

SIGNALLING & TRAFFIC 326 Signalling and Membrane Traffi cking in Transformation and Differentiation

TransDeath 328 Programmed cell death across the eukaryotic kingdom

Peroxisomes 330 Integrated Project to decipher the biological function of peroxisomes in health and disease

DNA Repair 334 DNA Damage Response and Repair Mechanisms

STEROLTALK 338 Functional Genomics of Complex Regulatory Networks from Yeast to Human: Cross-Talk of Sterol Homeostasis and Drug Metabolism

RUBICON 342 Role of Ubiquitin and Ubiquitin-like Modifi ers in Cellular Regulation

EndoTrack 346 Tracking the Endocytic Routes of Growth Factor Receptor Complexes and their Modulatory Role on Signalling

AnEUploidy 350 AnEUploidy: understanding gene dosage imbalance in human health using genetics, functional genomics and systems biology


12 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

7.2 Tissue and organ development and homeostasis

7.3 Stem cells

7.4 RNA biology

7.5 Chronobiology

7.6 Biology of prokaryotes and other organisms

BACELL HEALTH 426 Bacterial stress management relevant to infectious disease and biopharmaceuticals

DIATOMICS 428 Understanding Diatom Biology by Functional Genomics Approaches

NFG 356 Functional Genomics of the Adult and Developing Brain

LYMPHANGIOGENOMICS 358 Genome-Wide Discovery and Functional Analysis of Novel Genes in Lymphangiogenesis

EuroHear 362 Advances in hearing science: from functional genomics to therapies

MYORES 366 Multiorganismic Approach to Study Normal and Aberrant Muscle Development, Function and Repair

EuReGene 370 European Renal Genome Project

EVI-GENORET 374 Functional genomics of the retina in health and disease

FunGenES 380 Functional Genomics in Engineered ES cells

Plurigenes 384 Pluripotency Associated Genes to Dedifferentiate Neural Cells into Pluripotent Cells

ESTOOLS 386 Platforms for biomedical discovery with human ES cells

EuTRACC 390 European Transcriptome, Regulome & Cellular Commitment Consortium

RIBOREG 396 Novel non-coding RNAs in differentiation and disease

FOSRAK 398 Function of small RNAs across kingdoms

Callimir 400 Studying the biological role of microRNAs in the Dlk1-Gtl2 imprinted domain

Eurasnet 402 European Alternative Splicing Network of Excellence

BACRNAs 408 Non-coding RNAs in Bacterial Pathogenicity

RNABIO 410 Computational approaches to non-coding RNAs

Sirocco 412 Silencing RNAs: organisers and coordinators of complexity in eukaryotic organisms

EUCLOCK 418 Entrainment of the Circadian Clock

TEMPO 422 Temporal Genomics for Tailored Chronotherapeutics




8. Systems Biology

Part C Indexes

EUSYSBIO 434 The Take-off of European Systems Biology

SYMBIONIC 436 Towards European Neuronal Cell Simulation: a European consortium to integrate the scientifi c activities for the creation of a European Alliance devoted to the complete in-silico model of Neuronal Cell

EMI-CD 438 European Modelling Initiative combating complex diseases

QUASI 440 Quantifying signal transduction

COMBIO 442 An integrative approach to cellular signalling and control processes: Bringing computational biology to the bench

COSBICS 444 Computational Systems Biology of Cell Signalling

DIAMONDS 446 Dedicated Integration and Modelling of Novel Data and Prior Knowledge to Enable Systems Biology

EU-US Workshop 448 Workshop on “Systems biology of DNA-damage- induced stress responses”

ELIfe 450 The European Lipidomics Initiative: Shaping the life sciences

ESBIC-D 452 European Systems Biology Initiative for Combating Complex Diseases

YSBN 454 Yeast Systems Biology Network

AMPKIN 456 Systems biology of the AMP-activated protein kinase pathway

RIBOSYS 458 Systems Biology of RNA Metabolism in Yeast

EuroBioFund 460 A Strategic Forum for the Dialogue and Coordination of European Life Sciences, Funders and Performers

VALAPODYN 462 Validated Predictive Dynamic Model of Complex Intracellular Pathways related to cell death and survival

AGRON-OMICS 464 Arabidopsis growth network integrating OMICS technologies

BaSysBio 468 Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach

BioBridge 472 Integrative Genomics and Chronic Disease Phenotypes: modelling and simulation tools for clinicians

SYSBIOMED 474 Systems Biology for Medical Applications

SysProt 476 System-wide analysis and modelling of protein modifi cation

Streptomics 478 Systems biology strategies and metabolome engineering for the enhanced production of recombinant proteins in Streptomyces

SYSCO 482 Systematic Functional analysis of Intracellular Parasitism as a model of genomes confl ict

Proust 484 The temporal dimension in functional genomics

PROJECTS ACRONYM INDEX 488

INSTITUTION AND COORDINATOR INDEX 493

KEYWORDS INDEX 498


14

The last decade has witnessed unprecedented advances in the life sciences. The sequenc-ing of the human (2001) and other genomes has revolutionised biology, with genome sequences becoming the ‘periodic table’ of biology. The global understanding of the com-plete function of approximately 22 000 human genes constitutes a major challenge for understanding normal and pathological situations. Therefore, to tackle this challenge, the European Commission made fundamental genomics research into health and disease one of the main action lines in the Life Sciences thematic priority under the Sixth Framework Programme for RTD (FP6) (2002-2006).

The European Commission identified the importance of genomics quite early, and has played a cohesive role in addressing the fragmentation of the genomics and post-genomics research community in Europe by funding collaborative research projects via the EU Framework Pro-grammes for RTD. The rationale for structuring and integrating fundamental genomics research at European level to tackle fragmentation and research capacity gaps is based on its immense potential contribution to the understanding of the processes underlying human disease, and hence offering unprecedented opportunities to improve human health and stimulate industrial and economic activity. This research requires a collaborative approach, is by nature highly multidisciplinary, and needs expertise and critical mass that do not exist in a single laboratory. Integrated multidisciplinary research and a strong interaction between high-throughput tech-nology development and biology are vital in the fundamental genomics field for translating genome data into practical applications.

The European Commission has allocated some 594 million over four years in FP6 for fun-damental genomics research activities with the overall aim to foster the basic understanding of genomic information by developing the knowledge base, tools and resources needed to decipher the function of genes and gene products relevant to human health, and to explore their interactions with each other and with their environment. The present publication provides a brief description of the goals, expected results, achievements and expected impact of all the projects supported during FP6 in the Fundamental Genomics priority area in the following sub-areas: tools and technologies development for functional genomics; regulation of gene expression; structural genomics and proteomics; comparative genomics and models organ-isms; population genetics and biobanks; bioinformatics; and multidisciplinary fundamental genomics research for understanding basic biological processes in health and disease and the emerging area of systems biology. During FP6, the European Commission supported sev-eral systems biology initiatives which paved the way for further developing the genomics and systems biology programme in the Seventh Framework Programme for RTD (FP7) (2007-2013). The introduction provides an overview on FP6 research policies and the steps taken to strengthen the European Research Area in each of the scientific sub-areas, as well as the FP7 concept in genomics and systems biology collaborative research.

The European Commission via its Life Sciences and Health programme has been acting as a catalyst for strengthening European excellence in genomics and systems biology research. The path to scientific discovery and innovation is long and complex and we have realised that further investment will continue to be necessary for this important area. We are proud of the European scientists who collaborate in top-class research projects and we are certain that these projects will lead to substantial advances in the understanding of the links between the human genome and diseases, strengthen Europe’s position in this important field of research, and eventually benefit society.

Manuel HallenActing Director

Health Research

Foreword



15From Fundamental Genomics to Systems Biology: Understanding the Book of Life

AG (Advisory Group) CA (Coordination Action) CP (Collaborative Project) CP-FP (Small-Medium Scale Focused Research Collaborative Project) CP-IP (Large Scale Integrating Collaborative Project) EC (European Commission) ERA (European Research Area) EU (European Union) FG (functional genomics) FP (EU’s Framework Programme) FP5 (Fifth Framework Programme for RTD) FP6 (Sixth Framework Programme for RTD) FP7 (Seventh Framework Programme for RTD) GDP (gross domestic product) HTP (high-throughput) INCO target countries (International Cooperation target countries) IP (Integrated Project) NoE (Network of Excellence) RNA (ribonucleic acid) RTD (Research and Technological Development) SB (systems biology) SG (structural genomics) SME (small- to medium-sized enterprise) SME-STREP (SME-Specific Targeted Research Project) SP (structural proteomics) SSA (Specific Support Action) STREP (Specific Targeted Research Project)

Abbreviations



Part A: Overview of FP6 and FP7 research policiesin Fundamental Genomics and Systems Biology

Section 1 The importance of fundamental genomics research in the European Union’s framework programmes for RTD

Over the last 23 years, the European Union (EU), via the implementation of subsequent EU Framework Pro-grammes (FPs) for supporting Research and Technological Development (RTD) activities in the European Union, has funded European collaborative and multidisciplinary research projects. This multi-laboratory, multinational collaboration represents the ‘reason of existence’ of the FPs for RTD, often essential for assembling critical mass, tackling fragmentation and strengthening European excellence in important research areas. The expected impact lies in enabling breakthroughs in important research areas in order to boost European biomedical and biotech industry competitiveness, and ultimately to improve citizens’ quality of life.

A signifi cant part of different FPs’ budgets is dedicated to supporting collaborative research in life sciences and biomedical research. The overall budget of the Sixth Framework Programme for RTD (FP6) was 17.5 billion, of which an important proportion of 2.5 billion was allocated to the thematic priority of ‘Life Sciences, Genom-ics and Biotechnology for Health’ in the period 2002 - 2006. The overall budget of the Seventh Framework Programme for RTD (FP7) is 50.5 billion; it will run for seven years, with approximately 6 billion dedicated to health-related collaborative research support.

The European Research Area (ERA) was launched in 2000 by the EU as a key concept in implementing the Lisbon strategy to make the EU “the most dynamic and competitive knowledge-based economy” by 2010; this was later followed by the goal to increase spending on R&D in the EU up to 3% of the gross domestic product (GDP), where two thirds would originate from private investments. FP6 set the implementation of the ERA as its major objective and addressed the fragmentation of EU research more intensively.

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of the EU Framework Programmes for RTD (FP1–FP7, 1984–2013)



The ERA concept encompasses three interrelated aspects:

■ a European ‘internal market’ for research, where researchers, technology and knowledge can circulate freely;

■ effective European-level coordination of national and regional research activities, programmes and policies; ■ initiatives implemented and funded at European level.

The FP is the main fi nancial instrument to implement the ERA at EU level, but it is clear that many other EU initia-tives and particularly initiatives at national and regional level will have to be undertaken.

The European Commission (EC) identifi ed the importance of genomics quite early, and has played a cohesive role in addressing the fragmentation of the genomics and post-genomics research community in Europe by fund-ing collaborative research projects via the EU FPs for RTD. The rationale for structuring and integrating funda-mental genomics research at European level to tackle fragmentation and research capacity gaps is based on its immense potential contribution to the understanding of the processes underlying human disease, and hence offering unprecedented opportunities to improve human health and stimulate industrial and economic activity. This research is by nature highly multidisciplinary, requires a collaborative approach, and needs expertise and critical mass not available in any single laboratory. Integrated multidisciplinary research and strong interaction between high-throughput (HTP) technology development and biology is vital in the fundamental genomics fi eld for translating genome data into practical applications.

A New European Research Strategy

European Research Area (ERA)

European Research Area

A joint effort by the EU and MS to address structural deficits in European research

European research policy

Fragmentation

Under-resourcing

Unfavourable environment for research and innovation

National programmes

Framework programme

European organisations

Open Coordination

Fig. 2: Graphical representation of the concept of ERA



Between 1990 and 2002 (from the Third Framework Programme (FP3) through the Fifth Framework Programme (FP5)), the EU invested in genomics research. This resulted in several major breakthroughs: the sequencing of the first eukaryotic genome (yeast), the sequencing of the first plant genome (Arabidopsis thaliana), and the assem-bling of the physical and genetic maps of the human genomes — important and necessary tools for the further sequencing of the human genome.

During FP5 (1998–2002), the EC invested 120 million in genome research. In 2002, 39.4 million was pro-vided to three large-scale research projects in genomics research for human health: GenomEUtwin, a major effort in population genetics (see www.genomeutwin.org); EUMORPHIA, a large integrated project (IP) devoted to the development and standardisation of mouse models phenotyping tools (see www.eumorphia.org); and SPINE, a major structural proteomics effort that solved approximately 300 new protein structures (www.spineurope.org). These three projects, the first of such scale in FP5 in the life sciences, played an important role in structuring the research community in the respective areas.

The publication of the first complete sequence of the human genome in 2001, as well as the sequencing of many other genomes, heralded a new age in modern biology and biomedicine, offering unprecedented opportunities to improve human health and to stimulate industrial and economic activity. If science was looking for a milestone to mark the entry into the 21st century, it seems that revealing the sequence of the letters of the ‘book of life’ was the most important one. Researchers in the post-genomics era have doubled their efforts, with the major goal of ‘reading’ the ‘book of life’, and understanding its ‘syntax’ and ‘language’ by putting the ‘words’ (our genes and their functions) in the correct order.

The three billion ‘letters’ that make up our genetic code contain all the information needed to turn a fertilised egg into an adult human being. Thanks to the human genome project, we now know the sequence of letters constitut-ing the approximately 22 000 human genes.

However, the global understanding of the complete function of our genome, including the function of approxi-mately 22 000 human genes and the interactions amongst them and with the environment, still constitutes a major challenge for the understanding of normal and pathological situations.

DNA and protein microarrays and other technologies for HTP molecular profiling have expanded our horizons and have provided a context for the information on the human organism: there are approximately 20 000 to 25 000 protein-encoding genes, more than 100 000 transcript splice variants of those genes and perhaps 106 protein states of possible functional significance.

Why research at European level?

Resources are pooled to achieve critical mass Leverage effect on private investments Interoperability and complementarity of big science

Stimulate training and international mobility of researchers Improve S&T capabilities Stimulate competition in research

Create scientific base for pan-European policy challenges Encourage coordination of national policies Effective comparative research at EU-level Efficient dissemination of research results

Fig. 3: The importance of European collaborative research


http://www.genomeutwin.org

http://www.eumorphia.org

http://www.spineurope.org


Early results in post-genomics research have already challenged established views about the nature of the ge-nome. A surprising result of the human genome sequencing experiments was that only a very small proportion (1.5%) of the entire genome encodes for proteins. It was once thought that a large proportion of our genome was inactive ‘junk DNA’, but today we know that many of these genomic regions have turned out to be regula-tory sequences, which are responsible for activating or silencing genes when necessary.

All the latest technological and knowledge breakthroughs and the accumulation of HTP novel data continue to highlight how little we still know about the effect of genes on the development of healthy and diseased phenotypes.

Therefore, to tackle these challenges, the EC made genomics and post-genomics research a research priority in FP6 (2002–2006). Indeed, of the total 2 500 million allocated to the priority of ‘Life Sciences, Genomics and Biotechnology for Health’, approximately 594 million was invested over four years in the FP6 Fundamental Genomics programme. Investing substantially in this EU Fundamental Genomics programme area was also im-portant in meeting the scientifi c community’s strong expectations, illustrated by the high number of expressions of interest (550) submitted in this area during the 2002 launching of FP6.

Section 2The Fundamental Genomics Programme in FP6: sub-areas and their objectives

Functional genomics is the branch of genomics that determines the biological function of the genes and their products using the development and application of global (genome-wide or systems-wide) experimental ap-proaches (i.e. genomics, transcriptomics, proteomics, in silico functional prediction, etc.).

The EU FP6 Fundamental Genomics Programme identifi ed its strategic objectives: to foster the basic understand-ing of genomic information by developing the knowledge base, tools and resources needed to decipher the function of genes and gene products relevant to human health, and to explore their interactions with each other and with their environment.

Life sciences R&D - chain

sequencesvariationfunctioncellssystems

microarraysNMR, specgenotypingsiRNAmodel organismsimaging

bioinformaticscomparative genomicsstructural genomics

further researchdiagnostics + disease markerstarget validationdrugs / therapiespharmacogenomics

Biology: DNA, RNA, protein Tools/assays Analysis/

interpretation Applications

Fundamental genomics

Fig. 4: Fundamental genomics research in the life sciences and biomedicine landscape



Research in FP6 supported the following scientific sub-areas:

■ Gene expression and proteomics with the aim of enabling researchers to better decipher the functions of genes and gene products, as well as to define the complex regulatory networks (biocomplexity) that control fundamental biological processes. Research focused on developing high throughput tools and approaches for monitoring gene expression and protein profiles and for determining protein functions and protein interactions.

■ Structural genomics with the overall objective to enable researchers to determine, more effectively and at a higher rate than currently feasible, the three-dimensional (3-D) structure of proteins and other macromolecules, important for elucidating protein function and essential for drug design. Research focused on developing HTP approaches for determining high-resolution 3-D structures of macromolecules.

■ Comparative genomics and population genetics with the goal of enabling researchers to use well-characterised model organisms for predicting and testing gene function and to take full advantage of specific population cohorts available in Europe, so as to determine the relationship between gene function and health or disease. Research focused on developing model organisms and transgenic tools, and developing genetic epidemiology tools and standardised genotyping protocols.

■ Bioinformatics with the aim of enabling researchers to access efficient tools for managing and interpreting the ever-increasing quantities of genome data, and for making it available to the research community in an accessible and usable form. Research focused on developing bioinformatics tools and resources for data storage, mining and processing, and on developing computational biology approaches for in silico prediction of gene function and for simulation of complex regulatory networks.

■ Multidisciplinary functional genomics approaches to basic biological processes with the overall objective of enabling researchers to study fundamental biological processes by integrating the above mentioned innovative approaches. Research will focus on elucidation of the mechanisms underlying fundamental cellular processes, to identify the genes involved and to decipher their biological functions in living organisms.

With the rise of the era of systems biology, which signalled a new approach in understanding biological processes, the latter sub-area supported pilot projects applying systems biology approaches for understanding basic biological processes in health and disease.

Although these areas represent different sections of the fundamental genomics programme during FP6, many projects were found to be cross-cutting in nature, using multidisciplinary approaches. For this reason, the authors decided to present the projects funded in fundamental genomics according to common scientific theme, rather than to use the ‘artificial’ sections mentioned above: this is more comprehensible for the reader. The grouping of all the projects funded in FP6 in scientific sub-areas is presented in Section 7, along with an introduction explaining which EC Actions reinforce which areas, the steps taken towards the ERA and a set of representative project examples.

Section 3Scientific excellence and impact of European fundamental genomics collaborative research

The EC identified the importance of genomics quite early, and has played a cohesive role in addressing the frag-mentation of the genomics and post-genomics research community in Europe by funding collaborative research projects via the EU FPs for RTD. The rationale for structuring and integrating fundamental genomics research at the European level to tackle fragmentation and research capacity gaps is based on its immense potential contribution



to the understanding of the processes underlying human disease, and hence offering unprecedented opportunities to improve human health and stimulate industrial and economic activity. This research is by nature highly multidisci-plinary, requires a collaborative approach, and needs expertise and access to methodologies, technologies, data, facilities and critical mass not accessible in any one laboratory, in order to accelerate breakthrough discoveries. Integrated multidisciplinary research and strong interaction between high-throughput (HTP) technology development and biology is vital in the fundamental genomics fi eld, for translating genome data into practical applications.

While it is still premature to predict the success of European projects supported under the Fundamental Genomics programme under FP6, one may conclude that EU is funding top-class, ambitious and state-of-the-art projects, involv-ing excellence in Europe (as exemplifi ed by the seven European Nobel prize winners participating in projects in fundamental genomics):

■ Harmut Michel: Nobel Prize Winner in Chemistry 1988 (project E-MEP)

■ Christiane Nüsslein-Volhard: Nobel Prize Winner in Physiology or Medicine 1995 (project ZF-MODELS)

■ Rolf Zinkernagel: Nobel Prize Winner in Physiology or Medicine 1996 (project MUGEN)

■ John E. Walker: Nobel Prize Winner in Chemistry 1997 (project E-MeP)

■ Tim Hunt: Nobel Prize Winner in Physiology or Medicine 2001 (project MITOCHECK)

■ Kurt Wüthrich: Nobel Prize Winner in Chemistry 2002 (project UPMAN)

■ Aaron Ceichanover: Nobel Prize Winner in Chemistry 2004 (project RUBICON)

The fi rst FP6-funded projects started in 2004, some have already been fi nalised, others are still ongoing. It is al-ready evident that many of these projects have already generated major discoveries on novel gene functions, and resulted in high-level publications (see project websites for further details). Most importantly, these projects have played an important role in integrating the research community in Europe, thereby increasing their visibility at na-tional, European and international level. They have also substantially contributed towards reducing fragmentation of research in Europe in their respective fi elds, thereby implementing the concept of the ERA and creating a real multidisciplinary integrated programme of activities, as is illustrated with relevant fi gures in each sub-area’s activi-ties description (see Section 7).

All the projects funded in the area of fundamental genomics have very ambitious objectives. To achieve these objectives, it is necessary to apply a multidisciplinary transnational approach and to create the necessary critical mass of researchers utilising a large set of different cutting-edge technologies. This multidisciplinary approach is only possible at European level by networking the research capacities and excellence available in different countries via the EU collaborative projects (CPs).

KI

LU

MPI-F

MPI-B

BIOZ

CNRSLAU

EMBL

CSIC

EBIUOXF

Birkbeck

ImperialUU

FEI

LAU

CNRS

EMBI

EBI

UOXF

Birkbeck

Imperial

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MPI-B

BIOZ

CSIC

KI

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MPI-F

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Fig. 5: The structuring effect and the added value of collaborative projects: an example of active interactions between partners at the start point to the mid-term of a four year project



Section 4The way forward in FP7:from fundamental genomics to systems biology

The last decade has witnessed unprecedented advances in the life sciences. The rise of genomics after the se-quencing of the human and other genomes has revolutionised biology, with genome sequences becoming the ‘periodic table’ of biology. The spectacular development of the field of functional genomics and other ‘-omics’ research has dramatically changed the research landscape in the life sciences.

Life sciences research is moving away from a reductionist approach towards a new paradigm shift and a systems biology approach that attempts to understand biology in an integrative manner as large amounts of novel data become available.

In this new era of biology, scientists combine data, produced by a multidisciplinary set of functional genomics tools and technologies, into biological models with the power of computer science, mathematics or engineering to understand the phenomena of life. Researchers are increasingly realising that complex organisms cannot eas-ily be subdivided into individual, independent components. Rather, genes, proteins, cells and organs interact with each other and the environment in numerous, complex ways.

Systems biology aims to shed new light on these interactions, which are vital for the holistic understanding of many major diseases such as cancer and diabetes.

The FP7 programme (2007–2013) has already been launched and is expected to play an important role in devel-oping the field of systems biology in Europe by supporting the necessary critical mass of multidisciplinary expertise (‘-omics’, mathematics, physics, etc.) needed to produce the complex models underlying important biological proc-esses. This will require modelling of complex systems involving networks of tens of thousands of genes, gene prod-ucts and other molecules. By understanding these biological processes in their complexity, systems biology promises to make real progress towards understanding, preventing and combatting major complex diseases.

Although the deciphering of the human genome sequence represents a major step towards understanding human biology, many questions still remain unanswered, including the function of most of the genes. New large-scale data-gathering initiatives (e.g. population genetics including biobanks, large-scale proteomics, etc.) will be es-sential for generating new knowledge on gene functions and their interactions in complex regulatory networks in health and disease for future systems biology approaches.

Furthermore, to catalyse progress in functional genomics and systems biology, it is important to develop new and improve existing ‘-omics’ high-throughput (HTP) research tools. The tools will catalyse experimental progress by enhancing the generation and acquisition of data by orders of magnitude, and by significantly increasing our knowledge base to gain insight into the functioning of cells, tissues, organs and entire organisms.

Based on the continuation concept and building on the strong FP6 European collaborative activities that have tak-en place, the priority area of fundamental genomics is evolving towards the systems biology era. The structure of the Genomics and Systems Biology programme in FP7 (2007–2013) ) is subdivided in the following sub-areas:

■ High-throughput research

The objective of this activity is to develop new research tools for modern biology that will significantly enhance data generation and improve data and specimen (biobanks) standardisation, acquisition and analysis. The focus will be on new technologies for:



■ sequencing

■ gene expression

■ genotyping and phenotyping

■ structural genomics

■ bioinformatics

■ systems biology

■ other ‘-omics’ fields

Potential impact and European added value of high-throughput research initiatives

Functional genomics is a field of research offering many opportunities for technological innovation. New tools and technologies will be essential to enhance our knowledge on gene functions in health and dis-ease: increasing data output and considerably decreasing the cost for sample analysis will permit the transfer of these technologies to the clinical environment. Developing new HTP research tools and technolo-gies for collecting and processing vast amount of new and high-quality data will dramatically increase our knowledge of complex biological processes.

The development of these new tools and technologies requires a large multidisciplinary and coordinated

effort, involving expertise in molecular biology, engineering, robotisation, electronics, material sciences and physics. Only coordinated efforts at European level can harvest this diverse expertise with the common goal of developing new cutting-edge technologies. Importantly, any technological innovation obtained through a coordinated European effort greatly facilitates wider access to these new technologies in Europe.

In several technological areas (e.g. imaging, proteomics, structural genomics, transgenics), Europe is very competitive and a wide range of direct medical applications have been or are being developed. The integrated collaborative efforts launched in FP6 and future efforts in FP7 will reinforce this competitive posi-tion. The development of groundbreaking technologies will support knowledge-based European competi-tiveness and their applications are expected to have a great impact on biomedical and biotechnological industry, including small to medium-sized enterprises (SMEs).

■ Integrating biological data and processes: large-scale data gathering and systems biology

■ Large-scale data gathering

The objective is to use HTP technologies to generate data for elucidating the function of genes and gene products and their interactions in complex networks. The focus will be on the following:

■ genomics

■ proteomics

■ population genetics

■ comparative genomics

■ functional genomics



Potential impact and European added value of large-scale data gathering initiatives New large-scale and systematic data-gathering initiatives in functional genomics (e.g. on the human pro-

teome) will be essential for human biology in providing new knowledge on gene functions. Furthermore, standardisation of approaches will be achieved by developing European norms to facilitate efficient data interchange. The data will be freely available for the scientific community in Europe.

In the recent past, several large-scale European initiatives were proven to be successful. In FP6, several new initiatives have been initiated, including, for example, the large-scale genome annotation programme, the whole mouse genomes in situ hybridisation projects and several structural genomics efforts.

Many Member States have cutting-edge post-genomics infrastructures, capacities and expertise. However, to launch new large-scale data-gathering initiatives, these will need to be networked in a well-coordinated and integrated effort that will generate the necessary critical mass of scale and scope. They will offer pos-sibilities to smaller Member States with more limited resources and capacities. Furthermore, considerable economy of scale and resources can be achieved by networking these research capacities in a coordi-nated and integrated way. This coordinated approach at European level has proven to be successful for several large data-gathering initiatives: the sequencing of the first yeast and plant genomes, and more recently, the determination of the 3-D structure of proteins important for human health, via the structural genomics collaborative efforts.

These large-scale initiatives require a multidisciplinary approach involving different types of expertise. One of the bottlenecks in the translational process is how to translate a massive amount of data into useful knowledge that is directly applicable. For this purpose, it is important to closely associate the bioinfor-matics communities with these initiatives, so as to develop the integrated databases necessary for wide dissemination of results. Industry must be closely associated with these efforts, providing the required technical innovation and assistance.

■ Systems biology

The focus will be on multidisciplinary research that will integrate a wide variety of biological data and will de-velop and apply system approaches to understand and model biological processes.

Potential impact and European added value of systems biology initiatives

Solving biological problems in health and disease requires understanding of complex networks, involving tens of thousands of genes, gene products and other molecules. To further our understanding of biologi-cal phenomena, there is a need for quantitative approaches and systematic modelling, and analysis of the enormous amounts of information gathered by HTP technologies. With such approaches, collectively termed ‘systems biology’, we can gain new insight into the functioning of living systems, from the mo-lecular levels to the organism and population levels. This research involves a wide variety of disciplines, including modelling and simulation of the complex dynamic interactions. Eventually, systems biological research will open the way towards predictive biology and medical applications, when sufficiently power-ful models, fed with enormous amounts of data from different sources, become widely available.

Projects operating in this category will contribute to the ERA by combining dispersed forces from around Eu-rope. Scientists working on a particular system system (e.g. a cell, an organ or a disease) in different locations will be able to work together towards a thorough understanding of the systems. Enabling this type of research to be carried out at European level will secure Europe’s place in an increasingly competitive field and so help employment prospects, industrial development (including SMEs) and wealth creation. Exploiting biological data in an integrated way is one of the most cost-effective means of supporting all life sciences, as well as helping to achieve the Lisbon objectives with the move towards a dynamic knowledge-based society.

Such an interdisciplinary approach is difficult, if not impossible, to carry out in a single institute, company or even a single country. This research can only be undertaken in a large consortium which ideally should be multinational. The requirement for such varied expertise renders the area ideal for European pro-



grammes, where national strengths in different disciplines can be combined for the benefit of all. Europe-wide collaboration best averts the duplication of efforts and is a strong starting point for joining or driving international collaboration.

Under FP6, several projects are under way, that either work towards enabling system biology, or gather data that are suitable for such approaches (examples are Biosapiens and Eurohear). Many researchers currently working on various systems are moving into systems approaches and the trend is likely to con-tinue in the coming decade. The genome era has enabled us to accumulate enormous quantities of data on both our genome and that of other organisms. The amount of data is certain to increase exponentially for the foreseeable future. Paradoxically, utilising this data is becoming feasible on the one hand, and increasingly complex on the other. The high hopes for new drugs and other treatments from the genomic data can only become reality if the potential is realised through approaches such as systems biology.

Section 5Content of the present publication

Although the sub-areas set out in Section 2 represent different sections of the fundamental genomics programme in FP6, many projects were found to be cross-cutting in nature, involving multidisciplinary approaches. For this reason, we thought the reader would find it clearer to present the list of projects funded in fundamental genomics arranged according to common scientific theme rather ‘artificially’ distributed based on the action lines mentioned above.

The present publication provides a brief description of the goals, expected results, achievements and expected impact of all the projects supported during FP6 in the fundamental genomics priority area in the following scien-tific sub-areas:

■ tools and technologies development for functional genomics

■ regulation of gene expression

Multidisciplinary projects :

in a holistic approach to address complex biological systems in health and disease

Fig. 6: The multidisciplinary nature of systems biology



■ structural genomics and proteomics

■ comparative genomics and models organisms

■ population genetics and biobanks

■ bioinformatics

■ multidisciplinary fundamental genomics research for understanding basic biological processes in health and disease

■ the emerging area of systems biology.

For each of these sub-areas, an introductory section describes the importance and impact in the post-genomics era of each field, including highlights from several projects and a short description of the activities implemented in the FP7 first call for proposals. The introductory section also provides an overview of FP6 research policies and the steps taken to strengthen the ERA in each of the scientific sub-areas, as well as the FP7 vision in genomics and systems biology collaborative research. However, owing to space limitations in this publication, we could not highlight all 130 projects funded in the fundamental genomics programme, in the introductory section. Naturally, this by no means minimises the importance of the projects not cited.

Table 1: EC Funding of different thematic sub-areas in fundamental genomics and systems biology collaborative research in FP6 and in FP7’s first call selected projects

Fundamental Genomics Research in FP6 (2002–2006)

Scientific sub-area Number of projects

EC financial contribution(million )

Tools and Technologies for Functional Genomics 20 68.0

Regulation of Gene Expression 6 32.6

Structural Genomics and Structural Proteomics 19 87.2

Comparative Genomics and Model Organisms 15 82.4

Population Genetics and Biobanks 10 19.4

Bioinformatics 5 32.0

Multidisciplinary Approachesfor Basic Biological Processes 32 219.4

FP6 Pilot Projects on Systems Biology 23 53.0

Genomics and Systems Biology Research in FP7 (2007–2013) (first call)

Tools-Technologies for HTP research 3 35.7

Large-Scale Data Gathering 7 80.0

Systems Biology 4 45.8



All the projects are highly multidisciplinary and include several areas of fundamental genomics in their research plan. We thought it would be easier for the reader if we classified the projects using the respective scientific themes they have in common. Having said that, there are several areas, like bioinformatics and databases, which are an essential part of all the projects and particularly of all the projects funded in the area of multidisci-plinary functional genomics, for understanding basic biological processes.

Section 6EC financial contribution in fundamental genomics and systems biology collaborative research

The EU FP6 thematic activity on ‘Life Sciences, Genomics and Biotechnology for Health’ has had a clear focus in the post-genomics era, rising to the challenges following the sequencing of the human and other organisms’ genomes. More specifically, the Fundamental Genomics Research programme received support of approximately

594 million under FP6 for a large number of collaborative projects (CPs) (small- to medium-scale (89) and large-scale (41)), out of a total 2 500 million allocated to the priority of ‘Life Sciences, Genomics and Biotechnology for Health’. The EC has committed approximately 635 million for 87 projects under Health research for the FP7 first call selected projects which started in the beginning of 2008. More specifically, in the Genomics and Systems Biology area, 14 large-scale integrating projects were supported, constituting 161.5 million (for further details, see Table 1). Specific explanatory notes on the definition of the funding instruments in FP6, namely Integrated Projects (IPs), Networks of Excellence (NoE), Specific Targeted Research Projects (STREPs), Co-ordination Actions (CAs) and Specific Support Actions (SSAs) are presented in Annex I of this publication.

Section 7Scientific sub-areas supported in FP6 and FP7in fundamental genomics and systems biology

All processes in biology and medicine reflect the flow of information from the genome of the organism to its phenotype. Since the identification of the structure of the DNA molecule more than 50 years ago, progress in understanding these processes has been driven by new technologies such as cloning, DNA sequencing, meas-urements of ribonucleic acid (RNA) and protein, and use of robotics and microarrays. The genome sequencing project has created a milestone for the deeper understanding of the function of the genes in a genome-wide, HTP manner and set the challenges for the post-genomic era in the area known as functional genomics.

Functional genomics focuses on a series of dynamic aspects of cellular biology such as gene transcription, translation and protein-protein interactions, including function-related aspects of the genome itself, such as muta-tion analysis and the measurement of molecular activities. It utilises the development and application of global (genome-wide or systems-wide) experimental approaches e.g. genomics, transcriptomics, proteomics, in silico (in italics) functional prediction, etc.). HTP technologies are a hallmark of functional genomics experimentation, with their capacity for collecting data on a genome-wide scale.



Functional genomics is a field of research offering many opportunities for technological innovation. These tech-nologies have proven strategically important for both academia and industry. Developing new HTP research tools and technologies for collecting and processing vast amounts of new and high-quality data will dramatically increase our knowledge of complex biological processes.

Despite all the progress being made, there are a number of bottlenecks currently affecting functional genomics research. The success of functional genomics lies in the development of novel tools to solve the practical limitations it suffers today. It should also be noted that there is a high degree of fragmentation of technologies, resources and expertise, which makes it difficult to exchange information and address the bottlenecks in a coordinated effort. Such collaboration is particularly important in view of the speed with which these technologies are moving and also because of their multidisciplinary nature. Another important issue is the tools standardisation aspect: this is required to provide high-quality reproducible data and to enable valid exchange and comparison of experimental data. In addition, due to the large quantity of data produced by these techniques, the development of sophisticated bioinformatics tools is necessary to increase the power of the functional genomics technologies. Most importantly, the development of new tools and technologies in functional genomics requires a large multidisciplinary and coor-dinated effort involving expertise in molecular biology, engineering, robotisation, electronics, material sciences and physics. Only coordinated efforts at European level can bring together this diverse expertise with common goals of developing new cutting-edge technologies, and therefore the area is well suited for EU support.

FP6 activities

In order for Europe to keep its competitive position in the development of new and improved functional genom-ics tools, a substantial number of projects have been supported in FP6 and several important actions have been launched in the first three FP7 calls for proposals.

In summary, the fundamental genomics programme in FP6 supported projects that aimed to improve existing or develop new tools and technologies for functional genomics research. The projects addressing such technologies are grouped in four categories, namely:

■ technologies for gene expression

■ technologies for proteomics

■ technologies for molecular imaging

■ tools and technologies for gene integration

Plenty of other projects developing tools and technologies are presented in the different sub-areas of structural genomics, model organisms, population genetics and bioinformatics in the following sections.

The FP6 European projects have been successful in bringing together the tools, the developers and the experi-mentalists for developing the most appropriate state-of-the-art technology and for validating them in experi-mental conditions. The HTP, high-precision technologies that are being established as a result of FP6-related projects are expected to be of major importance to research, improving the competitiveness of Europe on the world stage. Importantly, any technological innovation obtained through a coordinated European effort greatly facilitates wider access to these new technologies in Europe and to the international scientific community. The future applications of functional genomics technologies in health research are endless: cellular mechanisms can be delineated, gene expression chips are already being used in early diagnosis, and proteins potentially have enormous value as clinical biomarkers.

FP7 activities

The EC recognises the immense potential of the technologies in functional genomics for innovation and strength-ening of European biotechnological and biomedical industry competitiveness. Therefore, FP7 has prioritised the



area of HTP research with a focus on new technologies for the following: sequencing, gene expression, genotyp-ing and phenotyping, structural genomics, bioinformatics, systems biology and other ‘-omics’ fields.

During the FP7 first call for proposals, EC supported three large integrating projects launched in 2008, amount-ing to 36 million overall, in the following subjects:

■ development of human genetic variation databases integration (Gen2Phen);

■ tools and technologies development for spatial and temporal proteomics (PROSPECTS);

■ on technologies for DNA sequencing and genotyping (READNA).

During the FP7 second call for proposals, a broad topic on SME-driven small-scale focused research CPs for developing tools and technologies for HTP research was published. Several projects were selected for funding amounting to approximately 30 million, covering areas on tools for gene expression, proteomics, sequencing, phenotyping (currently under negotiation). The funding upper limit was 3 million EC contribution per project, with 40% allocated to SMEs, which is expected to reinforce SMEs’ scientific and technological bases.

The EC, continuing its efforts in the functional genomics tools area, published the FP7 third call for proposals in September 2008, with the aim of attracting proposals in the following areas:

■ computational tools for genome annotation and genotype/phenotype data integration tools, which will enable integration of the vast amounts of functional genomics data, facilitate data mining and catalyse progress in systems biology;

■ HTP tools and technologies to analyse samples in large-scale human biobanks, which will deliver high-quality and standardised data and accelerate epidemiological studies and biomarker discovery;

■ tools, technologies and resources for the characterisation of protein functions, which will help to overcome bottlenecks in the investigation of protein functions in cells, leading to a better under-standing of biological processes in health and disease.

For the first time in EU CPs in health research, a two-stage selection process will be implemented, with proposal topics that are broader in scope and that will invite a larger number of pre-proposals (of maximum 5 to 10 pag-es) for the first stage. In this way, the scientific community will be consulted for their ideas on research projects, aiming to keep Europe at the forefront of technology and resources development in HTP research.

Europe is very competitive in the development of several groundbreaking technologies for functional genomics, and their applications are expected to have a great impact in biomedicine and in the biotechnology industry, including SMEs. Only coordinated efforts at European level can gather this different expertise with the common goal of developing new cutting-edge technologies. Therefore, the FP7 Health priority via its Genomics and Sys-tems Biology programme will continue its support for catalyzing progress in this important area.

The ability to functionally explore the effect of genes on cellular phenotypes and signalling in a HTP fashion is of fundamental importance in all fields of life sciences and biomedicine and has also attracted the attention of the biotechnology and biomedical industries.

Developments in large-scale, high throughput technologies and robotics now allow researchers to simultaneously profile vast numbers of different genes and gene products in parallel. Examples are DNA microarrays, where many thousands of genes are spotted onto an area no bigger than a microscope slide, allowing researchers to sample thousands of genes in parallel for expression analysis in health and disease.



The ability to monitor the activity of the genome by simultaneously measuring the expression of the transcribed genes provides a broader view of the cellular response under specific conditions, such as a particular develop-mental state, a specific cell type or a certain disease state. Studies in major diseases like cancer demonstrate that genome-wide gene expression profiles could identify molecular profiles correlated to disease states; this approach could have enormous potential for the development of novel diagnostic tools.

Recent years have seen the rapid growth of techniques for HTP analyses of genes, transcripts, proteins and cells using microarrays, but current methods still capture only a small fraction of the information embodied in the biological molecules. Methods are needed to detect nucleic acids and proteins in single cells, and in complex samples even at the level of single molecules, to overcome the limitations imposed by techniques currently being applied in heterogeneous populations of cells. The success of novel technologies will lie in breaking through the practical limitations it suffers today, in terms of sensitivity, accuracy, and ‘noise’ levels. A great challenge still remains the intensive interplay between tools developers and experimentalists, and between academy and industry: collaborative and coordinated efforts at the European level are required to tackle this. In addition, the optimisation of standardised HTP technologies to study gene expression will remain a requirement for the future, as well as the development of ultra-precision technologies and devices.

FP6 activities

In summary, the FP6 projects funded in this sub-area may be classified into two categories:

1. Projects overcoming existing bottlenecks and developing tools and technologies for the study of gene expression

With already existing array technologies serving as a starting point, the IP MolTools is developing a new set of HTP methods with the aim of increasing sensitivity and precision, and enabling analyses at the level of single DNA, RNA or protein level at a considerable lower cost. EMERALD aims to coordinate a discus-sion on reproducibility, variability and comparability of microarray experiments at different platforms and to overcome the limitations of microarray technologies in terms of reproducibility and sensitivity. The resolution of these issues will facilitate the translation of microarray technology in a clinical setting. TRANSCODE develops open source tools using bioinformatics and large-scale experimental approaches for the prediction and verification of the functional role of regulatory elements controlling gene expression, and for the identifi-cation of transcription factors (TFs) binding sites. AUTOSCREEN’s goal is the establishment of an innovative, automated instrument for HTP and high-content screening that will permit the qualitative and quantitative monitoring of cellular constituents (RNA, proteins, and metabolites) in living cells.

2. Projects developing tools for gene expression, which are applied to the study of disease mechanisms

REGULATORY GENOMICS aims to develop novel tools and methods for the determination of tran-scription factor binding specificity, and to apply these techniques for determination of the binding spe-cificities of TFs linked to cancer. This information will subsequently be used for computational identifica-tion of ‘regulatory’ SNPs (rSNPs) that are predicted to affect transcription factor binding. The principle objective of the project MODEST is the development and use of modular devices as well as protocols for highly efficient, small-volume ultra-HTP screenings of primary cells, in areas such as neurology and liver metastasis, to accelerate basic research, target identification and drug validation. FGENTCARD’s major goal is to develop methodologies that integrate functional genomics tools and genetic strategies to address major unresolved questions concerning the molecular basis of common diseases with a focus on coronary artery disease. TargetHerpes focuses on improving tools for producing novel antivirals.

These projects have already shown a clear added value in carrying out the work at an extremely cooperative and integrated European level, by establishing tools with international visibility, that have been developed through close collaboration of partners, both across European countries and via international cooperation.

FP7 future actions will continue to support projects developing tools for gene expression under the FP7 priority sub-area for HTP research.



The term proteome describes the full set of proteins encoded by the cell’s genome which are constantly changing, reflecting the dynamic response of cells to their environment. Proteomics is the study of the proteome in a HTP manner. In recent years, the term proteome has been expanding to include the study of all the protein isoforms, their post-translational modifications, their interactions, and their structural analysis.

Following the technological development in genomics, the interest in the simultaneous analysis and measure-ments of genome-wide protein levels will be of central importance in biological studies, since proteins are the main regulators whose concentration and modification define the cells responses to the environment.

Proteomics complements other functional genomics approaches, including microarray-based expression profiles, systematic phenotypic profiles at cell and organism level, systematic genetics and small-molecule-based arrays. Additionally, proteomics is set to have a profound impact on clinical diagnosis and drug discovery via the detec-tion of protein profiles associated with disease states, since most currently used drug targets are proteins.

Tremendous progress has been made in the past years in generating large-scale data sets for protein-protein interactions, organelle composition, protein activity patterns and protein profiles in healthy and diseased situa-tions. Moreover, large-scale data sets will be crucial for the emerging field of systems biology. But further techno-logical improvements, coordination of European and international proteomics efforts, as well as open access to results are needed for the field of proteomics to realise its full potential.

Proteomics advances would not be possible without the previous achievements of genomics, which provided the ‘blueprint’ of possible gene products that are the focus of proteomics studies. Unlike the challenges faced with the human genome projects, proteomics faces inherent challenges which deal with problems of material limitations and variability, sample sensitivity and degradation, low to high abundance, a plethora of post-translational modi-fications and unlimited tissue, developmental and temporal, diseased state and drug responses variations. In addition, over of the last years, vast amounts of heterogeneous data has been generated in proteomics research as well as different bioinformatics software and formats, a fact that creates barriers for the direct comparison and the sharing of data.

FP6 activities

To address the current challenges and the immense potential of the proteomics field, the majority of FP6-funded projects were oriented towards improving throughput potential, sensitivity and accuracy of detection of the proteomes, as well as the standardisation of data. INTERACTION PROTEOME, the largest effort established at the European level, has objectives focused on the future of the functional proteomics field, via the develop-ment of a broadly applicable platform of innovative methods for the analyses of protein-protein interactions. A multidisciplinary approach has been established to address different aspects of protein-protein interaction data: their validation by cell biology, biochemical and biophysical methods; the improvement of in silico (in italics) methods for prediction of protein interactions; and ultimately the development of a new type of public database for protein-protein interaction data.

The ProDac CA is contributing to the international proteome standards initiative for HTP proteomics by implementing these standards in public repositories and data submission pipelines, and demonstrating the practical use of improved, standardised proteomics data collection and analysis to the proteomics community. NEUPROCF, a project with a more specific focus, is further developing and applying a set of proteomics tools for the detection of low-abundance proteins to help the study of disease phenotype (i.e. cystic fibrosis). With the project CAMP, the new emerging field of chemical genomics has also been addressed.

FP7 activities

Establishing how networks of proteins associate in time and space to generate function is an important goal in post-genomics research. The formation of interaction networks is essential for cellular function and requires pro-teins to be at the right place, at the right time and in the right concentration.



In view of the importance of spatial and temporal proteomics in the area of HTP tools development, at the FP7 first call for proposals the EC supported the project PROSPECTS, a large scale integrating project funded with 12 million, to overcome current bottlenecks in the proteomics technologies. This multidisciplinary project brings together the world leaders in proteomics to make a major advance, both by developing much more powerful instrumentation and by applying novel proteomics methods that will quantitatively annotate the human proteome with respect to protein localisation and dynamics. These technological developments will be applied so as to gain unique insights into the molecular basis of multiple forms of human disease, specifically neurode-generation and other diseases related to folding stress.

To keep Europe at the forefront of technology development in proteomics research, the EC, via its Health priority, published the FP7 second call for proposals for SME-targeted focused CPs in HTP research. Several proteom-ics projects have been selected for funding and are currently under negotiation. Continuing the efforts, the EC published the FP7 third call for proposals in September 2008 with the aim of developing tools, technologies and resources for the characterisation of protein functions, to be implemented via a bottom-up approach and a two-stage selection procedure. In this way, the scientific community will be consulted for their ideas on research projects developing state-of-the-art proteomics research.

Further advances in proteomics techniques will help overcome bottlenecks in the investigation of protein functions in cells, leading to a better understanding of biological processes in health and disease, and fostering European research excellence and technological innovation.

Although we need to continue to sequence genomes and to indentify individual proteins involved in a given bio-logical response, the ultimate challenge will be to utilise the enormous amount of data generated and to convert this into a dynamic picture of the subcellular, cellular or whole organism level. In the dynamic cellular environ-ment, proteins and other cellular components undergo many processes — all primarily designed to maintain cellular function and homeostasis.

Most of the current knowledge on gene expression, regulation and delivery in mammalian systems results from in vitro or ex vivo studies. It is worthwhile reflecting on the fact that study of a biological system over time is gener-ally constructed from a series of data obtained from different specimens, which often fail to represent accurately the true order of events in vivo. This situation, coupled with our inability to easily monitor multiple molecular species simultaneously, seriously limits our ability to study cellular processes, keeping in mind that biology is fundamentally dynamic.

Biomedical methods have elucidated many cellular pathways and continue to do so. However, the desire to capture microsecond and nanosecond cellular changes and interactions in living cells in their natural environment, as well as the need for high spatial and temporal specificity have led to the development of increasingly sophisticated imag-ing technologies. These techniques are becoming more powerful with the contribution of computing power.

FP6 activities

The EC has supported FP6 collaborative projects (CPs), aiming at the development of new imaging technologies for monitoring gene and protein expression in situ and in vivo (often in tissues or living cells and whole animals). MOLECULAR IMAGING is an IP aiming to develop novel non-invasive imaging techniques that enable monitoring of the dynamics of multiple molecules within living systems, and whole animals .

The Tips4Cells focused project aims at further developing scanning probe microscopy (SPM); this is currently the imaging method of choice for measuring intermolecular and intramolecular forces in biomolecules at the single molecule level and for providing high-level information on structural details of biological samples in their native environment. The COMPUTIS focused project is developing new and improved technologies for molecu-lar imaging mass spectrometry (MIMS), enabling innovative methods of investigation in functional genomics, proteomics and metabolomics, as well as investigation in cells and tissues.



High-resolution imaging of living cells and subcellular components is essential for functional and structural genomics. Developments in this field are expected to transform our understanding of biology, making experimental investigations much more efficient, speeding up research into life sciences. Multidisciplinary consortia established in FP6, comprising physicists, mathematicians, biologists and chemists, addressing in vivo molecular imaging, resulted in the formation of ‘centres of excellence’, enabling greater technological developments and commercial opportunities. Imaging tools have potential for direct applicability in the biomedical sector; therefore partnerships amongst academy, industry and the medical sector would facilitate the future transition from the laboratory and a wider diffusion and application of these technologies.

One of the most important goals in the post-genomics era is to systematically determine the function of all genes and regulatory sequences within living cells. The so-called reverse genetics approaches rely on the targeted integration of artificial gene constructs by homologous recombination to delete (knock-out) or alter (knock-in) chromosomal sequences.

The modification of the cell’s genome by methods of gene targeting has traditionally been used in modern biol-ogy for gene function analysis and for development of tools for gene therapy. Therefore, controlled gene integra-tion and in particular targeted integration are key technologies for the exploitation of the full function of genomic information. Targeted gene integration also fulfils a critical role in medical research, as it allows the establishment of animal disease models for advancing research in disease pathogenesis and treatment.

Gene targeting allows researchers to precisely modify the genetic blueprint of living cells in vivo. The mechanism of gene integration into the chromosomes of living cells is far less known, and can occur either randomly or be targeted by homologous recombination. In FP6, the EC supported several focused research projects developing tools for gene integration and the study of the mechanisms of gene integration in different model organisms.

The GENINTEG project seeks to establish a greater understanding of the mechanism of gene targeting and devel-op new generic tools for enhancing gene integration by applying an interdisciplinary and multi-organism compara-tive approach. TAGIP is a focused project that aims to develop gene targeting via homologous recombination as a routine technology in plants that will facilitate the cost-efficient and large-scale production of therapeutic proteins.

The PLASTOMICS project will define the mechanisms and improve the understanding of the genes and proteins involved in several key stages of plastid transformation and foreign proteins expression. The focused project MEGATOOLS studies meganuclease-induced recombination; this approach could provide a practical alterna-tive to current approaches and represents an extremely powerful tool for gene alteration.

The clarification of gene function by transgenesis is important for our understanding of biological processes and disease pathogenesis. Therefore, investment in further developing gene integration technology promises advances not only in basic research, but also in drug development.

Research into regulation of gene expression will enable scientists to decipher the functions of genes and their protein products, and acquire a clearer picture of the complex regulatory networks that control fundamental biological processes.

The gene expression process is of fundamental importance for all living organisms. Regulation of gene expression refers to cellular control of the quantity and the timing of changes to the appearance of the functional product of the gene. Most genes reside in the chromosomes located in the cell nucleus and express themselves via proteins synthesised in the cytoplasm. The genetic information is transcribed from DNA to RNA, and then translated from



RNA into protein, the so-called central dogma in biology. Any of the steps leading to the expression of a gene may be modulated, from DNA or RNA transcription to the post-translational modification of a protein. Gene regulation allows a cell to have control over its structure and function, which is the basis for cellular differentia-tion, morphogenesis and the versatility and adaptability of any organism to its environment.

The sequence of an organism’s genome does not directly determine how the genome is used to build the organ-ism. Buried deep in the primary code is a second regulatory code, which must also be deciphered.

To address the importance of the gene regulation in the post-genomics era, the majority of FP6-funded projects were oriented towards the understanding of:

■ transcription regulation

■ epigenetic regulation.

The knowledge and methods developed within the FP6-funded projects will improve EU scientific competitive-ness in the rapidly developing field of regulatory genomics, hopefully giving European scientists a head start in the race to decipher the regulation of the genetic code.

Our genome consists of approximately 22 000 protein coding genes. However, only a fraction of these are used in each cell. Which genes are expressed (i.e. govern the synthesis of new proteins) is controlled by the machinery that copies DNA to mRNA in a process called transcription. In the gene expression pathway, the first regulated and in most cases rate-limiting step is the process of transcription. This process, in turn, can be modulated by various factors. A number of conceptual as well as mechanistic questions still need to be answered before we can attain a complete picture of the principles employed by living organisms to control this process. One of the main gaps in our knowledge is the limited insight we have regarding transcription regulation in the nuclear environment.

The goal of the TRANS-REG focused project is to obtain a comprehensive knowledge of the mechanism of regulation of model genes during cell differentiation, cell proliferation and signal transduction. The consortium is undertaking concerted efforts to develop and apply different molecular and cell biology approaches to study the molecular characteristics.

The X-TRA-NET project develops and employs chromatin immunoprecipitation technology combined with sequenc-ing to explore the complex transcriptional network of nuclear receptors signalling pathways and regulation. These unique methods will be used to investigate the impact of binding site diversity on the mechanism of gene activation with potential impact in the treatment of major diseases such as cancer, insulin resistance and atherosclerosis.

The completion of the human genome has provided a wealth of information about our genetic wiring. Epige-netics is defined as the study of the heritable changes in genome function that occur without a change in DNA sequence. It seeks to determine how genome function is affected by mechanisms that regulate the ways the genes are controlled. There are hundreds of different kinds of cells in our bodies. Although each one derives from the same starting point, the features of a neuron are different from a liver cell. As cells develop, their fate is governed by the selective use and silencing of genes. This process is subject to epigenetic factors where DNA methylation plays an important role in all the phenomena where genes are switched on and off. Epigenetics also provides a means by which genetic material can respond to changing environmental conditions.

Over recent years, the study of epigenetics (chromatin and/or DNA modifications not attributed to changes in the DNA sequence but surviving across generations) has received increased attention due to its possible role in pathogenesis and in a series of the organism’s phenotypic characteristics.



The huge interest in epigenetic regulation of gene expression has led to a number of excellent European-funded initiatives. In the later stages of FP6, strong links were established between these projects, thereby developing a European critical mass in this field.

The EPIGENOME project has established a network of excellence (NoE) providing a platform for the development of the European epigenetic research. It seeks to promote the ERA in the field, not only by means of a strong research programme, but also by integrating and disseminating the project’s activities, including an efficient communication infrastructure to enable internal communication of geographically dispersed teams and to foster public dialogue.

The HEROIC project advances epigenetic research with HTP technology in the context of the whole genome to help unravel the meaning of the epigenetic code. It performs research into gene regulatory systems at the level of the chromatin structure and nuclear organisation, employing the most extensive multidisciplinary con-sortium ever assembled at European level. Although the chromatin immunoprecipitation (ChIP) assay plays a crucial role in deciphering patterns of epigenetic marks that govern gene transcription, it still suffers from low resolution and low sensitivity. The CHILL project will overcome this by developing Chromatin Immuno-Linked Ligation (ChILL) technology resulting in a better understanding of the epigenetic code. The SMARTER project will help in the treatment of cancers by investigating the small molecules that target histone deacetylases and by opening up new avenues of research.

Epigenetic research is anticipated to have far-reaching implications for medicine. Using a combination of ge-nomic tools, researchers are trying to better understand processes like DNA methylation in order to use the information for more effective early diagnosis of complex diseases (such as cancer) and to develop innovative treatments directly targeting the molecules involved in these processes.

The way molecules such as proteins and ribonucleic acids (DNA and RNA) interact with one another and with other molecules (such as drugs) is determined by their 3-D structure. Understanding the 3-D structure of these mac-romolecules is critical for the understanding of their role in complex biological processes, and is essential for drug design. Most molecular interactions can only take place as a result of the molecules’ chemical architecture, creating active sites where they can link together with complementary molecules or interact as a part of cellular machinery, in order to acquire the functional state required in a living organism. In proteins, these sites depend on the way the long chains of amino acids of which they are constituted are intricately folded to give a final 3-D structure. Most drugs target particular protein functions, either of proteins of human origin or of a specific pathogen, and the de-velopment of new drugs relies heavily on knowledge of the targeted protein’s structure. Compounds with potential pharmaceutical activity can be designed and tested to determine their potential by altering the protein structure.

Structural genomics researchers are using and developing a variety of techniques to study the 3D structure of mac-romolecules ((X-Ray crystallography, nuclear magnetic resonance or NMR, 3-D Electron Microscopy). During, the last decade, the major bottleneck in the technological developments described above, from the stage of sample preparation to the analysis of structural data, has been the low-throughput outcome. The techniques did not permit a sufficiently HTP analysis of samples and the determination of the structures of the thousands of macromolecules is still to be solved. Research effort has therefore been focused on the automatisation of many stages in the procedures to reduce bottlenecks and increase throughput.

The concept of structural genomics arose in the late 1990s in the US and Japan as a response of the success of HTP sequencing methods applied to whole genomes. It was anticipated that similar HTP methods could be applied to obtain 3-D structures of all the proteins. This vision led to the investment of substantial funds into large-scale structural genomics projects in the US (between 2000 and 2005) and in Japan. Europe was slow to enter the area of structural genomics and proteomics, and European investment in this area has been on a consider-ably smaller scale.

In Europe, the first large collaborative initiative in implementing HTP approaches to structural biology was launched in 2002 (pilot FP5 IP) with the project SPINE: Structural Proteomics in Europe (www.spineurope.org). The challenge set for SPINE was to push forward cutting-edge technologies aimed at biomedically relevant tar-




gets, while at the same time generating a pan-European integrated effort directed towards biomedically oriented structural proteomics. The project produced approximately 300 novel protein structures and also developed Eu-ropean standards in protein crystal handling for X-ray crystallography studies. The success of the SPINE project, and its catalytic effect on the area, led to a new generation of CPs.

FP6 activities

The effort in structural genomics and structural proteomics activity area was substantially increased in the EU’s FP6 Programme for RTD (2002–2006), with objectives to enable researchers to determine, more effectively and at a higher rate than was currently feasible, the 3-D structure of proteins and other macromolecules, which is important for elucidating protein function and essential for drug design.

Whereas, in general, the projects elsewhere have tended towards a HTP approach, which would cover an organism, an organelle or a category of proteins, most of the European projects are oriented towards technol-ogy development or high-value targets, in most cases associated with diseases (drug targets, viral pathogens, membrane receptors, signalling complexes involved in neuronal development and degeneration, immunology, and cancer).

The FP6-funded projects in structural genomics and proteomics, whose objectives, results and potential impact are presented in this publication, cover the three main technological disciplines (X-Ray crystallography, NMR, and Electron Microscopy), which in many cases are integrated into the same consortium for the first time.

In summary, the FP6 projects can be classified into three categories:

1. Projects that are biologically focused and generate high-value 3-D structures of proteins and complexes of fundamental and biomedical importance. These projects aim at the following:

■ 3-D structure determination of viral pathogens VIZIER: The aim of this IP is to gather knowledge on viral replication needed to develop new drugs to

prevent new viral outbreaks. RNA viruses include more than 350 different major human pathogens. The project, unprecedented in size, has set out the sequence of the genomes of hundreds of viruses, defined the proteins essential for replication, and through a major 3-D structural effort is identifying common sites of these proteins that could be a target for new antivirals with a large spectrum of action. FSG-V-RNA is a more targeted complementary project, which aims at developing and improving tools for the rapid structural analysis of RNA and RNA-protein complexes in several RNA viruses.

■ 3-D structure determination of membrane proteins E-MeP is an IP that aims at solving the bottlenecks that preclude the determination, at HTP, of high-

resolution structures of membrane proteins and membrane protein complexes; an integrated database cataloguing E-MeP’s results, protocols and other pertinent data is being developed.

■ 3-D structures of components of important signalling pathways SPINE-2-COMPLEXES is a second-generation SPINE project that aims at investigating signalling path-

ways from receptor to gene by combining the knowledge of genomes with HTP methods for structural proteomics. The complexes under study are extremely important with respect to human health and are drawn from the common theme of signalling pathways with targets from key areas of biology, including cell cycle, neurobiology, cancer and immunology, as well as pathogen proteins that modulate or subvert human signalling pathways.

■ 3-D structures of large complexes 3D-Repertoire aims at determining the structures of all amenable complexes from the budding yeast

at medium or high resolution by electron microscopy, X-ray crystallography, and in silico methods; these structures will serve to integrate toponomic and dynamic analyses of protein complexes in a cell.



2. Projects that develop new and/or improving existing technologies and methods as well as bioinformatics tools for structure determination of proteins and complexes.

These projects aim at the following:

■ New and improved tools for 3-D electron microscopy 3D-EM is bringing together European excellence in electron microscopy approaches for studying protein

complexes and cellular supramolecular architecture. This NoE addresses the development and improve-ment of existing 3D-EM techniques, the standardisation of data processing, the integration of research activities and the transfer of knowledge. HT3DEM is a more focused project aimed at developing an innovative technological platform for HTP screening and analysis of native protein complexes and protein crystals that will reduce processing time and cost.

■ New and improved tools for X-ray crystallography BIOXHIT is mobilising both all European synchrotron facilities with beamlines equipped for macromolecu-

lar crystallography (either already in existence or planned for the future), and also most of the software developers active in fields relevant to HTP structure determination. It aims to build a common platform for European researchers in the field of biological crystallography. It focuses on the development of hardware synchrotron technologies, HTP crystallisation technologies and standardisation of methodologies in syn-chrotron data acquisition and treatment. This IP represents the greatest possible mobilisation of resources at the European level, both in terms of infrastructure and scientific excellence.

Furthermore, the optimisation of methods for the production of proteins is important for retrieving suf-ficient quantities for crystallisation purposes. OptiCryst is a focused project with the goal of improving and automating methods for protein crystallisation and the objective of increasing speed and crystallisa-tion success rates. IMPS aims at innovative techniques for expressing, stabilising, purifying and crystal-lising membrane proteins.

■ New and improved tools for NMR structure determination NDDP is a focused project that develops cutting-edge NMR techniques for the dynamic characterisation

of drug-receptor interactions to support structure-based drug design for phosphatases, a major class of proteins for a broad range of medical applications. UPMAN is studying the structural states of proteins from unfolded monomers to oligomers and fibrillar aggregates. A variety of NMR techniques coupled with novel computational approaches are used in order to define the misfolded structures’ characteristics and are then applied to representative samples of the various types of proteins that are associated with misfolding diseases.

■ In silico tools for structure determination Extend-NMR deals with the development of novel computational tools that extend the scope of NMR

and that make possible functional and structural studies of larger proteins and biomolecular complexes which are not amenable to crystallisation. is developing improved bioinformatics tools for reliably assigning function to genes, with an emphasis on in silico protein-protein interaction and 3-D structure determination. The developed function prediction methods should improve the in silico func-tional annotation of the genome.

3. Projects that network and coordinate research efforts in Europe, as well as promoting high-level training. These projects aim at the following:

■ High-value training in structural genomics in Europe E-MeP-Lab is an SSA, where for the first time Europe’s membrane protein structural biology community

will organise high-level training with advanced practical courses in the best-equipped laboratories in Eu-rope. TEACH-SG is an SSA that provides a platform for training young scientists and those from smaller laboratories and new EU Member States in the HTP technologies developed in the area of structural genom-ics, by organising a series of workshops and meetings with hands-on training.

■ Networking and coordination in SG/SP NMR-Life promotes the networking and coordination of NMR research in structural genomics via the

exchange of personnel and good practices, the organisation of meetings and the implementation of a vir-


38

tual laboratory. FESP is a CA that aims at a thorough assessment of the existing structural genomics and structural proteomics projects and infrastructures at national, European and international levels. Its major goal is to develop a strategy for structural genomics and structural proteomics in the broader context of anticipated developments in biological research, resulting in recommendations for future European poli-cies in this area.

In total, the EU investment in structural proteomics increased substantially in FP6, reaching more than 90 million. Thanks in large part to EU-funded projects, in the last few years the structural proteomics field has had good publicity and achieved international stature comparable to large-scale projects in the US and Japan. While it is still premature to predict the success of the FP6 structural genomics projects, we could say that these projects have played an important part in integrating the research community in Eu-rope, thereby increasing visibility at national, European, and international level, and improving the capacity to tackle ambitious challenges in research in a collaborative manner. By doing so, these projects are reducing the fragmentation of research in Europe and are realising the concept of the ERA in structural genomics. In figure 7, the steps towards the ERA in structural genomics are presented.

FP7 activities

The future of the field relies on combining integrated structural biology with cell biology so that the atomic dissec-tion of the cell can be reconstituted into a functional system (3-D cellular structural biology). FP7 will continue to support projects aiming at developing new and/or improving existing tools and technologies for protein and pro-tein-complex structure determination. Most importantly, in FP7, structural genomics projects will be implementing


Biologically-Focused Research

Technological Developments

Coordination, Fora,Workshops, Training

European FP5 Pilot project

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

STREP, CA, SSA

IP, NoE

IMPS (tools forMembrane proteins)

OptiCryst (Protein Crystallization)

Extend-NMR(NMR)

HT-3DEM (high-throughput 3D-EM)

GeneFun (in silico strucure prediction) BIOXHIT

(X-ray Crystallography)

UPMAN (protein misfolding-

aggregation) 3D-EM(Electron

Microscopy)NDDP (NMR-phosphatases)

3DGENOME(3D microscopy)

FESP (Forum for European Structural

Proteomics)

NMR-Life (coordination

action)

E-Mep-Lab(Training in

Membrane proteins)

TEACH-SG (Training in

Structural Genomics)

FP5 foundations for European Structural Genomics: SPINE (pilot IP 2002-2005)

Interdisciplinary Initiatives in Structural Genomics/Proteomics

VIZIER(RNA Viruses)

FSG-V-RNA(viral RNA)

E-MeP(Membrane

proteins)

3D-Repertoire (Large Complexes)

SPINE2-COMPLEXES Signalling Pathways-

Structures of complexes

Mature Field

Fig. 7: Steps to ERA in Structural Genomics and Structural Proteomics in FP6 (2002-2006)



large-scale data gathering initiatives, but will also participate in multidisciplinary systems biology approaches.Understanding membrane protein function remains one of the research frontiers in cellular biology. Membrane proteins constitute approximately one third of all human proteins and are important drug targets. However, in the current literature, membrane protein structure determination represents only 0.3% of all the protein structures existing in the public databases. To increase our knowledge in this important family of proteins, the EC set as a priority the structure-function analysis of membrane transporters and channels for the identifi cation of potential drug target sites, in the FP7 fi rst call for proposals in large-scale data gathering functional genomics initiatives.

The following two complementary large IPs were funded and started in the beginning of 2008.

EDICT: European Drug Initiative on Channels and TransportersAt a funding level of 12 million, this IP aims at characterising the structure-function of membrane superfamilies in human and pathogenic microorganisms, covering a wide variety of human diseases. The main strength of EDICT (where two of the partners are Nobel Prize winners) is its powerful HTP structural genomics pipeline. In ad-dition, high-resolution images coupled with sophisticated computational methods will identify new drug targets.

NeuroCypresAt a funding level of 11 million, this IP focuses on channel proteins of the central and peripheral nervous system involved in severe neurodegenerative diseases. Its main strength is its multidisciplinary approach with a focus on biology for understanding the link between dysfunction and disease.

Figure 8 shows the runtime of current EU-funded CPs in structural genomics and structural proteomics between 2002 and 2008, including all FP6 and the FP7 fi rst call funded projects.

This drastic change in investment implemented via the European FPs for RTD (FP5, FP6 and FP7 fi rst call for proposals), resulted in a major investment of approximately 120 million allocated to Collaborative Structural Genomics projects between 2002 and 2008.

Project Acronym 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 FP

FP5FP6

FP7

SPINEBIOXHIT3D-EM3DGENOMEE-MePVIZIERNDDPUPMANGeneFunFSG-V-RNA3D-RepertoireExtend-NMRHT3DEMIMPSOptiCrystSPINE2-COMPLEXESFESPE-MeP-LabNMR-LifeTEACH-SG

EDICTNeuroCypres

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

IP 13.7mIP 10m

IP 13mIP 10.35m

IP 13m

IP 12m

IP 11.9m

IP 11.03m

NoE 10m

STREP 2.2m

STREP 1m

STREP 1.9mSTREP 1.5m

STREP 2.4m

STREP 2mSTREP 1.8m


SSA 0.3mSSA 0.3m

SSA 0.5mCA 1.1m

Fig. 8: Runtime of current EU-funded collaborative research projects in structural genomics and structural proteomics(funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)



Comparative genomics is the analysis and comparison of genomes from different species. The purpose is to gain a better understanding on the genetic differences between species and to determine the function of the genes. Researchers have learned a great deal about the function of human genes by examining their counterparts in model organisms such as the mouse.

The sequencing of the human genome has revealed that our genetic material is composed of about 22 000 different genes. Despite their morphological differences, model organisms and humans share a strong conservation of genes as well as fundamental biological pathways. This extensive conservation has promoted the use of model organisms as a means to study conserved processes.

However, just identifying a gene does not tell us much about its potential function in health and disease. To in-vestigate this, it is necessary to mutate the gene in a model organism. Several model organisms are extensively studied to understand particular biological phenomena, with the expectation that discoveries made in these models will provide insight into the workings of other organisms. In particular, model organisms are widely used to explore potential causes and treatments for human disease in instances where experimentation on humans would be unfeasible or unethical.

FP6 activities

In FP6, substantial resources were invested in comparative genomics, in particular for research in rodent models like the mouse and the rat, but also in other vertebrate models like the zebrafish and the frog. Projects involving invertebrate models (e.g. nematodes, yeast, etc.) were been funded in FP6. Finally, bacterial and plant functional genomics projects were also partially supported as cross-cutting activities with other FP6 fun-damental genomics thematic areas.

The identification of all the genes in mice and humans in the Human Genome Project has shown that about 99% of the genes in mice have an equivalent gene (or homologue) in humans. This is important as, to date, around 5 000 diseases have been shown to be caused by an error in our genetic make-up (in our genes), for example cystic fibrosis and Down’s syndrome. In several more complex diseases, such as diabetes, an error in the genetic make-up is a contributory factor.

In addition, powerful conditional mutagenesis technology has been developed that currently can only be applied in the mouse to specifically inactivate any gene in a time- and space-dependent manner. This approach allows us to very precisely unravel the genetic networks underlying disease. All things considered, the mouse is one of the model organism of choice for human disease research.

EUMORPHIA was the first major integrated research programme (funded at the end of FP5) on mouse re-search that brought together a large consortium of 18 mouse research centres in 8 European countries. The main goal of this large initiative was the development and standardisation of new approaches in phenotyping, mutagenesis and informatics leading to improved characterisation of mouse models for the understanding of human physiology and disease. The project delivered an extensive database of standardised phenotyping protocols (EMPReSS) that is now widely used in many mouse laboratories across Europe (Brown S.D. et al., Nature Genetics, 2005, 11, 1113–20). Furthermore, this project has also played an important role in structur-ing the research landscape in mouse research in Europe.

In FP6, building on the success of EUMORPHIA, several mouse large-scale functional genomics initiatives (EUCOMM, EUMODIC, EUREXPRESS, and MUGEN) were funded that may be grouped as follows:



1. Projects that develop tools and resources for mouse functional genomics

EUCOMM integrates European skills, resources, and infrastructure to produce, in a systematic, HTP way, mutations throughout the mouse genome. A collection of up to 20 000 mutated genes will be generated in mouse embryonic stem (ES) cells using conditional gene trapping and gene targeting approaches. This mutant resource will be of crucial importance for health research since it will allow scientists to dissect gene functions within a living organism (in vivo) more accurately and to mimic human disease conditions more closely. By networking their effort at the European level with the EUCOMM project, Europeans researchers are playing a leading role in the International Mouse Knockout Consortium that was launched recently (Collins F.S., Cell 2007, 128, 9–13; Qiu J., Nature 2006, 444, 814–816) and which joined EUCOMM, KOMP (funded by the National Institutes of Health) and NorCOMM (funded by Genome Canada). FLPFLEX is a more focused project aiming to develop flexible genomic insertion cassettes carrying modifications to allow recombinase-mediated cassette exchange of effector genes of interest. Molecular Imaging is another project (mentioned earlier in the functional genomics tools section) which aims to develop non-invasive imaging tools for whole animals (mice) in vivo.

2. Projects that develop tools and technologies for large-scale and HTP phenotyping studies

EUREXPRESS and EUMODIC are both focused on phenotyping. EUREXPRESS’s main goal will be to deliver expression patterns for 20 000 mouse genes during embryonic development and in adult tissues. EUMODIC will phenotype in depth, using the EMPReSS standardised protocols (about 650 mutant lines) produced from the EUCOMM project. MUGEN is another FP6 major research initiative using functional genomics tools to analyse more that 200 mouse mutant strains showing defects in the immune systems in a standardised way.

3. Plenty of projects support biologically focused research, using mouse as an essential model to understand diseases mechanisms

These projects cover a great variety of basic biological processes; several projects use predominantly mouse as the animal model of choice.

MUGEN aims to structure and shape a world-class network of European scientific and technological excellence in the field of murine models of human immunological diseases that will advance understanding of the genetic basis of disease and enhance the innovation and translatability of research efforts.

The main objective of HEROIC is to make significant advances in the mechanistic questions of epigenetic regulation, characterise the epigenetic modifications that occur, and then understand the implications for gene expression in different cell types. The approach focuses on the use of HTP-enabling technologies on predominantly primary and established mouse cell lines, particularly ES cells.

The majority of the projects funded under the areas on multidisciplinary approaches to basic biological processes (see Part B,Chapter 7) are either using established mouse models or creating novel mouse models to understand health diseases. One example is the FunGenES consortium, which addresses fundamental issues of stem cell biology differentiation and functional genomics, pursuing an integrated strategy based on cultured mouse ES cells. Another, the EUROHEAR IP develops novel mouse models to understand the mechanisms of hearing deficiencies.

4. Projects that network and coordinate research efforts in Europe

Along with the research initiatives, the EC has financed two CA projects: PRIME and CASIMIR. The aim of PRIME is to build on existing national and European mouse research programmes, resource centres and infrastructures by focusing and integrating them, rather than establishing new programmes. The long-term aim is to establish mechanisms to define future research policies and directions in a coordinated manner across Europe. CASIMIR focuses on coordination and integration of databases set up in support of FP5 and FP6 projects containing experimental data, including sequences, and material resources such as biological collections, relevant to the use of the mouse as a model organism for human disease.



Europe has a large community of researchers using the rat as a model. Indeed, over the last 50 years, the rat has also intensively been used by physiologists to investigate molecular determinants of diseases such as diabetes. The availability of the rat genome sequence (since December 2004) and genome-scale technologies, along with the ability to clone fertile adult rats, has substantially advanced the potential for functional genom-ics research in the rat model.

The EURATools IP draws together leading European researchers in rat genetics, pharmacology, toxicology, dis-ease pathophysiology, and genome biology and informatics. The central aim of this project is the development of integrated genome tools that will generate knowledge that can be translated into improvements in healthcare for highly prevalent diseases in the EU. Besides scientific excellence, EURATools is expected to have a strong European structuring effect in the rat research community.

In addition, two smaller-scale projects, MED-RAT and STAR, were also funded in FP6. These two projects are complementary to the EURATools project: one is developing new tools to generate transgenic and knock-out rat models (MED-RAT) while the other is generating a SNP and haplotype map for the rat model (STAR).

Integrated European Mousefunctional Genomics Programme

FLPFLEX (transgenic tools)

FP5 foundations for European Mouse Functional GenomicsProgramme: EUMORPHIA (pilot IP 2002-2005) on

standardised phenotyping protocols

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

BiologicallyFocused Research

Phenotyping

Tools and Resources

Coordination, Fora,Workshops

European Pilot projectSTREP, CA, SSA

IP, NoE

MUGEN(mouse models

for immunological diseases)

EURExpress (high-throughput

in situ hybridisation)

FunGenES(mouse ES cells differentiation)

Molecular Imaging(in-vivo imaging

technologies)

HEROIC (Epigenetics in

Mouse ES cells)

EUCOMM(genome-widemutagenesis)

EUMODIC (European mouse

Disease clinic)

EUROHEAR (mouse models

for hearingdeficiencies)

PRIME(Co-ordination of mouse functional

genomics programmes)

CASIMIR (Co-ordination/integration

of databases)

Fig. 9 : Steps to ERA in mouse functional genomics research in FP6 (2002-2006) In FP5 and FP6 the European Commission has invested substantially in mouse functional genomics.

All projects are very ambitious and highly complementary to each other, thereby creating an integrated European Research programme in mouse functional genomics. By joining their forces at the European level via these collaborative projects,

Europe is now at the forefront of mouse functional genomics research at the international level.



Zebrafish is a vertebrate model that offers numerous advantages compared to the rodent models. It is smaller in size and less costly to grow and maintain. Many transgenic approaches are also possible in this animal, facilitat-ing the study of genes highly conserved in vertebrates and having functions in health and diseases.

Furthermore, for developmental biologists, the zebrafish model offers additional advantages. Indeed, the devel-opmental processes can be easily observed in the fish since the embryo develops outside the mother body and is also fully transparent. ZF-MODELS IP aims to utilise the zebrafish model to harvest large datasets on gene functions underlying development and disease. Fish with genetic disorders corresponding to human diseases are produced by chemical mutagenesis (forward genetics) and targeted knock-out (reverse genetics) and are phe-notypically characterised. These disease models will aid clinical researchers and the European pharmaceutical industry in the development of new therapies. This project will also contribute to improving basic knowledge of human development, since key genes involved in development are often reactivated in adult life in many con-genital diseases and cancers.

Furthermore, the zebrafish embryo model also shows great potential to be incorporated into preclinical drug screening pipelines. ZF-TOOLS aims to develop a case study for an anti-tumour drug screening system, based on implantation of fluorescently labelled tumour cells into zebrafish embryos. This system allows for the powerful combination of visual monitoring with HTP analysis of expression of marker genes with a predictive value for tumour progression or for defence responses to developing tumours.

The EC is also supporting functional genomics research projects in other model organisms including Xenopus laevis (X-OMICS) and C. elegans nematode (NEMAGENETAG). Under the Systems Biology umbrella, the EC is also supporting a large IP (AGRONOMICS) on leaf development in Arabidopsis thaliana and a large IP (BaSysBio) in Bacillus subtilis. These projects are also cross-cutting in nature, relating to other FP6 thematic priorities, in particular with Priority 2, related to Food Safety.

Importantly, an essential part of the thematic sub-area ‘Multidisciplinary functional genomics approaches to study basic biological processes’ is devoted to model organism research used as tools to understand a particular basic biological process. These projects are presented in a separate section in the current publication.

In conclusion, between 2002 and 2007, the EC’s FPs (FP5, FP6) provided more than 150 million for collaborative research projects on model organisms, such as mouse, rat, zebrafish, plant, nematode worm and bacteria. These projects are playing an important role in structuring the research landscape in Europe and creating the knowledge base to understand health and disease. Furthermore, they are generating important and freely available data and/or animal resources that will catalyse progress in biomedical research.

FP7 activities

In FP7, support of research on model organisms continues, and considering that FP6 funded several projects in rodent models, we have proposed calls for proposals on establishing consortia on genome-wide association studies in non-rodent mammalian models that develop diseases analogous to those seen in humans.

At the beginning of 2008, the EC launched the 12 million IP LUPA, which aims at elucidating the molecular basis of common complex human disorders using the dog as a model system. This project brings together ex-perts in genomics, the world’s leading scientists in complex trait genetic analysis, and interconnects the major veterinary centres of Europe, utilising HTP molecular tools. It should also be emphasised that particular attention is being paid to following strict national guidelines for animal welfare.



For the fi rst two calls of the FP7, in the genomics and systems biology area, no specifi c topics related to large IPs in rodent model organisms were proposed. This area, and in particular research in mouse, was well covered in FP6 and there was a need for the currently funded projects to reach the required maturity for novel evolving ideas.

A policy workshop was organised by the Genomics and Systems Biology unit in the Health Directorate in March 2007, in cooperation with other funding agencies, (including, the US National Institutes of Health and Genome Canada), to explore the future research needs in the fi eld of mouse functional genomics. The recommendations of that workshop, which brought together the world-leaders in the fi eld, also served as a foundation to refl ect on future FP7 activities in the area. In the FP7’s third call for proposals, published in September 2008, the EC proposed a bottom-up approach, implementing (for the fi rst time in the Health priority) a two-stage selection procedure, to attract proposals on large-scale functional genomics efforts in multicellular model organisms. The expected impact is to continue progressing in the understanding of the function of all human genes, their complex interactions, and their role in disease.

Common diseases of major public health importance are phenotypically complex, with many having a heritable component. Population genetics approaches are used to characterise complex diseases and associated pathophysi-ological states in respect to the genetic and environmental determinants involved. An important element of popu-lation genetics research is the study of the genetic variations and/or mutations that are correlated to the healthy and diseased phenotype. The estimated 22 000 protein-encoding genes are calculated to contain myriad possible variations, called polymorphisms, which increase the complexity of our genes. The human genome comprises about 3 x 109 base pairs of DNA, and the extent of human genetic variation is such that no two humans, even identical twins, will be genetically identical. The amount of genetic variation is about 0.1%, meaning that about 1 base pair out of every 1 000 will be different between any 2 individuals. Some of these variations determine physical char-acteristics, but others can determine the susceptibility to certain diseases, or the response to drug therapies.

Access to databases containing genotypic, clinical, and environmental and lifestyle information on individuals, along with corresponding clinical samples/specimens (biobanks), are an essential component for population genet-ics research. The systematic collections of genetic material and other relevant information on individuals, namely biobank collections, make it easier for researchers — using HTP analytical tools for monitoring DNA variations combined with powerful bioinformatics — to systematically search for links between gene variation and disease.


EUMORPHIAEURExpressMUGENFLPFLEXEUCOMMPRIMEEUMODICCASIMIRSTARMED-RATEURAToolsZF-MODELSZF-TOOLSTP PlantsNEMAGENTAGX-OMICS

LUPA

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

IP 17.3mIP 10.8m

IP 11.9m

IP 12m

IP 10.3m

NoE 11mSTREP 1.7m

IP 11mIP 12m

STREP 2.4m

SME-STREP 1.7m

SME-STREP 1.8m

STREP 1.6m

SSA 0.56m

CA 0.8m

CA 0.8m

CA 1.3m

Fig. 10: Runtime of current EU-funded collaborative research projects in model organisms(funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)



There has been relatively little success in finding genes for complex disease or complex traits, most likely due to the expected small effect of individual genes on complex disease. Because of the complex relationship between disease and genetic, environmental and lifestyle factors, population geneticists need access to very large num-bers of samples to ensure that any patterns they observe are statistically significant. For this reason, population studies increasingly necessitate international collaboration to ensure that large data sources can be shared. The ethical, legal and social aspects of this type of research are also extremely important factors in ensuring that individuals’ data are respected.

In several European countries, a multitude of national and regional population and disease-oriented biobanks have been systematically collected for decades via the national healthcare systems, representing a unique European strength. Significant advantage could be gained by pooling the resources already available or under construction. This could give researchers access to greater cohort size and data sets, so that the re-search outcome from associations’ studies between genotype, environment, and lifestyle at individual and population level could lead to greater statistical significance and prediction. The lack of standardised and quality-controlled protocols for data and sample collection, storage, retrieval, analysis and access, as well as the diversity of national legal regulations, have created a great deal of fragmentation and created obstacles for collaboration at European level. It would make an enormous difference if the protocols involved in human population genetics research at national level could be harmonised to become representative and accessible at European and international level.

Building the ERA in population genetics research via a coordinated and collaborative approach will address the existing bottlenecks and would pave the way for advances in biomedicine and improvement of the public health.

The EC, recognising the power of population-based approaches in the study of genetic susceptibility for disease, has funded a number of networking activities and collaborative research projects between 2002 and 2008.

In Europe, the first large collaborative initiative on genetic epidemiology on common diseases utilising samples from large- and medium-sized population biobanks and involving cross-border transfer of data and samples was launched in 2002 (pilot FP5 IP) with GenomEUtwin (www.genomeutwin.org). The main objective for Genom-EUtwin was to perform genome-wide analyses of European twin and population cohorts with the aim of identify-ing genes predisposing the carrier to common diseases. During the four-year period, the partners harmonised and integrated the study cohorts’ data (a combined cohort of 850 000 twins and a cardiovascular diseases cohort of 160 000 volunteers). Genome-wide studies have the potential to systematically identify the contribu-tions of common genetic variants to human disease. This unique project has provided the basis for the detection of small genetic infuences on common diseases, which may not be detected in small-scale family studies. Impor-tantly, the project has developed an Ethics Manual defining policies for the transfer of data and samples between countries. GenomEUtwin is a cornerstone of European genetic epidemiological research, because it paved the way for harmonisation of collected data, easy access to available data by creating a unified database structure and genome-wide analysis of the existing cohorts.

FP6 activities

The success of the GenomeEUtwin project, and its catalytic effect on the area, led to new CPs in FP6. These projects are taking full advantage of specific population cohorts available in Europe for determining the re-lationship between gene function and health or disease. These projects may be classified into the following general categories.

1. Projects developing tools and technologies

These projects bring together the critical mass to catalyse the development of techniques and technologies for population genetics research.

MOLPAGE is an IP that develops and validates a range of ‘-omics’ technology platform tools (metabo-nomic, genomic, proteomic) for molecular phenotyping in large epidemiological studies. These tools will be used for identification of biomarkers, prediction of disease, and risk determination or response to therapy. The consortium develops and disseminates standards for the collection, processing and storage of biologi-


http://www.genomeutwin.org


cal samples that are suitable for use in large sets of individuals, applicable to biological fluids and solid tissue samples, and optimised for future ‘-omics’ platform analysis. The project is expected to significantly contribute to the development of international scientific standards in molecular phenotyping.

2. Projects performing large and medium-scale epidemiological studies

All these projects perform large-scale studies on genetic epidemiology on common diseases and related traits, utilising samples in large- and medium-sized biobanks and involving cross-border transfer of data and samples.

The EUROSPAN focused project has the objective of quantifying genetic variation in established diseased genes across population cohorts in Europe, with the goal of identifying novel disease variants. It will cre-ate a large database of phenotypic and genotypic data from genetic isolated populations and will thus improve European competitiveness in gene discovery.

GenOSept is a STREP which uses a multidisciplinary fundamental genomics approach to examine genetic predisposition to sepsis by harmonising HTP genotyping and quality control between major European centres.

3. Projects for networking and coordination

The EC is also financing several CAs (such as PHOEBE and IMPACTS), as well as SSAs (such as DanuBiobank and EUHealthGen). PHOEBE promotes harmonisation of epidemiological biobanks in Europe. IMPACTS coordinates the standardisation of tissue archives. EUHealthGen organised a Wellcome Trust/EU EC con-ference (‘From Biobanks to Biomarkers’) to enable dialogue on the potential of human population genetics research. The aim of Danubiobank is to establish a biobank foundation for ageing disorders by networking universities, teaching in hospitals, developing prevention programmes and clinics along the Danube River, via the organisation of workshops and conferences.

On the whole, these projects have the following aims: to exchange information on research biobanks in Europe and beyond; to standardise and harmonise existing protocols for the acquisition, management and analysis of data and samples from different sources; to develop common quality assurance schemes; and to standardise approaches to ethical and legal issues.

By networking existing national capacities, FP6-funded projects have provided the critical mass to catalyse the development of techniques and technologies for population genetics and to conduct large epidemiological stud-ies. Together, these projects will enable researchers to better understand the ways in which interactions between genes and environmental factors are involved in the causes of common diseases and to determine the influence of specific genetic variations on the development or severity of these diseases.

FP7 activities

The FP7 Health theme has several objectives, one of which is to integrate the vast amounts of genomics, epide-miological and biological data with a view to translating this data into the understanding of major diseases and the ultimate development of new preventive, diagnostic and therapeutic methods. That is why population genet-ics and biobanks research aiming to develop tools and harmonisation principles is essential in FP7.

In the future, the integration of traditional population epidemiological genetic studies with HTP ‘-omics’ tools (genomics, transcriptomics, and metabolomics) and bioinformatics as an essential component, is expected to tremendously boost the field of population genetics.

With this in mind, in the FP7 first call for proposals under the HTP research activity area, the EC funded a large scale integrating project to develop groundbreaking techniques for DNA sequencing and genotyping, which is expected to increase the efficiency and cost of existing tools and lead to wider applicability in the clinical environment.

The READNA project, with 12 million of funding, focuses on next-generation nucleic analysis technologies and devices. The tools developed should increase the sensitivity, rapidity and efficiency of existing tools for sequenc-



ing and genotyping, with a target of 1 000 for the sequence of a complete human genome, while at the same time leading a revolution in cost-effective, non-invasive early screening of large cohorts for diseases.

In FP7’s first call for proposals, the large-scale data-gathering activity area supported two highly complementary projects (started in 2008) for performing molecular epidemiological studies in existing well-characterised Euro-pean population cohorts, with the objective of identifying candidate susceptibility genes to multifactorial diseases by integrating genome-wide association studies and the advances of ‘-omics’ developments.

The ENGAGE project, with 12 million of funding, sets as its main objective the integration of the results from many large-scale genetic studies underway in Europe and Australia, and the identification of novel disease- and trait-susceptibility variants for multifactorial diseases. The scale is large, with more than 650 000 DNA samples from various cohorts involved; the focus is primarily on cardiovascular and metabolic diseases, but can be expanded to other common disorders.

The HYPERGENES project, with 10.2 million in funding, aims to dissect complex genetic traits using hyper-tension as the disease model. The consortium will identify, by means of a whole genome association approach, genes contributing to essential hypertension (EH) and to EH-associated target organ damage, utilising well-characterised European cohorts. A combination of the most up-to-date methods of genomics, molecular genetics, molecular epidemiology and bioinformatics, together with learning-based modelling of the data, is expected to produce a disease model.

To keep Europe at the forefront of technology development in population genetics and biobanks research, the EC published the third FP7 call for proposals in September 2008, via its Genomics and Systems Biology programme; a bottom-up approach via a two-stage selection procedure was implemented for the first time in the Health priority. In the activity area of HTP research, the scientific community is invited to submit proposals for large integrating projects on the following topics:

■ The development of HTP tools and technologies to phenotype samples in large-scale human biobanks.

The projects are expected to accelerate epidemiological studies and biomarker discovery by increasing the molecular analysing capacity of biobanks, and will deliver high-quality and reproducible data set to enable standardised approaches for large-scale biobanks.

In the activity area of large-scale data gathering initiatives, the FP7 third call for proposals invites proposals on the following topics:

■ Characterisation of human genetic variation in Europe.

The projects should aim at characterising genetic variation in populations from different regions and ethnic minorities in Europe, involving normal and/or disease phenotypes. A large-scale comparative study of ge-netic variation in human populations in Europe is expected to facilitate ongoing and new epidemiological studies, and fill in the information gaps on genetic variability in healthy and/or disease phenotypes.

■ Large-scale functional genomics efforts to identify molecular determinants of cancer. The projects should implement multidisciplinary functional genomics approaches (e.g. sequencing, tran-

scriptomics and/or epigenetics) to characterise in detail a large number of human cancer tumour samples, so as to identify molecular determinants that contribute to human oncogenesis. They should establish the standards and norms on the manipulation and storage of tumours samples, thereby facilitating the compari-son between different data sets.

Recognising the power of population-based approaches in the study of genetic susceptibility for disease, the EC’s FPs for RTD provided more than 60 million to collaborative research projects in this area between 2002 and 2008 (see fig.11 representing the steps towards the ERA in population genet-ics research). In future calls, the Health theme will continue supporting this area, which will allow the EU to develop and maintain a leading global position in genetic epidemiology and population genetics.


48

As we move towards understanding biology at the systems level, access to large data sets of many different types has become crucial. The data obtained from such technologies (such as genome-sequencing, microarrays, proteom-ics and structural genomics) have provided ‘parts lists’ for many living organisms, and bioinformatics provides the systematic cataloguing and interpretation of this data. Researchers are now focusing on how the individual compo-nents fit together to build systems. The hope is that scientists will be able to translate their new insights into improving quality of life. The functional genomics HTP revolution is generating a vast amount of data. There is an ongoing (and growing) need to collect, store and curate all this information in ways that allow its efficient retrieval and exploita-tion. By making these data available to the academic and industrial research communities in an accessible and usable form, bioinformatics research ensures that the potential for genomics and health research is maximised.

FP6 activities

The FP6 objectives for the field of bioinformatics were to enable researchers to access efficient tools for manag-ing and interpreting the ever-increasing quantities of genome data, and for making it available to the research community in an accessible and usable form.

The foundations for meeting these challenges were laid in FP5, especially with the major large-scale IP TEM-BLOR, which supported the development of major databases, including those for protein structure and sequence, protein-protein interaction, gene expression and integration of this and other data. The capabilities established and strengthened by TEMBLOR brought Europe to a level similar to that of other major world centres in the key areas of life sciences research.

In FP6, an ERA has been established in bioinformatics, building on the foundations in FP5. This bioinformatics ERA forms the basis for a wide range of applications for health research, and will be a key element in a future ERA in systems biology, already under development in FP6 as well.

Integrated research in Population Genetics & Biobanks

GenOSept (genetic predisposition

sepsis)

FP5 foundations for Population Genetics: GenomEUtwin (pilot IP 2002-2005)

ENGAGE(genetic epidemio-

logy-Common diseases)

EUROSPAN (genetic variation)

EUHEALTHGEN (impact of

population genetics)

Impacts(Tissue archivesstandardisation)

PHOEBE (harmonisation of

population biobanks)

EpiGenChlamydia(host-pathogen

genomics)

HyperGenes(genetic

epidemiology-hypertension)

Genetic epidemiologyof common diseases

Technological Developments

Coordination, Fora,Workshops

FP5 EuropeanPilot project

MolPAGE(molecular

phenotyping tools)

READNA(sequencing/genotyping

technologies)

Microsat(workshop on

microsatellites)

DanubioBank(age-related

biobanks)

HUMGERI(Human Genomics

Integration)

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

FP7 1st call - 2006

STREP, CA, SSA

IP, NoE


Fig. 11: Steps to ERA in Population Genetics and Biobanks in FP6 (2002-2006) and FP7 first call projects


49

Three major NoE in bioinformatics were established in FP6, which constitute the core of the bioinformatics ERA. All of them also involve the European Molecular Biology Laboratory and the European Bioinformatics Institute (EMBL-EBI), which is a major core facility in Europe, and dozens of other major and smaller partners in Europe and worldwide.

In bioinformatics, BIOSAPIENS has created a European Virtual Institute for Genome Annotation, bring-ing together the best laboratories in Europe, including informaticians and experimentalists. The institute has greatly improved bioinformatics research in Europe by providing a focus for annotation, and by organising European meetings and workshops to encourage cooperation, rather than duplication of effort. The Institute has established a permanent European School of Bioinformatics, to train bioinformaticians and to encourage best practice in the exploitation of genome annotation data for biologists. The tools developed have already been applied to gain important insights into the mechanisms of genetic mutation in major diseases such as HIV/AIDS and Down’s syndrome.

The EMBRACE NoE integrates the major databases and software tools in bioinformatics in Europe by creating a bioinformatics computer grid for easy and integrated data access, analysis and services. The integration efforts are being driven by an expanding set of test problems representing key issues for bioinformatics service providers and end-user biologists. As a result, groups throughout Europe will be able to use the EMBRACE service interfaces for their own local or proprietary data and tools. ATD aims to understand the mechanisms that are responsible for the formation of transcript isoforms on a genome-wide scale by creating a value added database of alternate transcripts from human and model species.

Finally, ENFIN is connecting bioinformatics and wet-lab capabilities with a Europe-wide integration of computa-tional approaches in systems biology. Computational work includes the development of a distributed database infrastructure appropriate for small laboratories and development of analysis methods including Bayesian net-works, metabolite flux modelling and correlations of protein modifications to pathways. ENFIN will deliver a platform for database provision of diverse biological data, integrated analysis tools, guides for wet laboratory utilisation, and ‘best practice’ guidelines for systems biology.

Furthermore, bioinformatics is included as an essential component by creating integrated databases in many multidisciplinary functional genomics projects aiming to understand basic biological processes in health and dis-ease (see next section). There are several characteristic project examples: MITOCHECK (which creates a publi-cally accessible database for all the proteins involved in mammalian cell cycle), MYORES (a NoE on muscle development in different model organisms, which implements a database for muscle research), EVI-GENORET (which is creating a state-of-the-art relational database integrating functional genomics data and clinical disease data for genes involved in retina development, degeneration and disease).

The development of computational biology and integrated bioinformatics databases of diverse ‘-omics’ data is an essential component for the successful implementation of systems biology approaches. Several systems biology projects funded in FP6 (see following section) are focused on the development of computational tools. There are several characteristic examples: EMI-CD is developing a software platform connecting several modules neces-sary for the in silico modelling of complex disease processes, while COMBIO combines a unique group of ex-perimentalists, bioinformaticians and simulation groups in order to gain detailed understanding of key processes like the P53-MDM2 regulatory network. Also, COSBICS is establishing and applying a novel computational framework to investigate cellular signalling pathways and subsequent target gene expression. The DIAMONDS project aims to demonstrate the power of a systems biology approach in the study of the regulatory network structure of the most fundamental biological process in eukaryotes: the cell cycle, in different species.

FP7 activities

Continuing the efforts to strengthen the ERA in bioinformatics, in the FP7 first call for proposals under the HTP research activity area, the EC funded a large scale integrating project to unify human and model organism ge-netic variation databases; this is expected to achieve effective linkage between databases and would facilitate analysis in population genetics studies.

The GEN2PHEN project, with 12 million level of funding, implements an integrated approach towards unifying




human- and model-organism genetic variation databases, in such a way that the resulting holistic view of genotype-to-phenotype data can be blended with other biomedical databases via the central genome browser ENSEMBL. The project will help to overcome existing access and usage barriers for genotype-to-phenotype relationships, by providing an integrated informatics structure. It will further facilitate easy access to the stored information and as-sociated resources through development of a Web portal knowledge centre.

To keep Europe at the forefront of bioinformatics developments, the EC, via its Genomics and Systems Biology programme, published the third FP7 call for proposals in September 2008, implementing a bottom-up approach via a two-stage selection procedure for the first time in the Health priority.

In the activity area of HTP research, the scientific community is invited to submit proposals for large IPs on the following topic.

■ Computational tools for genome annotation and genotype/phenotype data integration. The projects are expected to develop new computational tools and methods for genome/proteome annota-tion to catalyse the progress of systems biology by describing, for example, molecular interactions, path-ways and networks. The development of new computational tools for genome annotation and genotype/phenotype data integration will enable integration of vast amounts of data generated on gene function genomics to facilitate data mining and catalyse progress in systems biology.

In summary, between 2002 and 2008, the EC’s FPs for RTD provided approximately 75 mil-lion to collaborative research projects in the area of bioinformatics. Before FP6, although there was a strong European core at the European Bioinformatics Institute, there were a wide range of databases and capabilities scattered across Europe with suboptimal access and interaction. By the end of FP6, databases, services, analysis tools, and scientific research were strengthened locally and linked together at European level to produce highly coordinated resources in support of biology and health-related research, a fact that has greatly increased our understanding of the wealth of data being generated in Europe and the rest of the world.

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

FP7 1st call - 2006

Computational Biology

Databases focusedon a biological theme

Classical Bioinformaticsand Databases

European FP5 Pilot project

STREP, CA, SSA

IP, NoE

Bioinformatics Databases,Computational tools for Systems Biology

ENFIN(computational

tools for SB)

COSBICS (modellingCellular signalling)

DIAMONDS (cell cycle modelling)

EMI-CD(Disease modelling)

COMBIO(P53 and spindle

modelling)

MYORES(muscle development

network)

MITOCHECK (mammaliancell cycle)

EVI-GENORET(retina development

& disease)

BioSapiens (Genome

Annotation)

EMBRACE (Bioinformatics

Grid)

ATD(Alternativetranscripts)

GEN2PHEN(genotype/phenotype

Databases grid)

FP5 foundations for European Bioinformatics: TEMBLOR (Cluster of 4 proposals) 2002-2004

Plus individual smaller projects

Fig. 12: Steps to ERA in Bioinformatics in FP6 (2002-2006) and FP7 first call projects



Extremely strong bases in the bioinformatics area have been established. However, just as existing fields are showing an ‘explosion’ of data (as new fields are being established in the various ‘-omics’ disciplines such as metabolomics, regulomics) and as these data and analysis tools are being linked together and used as the driving force for systems biology analysis, so bioinformatics research also needs to grow.

The full potential of systems biology research has not yet been achieved in Europe, because basic databases and research methods have not yet provided the entire basis needed to fully apply a systems approach. The approaches planned in FP7 should allow us to overcome the future challenges in bioinformatics and computational biology.

The different approaches to functional genomics described in the earlier sections — gene expression, proteom-ics, structural genomics, model organisms and population genetics and bioinformatics — provide researchers with an extremely powerful multidisciplinary ‘toolbox’ which they can use to study and manipulate fundamental biological processes.

By picking the most appropriate genomic tools, or combination of these tools, researchers are developing inno-vative ways to study the basic understanding of cellular processes, by revealing the function and interactions of cellular components in health and disease. The multidisciplinary approaches provide opportunities to view these processes from different angles and gain new insights into the underlying cellular functions.

Diseases are often the result of important biological processes dysfunctioning, either because of external stimuli, such as pathogens or environmental factors, or because of inherited or acquired gene mutations resulting in incorrectly coded gene products unable to perform the appropriate cellular function. By understanding normal cellular processes in organisms as diverse as micro-organisms, plants and animals, researchers will be able to manipulate the cellular processes involved in disease, enabling therapeutic advances.

In FP6, this research sub-area funded projects implementing innovative and multidisciplinary approaches of func-tional genomics to study basic biological processes in health and diseases. A series of large-and medium-scale transnational projects were supported in FP6, where the main goal is to develop innovative ways to understand basic biological processes such as transcription regulation, DNA repair, cell cycle, epigenetics, hearing and vision processes, immune system, intra- and inter-cellular signalling, and developmental processes. The innovation is a result of the integration of the most appropriate multidisciplinary functional genomics tools; in this way we can gain new knowledge on the complexity of the underlying mechanisms of life that constitute the footprint of a physiologi-cal and/or pathological situation.

In summary, the sub-area of multidisciplinary approaches to basic biological processes in FP6 supports projects that may be grouped into the following categories:

■ basic biological pathways in intracellular and extracellular signalling

■ tissue and organ development, homeostasis and diseases

■ stem cell biology

■ RNA biology

■ chronobiology

■ biology of prokaryotes and other organisms



Several projects aim to discover the genes involved in the regulation of fundamental processes such as cell cycle, DNA repair (examples are MITOCHECK, DNA REPAIR, RUBICON). A series of projects, such as EVI-GENORET, EUROHEAR and MYORES, provide new knowledge on the fundamental molecular and cellular biology of differ-ent tissues/organs as well as their development and malfunction, with the ultimate goal of therapeutic advances. Large-scale functional genomics initiatives were funded to shed light to fundamental questions in embryonic/adult stem-cell research: how multipotent stem cells and early progenitors become committed to a single devel-opmental pathway and then differentiate to the specific cell type (examples are FunGenes and ESTOOLS). The exciting discoveries in RNA biology of the ‘second genome’ and the non-protein coding genes as organisers and coordinators of the organism’s complexity are tackled by several projects (SIROCCO and RIBOREG), including the increasing importance of post-transcriptional regulation of gene expression (EURASNET).

In FP6, between 2002 and 2006, the EC provided approximately 220 million to collabora-tive research projects in the area of multidisciplinary approaches for fundamental biologi-cal processes. All these European efforts have created the critical mass that will boost European excellence in the respective fields by increasing integration and reducing fragmentation. It is important to mention that even though the projects are focused on fundamental biology, for the first time several of them are integrating basic biologists, clinical scientists and industry (including SMEs) where appropriate, to facilitate the transfer of basic knowledge to clinical applications. Several projects are improving functional genomics tools for the genome-wide understanding of gene function that would be applicable in all areas of cell biology. Training courses in multidisciplinary expertise of the next generation of biologists has been implemented in several, mostly large-scale projects. Importantly, the issues of setting up standard operational procedures on method-ologies and data collection, and the creation of integrated bioinformatics databases have been addressed — the latter being an essential element of collaborative effort in Europe.

In summary, the FP6 projects have already generated a comprehensive list and map of the multiple set of genes and proteins related to a basic biological process in normal and/or pathological situations. Indeed, major discoveries on novel gene functions have already been made that have resulted in high-level publications by collaboration of various laboratories, previously working in isolation. Most importantly, these projects have played an important role in integrating the research community in Europe, thereby increasing their visibility

Multidisciplinary Initiativesfor understanding basic biological processes

Basis for advances in post-genomics era: High-throughputTools for Proteomics, transcriptomics, model organisms, imaging

EUROHEAR(Hearing process and deficiencies)

EureGene (kidneydevelopmentand disease)

EuTracc(transcriptional

regulation in ES cells)

ESTOOLS(hES

differentiation)

MAINChronic

inflammationDNA Repair

BIOSAPIENS (Human Genome

Annotation)

EMBRACE(Bioinformatics

grid)

EndoTrack (endocytosis)

SIRROCO(Small

regulatory RNAs)

Tissue/organDevelopment and disease,

Stem cell biology

Biological pathwaysand signalling

In silico tools,Integrated bioinformatics

databases

Tools and technologicsfor ”-omics”

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

CA, STREP

IP, NoE

Fig. 13: Steps to ERA in multidisciplinary functional genomics approaches for understanding basic biological processes in FP6 (2002-2006)



at the national, European and international level. They have also substantially contributed towards reducing fragmentation of research in Europe in their respective fields, thereby implementing the concept of the ERA and creating a real multidisciplinary integrated programme of activities, as is illustrated in Fig. 13.

The FP6 investment constitutes the largest programme ever (in Europe and worldwide) that addresses fundamental biology in such a multidisciplinary collaborative way, implementing state-of-the-art functional ‘-omics’ approaches.

However, it must be recognised that cellular components interact in subtle and complex ways, even in the simplest organisms. The understanding of the enormous complexity of the interacting gene networks that are responsible for most biological processes will require integrative and quantitative forms of analysis of diverse data. It is important to emphasise that the ‘multidisciplinary approaches to basic biological processes’ action line, has already provided a richness of large-scale ‘-omics’ data that constitutes the foundation for future systems biology initiatives in Europe.

Cellular signalling helps govern basic cellular activities and coordinates cellular function. A cell’s ability to re-spond correctly to its surrounding environment is the basis of normal cellular growth and tissue homeostasis, as well as development and repair. Dysfunctions of the transmission and process of signalling within the cell may result in many diseases. An improved understanding of the basic biological pathways involved in intracellular and extracellular signalling will lead to more effective therapies for these diseases.

In general, the FP6 projects funded in this broad sub-area could be classified into two groups: those focusing on basic biological processes in healthy conditions, and others focusing on disease.

1. Projects applying multidisciplinary approaches for understanding basic biological processes in healthy conditions

MITOCHECK involves research into the regulation of mitosis and into the mammalian cell cycle, ab-normalities of which can contribute to cancer. The project applies cutting-edge technologies: the use of RNA interference genome-wide screens to identify in a systematic manner (functional genomics) all genes involved in mammalian cell-cycle, and proteomics approaches to identify novel protein complexes and phosphorylation sites. A web-based database is created with such information as, the list of genes required for mitosis, the sub-unit composition of mitotic complexes, and genome-wide RNAi screens phenotypic data that will provide a valuable source of information to the whole cell biology community.

The RUBICON NoE focuses on the better understanding of post-translational modifications of proteins by ubiquitination. It will establish the link to diseases such as infectious and inflammatory conditions, cancer, and neurodegenerative disorders. This goal is achieved by applying multidisciplinary functional genomics to elucidate the functions of genes and gene products, and by defining the regulatory networks controlling ubiquitination.

The EndoTrack project aims at gaining conceptual advances into the signalling function of growth factors from an unconventional perspective, namely by exploring the role of endocytic trafficking in the modula-tion of signalling and gene expression regulation. It further aims to translate such basic knowledge into novel opportunities for the development of a new generation of tools to combat diseases like cancer, and cardiovascular, metabolic, and infectious and neurodegenerative diseases

The PEROXISOMES project, using cutting-edge proteomics tools, identifies and characterises the func-tions of novel peroxisomal proteins and establishes a catalogue of peroxisomal proteins in human liver, kidney and brain. The consortium will evaluate the role of peroxisomes as modulators or modifiers of dis-eases of complex inheritance, such as cancer and neurodegenerative disorders.

TRANSDEATH will investigate the functional relationships between the different forms of programmed cell death by using appropriate models. These mechanisms will then be used to understand corresponding types of cell death in mammals, and particularly in humans.



SIGNALLING & TRAFFIC will establish the connections between signalling pathways and membrane trafficking in the context of migrating, dividing and adhering mammalian cells. Through the study of membrane traffic in the course of cell differentiation, dedifferentiation, and during mitosis, the project explores how membrane traffic can influence signalling cascades.

2. Projects applying multidisciplinary approaches for understanding basic biological processes in disease

The MAIN project is identifying and characterising the molecular mechanisms underlying chronic inflam-matory responses and will produce cutting-edge technological approaches for use in cell migration. It primarily studies the migration of leukocytes from the bloodstream into inflamed tissues, and their local ac-tivation by inflammatory substances and pathogens. A bioinformatics database is being created, enabling rapid data retrieval and analysis, and cross-correlation of functional genomic and functional proteomic data, facilitating biological hypothesis-making and ‘systems’-level investigations.

Aneuploidy is the term used to describe the abnormal copy number of genomic elements. The ANEU-PLOIDY project is studying the phenotypic consequences of gene dosage imbalance in humans at cellular and organism level, by focusing on two prototype human model phenotypes: trisomy 21 and monosomy. The project will allow the identification of genes and biological pathways potentially involved in new aneu-ploidy syndromes.

The DNA REPAIR consortium is using an integrated multidisciplinary approach to improve understanding of DNA damage response and repair systems in living organisms. Genomics tools are used to identify new components of DNA damage response pathways. The project will extrapolate the findings from model organisms to humans, by the investigation of cells from patients suffering from genome instability, cancer predisposition and premature ageing syndromes.

WOUND will identify evolutionary conserved genes and major signalling pathways involved in epithelial fusion and wound healing, using model systems.

The project STEROLTALK has undertaken a systematic post-genomic evaluation of cholesterol home-ostasis and its cross-talk to drug metabolism and will contribute towards understanding the effects and side-effects of hypolipidemic therapy and combined therapies.

All the projects described in this section have set very ambitious and technically challenging objectives which clearly exceed the capacity of a single laboratory. The combination of a critical mass of excellent European researchers with a readiness to develop new concepts and highly innovative methods as part of European con-sortia has stimulated a European corporate identity in their respective fields and is expected to greatly reinforce competitiveness. To overcome the duplication of efforts in the production of research tools and data, the majority of the projects have established shared databases to include ‘-omics’ data which are shared between collabora-tive laboratories. The availability of state-of-the-art HTP technologies is currently restricted to a relatively small number of laboratories at larger institutions. All these projects have promoted access to advanced technology. The development of these technologies, as well as the integration of industry and SMEs in most of the projects, further facilitates the transfer of basic knowledge to future commercial applications.

FP6 has built a strong basis by funding several projects applying multidisciplinary ‘-omics’ approaches to under-stand the molecular pathways and identify novel genes involved in tissue and organ development, degeneration and disease. All projects apply functional genomics approaches and bring together multidisciplinary expertise in the same consortium for the first time, and several of them are validating the knowledge produced for devel-opment of gene and stem cell therapies. The focal point for most of these projects lies in fundamental research. However, the involvement of clinical expertise, the use of disease population cohorts and industry (including SME) involvement, promises rapid translation of the basic knowledge to clinical applications.



The LYMPHANGIOGENOMICS consortium brings together leading researchers established in the field of lymphangiogenesis and provides fundamental insights into the molecular and cellular basis of the lym-phatic diseases. The project promotes the development of therapies for the treatment of cancer, inflamma-tory disease, tissue ischemia and lymph oedema, and has been one of the main drivers behind the recent growth in the field of lymphatic biology.

The MYORES NoE integrates the work of European laboratories previously working in isolation. The project aims at identifying the genetic determinants of muscle normal development, degeneration and dis-ease, and at developing technologies for HTP screening in order to isolate novel molecules and rapidly test their suitability for muscle function and repair in animal models. The creation of the MyoBase database as a main integrating activity will become the main source of information in muscle biology.

The aim of EVI-GENORET is to understand the fundamental molecular and cellular biology of the retina, of its development and of the way it is perturbed by genetic mutation, environmental factors and age. The project integrates population genetics, clinical and experimental phenotyping, molecular genetics approaches, and HTP transcriptomics and proteomics analysis for the pathophysiology of the retina. The creation of a state-of-the-art bioinformatics database that will integrate diverse ‘-omics’ data with clinical data it is expected to accelerate diagnosis, disease screening, drug target evaluation and the development of new therapeutic strategies for inherited and age-related retinal diseases.

The EUROHEAR IP has two closely interrelated objectives: to provide fundamental knowledge on the development and function of the inner ear and to identify the molecular effects underlying hereditary hear-ing impairments, including presbycusis. The involvement of hearing-impaired individuals and their families in research is essential for the understanding of normal and abnormal auditory function. The EUROHEAR project demonstrates vigorous cross-disciplinary expertise with strong interaction between human and ani-mal models geneticists, development of biophysical and bioimaging techniques combined with functional genomics, as well as a sound inner-ear training programme for young European scientists.

EuReGene integrates European excellence in research relevant to renal development, pathophysiology and genetics. The main objective is to discover genes responsible for renal development and disease. The consortium involves the multidisciplinary expertise of leading scientists, including clinicians and SME partners, and focuses on the development of novel technologies and discovery tools in functional ge-nomics and their application to kidney research. Knowledge generated will be available to the scientific community and to the stakeholders through freely accessible databases and repositories.

All of the above projects, representing an investment of more than 60 million, constitute the most coordinated and integrated approach in Europe and internationally in the fields of kidney, inner ear, retina, muscle and lym-phatic tissue health and disease.

All the above projects are developing standardisation of protocols, and several of them standard operating pro-cedures facilitating the cross-comparison of results between geographically isolated laboratories. Several of them are developing a strong bioinformatics database that for the first time will integrate diverse data existing in differ-ent laboratories to be shared and analysed by members of the consortia in collaboration. An advantage in these fields is access to large-scale population cohorts as well as access to HTP genomics and genetic platforms.

Given the genetic complexity of different organs and tissues, the cooperation between the European groups is expected to be instrumental both in terms of resource sharing and complementary expertise. These consortia by uniting their efforts, have created a structure unequalled elsewhere.

Disorders affecting normal organ and tissue function have an impact in the quality of life of large populations and have a serious economic impact on the European economy. The knowledge produced will contribute strategies to combat common and rare diseases as well as inherited and age-related diseases related to organ development and degeneration, and to identify novel disease genes and novel targets for diagnosis and therapy.



The EU has supported stem cell research for a number of years in successive FPs. Stem cells have enormous po-tential, not only in regenerative medicine for replacing damaged tissue in various diseases, but also for applica-tions in drug discovery, toxicology and pharmacogenomics. Stem cell research is also crucial in understanding the basic underlying processes that lead to serious pathological conditions.

In fundamental genomics and under the area in which multidisciplinary approaches are applied to basic biologi-cal processes, the EC funds several projects with the aim of generating knowledge on the fundamental processes governing stem cell differentiation in human and model organisms. If we can learn more about this fundamental process, we might be able to reprogramme the body’s own cells, for example, to replace diseased or damaged tissue. Various sources of stem cells are studied and compared, including ES cells, adult stem cells and induced pluripotent stem (iPS) cells originating from somatic cells.

FUNGENES applies multidisciplinary approaches with an emphasis on microarray expression analysis to mouse ES cells that are in a state of self-renewal or that have been induced to differentiate in various tissues of the three major differentiation pathways. It delivers a gene expression atlas on the genetic pathways for cell differentiation into heart cells (cardiomyocytes), nerve cells (neurons), smooth muscle cells, vascular endothelial cells, fat cells (adipocytes), liver cells (hepatocytes) and insulin-producing cells of the pancreas. The data are analysed by meth-ods of bioinformatics to produce new knowledge regarding genetic pathways, to identify novel genes that are involved in different aspects of development, and lastly to validate the candidate genes by genetic engineering of mouse ES cells. The project is expected to have an impact on future novel therapeutic strategies for diseases including cancer, liver disease, diabetes and cardiovascular and neurodegenerative diseases.

ESTOOLS applies multidisciplinary genomic techniques and genetic tools to uncover the basic mechanisms con-trolling the choice that human ES cells make between self-renewal and differentiation into the neuronal lineage, by utilising 52 human ES cell lines. It will develop internationally agreed standardised protocols and tools for growing and manipulating ES cell lines, and for monitoring their phenotypic, genetic and epigenetic stability. This knowl-edge will be disseminated to the wider scientific community to make the best use of the existing stem cell lines, and ultimately will allow the culture and exploitation of hES cells.It will also address the technology for deriving induced Pluripotent Stem (iPS) cells and explore whether iPS cells have genetic, epigenetic and developmental properties equivalent to human ES cells. If this technology can be established, and if the derived cells are indeed identical to ES cells, then this approach may in the future reduce the need for working with embryo-derived stem cells. A first step towards regenerative medicine involves finding a means to cause controlled dedifferentiation of adult tissue. The project PLURIGENES investigates the controlled de-differentiation of adult tissue in order to discover the function of genes controlling pluripotency and de-differentiation in the central nervous system, so as to ultimately combat diseases such as brain injury and/or ageing. The project is based on the identification of candidate pluripotency associated genes evolutionarily conserved between different model organisms. The knowledge generated on self-renewal pathways (which are often deregulated in cancer stem cells) might also lead to improved outcomes in the treatment of human tumours.

One of the big challenges for the next decade is to understand the regulatory network of TFs that control cel-lular functions. EuTRACC determines the regulation of the genome by mapping the regulatory pathways and networks of TFs (the ‘Regulome’) that control the activity of ES cells and the process of differentiation into neural tissues and the blood system. The project utilises multidisciplinary approaches by applying genetics, proteomics and genomics tools in the mouse mainly, which are complemented by functional assays in other model organ-isms. The neural and hematopoietic tissue types were selected because of their well-characterised differentiation pathways and their existing clinical applications.

Several of these projects cooperate closely with international efforts. ESTOOLS will play a significant role in the development of standardised techniques for hES cells not only in Europe, but throughout the world, by working together with the International Stem Cell initiative (ISCI), which addresses issues of standardisation of markers and techniques for studying human ES cell lines. will collaborate with the International Regulome Consortium (IRC), a worldwide consortium that will map the genetic regulatory nodes and networks that control the function and lineage determination of embryonic and adult stem cells, with immense implications for devel-opmental biology, disease and regenerative medicine.



The flow of genetic information from DNA via mRNA to protein has been termed as the central dogma of molecular biology. Early results in post-genomics research have already challenged established views about the nature of the genome. A surprising result of the human genome sequencing experiments was that only a very small proportion (1,5%) of the entire genome encodes for proteins. It was once thought that a large proportion of our genome was in-active ‘junk DNA’, but today we know that many of these genomic regions are regulatory sequences responsible for activating or silencing genes when necessary. A major surprise in the human and mouse genome sequences was the discovery that humans do not have considerably more genes than other mammals. However, the mammalian transcriptome is largely constituted of many non-protein coding transcripts (many more than the number of genes), which might be associated with the level of cellular complexity in mammalian species. Many of these transcripts are non-coding RNAs, while others are conserved across species and others are unique in species, yet their functions in health and disease remain largely unknown.

The discovery of the RNA-interference mechanism that can degrade mRNA from a specific gene was reported in 1998 and led to the 2006 Nobel Prize in Medicine and Physiology. This mechanism is activated by double-stranded RNA which leads to degradation of the target mRNA so that the corresponding gene is silenced and no protein is produced. RNA interference occurs in plants, animals, and humans and is already being widely used in basic science as a method to study the function of genes and it may lead to novel therapies in the future. These discoveries have revealed a previously unknown role for RNA as a silencer of gene expression, to its previously understood role as a cellular messenger that directs protein synthesis.

The exciting discoveries in RNA biology and the non-protein coding RNAs as the ‘second genome’ are tackled by several FP6 CPs (SIROCCO and RIBOREG are examples), including the increasing importance of post-tran-scriptional regulation of gene expression (an example is EURASNET).

The SIROCCO project studies the role of non-protein coding genes as organisers and coordinators of the organ-ism’s complexity. It investigates the role of small regulatory RNAs (sRNAs) in health and disease, with particular emphasis on cancer, neurological diseases and developmental regulation, by using HTP technologies and bio-informatics. It will determine the tissue and cell-type miRNA expression, optimise methods of sRNAs detection, characterise the molecular machines responsible for both miRNA and siRNA biogenesis, and dissect sRNA regulatory networks through the combination of multidisciplinary methods.

The RIBOREG project identifies novel non-coding RNA (ncRNA) genes linked to cell differentiation and disease and analyse their mechanisms of action by developing a multidisciplinary approach integrating bioinformatics, cell biology, genetics and genomic strategies. The BACRNAs project will identify non-coding RNAs involved in bacterial pathogenicity and the identification of targets (virulence factors) controlled by ncRNAs involved in virulence. RNABIO is an SSA: its main contribution was the organisation of an international workshop on com-putational approaches to non-coding RNAs, with the main objectives of presenting and discussing the state of RNA computational biology so as to identify needs and propose new developments.

The human genome contains a surprisingly low number of protein-coding genes — approximately 22 000. However, the human proteome consists of approximately 100 000 protein isoforms. Part of the answer is alternative messenger RNA (mRNA) splicing. The EURASNET NoE aims to develop an integrated approach to the study of alternative splic-ing: it will provide durable structures that will change the way research in this field is carried out in Europe; establish an ambitious, innovative and multidisciplinary programme of joint research activities with high impact; spread ex-cellence within Europe; disseminate knowledge about alternative splicing in molecular biology and particularly in medical communities; and foster public awareness of genomics and RNA research and their applications.

The circadian clock is a basic biological process that enables organisms to anticipate daily environmental changes by adjusting behaviour, physiology and gene regulation. It impacts health and quality of life in regulating sleep and well-being, in the consequences of shift work, in medical diagnosis and therapy, and in age-related changes.



In EUCLOCK, European researchers join forces to investigate the circadian clock under entrainment. Utilising the most advanced methods of functional genomics and phenomics, the team will compare genetic model organisms and humans. Important findings such as the prerequisites for large-scale non-invasive research on human entrainment as well as the first animal models for shift-work will be developed. These findings will en-able the field of chronobiology to exploit the advantages of systems biology research on circadian timing, and to perform and integrate findings at the level of the genome, the proteome, and the metabolome.

The general objective of TEMPO combines functional genomics, proteomics, cell signalling, systems biology and pharmacokinetics, and will design mouse and in silico models to allow the prediction of optimal chronotherapeu-tic delivery patterns for anti-cancer drugs.

The EC is also supporting multidisciplinary functional genomics research projects in prokaryotic organisms such as bacteria and other organisms.

The BACELL HEALTH consortium aims to unravel the integrative cell stress-management systems and stress-resistance processes required to sustain a bacterial cell when exposed to types of environmental signals. There are also other projects using bacteria to understand the function of basic biological processes (like BaSysBio) and applying systems approaches to understand transcriptional regulation.

DIATOMICS will make use of whole genome sequences from diatoms to provide information on gene function and its relationship to ecology and evolution.

Systems biology, now an emerging discipline, has gained popularity over the past few years. Each cell, organ or tissue is a dynamic biological system. The cellular functions are controlled by many genes, proteins and sig-nalling and metabolic processes. Technological and computational advances have enabled the acquisition and analysis of large datasets obtained by diverse biological systems at multiple levels. Global measurements of DNA have yielded data on sequence and genotype and information about chromatin structure. RNA measure-ments have enabled genome-wide transcriptional profiling and information about alternative splicing and non-coding RNAs. Proteomics approaches using mass spectrometry and more recently protein arrays have permitted the global identification and quantification of proteins in their biological context. Furthermore, these technologies have allowed the quantification of post-translational modifications and revealed dynamic protein-protein and protein-DNA interactions. Great progress has also been made in measuring metabolic fluxes, and emerging imaging technologies are providing important insights into biological function.

However, despite these advances, the link between complex biological networks and phenotype remains an enormous challenge.

In order to gain deeper insights and ultimately a quantitative understanding of the complex and dynamic proc-esses of living organisms (e.g. environmental adaptation, ageing, and immune defence) of the cells, it is neces-sary to view the systems as a whole.

Systems biology promises to build up an integrated picture of the regulatory processes at all levels, from genome to proteome, from organelles to cells and tissues, and the understanding of the whole organism, by integrating functional data into a cohesive model. This stands in contrast to the standard reductionistic approaches of the twentieth century, with biologists analysing functional information on organisms based on a single gene or a single protein at a time.

There are two approaches proposed in systems biology. The top-down approach presupposes that it is not neces-sary to know all the details of the ways in which cells work in order to make useful predictions about how organism



cells work. This method starts with a model of how the system works and then compares the model with information from the real biological system. At the opposite end, stands the ‘bottom-up’ approach, which starts from the prop-erties of individual molecules and builds models at increasingly higher scales. Therefore, the bottom-up approach essentially requires complete information, including the dynamics of each step, to build a system model. When complete, such a detailed model should be capable of describing exactly how the system works under any circum-stance. The combination of the advantages of the above approaches leads to the so-called ‘middle-up’ approach.

The ultimate goal of biology is to understand biological systems in sufficient detail to enable accurate, quantita-tive predictions about the behaviours of biological systems, including predictions of the effects of modifications of the systems such as disease. The hope of the rapid translation of genomic information into novel drugs has foundered on the reality that disease biology is complex. Systems biology aims ultimately to develop predictive models of human disease. Currently, integration of ‘-omics’ data within the context of controlled gene expression or drug perturbations of complex cell and animal models (and in the context of clinical data) is the basis for systems biology efforts at a number of drug companies.

Such research has a strong multidisciplinary nature and the collaboration between different stakeholders, univer-sity, research institutes, biotech companies and clinical centres is a prerequisite for success. The subject requires collaboration between a broad spectrum of scientific disciplines including biology, physics, chemistry, computer science and engineering. A collaborative approach is a prerequisite to achieving major breakthroughs.

FP6 activities

The EU is emerging as a major world player in the development of systems biology in Europe. An important fund-ing effort has been initiated in FP6 through the support of collaborative research projects and through a number of key studies and workshop events that have helped to integrate this emerging community.

In FP6, a number of systems biology projects predominantly initiated in 2005 have already demonstrated that a systems approach can indeed work, to provide both a deeper understanding of biological processes and pre-dictive potential for applications. These projects have major links to ongoing worldwide research programmes, national programmes, and Europe-wide support and links (EMBL, EMBL-EBI).

Within FP6, the EC has already funded several pilot research projects paving the way toward systems biology. These projects may be grouped into the following general categories:

1. Projects applying systems biology approaches in fundamental cellular signalling pathways

Some of these projects (COMBIO, COSBICS and DIAMONDS) are already applying systems biology ap-proaches to model cellular signalling pathways. Other projects (QUASI and AMPKIN) aim for a systematic quantitative understanding of intracellular and extracellular signalling pathways of disease relevance, with ultimate goals of building predictive pathway models. All of these projects demonstrate that the develop-ment of computational biology and integrated bioinformatics databases of diverse ‘-omics’ data is an es-sential component for the successful implementation of systems biology approaches.

COMBIO implements an integrative approach to cellular signalling by combining a unique group of experimentalists, bioinformaticians and simulation groups in order to gain detailed understanding of key processes, like the P53-MDM2 regulatory network. COSBICS establishes and applies a novel computa-tional framework to investigate cellular signalling pathways and subsequent target gene expression.

The DIAMONDS project aims to demonstrate the power of a systems biology approach to study the regulatory network structure of the most fundamental biological process in eukaryotes, the cell cycle, in different species.

In the AMPKIN project, experimental and theoretical studies will be integrated to achieve an advanced under-standing of the dynamic operation of the AMP-activated protein kinase signalling pathway. This pathway plays a central role in monitoring the cellular energy status and controlling energy production and consumption.



In the last FP6 call, the EC also financed an integrated project (BaSysBio) which uses systems biol-ogy approaches for the understanding of the dynamic transcriptional regulation in bacteria. It studies the transcriptional regulation and metabolism in B. subtilis and B. anthracis, and the cellular transcrip-tional responses in pathogenesis. The project AGRONOMICS applies integrative functional genomics approaches to systematically investigate the components controlling growth processes in plant cells (genome sequences, proteins and metabolites) and to explain quantitative growth phenotypes at the molecular level. Finally, mathematical and statistical methods will be employed in order to model basic plant processes. The aim is to investigate those further and test them in close collaboration with computer scientists, statisticians and experimentalists.

2. Projects applying systems biology approaches for understanding complex diseases phenotypes

EMI-CD, ESBIC-D and BioBridge are using systems biology approaches to gain new insight into highly complex diseases, such as trisomy related illnesses (Down’s syndrome) and various cancers.

The main purpose of EMI-CD is to provide a software platform complex enough to cope with various ex-perimental techniques, connecting several modules necessary for the in silico modelling of complex disease processes such as cancer and diabetes.

VALAPODYN validates predictive dynamic models of complex intracellular pathways related to the cell death and survival. It develops a new systems biology approach to model the dynamics of molecular inter-action networks related to neurodegeneration. The ultimate goal is to select and validate drug targets for human pathologies associated with neurodegeneration.

SysProt develops a new paradigm for the integration of proteomics data into systems biology. It will produce quantitative proteomics data, and study post-translational protein modifications via the development of compu-tational analysis, in order to gain understanding on the progression of complex diseases such as diabetes.

BioBridge focuses on the application of simulation techniques for integrated genomic, proteomic, metabo-lomic and kinetic data analysis, in order to create models for understanding complex diseases at the systemic level, with an emphasis on heart failure, chronic obstructive pulmonary disease and type II diabetes.

3. Projects aiming at coordination and networking in systems biology

To prepare the best research environment in Europe for systems biology, the EC is already supporting several SSAs and CAs.

EUSYSBIO laid the foundations for the successful start of European systems biology research, implementing networking activities and identifying the strengths and weaknesses in European systems biology. SYMBIONIC is creating a broad European network of research institutions and industries with interdisciplinary expertise in the systems biology field, which will be a driving force for future ambitious initiatives in neuronal cell modelling.

ESBIC-D aims at organising a Europe-wide systems approach to combat complex diseases. The project will network leading groups in the fields of cancer research, genomics, proteomics and computational biol-ogy to strengthen the expertise and research infrastructure in Europe.

SYSBIOMED explores the potential application of SB to medical research in major disease areas (infec-tious, neurodegenerative, metabolic and cardiovascular diseases and cancer), and its applications in drug development. A series of workshops will be organised to promote European collaboration and to contribute to the breaking down of barriers — between theoreticians, basic researchers and clinicians interested in medical applications.

YSBN is a CA which focuses on defining standards, methods and concepts of systems biology using the model organism S. cerevisiae.



It is worth mentioning that the EU-supported large-scale functional genomics initiatives in FP6 have produced a richness of HTP ‘-omics’ data, which has provided new knowledge on basic biological processes such as the mammalian cell cycle, tissue development and degeneration (muscle, retina, inner ear and kidney), human and animal stem cell differentiation processes, organelle function, endocytosis and post-translational modifications. These large initiatives will pave the way for future systems biology initiatives in Europe. An essential element in future systems biology are the integrated bioinformatics and computational biology tools. In FP6, important fund-ing has been provided in the area of bioinformatics, which will contribute to the ERA of systems biology.

FP7 activities

The EU FP7 programme is already playing a major role in this important and rapidly expanding research field by establishing multidisciplinary networks in Europe that will catalyse progress and excellence in this field. The FP7 first call for proposals provided an important boost for large-scale European initiatives, by allocating a total budget of 45 million to the following large scale integrating projects.

SYBILLA, a large scale integrating project, aims to understand at the systems level, how T-cells discriminate foreign from auto-antigens and will address modelling of T-cell activation. The project will develop technologi-cal and mathematical tools to generate and integrate high-density quantitative data describing T-cell activation in health and disease, placing particular emphasis on multiple sclerosis. T-cell activation is a complex process, relying on multiple layers of tightly controlled intracellular signalling modules, defects in which can cause severe and chronic disorders such as autoimmune diseases.

The APOSYS project studies the basic cellular mechanisms of apoptosis. This multidisciplinary consortium brings together and networks experimental biologists, biomathematicians, biostatisticians, computer scientists and clini-cal scientists to examine cell death pathways in health and disease, with an emphasis on cancer and AIDS. It complements the systems approach with a series of in silico, in vitro and in vivo model organisms and tissue

FP6 Pilot SystemsBiology Projects

Fundamental genomics forbasic Biological processes;

“-omics” data gathering

Integrated bioinformatics,databases,

Computational biology

Experimental Tools and technologies for ”omics”

1st call - 2002

2nd call - 2003

3rd call - 2004

4th call - 2005

CA, STREP

IP, NoE

DIAMONDS(modelling cell cycle)

SysProt (systemsanalysis of protein

Modification)

BaSysBio (Bacterial Transcription

Regulation)

ESBIC-D (SB for complex diseases)

QUASI (MAPK-kinase signalling)

COMBIO(P53 pathway)

COSBICS (modellingCellular signalling)

BioBridge(SB for

chronic diseases)

MITOCHECK (mammaliancell cycle)

EUROHEAR(Hearing process and deficiencies)

ESTOOLS(hES

differentiation)

SIRROCO(Small regulatory

RNAs)

BIOSAPIENS (Human Genome

Annotation)

EMBRACE(Bioinformatics

grid)

ENFIN(computational

tools for SB)

Tools for Proteomics, transcriptomics, structural genomics, population genetics, metabolomics, imaging

ERA in Systems Biology

Fig. 14: Steps to ERA in Systems Biology in FP6 (2002-2006)



samples from patients suffering from cancer and AIDS. The project is expected to enhance our understanding of clinical data and lead to the development of new diagnostic tools and drugs.

UNICELLSYS set as an overall objective the quantitative understanding of fundamental characteristics of eukaryotic unicellular organism biology, using yeast as model organism. The project goes far beyond the state of the art in terms of dynamic modelling of cellular subnetworks controlling complex biological processes such as control of cell growth and proliferation. It is expected to deliver new knowledge on important biological processes relevant to human health (cell growth and proliferation) but will also generate economic value in the form of new computational tools and ap-proaches for systems biology that will be of general applicability to other systems in more complex organisms.

EuroSyStem is a large European effort that brings together elite European research teams to create a world-leading programme in fundamental stem cell biology, with the main focus on the paradigmatic mammalian stem cells: haematopoietic, epithelial, neural and embryonic. Cutting-edge multidisciplinary technologies such as cytometry, transcriptomics, RNA interference, proteomics and single cell imaging, will be used to generate new knowledge on stem cells differentiation in terms of cellular hierarchy, signalling, epigenetics, de-regulation, and plasticity. An important bioinformatics and computational platform will be established to mine information and subsequently to model these complex differentiation pathways.

From biological pathways in unicellular eukaryotic organisms to human cells and organs, there is a need to combine, integrate and extend existing data sources and screen different heterogeneous data resources. These large-scale projects on systems biology are expected to integrate dispersed capabilities and assemble the critical mass necessary to enable systems approaches, as well as to secure European excellence and competitiveness and the exploration of new directions for the fi eld. The quantitative data delivered should serve as the basis from which to design robust models with predictive value. They should produce new knowledge on basic biological processes relevant to health and diseases.


FP

EYSYSBIOSYMBIONICEMI-CDQUASICOMBIOCOSBICSDIAMONDSEU-US WorkshopELifeESBIC-DYSBNAMPKINRIBOSYSEUROBIOFUNDVALAPODYNAGRON-OMICSBaSysBioBioBridgeSYSBIOMEDSysProtStreptromicsSYSCOProust

APOSYSSYBILLAUNICELLSYSEuroSysStem

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

2013

2013

FP7

FP6

IP 12mIP 12m

IP 11.1mIP 11.1m

IP 11.03mIP 11.03m


STREP 2m


SME-STREP 1.5m

SME-STREP 1.8m

SME-STREP 2.1mSME-STREP 2.9m

SME-STREP 1.8m

STREP 1.9m


SSA 0.5m

SSA 0.48m

SSA 1.5m

SSA 0.9m

SSA 0.36m

CA 1.3m

SSA 0.2m

SSA 0.06m

Fig. 15: Runtime of current EU-funded collaborative research projects in systems biology (funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)



In systems biology, not every research area requires a large collaborative effort. During the FP7 second call for proposals, approximately 15 small-scale research projects were selected, and are cur-rently under negotiation with a total of 45 million to be committed at the end of 2008 or be-ginning of 2009. These projects may be categorised as follows: (i) projects aiming to enable systems biology approaches for diseases like inflammatory response, cancer, neurological diseases, and bacterial infections; (ii) projects applying systems biology for basic signalling pathways like DNA damage and repair, oxidative stress, cellular organelle function, and stem cell differentiation; and (iii) support actions for tackling future challenges in systems biology. All these projects are multidisciplinary and they are focused on collecting, analysing and apply-ing quantitative data to enable systems biological approaches.

For an emerging and booming field like systems biology, it is rather difficult to identify which are the timely ideas to investigate using an EU large-scale coordinated approach. The large-scale CPs will create the critical mass of multidisciplinary expertise that is necessary for enabling complex systems approaches. Therefore, the EC via its Genomics and Systems Biology programme published the FP7 third call for proposals in September 2008, implementing a bottom-up approach via a two-stage selection procedure for the first time in the Health priority. The scientific community is invited to submit proposals for large integrating projects on the following topic:

■ Systems biology approaches for basic biological processes relevant to health and disease The projects should focus on modelling important biological processes at any appropriate levels of system

complexity by generating and integrating quantitative data sets (e.g. transcriptomics, proteomics, metabo-lomics, structural biology, RNAi screening, physiology and/or pathophysiology). These large multidiscipli-nary efforts should integrate the critical mass of excellence in Europe that is necessary for generating and validating the models using systems biology.

In summary, to face the challenges of the systems biology era, the EC’s FPs for RTD have al-ready provided, between 2003 and 2008, more than 150 million for collaborative research projects. With such substantial funding, the EU is emerging as a major world player in the development of systems biology in Europe and will continue to do so in the future.

System Biology in FP7 & Health

Biological processes: data gathering

Bioinformatics/ Data bases/software/computational biology

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

2016

2017

2018

2019

2020

2021

FP6

FP7

SB: pathways

SB: organisms

SB: tissues/organs

SB: Cells: Mammalian cells

SB: Cells: yeast/bacteria

Fig. 16: The future developments of systems biology in FP7 The FP6 fundamental genomics programme paved the way by supporting multidisciplinary projects collecting large amounts

of “-omics” data on basic biological processes, and by developing the bioinformatics and computation tools base.



AnnexesBasic facts and figures for the Fundamental Genomics activity area

Annex IFunding instruments and schemes in FP6 and FP7

Compared to FP5 (1998–2002), which mainly supported small and medium collaborative research projects, FP6 (2002–2006) has additionally offered more ambitious ‘new funding instruments’, namely IPs and networks of ex-cellence (NoE). These two project types are more ambitious in size and scope than the research projects funded previously by the EU. Both types of projects aim to stimulate and sustain world-class research in a specific area of fundamental genomics and to improve the organisational aspects of European research in the specified topic. How-ever, IPs and NoE have a different centre of gravity. With an IP the balance is towards achieving ambitious, clearly defined scientific objectives; with a NoE the balance is shifted towards tackling the fragmentation of European research in a specific field, so as to provide an improved organisational structure in which research can flourish.

It is clear that the ‘new instruments’ of FP6 have enabled European scientists to achieve a major critical mass in very competitive areas of functional genomics and have really given European research a global profile.

For further information, see http://www.cordis.lu/fp6/instrument-ip/.

Integrated Projects (IPs)

IPs are large-scale projects aiming to support world-class objective-driven research, where the primary deliver-able is generating new knowledge. In addition, by mobilising a critical mass of resources, IPs should also have a structuring effect on European research (see Figure 17 for the graphical representation on the goals of an IP).

The activities integrated by an IP may cover the full research spectrum from basic to applied research, and should contain:

■ objective-driven research;

■ technological development, innovation-related and demonstration components, as appropriate;

■ the effective management of knowledge and, when appropriate, its exploitation;

■ a training component, where appropriate.

All these activities should be integrated within a coherent management framework.

An IP should bring together a critical mass of research excellence and resources to achieve its ambitious objec-tives. The European Community funding for an IP in the fundamental genomics programme ranges from 8 to

13 million, their duration from 36 to 60 months, with an average of 11.2 million per project and 48 months duration for the majority of the projects.


http://www.cordis.lu/fp6/instrument-ip


Networks of Excellence (NoE)

NoE are large-scale projects with the goal of overcoming fragmentation in the European research landscape and strengthening European excellence in a given area (see Figure 18 for a graphical representation of the goals of a NoE). Their purpose is to reach a durable restructuring/shaping and integration of efforts and institutions or parts of institutions (labs, departments, units, teams, etc.) in areas where this is necessary. The success of a NoE is not measured only in terms of scientifi c results, but also by the extent to which the fabric for researchers and research institutions in a given fi eld has changed due to the project, and the extent to which the existing capacities have become more competitive as a result of this change.

A NoE is implemented through a Joint Programme of Activities, which encompasses the following:

■ Integrating activities: These aim at structuring and shaping the way participants carry out research in the topic (e.g. coordinated programming, sharing research facilities, tools and platforms, joint management of the knowledge portfolio, schemes for increasing staff training and mobility, staff exchanges, shared information and communication systems).

■ Jointly executed research: A world-class research programme is an obligatory part of the Joint Programme of Activities or JPA (for example, to generate new knowledge in the research topic and to develop new research tools and platforms for common use).

■ Activities for spreading excellence: An essential mission of a NoE is to spread excellence beyond its boundaries. Typical examples of such activities would be the following: joint programmes for training researchers and other key staff to ensure the sustainability of Europe’s excellence in the topic, communication campaigns for disseminating results (and raising public awareness of science), and networking activities to encourage knowledge transfer and innovation.

NoE should pursue ambitious goals and gather the critical mass needed to ensure their achievement. The Euro-pean Community grant to a NoE in the fundamental genomics areas ranges from 10 to 12.5 million, their duration from 48 to 60 months, with an average of 10.7 million per project and 60 months duration for the majority of the projects.

Integrated Projects

Addressing major societal needs

Increasing EU competitiveness

To integrate the critical mass of activities/resources needed for :

Predefined S/Tresults and

clear deliverables

Strongmanagement

structure

ImplementationPlan

Ethical aspects, science-society dialogue

Technology transfer, exploitation

Management

Training

RTD 4 RTD 5

RTD 1

RTD 2

RTD 3

Demonstration

Fig. 17: Graphical representation of the structure and the goals of an Integrated Project in FP6 (2002-2006)



Specifi c Targeted Research Projects (STREPs)

STREPs are multi-partner research projects, with the goal to support research, technological development and demonstration or innovation activities of a more limited scope and ambition than IPs. They are an evolved form of the shared-cost RTD projects and demonstration projects used in FP5, and their main deliverables are to produce new knowledge and improved tools and technologies in fundamental genomics.

The European Community fi nancial support for a STREP in fundamental genomics ranges from 1.5 to 2.5 mil-lion, their duration from 36 to 48 months, with an average of 2.1 million per project and 36 months duration for the majority of the projects.

STREPs were also funded during the fourth call of FP6 with the specifi c goal of supporting projects for develop-ing and/or improving tools and technologies development, and of encouraging SMEs’ research and innova-tion efforts. The goal was that 30% of the EC contribution to be allocated to the SMEs. These projects are entitled SME-STREPs in the current publication.

Co-ordination Actions (CAs)

CAs do not support research and development activities per se; they promote and support the networking and coordination of research and innovation activities aiming at improved integration of European research. CAs are a continuation of the concerted actions/thematic networks used in FP5, in a reinforced form.

A CA could contain activities such as:

■ the defi nition, organisation and management of joint or common initiatives;

■ the organisation of conferences and meetings;

■ the performance of studies and analyses;

Networks of Excellence

Governing Council

ManagementGroup

Funding BodiesRepresentatives

Joint research activitiesIntegrating activitiesSpreading of excellence (training)Common management

Research team leaderPartner Organisation Representative

Euro

pean

Com

miss

ion To structure the EU research potential

by integrating existing research capacities

Fig.18: Graphical representation of the goals and the structure of a network of excellence in FP6 (2002-2006)



■ the exchange of personnel;

■ the exchange and dissemination of ‘good practices’;

■ the setting up of information systems and expert groups;

■ specific training courses or seminars.

The European Community financial contribution for a CA in fundamental genomics ranges from 0.5 to 1.3 million, their duration from 24 to 48 months, with an average of 0.8 million and 36 months respectively.

Specific Support Actions (SSAs)

SSAs are more limited in scope than the accompanying measures of the previous FPs. They aim to:

■ promote and facilitate the dissemination, transfer, exploitation, assessment and/or broad take-up of past and present programme results (over and above the standard diffusion and exploitation activities of individual projects);

■ contribute to strategic objectives, notably regarding the ERA (e.g. pilot initiatives on benchmarking, mapping, networking, etc.);

■ prepare future community RTD activities, (e.g. via prospective studies, exploratory measures, pilot ac-tions, etc.).

The European Community funding contribution for an SSA in fundamental genomics ranges from 0.06 to 0.5 million, their duration from 12 to 36 months, with an average of 0.3 million and 24 months respectively.

FP7 projects are all categorized with the general term collaborative projects.

Large scale collaborative Projects (Large scale integrating projects) (CP-IPs)

The large integrating projects could be considered an evolution of the IPs in FP6. These projects will support objective-driven research projects aiming at developing new knowledge, new

technologies, products, demonstration activities or common resources for research, to improve European competitiveness or to address major societal needs.

They include the following activities:

■ RTD — the core activities of the project;

■ demonstration, where applicable;

■ project management;

■ other activities such as dissemination of research results, etc.

The European Community funding contribution for CP-IPs in the Health theme should be more than 6 million and maximum of 12 million. In the Genomics and Systems Biology programme during the implementation of the FP7 first call for proposals, the funding ranges from 11 to 12 million, their duration from 48 to 60 months, with an average of 11.7 million and 48 months respectively.



Small or medium scale collaborative Projects (Small-Medium Focused Research Projects) (CP-FPs) These projects could be considered as a continuation of FP6 STREP projects and are research projects with

lower ambitions than IPs.

The European Community funding contribution for CP-FRPs in the Health theme should be 3 million to less than 6 million. In the Genomics and Systems Biology programme during the implementation of the FP7 second call for proposals (with a September 2007 deadline), currently under negotiation, the funding ranges from 2.5 to 2.99 million, their duration from 36 to 48 months, with an average of 2.7 million per project and 36 months duration for the majority of the projects.

Coordination and Support Actions (CSAs) These projects refer to Coordination and Support Actions (CSAs) and do not support research per se but

rather coordination activities with objectives similar to those of FP6.

The European Community funding contribution for CP-CSAs in the Health theme is generally in the range of up to 1.5 million, although there is no upper limit. In the Genomics and Systems Biology programme during the implementation of the FP7 second call for proposals (projects currently under negotiation), the EC funding ranges from 0.5 to 2.7 million, and the duration from 24 to 36 months.



Annex IIDevelopment of the specific scientific topics for calls for proposals in the FP6 Fundamental Genomics programme

At the beginning of FP6, a global expression of interest was established for the first time in the FP, and the most innovative ideas for European collaborative research were selected. This concept has been applied in the whole thematic area of Life Sciences, Genomics and Biotechnology for Health. In this section, we will concentrate on the Fundamental Genomics activity area. The European scientific community has submitted 550 expressions of interest, and these have been evaluated by eminent scientists both within and outside Europe. This high-level evaluation process led to the strategic areas of research that defined the specific topic for calls for proposals, mostly for the large-scale projects in the FP6 first, second and third call topics.

The rest of the calls have been developed by consulting the scientific community via EC’s strategic workshops (see Annex III). The Scientific Advisory group was set up by the EC to provide input on the strategy and the imple-mentation of the work programme in the Life Sciences theme in FP6: this group’s valuable advice is an important source of consultation on the work programmes (for more information, please see http://cordis.europa.eu/fp6/eags.htm and http://ec.europa.eu/research/fp7/index_en.cfm?pg=eag).

The EC also acknowledges the important role of the Member States’ recommendations in the final implementation of the work programme.


http://cordis.europa.eu/fp6

http://ec.europa.eu/research/fp7/index_en.cfm?pg=eag


Annex IIIThe EC organisation of strategic workshopsin different scientific areas of fundamental genomicsand systems biology

During FP6, the EC organised a number of successful workshops in collaboration with the scientific community, to identify the challenges and the future developments in different areas of fundamental genomics, along with new initiatives that have contributed to strategies in FP7. The following workshops were organised by the Unit of Fundamental Genomics — this name was updated to the Genomics and Systems Biology Unit in FP7 (for further information, see http://cordis.europa.eu/lifescihealth/genomics/home.htm).

■ Bioinformatics Structures for the Future, in March 2003, with the goal of setting a research agen-da in the field for structuring European bioinformatics research;

■ Workshop on Mouse Genetics, in July 2003, with the aim of setting priorities for mouse functional genomics research in Europe;

■ Computation Systems Biology: its Future in Europe, in September 2003, with the aim of defining a research and policy agenda to promote the field of computational systems biology (CSB) in Europe;

■ Meeting on population genetics in Europe, in September 2003, in order to identify priorities for research in population genetics and related areas;

■ Workshop on Structural Genomics, in October 2003, with the aim of identifying the strengths, weaknesses and future opportunities for structural genomics in Europe;

■ Conference on European Structural Genomics & Proteomics Research combined with the joint meeting of EU-funded projects, in October 2004, with the aim of creating synergies between the projects by clustering and networking, of disseminating best practices and success stories to establish gateways between disciplines; of debating and formulating a proposal on the current and future policies needed for SG in Europe;

■ Functional Genomics Research: Future Perspectives in October 2004, with the aim of identifying the future challenges and developments of the functional genomics field for future research policies actions, in view of establishing genomics research for FP7;

■ Workshop on Systems Biology in December 2004, where European scientists identified key areas in systems biology for development in the near future;

■ Conference on Funding Basic Research in Life Sciences: Exploring opportunities for Eu-ropean synergies in December 2004, a joint effort of Directorate F (Life Science, Genomics And Biotechnology for Health in FP6 & Directorate E (Food Quality And Safety);

■ EUROMOUSE conference: Understanding human disease through mouse genetics — The European Dimension in October 2005, for creating synergies among projects using mouse as a model organism and discussing priorities in mouse functional genomics;

■ Human genetic variation workshop in March 2006, exploring the need for a grid-linked set of databases in this area;

■ Mouse functional genomics workshop in March 2007, concluding with recommendations for international collaboration in the field of mouse as a model for human disease;


http://cordis.europa.eu/lifescihealth/genomics/home.htm


■ EU-US Task Force Workshop on Infrastructure Needs for Systems Biology in May 2007 (US), with the aim of making recommendations for infrastructure support to enable systems biology research;

■ EU-US workshop on ‘How Systems Biology Could Advance Cancer Research’ in May 2008, drawing up suggestions for international collaboration on systems biology of cancer.

For more information, including the published reports for some of the workshops, see http://cordis.europa.eu/lifescihealth/genomics/home.htm. Information can also be found on the FP7 Health website, at http://cordis.europa.eu/fp7/health/home_en.html.


http://cordis.europa.eu

http://cordis


Annex IVEvaluation process in the FP6 and FP7 Fundamental Genomics programme

The present section provides a short overview of the evaluation procedure in the thematic priority of Life Sciences, and more specifically focuses in the area of Fundamental Genomics.

The procedure for evaluation of proposals is based entirely on the ‘Guidelines on proposal evaluation and project selection procedures’, which can be found at: http://fp6.cordis.lu/lifescihealth/call_details.cfm?CALL_ID=148, and which serves as the basis for the following brief presentation.

Role and code of conduct of evaluators

The EC appoints independent experts to assist in the evaluation of proposals. In general, independent experts are expected to have skills and knowledge appropriate to the areas of activities in which they are asked to as-sist. Details of potential independent experts are maintained in a central database. This database may be made available, on request, to national authorities in the Member States and countries associated to the FPs. The names of the independent experts assigned to individual proposals are not made public; however, at regular intervals, the EC publishes the list of independent experts used per activity/research area, on the Internet.

The EC takes all reasonable steps to ensure that each expert is not faced with a conflict of interest in relation to the proposals on which he/she is required to give an opinion. To this end, the EC requires experts to sign a dec-laration that no such conflict of interest exists at the time of their appointment and that they undertake to inform the EC if one should arise in the course of their duties. When so informed, the EC takes all necessary actions to remove the conflict of interest. The experts are obliged to maintain the confidentiality of the information contained within the proposals they evaluate and of the evaluation process and its outcomes and to act with strict impartial-ity. A conflict of interest and confidentiality declaration will be signed by independent experts.

The proposal evaluation and project selection process

The overall evaluation and project selection process is summarised in the following diagram.

The evaluation procedure consists of the following steps:

Step 1: Briefing of the independent experts

All independent experts are briefed in writing and orally before the evaluation by representatives of the EC’s service in charge of the call, in order to inform them of the general evaluation guidelines and the objectives of the research area under consideration.

Step 2: Individual evaluation of proposals

The proposals are sent to the expert evaluators at their normal place of work. Each proposal is evaluated against the applicable criteria relevant to each funding instrument independently by several experts who fill in individual evaluation forms giving marks in each criterion and providing justification of marking. These comments serve as input to the consensus discussion and related consensus report that takes place in Brussels. The number of evaluators legally required is five for IPs/NoE and three for the other instruments. The EC has established as a general practice the evaluation by a number of seven to nine evaluators for IPs/NoEs and five for the other instruments, in order to further strengthen the quality of the evaluation procedure.

Written opinions from external reviewers are applied specifically for the large projects (IPs, NoE), where most of the top European specialists in the field are involved in a given proposal. Therefore, to obtain an independ-ent high-quality assessment, several specialists in the field, mainly from outside Europe, are invited to review


http://fp6.cordis.lu/lifescihealth/call_details.cfm?CALL_ID=148

73

each proposal. The external reviewers are asked to provide their written opinion of the scientific quality of the proposal. These written opinions are provided to the expert evaluators prior to the meeting of the consensus group in Brussels, but after the expert evaluators have completed and forwarded to the EC services their in-dividual assessment reports on the proposals assigned to them. Consideration of the written opinions of the external reviewers makes up an important aspect of the consensus group’s discussions in Brussels.

Different consensus groups operate in parallel in different groups of closely related topics. The propos-als passing the thresholds are reviewed by a final panel composed of several experts from each of the several consensus groups. The final panel produces a ranking list of proposals in order to advise the EC on which projects to select for funding.

Step 3: Consensus panels

Separate parallel consensus panels are convened in Brussels. The goal is that for each proposal all the experts reach an agreement on a consensus mark for each of the blocks of evaluation criteria based on the comprehensive discussion. They justify their marks with comments suitable for feedback to the pro-posal coordinator. The discussion of the proposal continues until a consensus is achieved, i.e. a conclu-sion with which all agree regarding the marks for each criterion and the accompanying comments. In the event of persistent disagreement, the EC official supervising the evaluation of that proposal may bring in up to three additional evaluators to examine the proposal.


(OPTIONAL)

Consultation of ProgrammeCommittee if required

Consensus

Hearings

Panel

Ranking by EC

Eligibility

Negotiation Result

Thresholds

Proposal

EC Funding Decision and/or Rejection Decision

EC Rejection Decision

Individual Evaluation

Ethical Issues

Negotiation

The Proposal Evaluation And Project Selection Process



In order to facilitate discussion among the experts, the EC officials act as moderators for the group and assign an expert as ‘proposal rapporteur’. The proposal rapporteur introduces the proposal(s) assigned to him/her and summarises the opinions of the external reviewers (in the case of IPs and NoE). The proposal rapporteur is responsible for amalgamating the individual experts’ views, for initiating the discussion and drafting the consensus report. The outcome of the consensus step is the consensus report signed by all inde-pendent experts and the moderator. The moderating EC official is responsible for ensuring that the consen-sus report faithfully reflects the consensus reached. For all proposals passing the thresholds, the consensus group is asked to give an opinion on the appropriateness of the level of Community funding requested in relation to the tasks and activities to be carried out.

Final evaluation panel

Immediately after completion of the consensus panels, an integrated final panel discussion is convened in Brus-sels to examine and compare the consensus reports and marks of the independent consensus panels, to review the proposals with respect to each other and, in specific cases (e.g. equal scores) to make recommendations on a priority order of proposals. A panel rapporteur (who may also be the panel chairperson) is appointed to draft the panel’s advice. An EC official may act as moderator of the panel. The role of the EC moderator is to ensure fair and equal treatment of the proposals in the panel discussions. The outcome of the panel meeting is the panel report recording the deliberations of the panel containing the following: an evaluation summary report (ESR) for each proposal and a ranked list of proposals passing thresholds, along with a final mark and the panel recom-mendations for priority order.

After the evaluation

At this stage, the EC services review the results of the evaluation by independent experts, make their assessment of the proposals based on the advice from these experts and prepare the final evaluation results.

The EC services draw up a final ranked list of all the proposals evaluated and of those passed the required thresh-olds. Due account is taken of the marks received and of any advice from the independent experts concerning the priority order for proposals. The list of proposals to be retained for negotiation takes into account the budget avail-able. Negotiation may cover any scientific, legal or financial aspects of the proposal, based on the comments of the independent experts and on any other issue that was taken into consideration at the ranking stage. If negotiations are successful, the EC may then enter into the contract with the coordinator and the other contractors.

Evaluation procedures in FP7

The procedure for evaluation of proposals is based entirely on the ‘Rules for submission and the related evalua-tion, selection and award procedures’, which can be found at ftp://ftp.cordis.europa.eu/pub/fp7/docs/calls/fp7-evrules_en_pdf.zip.

The basic structure of the procedure is similar to the one described in FP6, with some minor adaptations.The evaluation criteria in FP7 have been consolidated to avoid repetition and the high level of complexity expe-rienced during the FP6 evaluations.


ftp://ftp.cordis.europa.eu/pub/fp7/docs/calls


Annex VEvaluation criteria in FP6 and FP7

Evaluation criteria in FP6

The evaluation criteria applied for each funding instrument in FP6 are described below.Each of the criteria may differ depending on the type of the funding instrument (described in Annex I). The evalu-ation criteria are ranked as follows:

0: the proposal fails to address the issue under examination or cannot be judged against the criterion due to missing or incomplete information; 1: poor; 2: fair; 3: good; 4: very good; 5: excellent.

Evaluation criteria for an Integrated Project (IP):

■ relevance (threshold score: 3), which means the extent to which the proposed project addresses the objectives of the work programme/call;■ potential impact (threshold score 3);■ scientific & technological excellence (threshold score: 4);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3); ■ mobilisation of resources (threshold score: 3).

The total score for an IP could be a maximum of 30 with threshold 24.

Evaluation criteria for a Network of Excellence (NoE):

■ relevance (threshold score: 3, which means the extent to which the proposed project addresses the objectives of the work programme/call);■ potential impact (threshold score: 3);■ excellence of the participants (threshold score: 3);■ degree of integration & the joint programme of activities (threshold score: 4); ■ organisation and management (threshold score: 3).

The total score for a NoE could be a maximum of 25 with threshold 20.

Evaluation criteria for a Specific Targeted Research Project (STREP):

■ relevance (Threshold score: 3);■ scientific and technological excellence (threshold score: 4);■ potential impact (threshold score: 3);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3) ;■ mobilisation of resources (threshold score: 3).

The total score for STREP could be a maximum of 30 with threshold 21.



Evaluation criteria for a Co-ordination Action (CA):

■ relevance (Threshold score: 3);■ quality of the support action (threshold score: 4);■ potential impact (threshold score: 3);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3); ■ mobilisation of resources (threshold score: 3).

The total score for CA could be a maximum of 30 with threshold 21.

Evaluation criteria for a Specific Support Action (SSA):

■ relevance (Threshold score: 3);■ quality of the co-ordination (threshold score: 3);■ potential impact (threshold score: 3);■ quality of the management (threshold score: 3); ■ mobilisation of resources (threshold score: 3).

The total score for an SSA could be a maximum of 25 with threshold 17.5.

Evaluation criteria in FP7

Evaluation criteria for Collaborative Projects (CPs)

■ Scientific and/or technological excellence (relevant to the topics addressed by the call) (threshold score: 3). Under this criterion, the following aspects will be evaluated: soundness of concept and quality of objec-tives; progress beyond the state of the art; and quality and effectiveness of the S/T methodology and associated work plan. The relevance of a proposal is considered in relation to the topic(s) of the work programme open in a given call, and to the objectives of a call. When a proposal is partially relevant

* The total score is divided by the number of the criteria per funding instrument, in order to have a normalised score comparison between different types of projects.** The number of criteria has been reduced to 3 in FP7, and hence the maximum score is 15.


Funding instrument Range of total score in funded projects

Average normalised score in funded

projects*

Genomics and Systems Biology Research -FP7 (2007–2013) (first call)

Table 2: Quality of funded projects in the Fundamental Genomics area: an overview of the average total scores of the funded projects



because it only marginally addresses the topic(s) of the call, or if only part of the proposal addresses the topic(s), this condition is reflected in the scoring of the first criterion.

■ Quality and efficiency of the implementation and the management (threshold score: 3). under this criterion the following aspects will be evaluated: appropriateness of the management structure and procedures; quality and relevant experience of the individual participants; quality of the consortium as a whole (includ-ing complementarity and balance); and appropriateness of the allocation and justification of the resources to be committed (budget, staff, equipment).

■ Potential impact through the development, dissemination and use of project results (threshold score: 3). Under this criterion, the following aspects will be evaluated: contribution, at European and/or international level, to the expected impacts listed in the work programme under relevant topic/activity; appropriateness of measures for the dissemination and/or exploitation of project results, and management of intellectual property.

Impact is considered in relation to the expected impact listed in the work programme. The total score for a CP could be a maximum of 15 with threshold 10.


Call*Number of proposals evaluated

Number of proposals

funded

Average percentage of success rate**

All FP6 calls


Table 3: Number of proposals evaluated, proposals funded and success rates in all the calls for proposals in FP6 in the Fundamental Genomics activity area, including the first call of FP7

* Four calls for proposals with an overall budget of 594 million were open in the Fundamental Genomics programme in FP6 during 2002 and 2005. Some 441 proposals were evaluated and 127 projects were selected for funding, with an overall average success rate of 29%.

** The average success rate represents the success rate for all types of funding instruments. If we would calculate the success rate, separately for IPs/NoEs, STREPs/CAs and SSAs, which had different budget allocations, one would note a variation on the success rate. The average percentage per call is calculated by dividing the total number of proposals funded in all funding instruments by the total number of proposals evaluated.

*** In FP7, the success rate generally concerns the large IPs for the first call. On the whole, the average success rate for the Health theme ranges from 15% to 17% and could vary considerably in some areas, in relation to the higher number of applications received.



Annex VIBasic facts and figures for the Fundamental Genomics activity area


Funding instrument

Number of funded projects

Total ECfinancial

contribution (million )

Percentage budget spent/type of funding

instrument

Total FP6 130 594.1 100


Table 4: Number of funded proposals per funding instrument and total budget allocated per funding instrument




Funding instrument

Average EC contribution* (million /instrument)

Average number of partners**/ instrument

Average duration (months)/instrument


Table 5: Average funding level, average number of partners and average duration per funding instrument, in FP6 in the Fundamental Genomics activity area, including the first call of FP7

* The budget is indicative and is calculated based on the maximum EC contribution at the start of the project; it does not relate to the final spent by the project for projects not finalised.

** A partner is an independent legal entity, which might include several independent scientific groups belonging to the same legal entity; partners (independent legal entities) are calculated based on information including amendments of the FP6 projects until the end of 2007.




Activity type of partners*

Number partners/activity type of partners

Percentage EC contribution/activity

type of partners

Table 6: Distribution of partners and percentage of EC contribution per activity type of partner

* HES: higher education; RES: research institutes; IND: industry; OTH: other (for example, international organisations). The number of partners has been calculated based on information which includes amendments of the FP6 projects until the end of 2007. Figures do not include calculation of inclusion or termination of partners — with these included, numbers may vary. ** The total EC contribution allocated to SMEs in the fundamental genomics area constitutes approximately 7% of the total EC contribution during FP6 (2002–2006), with an allocated budget of more than 40 million; SME participation constitutes 84% of the number of industrial activity partners.




Countries Number of partners/country group

Percentage EC contribution/country

group

EU-25*

(New Member States)

Candidate countries**

Associated countries

Third countries***


Candidate countries Associated countries Third countries

Bulgaria (1)

Croatia (2) Australia (2)

Turkey (1) Canada (5)

China (1)

Gambia (1)

Japan (1)

Lebanon (1)

Russia (4)

South Africa (2)

Tunisia (2)

US (5)

Table 7: Distribution of partners and percentage of EC contribution among different groups of countries

Table 8: Distribution of non-EU-25 partners in FP6 Fundamental Genomics projects

* During FP6, the EU comprised 25 Member States; Bulgaria and Romania became Member States in 2007. The new Member States (from May 2004) are the Czech Republic, Estonia, Cyprus, Latvia, Lithuania, Hungary, Malta,

Poland, Slovenia, Slovakia. The associated countries are Switzerland, Israel, Iceland, Norway, and Lichtenstein

** Candidate countries for accession in EU during FP6 were Bulgaria, Romania, Croatia and Turkey; Bulgaria and Roma-nia were candidate countries and are therefore included in this group in the FP6 statistics for the Fundamental Genomics programme.

*** Third countries. The FP6 programme was open for participation to the International Cooperation target group countries, which may be found in the relevant FP6 work programmes Annexes. Other third countries, for example industrialised countries like the US, Canada, Australia and Japan may participate on a case-to-case basis if during the evaluation their participation is considered essential for implementing the objectives of the respective project; generally speaking, in FP6 the industrialised countries did not receive EC contributions.



TOOLS ANDTECHNOLOGIES FOR FUNCTIONAL GENOMICS1.



TOOLS & TECHNOLOGIES FOR GENE EXPRESSION

MolTools

REGULATORY GENOMICS

Tat machine

TransCode

EMERALD

AutoScreen

TargetHerpes

FGENTCARD

MODEST

1.1


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State-of-the-Art:The recording of complete genome sequences now for the first time, provides opportunities to characterise comprehensively the flow of information from genetic variation at the DNA level, over messages expressed as RNA and to their protein products, and to functions of the cell. By eavesdropping on these processes, it will be possible to identify genetic variations underly-ing malignancy, diabetes and other common diseases, and to monitor and ultimately explain molecular processes involved in these and other important conditions.

Recent years have seen rapid growth of techniques for high-throughput analyses of genes, transcripts, proteins and cells using microarrays, but current methods still capture only a small fraction of the information embodied in the molecules. This project brings together leading European laboratories and one American lab involved in the development of molecular tools, to study the molecules that make up our genomes and all their products. Our purpose is to build an infrastructure to develop a next-generation toolbox for large-scale molecular analy-ses. The suite of microarray-based technologies developed in the course of this project will be of strategic value throughout biological research, and for the biotech and pharmaceutical industries. Gradually the techniques should also become available to clinical medicine to guide diagnosis and therapy, and in agriculture and environmental monitoring.

Scientific/Technological Objectives:A series of interrelated research problems are being dealt with in collaboration between partners in academia and in biotechnology companies. The partners provide the comple-mentary expertise required to establish an individualised genome analysis technology by achieving the following objectives:

and haplotyping, and the elucidation of duplications

profiling

read out on microarrays

nucleic acids in the complexity of biological samples

alterations in cells by establishing technologies for cell array studies.

Expected Results:The ambitious plan for the MolTools project is to have developed, by 2007, a next-gen-eration toolbox for large-scale molecular analyses on arrays and in cells, with the ability to detect even single molecules. The tools will increase throughput and decrease costs for analyses of genomes, transcriptomes, proteomes and functional cells. Important progress towards these goals has been made during the course of the project.

Regarding the development of techniques for single-molecule detection and for the analy-sis of single cells, Uppsala and Aarhus Universities, in a joint project, have developed


www.moltools.org MolTools

Project Type:Integrated ProjectContract number:LSHG-CT-2003-503155 Starting date:1st January 2004 Duration:42 months EC Funding:

9 000 000


http://www.moltools.org

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a method for in situ genotyping, visualising single nucleotide allelic variations in single molecules, directly in cells and tissues, using a combination of padlock probes and rolling circle replication. An article was published in Nature Methods on how the technology was applied to genotyping mitochondria in individual cells. Since then, the technology has been further refined and now permits analysis of nuclear single-copy genes in fixed cell prepara-tions. The Uppsala lab has published a paper describing a related technology that allows individual and interacting pairs of protein molecules to be detected in cells.

Progress has also been made on working towards establishing methods for high-sensitivity, high-throughput and low-cost gene expression profiling. Very often the molecular characterisation of clini-cal samples is complicated and limited due to the available amount of samples. During the MolTools project, the so-called TAcKLE technique has been de-veloped at DKFZ. This method generates amplified, antisense-orientated fluorescent representations of initial mRNA for the sensitive parallel detection of transcripts on oligonucleotide arrays..

Potential Impact:The MolTools project brings together some of Europe’s leading groups developing technolo-gies for molecular medicine to overcome fragmentation, create synergy and speed up the development process. The high-throughput, high-precision technologies established in this programme are expected to be of decisive importance in many forms of molecular biologi-cal research, and the programme can therefore provide leverage in academic research, increasing competitiveness in the European Research Area in a global context. The project also addresses one of Europe’s main challenges in biotechnology: translating technological innovations into commercially successful products, thereby increasing competitiveness of the European biotech industry.

An image of serum analyses on arrays made of 700 antibodies

In situ genotyping single-nucle-otide variation in single mito-chondrial genomes. Larsson et al. Nature Meth., 1. 227-232 2004


Advanced Molecular Tools for Array-Based Analyses of Genomes,

Transcriptomes, Proteomes and Cells


88

MolTools participants have strong records of developing techniques, which are now used by companies such as Affymetrix, Agilent, Ap-plied Biosystems, GE Healthcare, BiopsyTec, Biotage, Bruker Dal-tonics, DynaMetrix, Epigenomics, GPC-Biotech, Hybaid, Integragen, Lynx, Micro Discovery, Molecular Staging, Mosaic Technologies, PEPperPRINT, Prot@gen, PSF AG and Scienion. By strengthening the interactions between research groups in this consortium, we hope to provide a critical mass that will stimulate the transfer of inventions from academia to es-tablished industries, and that will also promote the establishment of new companies. During the course of MolTools, one new com-pany, Olink, has been established in Sweden and another will soon be founded in Denmark. The MolTools

consortium at the 2004 annual meeting

in Berlin, Germany

Keywords: genomics, proteomics, diagnostics


MolTools


89

PartnersProject Coordinator: Prof. Ulf LandegrenUppsala UniversityDepartment of Genetics and PathologyDag Hammarskjoldsvag 20 P. O. Box 25675185 Uppsala, [email protected]

Project Manager:Dr. Carolina RydinUppsala University Department of Genetics and Pathology75185 Uppsala, [email protected]

Prof. Delores CahillUniversity College of Dublin in IrelandCentre for Genomics and BioinformaticsDublin, Ireland

Prof. Ivo GutCentre National de GénotypageEvry, France

Dr. Jorg HoheiselDeutsches KrebsforschungszentrumFunctional Genome AnalysisHeidelberg, Germany

Prof. Olli KallioniemiVTT Technical Research Centre of FinlandMedical Biotechnology Turku, Finland

Dr. Jorn KochUniversity of AarhusInstitute of PathologyAarhus, Denmark

Prof. Hans LehrachMax-Planck-Institute for Molecular GeneticsDept of Vertebrate GenomicsBerlin, Germany

Prof. Andres MetspaluEstonian BiocentreLaboratory of Gene TechnologyTartu, Estonia

Prof. Edwin SouthernOxford Gene Technology (Operations) Ltd Oxford, UK

Dr. Michael TaussigThe Babraham InstituteTechnology Research GroupCambridge, UK

Prof. Arvydas JanulaitisFermentas UABVilnius, Lithuania

Dr. Ove OhmanAmic AB Uppsala, Sweden

Prof. Anthony BrookesUniversity of LeicesterDepartment of GeneticsLeicester, UK

Prof. Marc ZabeauMethexis GenomicsGhent, Belgium

Dr. Michael DahmsFebit AGTechnology DepartmentMannheim, Germany


Advanced Molecular Tools for Array-Based Analyses of Genomes, Transcriptomes, Proteomes and Cells




90

State-of-the-Art:Determination of the sequence of the human genome, and knowledge of the genetic code through which mRNA is translated have allowed rapid progress in the identification of mammalian proteins. However, less is known about the molecular mechanisms that control expression of human genes, and about the variations in gene expression that underlie many pathological states, including cancer. This is caused, in part, by lack of information about the second genetic code – binding specificities of transcription factors (TFs). Deciphering this regulatory code is critical for cancer research, as little is known about the mechanisms by which the known genetic defects induce the transcriptional programmes that control cell proliferation, survival and angiogenesis. In addition, changes in binding of transcription factors caused by single nucleotide polymorphisms (SNPs) are likely to be a major factor in many quantitative trait conditions, including familial predisposition to cancer.

Scientific/Technological Objectives:We aim to develop novel genomics tools and methods for the determination of transcription factor binding specificity. These tools will be used for the identification of regulatory SNPs that predispose to colorectal cancer, and for characterisation of downstream target genes that are common to multiple oncogenic TFs. The specific aims are:

1. to develop novel high-throughput multiwell-plate and DNA chip-based methods for determination of TF binding specificity

2. to determine experimentally the binding specificities of known cancer-associated TFs 3. to predict computationally, and to verify experimentally, elements that are regulated

by these TFs in genes that are essential for cell proliferation4. to develop an SNP genotyping chip composed of SNPs that affect the function of TF-

binding sites conserved in mammalian species5. to use this chip for the genotyping of patients with hereditary cancer predisposition,

as well as controls in three European populations, for identification of regulatory SNPs associated with cancer.

Expected resultsThis project aims to understand the basic principles involved in growth regulation by on-cogenic TFs, and is expected to have a major impact on understanding cancer. Identifi-cation of SNPs associated with low penetrance cancer predisposition would be a major breakthrough in the effort to understand inheritance of quantitative trait loci, and will have implications on healthcare at the population level.

The methods developed within the project¹ have already allowed genome-scale prediction of regulatory elements in the human genome, and the methods developed should make feasible the analysis of DNA-binding specificities of all TFs, and consequently significantly improve our understanding of the regulation of gene expression.

¹ Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E and Taipale J: Genome-wide Prediction of Mammalian

Enhancers Based on Analysis of Transcription Factor Binding Affinity. Cell. 124:47-59, 2006.


Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-512142 Starting date:1st September 2004Duration:48 months EC Funding:

2 200 000

http://research.med.helsinki.fi/regulatorygenomicsREGULATORY GENOMICS


http://research.med.helsinki.fi/regulatorygenomics

91

Potential impactWe expect that the project will lead to the identification of genes that associate with color-ectal cancer. This will have direct implications on diagnosis and treatment of a cancer type that affects more than 200 000 Europeans each year.

Methods, tools and instrumentation for advanced genomics developed within the proposed project will improve EU scientific competitiveness in the rapidly developing field of regula-tory genomics, and will allow EU scientists to be in a very good starting position to decipher the genetic code controlling regulation of gene expression.

Keywords: genomics, molecular genetics, cancer, transcription factors

Project Coordinator:Prof. Jussi TaipaleUniversity of HelsinkiFaculty of MedicineGenome-Scale Biology Research ProgrammeYliopistonkatu 400014 Helsinki, [email protected]

Dr. Jörg HoheiselDeutsches KrebsforschungszentrumFunctional genome AnalysisHeidelberg, Germany

Dr. Markus BeierFebit Biotech GmbHHeidelberg, Germany

Prof. Torben ØrntoftAarhus University Hospital, Skejby SygehusMolecular Diagnostic LaboratoryDepartment of Clinical BiochemistryAarhus N, Denmark

Prof. Jan LubinskiPomeranian Medical UniversityInternational Hereditary Cancer CenterSzczecin, Poland

Partners


Advanced Genomics Instruments,Technology and Methods for Determination of Transcription Factor Binding Specificities:

Applications for Identification of Genes Predisposing to Colorectal Cancer



92

State-of-the-Art:Bacterial protein secretion is a fundamental biological process that is of the utmost relevance to human health. On the one hand, it can be exploited to enhance health through the bio-technological production of biopharmaceuticals. On the other hand, secreted bacterial toxins and virulence factors represent a major threat to health. The twin-arginine translocation (Tat) machinery represents a recently discovered, but highly conserved, system for bacterial protein secretion. This multi-sub-unit nanomachine can transport fully folded proteins, and thus has im-mense potential for biopharmaceutical production in the bacterial species already being used for this purpose, including , coli and . Moreover, it has been demonstrated that critical virulence factors are secreted via Tat in important pathogens, such as

and E. coli O157.

Scientific/Technological Objectives:The goal of the multidisciplinary Tat machine consortium is to carry out the functional ge-nomic characterisation of the Tat nanomachine, for both biotechnological and biomedical purposes. It has two specific objectives: firstly, to eliminate the current bottlenecks in the Tat nanomachine that limit biopharmaceutical production in , and , and secondly, to characterise the structure and function of Tat nanomachines in a few selected Gram-positive and Gram-negative bacteria, including major pathogens. To achieve these goals, the full potential of bioinformatics, comparative and structural genomics and proteom-ics will be exploited. The Tat machine consortium has a proven track record in the application of these cutting-edge technologies.

The consortium’s principal technological objective is to generate a platform for the secretion of a wide range of heterologous proteins, in particular those of therapeutic value, based on the Tat machinery. Its principal scientific objective is to obtain a clear picture of the ‘global’ role of Tat in a range of pathogenic and non-pathogenic organisms, and to obtain detailed information on the Tat structure that will lay the foundations for the future design of specific inhibitors. It is already clear that the Tat system is vital to the pathogenesis of a range of bacteria. Some bacteria export major virulence factors by this pathway, and disruption of the Tat pathway impairs the viability of others. Because Tat sub-units are also unique in structural terms, and completely absent from mammals, the Tat machine represents a superb target for novel anti-infectives.

Expected Results:The consortium aims to produce the following results: (1) A detailed structure of Tat complexes from representative Gram-negative and Gram-positive species. This is an ambitious target. The project is geared to the efficient delivery of a wide range of Tat complexes, to partners with track records in the elucidation of membrane protein structures; (2) Development of super-secreting strains of B. subtilis and S. coelicolor that are capable of exporting heterologous proteins with high efficiency. These strains will fill major gaps in the present repertoire of bac-terial vehicles for protein production; (3) Understanding of the overall role of Tat in a limited series of pathogenic bacteria, including identification of specific virulence determinants that employ this export pathway; (4) In-depth understanding of the Tat translocation mechanism. This will be achieved through a combined biochemical/genetic analysis of the Tat transloca-tion process, and the results will benefit all the elements of this project, mentioned above.

Potential Impact:The expected deliverables of the Tat machine project include knowledge of a fundamental biological system, the Tat nanomachine, which is of vital relevance to human health. The


Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-005257Starting date:1st November 2004Duration:48 monthsEC Funding:

2 000 000

Tat machinewww.tatmachine.net


http://www.tatmachine.net

93

results will serve to reinforce efforts to design anti-infectives and to produce novel biophar-maceuticals. In addition, the consortium will add to the stock of highly trained young Euro-pean scientists working in this area, and will disseminate knowledge via scientific books and journals, scientific meetings and practical training courses. These deliverables will be achieved through multidisciplinary research involving biochemistry, proteomics, functional genomics, structural genomics and comparative genomics approaches, in combination with robust project management.

Keywords: anti-infectives, biopharmaceuticals, human health, nanomachines, twin-arginine translocation, Bacillus, E. coli, Staphylococcus, Spe-cific Targeted, Research Projecttomyces, Mycobacterium, bioinfor-matics, structural genomics, drug targets

PartnersProject Coordinator:Prof. Jan Maarten van DijlUniversity Medical Center GroningenDepartment of Medical MicrobiologyHanzeplein 1P. O. Box 300019700 RB Groningen, The [email protected]

Project Manager:Dr. Sierd BronUniversity of Groningen and University Medical Center GroningenKerklaan 309751 NN Haren, The [email protected]

Prof. Colin RobinsonUniversity of WarwickDepartment of Biological SciencesCoventry, UK

Prof. Oscar KuipersUniversity of GroningenGroningen Biomolecular Sciences andBiotechnology InstituteMolecular GeneticsGroningen, The Netherlands

Prof. Marc KolkmanGenencor InternationalMicrobial and Molecular ScreeningLeiden, The Netherlands

Prof. Matthias MüllerUniversität FreiburgInstitute for Biochemistry and Molecular BiologyFreiburg, Germany

Dr. Tracy PalmerUniversity of DundeeCollege of Life SciencesDivision of Molecular & Environmental MicrobiologyDundee, UK

Dr. Long-Fei WuCentre National de la Recherche Scientifique (CNRS)Laboratoire de Chimie Bacterienne UPR 9043Marseille, France

Prof. Michael HeckerErnst-Moritz-Arndt-UniversitätInstitute for Microbiology and Molecular BiologyGreifswald, Germany

Prof. Werner KühlbrandtMax-Planck-Institute for BiophysicsStructural BiologyFrankfurt, Germany

Prof. So IwataImperial College of ScienceCentre for Structural BiologyDivision of Molecular BiosciencesLondon, UK

Prof. Roland FreudlJülich Research InstituteJülich, Germany


Functional genomic characterisation of the bacterial Tat complex as a nanomachine for biopharmaceutical production and a

target for novel anti-infectives




94

State-of-the-Art:The aim of this project is to develop open source tools enabling the identification of regula-tory elements controlling gene expression. In particular it is focused on elements which con-trol the expression of transcription factors, which in turn control expression of all other genes in the genome. This field has undergone a rapid expansion since the sequencing of several chordate genomes, which enabled researchers to identify elements through the discipline of comparative genomics, i.e. a comparison of sequenced genomes in search of conserved elements, which are likely to harbour functional elements. The great challenge is identifying effectively the elements that do not encode well-understood protein-coding genes but tend to act as regulators of expression. Recent advances have identified several such elements but they are likely to be the tip of the iceberg. TransCode aims to unravel many more such elements as well as some of the fundamental properties that characterise them.

Scientific/Technological Objectives:The project aims to perform medium-scale studies on conserved non-coding elements across several chordate organisms, as well as tackling fundamental questions related to transcription factor binding. The project will study a dozen transcription factor gene families and investi-gate in-depth for the presence of regulatory elements within the family across organisms. The following analyses will be performed on each gene family:

aims to identify elements which have remained conserved in position within a phylum and elements that have ‘shuffled’, i.e. changed position during evolution, when com-paring sequences across different phyla

-ing current algorithms with knowledge derived from the project

medium-scale verification of activity in mammalian cell-lines as well as Ciona embryos-

ferentiation assays and knock-out of transcription factors (TFs) in differentiated cells, to identify TFs involved in enhancer activity

in silico, in vitro and in vivo

This project represents a large-scale pluri-disciplinary effort to decipher the grammar of chor-date regulatory sequences, and will have a strong impact by building tools and resources that will enable devising more sophisticated hypothesis regarding regulatory networks, especially those of TFs which are involved in fundamental biological processes.

Expected Results:The project has completed its first year and has successfully completed the in silico analysis of selected transcription factor gene families, as well as the development of a central reposi-tory for both in silico and in vivo data that is being collected. The repository is available at the website (http://transcode.tigem.it/). It collates the in silico analyses so far performed, which indicate the sequence elements predicted to have functional potential based on pub-lished algorithms, as well as algorithms developed by project members. Some elements have undergone testing and for those tested in vivo results are also integrated, indicating those which have acted as enhancers or repressors and those which have yielded no results.


TransCode

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-511990 Starting date:1st January 2005Duration:39 months EC Funding:

1 000 000

http://transcode.tigem.it/


http://transcode.tigem.it

http://transcode.tigem.it

95

Partners

In the long term, the project aims to collate this data on a larger scale and with more in-depth information regard-ing the transcription factors responsible for the function of each element and their mode of action and interactions.

PotentialImpact:Throughout our project we are contributing widely to the creation, refinement and good use of standards. We are using open source software and XML data transfers, and generating novel tools and experimental protocols that will set new standards in both dry and wet areas of biology, which will help others to explore further the language of gene regulation. The identification of regulatory modules that are responsible for well-defined expression patterns will be very useful in gene therapy, thus having a direct impact on health issues. Finally we are reinforcing European competitiveness by carrying out a transnational and co-operative project of international visibility via a tight collaboration of partners across four European countries.

Keywords: comparative genomics, conserved non-genic sequences, bioinformatics algorithms, gene expression regulation

Project Coordinator: Dr. Sandro BanfiFondazione TelethonTelethon Institute of Genetics and MedicineMolecular Biology UnitVia G. Saliceto, 5000161 Rome, [email protected]

Dr. Patrick LemaireUniversité de la MéditerranéeCentre National de la RechercheScientifique (CNRS)Marseille, France

Dr. Cristian BrocchieriUniversity of CambridgeDepartment of OncologyCambridge, UK

Dr. Ferenc MullerForschungszentrum KarlsruheInstitute of Toxicology and GeneticsEggenstein-Leopoldshafen, Germany

Prof. Graziano PesoleUniversità di MilanoDipartimento di ScienzeBiomolecolari eBiotecnologieMilan, Italy

Dr. Elia StupkaCBM Scrl – Consorzioper il Centro diBiomedicina MolecolareBioinformatic UnitTrieste, Italy


Novel Tool for High-Throughput Characterisation of Genomic Elements

Regulating Gene Expression in Chordates



96

State-of-the-Art:Data quality and meta-data (documentation) are the key to all microarray implementations, ensuring that maximum information is extracted from the data. The microarray community has long realised the importance of structured documentation accompanying microarray data. To this end, a ‘grassroots movement‘, now the Microarray Gene Expression Data (MGED) Society, established guidelines for experimental description (Minimum Information About a Microarray Experiment, MIAME) and description of a structured data exchange model (Microarray Gene Expression Markup Language, MAGE-ML). MGED initiatives have mainly focused on data context, and only recently has this focus expanded to include data content. Quality and coherence of microarray data compendia (for example in ArrayEx-press) are major determinants of information extraction and model-building. EMERALD is designed to structure and organise these efforts at a European level, in close association with MGED and the External RNA Controls Consortium (ERCC).

Scientific/Technological Objectives:The EMERALD consortium aims to establish and disseminate quality metrics (QC), micro-array standards and best laboratory practices (QA) throughout the European microarray community, in order to improve the quality of microarray data. Its specific objectives are as follows:

1. To investigate existing microarray data resources in ArrayExpress, preparing a full inventory of these and deriving fair and meaningful QC from them;

2. To develop a normalisation and transformation ontology for the description of data pre-processing information;

3. To bring together all major players in the European microarray community; 4. To structure communication and information exchange within this community; 5. To obtain microarray community agreement on QA; 6. To assess microarray standards for QC. An analysis of QC relevant to vari-

ous data production protocols and available hybridisation standards (spikes, reference RNAs) will in turn facilitate the development of QA for high data quality;

7. Key microarray laboratory volunteers to validate QA/QC; 8. To validate the benefits of QA/QC in data compendium modelling; 9. To disseminate microarray standards and best practices to the microarray

community, through a user community website and information exchange and support networks, and to provide training in their proper implementation;

10. To extrapolate and apply these standards to developing technologies.

Expected Results:The main result of EMERALD will be a quality metrics system for microarray data, accompanied by ontologies for documentation of microarray meta-data. The project will also generate hy-bridisation standards and, in general, integrate European efforts towards laboratory standard-isation in this area. Recent scientific publications have shown that microarray data produced under a series of standardisation constraints show improved significance and sensitivity.EMERALD will bring together the main research and innovation operators involved in the devel-opment of microarray standards and quality metrics, with stakeholders in the data production process (core facilities, companies, technology innovators), data mining (computational and systems biology research teams) and data information (toxicology, clinical diagnostics, prog-nostics, etc). The coordination and amalgamation of the activities and interests of these diverse stakeholders will strengthen the European microarray community, consolidating an essential component of data-driven systems biology.

Intensity representation on an Affymetrix array (spatial plot). The false colours represent the

spatial intensity distribution of the array. The colour scale

was chosen proportional to the intensity ranks. This graphical

representation highlights problems that result from

the experimentation such as fingerprints, artifactual intensity gradient or dye specific failures

for instance.


Project Type:Co-ordination ActionContract number:LSHG-CT-2006-037689Starting date:1st November 2006Duration:36 monthsEC Funding:

1 300 000

EMERALD


97

Potential Impact:Data-driven modelling approaches that depend on data quality and coherence are es-sential to systems biology. EMERALD aims to bring about the implementation of QA/QC, especially in the building of high quality, compendium-style data repositories. The Seventh Framework Programme (FP7) is expected to place an emphasis on the development of new biological research tools that will significantly improve the acquisition and analysis of data, with a view to enhancing our understanding of complex biological systems. FP7 research will include the development of technologies related to sequencing, gene expression, geno-typing and systems biology. EMERALD will contribute to these research goals by improving large scale data gathering.

Keywords: microarray technology, quality control, quality assurance, systems biology, data modelling, technology development

Project Coordinator:Prof. Martin KuiperGhent University/Flanders Interuniversity Institute for BiotechnologyDepartment of Plant Systems BiologyComputational Biology groupGhent, [email protected]

Prof. Arne SandvikNorwegian University of Science and TechnologyNorwegian Microarray ConsortiumTrondheim, Norway

Dr. Alvis BrazmaEuropean Molecular Biology LaboratoryEuropean Bioinformatics Institute (EBI)Hinxton, UK

Dr. Carole FoyMicroarray Standardisation LGC LtdTeddington, UK

Prof. Joaquin DopazoCentro de Investigación Príncipe FelipeDepartment of BioinformaticsValencia, Spain

Dr. Heinz Schimmel, Joint Research Centre of the European CommissionInstitute for Reference Materials and MeasurementsGeel, Belgium

PartnersDr. Laszlo PuskasBiological Research Centre of the Hungarian Academy of SciencesLaboratory for Functional GenomicsSzeged, Hungary

Prof. Ulf Landegren Uppsala UniversityDepartment of Genetics and PathologyRudbeck LaboratoryUppsala, Sweden.


Empowering the Microarray-Based European Research Area to Take

a Lead in Development and Exploitation



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State-of-the-Art:As more and more genomes are being sequenced, efficient methods to elucidate the func-tions of the many unknown genes need to be developed. Such methods will be an essential prerequisite for turning biology from a qualitative, mostly descriptive, to a quantitative, ultimately predictive, science. Although quantitative tools such as DNA microarrays for transcriptome analysis have been available for some years, they have not yet been used to their full potential due to the overwhelming complexity. Cells are built from thousands of different proteins that are expressed, both temporally and spatially, over an extremely wide dynamic range. Proteins and other cellular components are regulated through variations of their location, their activity and their state of modifica-tion. Although DNA microarrays have proved to be important tools for gene discovery on the tissue level, and, moreover, hold great promise for diagnostic applications, they have major shortcomings in their lack of cellular resolution. In order to obtain qualitative and quantitative data on cellular pathways, new equipment needs to be developed.

Scientific/Technological Objectives: The overall objective of the AUTOSCREEN project is the establishment of an innovative and automated screening instrument for high-throughput and high-content screens. This instru-ment will allow standardised, robust, automated and ultrasensitive high-resolution analysis of RNAs and proteins at cellular and subcellular resolution.

The main goal of the project is to develop an innovative screening platform suitable for high-throughput and high-content cell-based assays and to demonstrate its suitability for high-res-olution in situ techniques. This instrument, named AUTOSCREEN, will not only provide the basis for intelligent and efficient high-content screens, but will also be designed for low cost genetic, medical, chemical and pharmaceutical screens. It will constitute a significant com-petitive advantage for the European pharmaceutical and agro biotechnological industry.

Expected Results: The main expected result of the project is the generation of an innovative screening instru-ment, named AUTOSCREEN. This instrument, which will consist of the modular iMIC imag-ing microscopy platform as a future microscopy standard, will integrate ultra-sensitive CCD-technology and novel software concepts that allow an adaptive, i.e. result-based, shaping of the ongoing experiment. An ultra-sensitive fluorescence-based scanning device for single-molecule measurements and a fully automated plate feeder station for automated sample handling and tracking will increase the flexibility and wide utility of AUTOSCREEN. This system will be tested in a large number of applications for performance and excellence.

The project is expected to permit the qualitative and quantitative monitoring of cellular con-stituents (RNA, proteins, and metabolites) in living cells at the highest possible cellular and subcellular resolution and with maximal sensitivity and specificity. This will allow quantify-ing protein expression and monitoring its subcellular localisation, its state of modification and its association with other proteins and ligands. Furthermore, it will allow measuring of the change of these processes over time.

Potential Impact: AUTOSCREEN will have a strategic impact on functional genomic, biotechnological and bio-medical research by permitting qualitative and quantitative monitoring of cellular constituents in cells at the highest possible cellular and subcellular resolution and with maximal sensitivity and specificity. This will allow, for example, quantifying protein expression, monitoring of sub-cellular protein localisation and state of modification, and characterisation of the toponome.


Autoscreen

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2007-037897Starting date:1st January 2007Duration:60 monthsEC Funding:

3 217 280


99

Partners

The demonstration of the wide applicability of AUTOSCREEN to the quantitative monitoring of biological processes, within living cells, at highest currently possible resolution and with sensitivity to the limit set by the laws of physics, will have a significant impact on biomedical research in general. By combining interdisciplinary activities from academic and industrial sources and by interfacing biological research with nanotechnology, computing and engi-neering, the team expects to create an important tool for biomedical research. Moreover, AUTOSCREEN-based assays will allow the monitoring of cellular networks and incorporate in vivo protein interaction assays and features like protein concentration and kinetic parameters. Thus, available information on gene expression networks will not only be useful for identifying points of the network affected by the drugs and for simulations of cellular processes, but will also allow the assessment of drug side reactions at an early stage and facilitate the design of novel, less toxic compounds. The project will reveal new, faster and better possibilities to determine gene functions and regulatory networks in a much shorter period of time. The implementation of these technolo-gies will lead to a higher competitiveness of European biomedical SMEs, in the sense that the instrumentation to be developed and assembled in this project will enable many European SMEs to efficiently perform their screens. The estimated low cost of this instrument is expected to be of great benefit for SMEs as it will promote their market success.

Keywords: imaging, screening, genomics, proteomics, drug screening, high-throughput technologies

Project Coordinator: Prof. Dr. Klaus PalmeUniversity of FreiburgInstitute for Biology IIFaculty of BiologyCenter for Applied BiosciencesFahnenbergplatz79085 Freiburg, [email protected]

Dr. Stefanie KlemmTILL ID GmbHGräfelfing, Germany

Dr. Andras FilepManz KftDebrecen, Hungary

Dr. Alois SonnleitnerUpper Austrian Research GmbHLinz, Austria

Dr. Colin CoatesAndor Technology PlcBelfast, UK

Dr. Carmen PlasenciaAromics SLBarcelona, Spain

Dr. Martin OheimInstitut National de la Santéet de la Recherche Médicale(INSERM)Neurophysiology andNew Microscopies LaboratoryParis, France

Dr. Hartmann HarzLudwig-Maximilians-UniversitätBioImaging ZentrumPlanegg, Germany

Dr. Benedetto RupertiUniversity of PadovaLegnaro, Italy


Autoscreen for Cell Based High-throughput

and High-content Gene Function Analysis and Drug Discovery Screens



100

State-of-the-Art:Herpes viruses cause many serious and life-threatening diseases, especially in immuno-compromised patients, such as transplant recipients and HIV-infected individuals. Even in healthy ones, herpesviruses can result in serious diseases. For example, the herpes simplex virus (HSV) remains one of the most common sexually transmitted diseases, while human cytomegalovirus (HCMV) is a leading cause of birth defects, and human herpes virus 8 (HHV-8) causes a number of cancers. At present, the options for antiviral therapy are lim-ited, and owing to toxicity, the current anti-herpesvirus drugs cannot be administered to pregnant women. There is a continuing need to develop new treatments, because drug-resistant viruses are constantly evolving.

A principal characteristic of herpesvirus infections, is that after primary infection (usually in childhood), the viruses establish a latent state that remains for life. Up to 90 percent of the population may be latently infected with one or more herpes viruses. The social and psychological consequences of the herpesvirus infections are severe.

Scientific/Technological Objectives: The major objective of TargetHerpes is to define novel drug targets and to identify new strategies, for the control of herpesvirus infections. These targets and strategies will help, in the long term, to provide the next generation of antiviral compounds, Specifically, TargetH-erpes will perform the following actions: (i) develop peptide inhibitors that interfere with virus entry; (ii) generate synthetic peptides that enable antibody-dependent cellular cytolysis against herpesviruses; (iii) define, investigate and apply RNA silencing reagents that block the expression of viral genes that enhance herpesvirus replication; (iv) define, investigate and apply RNA silencing reagents that interfere with proviral host genes; (v) identify viral and cellular genes involved in herpesvirus-mediated oncogenesis, and define RNA silenc-ing reagents and peptide inhibitors; and (vi) develop approaches to inhibit the reactivation of HSV from latency.

This programme of work will provide innovative technologies for the identification and de-velopment of future products targeted at preventive and therapeutic interventions for human herpesvirus diseases. Moreover, these strategies will likely be transferable to many other persistent infections.

Expected Results: The TargetHerpes project is divided into six experimental work packages (WPs). The aim of WP1 is the development of peptide molecules that will inhibit the functions of herpesvirus glycoproteins and elucidate their roles in entry of the virus particles into cells. Preliminary work has provided proof-of-principle that mimetic peptides to HSV gH inhibit infection.

Such peptides targeting HSV glycoproteins will be suitable for future animal experimenta-tion and translational research by partners PRIMM and IBA. WP2 will generate synthetic peptides that enable IgG antibodies to execute cell-mediated cytolysis against HSV and HCMV. Such peptides will be evaluated for their individual potency in vitro, then bioac-tive peptides will be evaluated with regard to safety and harmlessness to cells, as well as optimal stability in cultured cell systems. WP3, WP4, WP5 and WP6 will identify suitable molecular targets for antiviral intervention by RNAi.

These targets will include important herpes virus gene products that have known or sus-pected roles in promoting viral replication directly or indirectly. In case of WP5, siRNAs


TargetHerpes


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targeted at viral genes will be selected based on their capacity to interfere with HHV-8 me-diated cell transformation and immortalization. WP6 expects to identify the cellular interac-tion partners of ICP0 (the viral protein that is necessary for HSV to reactivate from latency), and to define those elements that are required for its activity.

Potential Impact: TargetHerpes will identify novel strategies, leading to the development of new approaches to inhibit replication of, or pathogenesis caused by, HSV, HCMV and HHV-8. Due to the conservation of genes and replication strategies within herpesviruses, the approaches dis-covered will be applicable to other human herpesviruses as well. For example, treatments that target HSV-1 are highly likely to be effective against HSV-2 and may be adapted to counteract varicella zoster virus (VZV). Similarly, treatments that are effective against HHV-8 may also be applicable to Epstein-Barr virus (EBV). Given the figures on the health burden and costs of herpesvirus infections, the potential impact of a successful outcome of the Tar-getHerpes project is considerable.

Keywords: herpesvirus; chemiotherapeutics; herpes simplex virus; human cytomegalovirus; human her-pesvirus 8; fusion; glycoproteins; siRNA; innate immunity; host response; IFN

Project Coordinator: Prof. Gabriella Campadelli-FiumeUniversity of BolognaCentro Interdipartimentale Galvani (CIG) via S. Giacomo 12I-40126 Bologna, [email protected]

Dr. Roger EverettMedical Research CouncilVirology UnitGlasgow, UK

Prof. Hartmut HengelUniversity of DuesseldorfInstitute for VirologyDüsseldorf, Germany

Dr. Joachim BertramIBA GmbHGöttingen, Germany

Dr. Frank NeipelUniversity of ErlangenInstitut fuer Klinische und Molekulare VirologieErlangen, Germany

Partners

Dr. Michael NevelsUniversity of RegensburgInstitute for Medical Microbiology and HygieneFaculty of Medicine, Molecular Virology UnitRegensburg, Germany

Dr. Angela PontilloPRIMM SrlMilan, Italy

Dr. Ivan RossiBioDec SrlBologna, Italy

Wolfgang Laepple-BoettigerARTTIC S.A.Office MannheimSchifferstadt, Germany


Molecular intervention strategies targeting latent and lytic herpesvirus infections



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State-of-the-Art:The general aim of FGENTCARD is to apply functional genomic and genotyping technolo-gies along with the knowledge arising from mammalian genome annotations, in order to define novel diagnostic tools for risk factors of Coronary Artery Disease (CAD) (glucose intolerance, insulin resistance, hypertension, dyslipidaemia and obesity). FGENTCARD, supported by available functional genomic technologies, will tackle these increasingly fre-quent and prevalent inherited diseases. The project will ultimately generate fundamental knowledge on the impact of functional genomics to identify disease biomarkers and test their use for disease prediction. The consortium is interested in focusing on CAD because of its frequency and prevalence in the general population, the strong impact on human health and the burden of related healthcare costs. Pathological elements of CAD have been shown to have complex etiology and pathogenesis that influence an individual’s relative risk of developing these diseases. The genetic input is complex, and involves combinations of multiple genes that contribute to susceptibility or resistance to CAD risk factors. In order to take advantage of high density multimodal phenotyping, the consortium is preparing an innovative infrastructure of both the techniques and materials that provide strategic support for CAD quantitative genetics in rodent models and humans.

Scientific/Technological Objectives: One of the major objectives of the FGENTCARD is to identify biomarkers associated with CAD risk factors, by means of network biology that can be used as disease prediction tools in clinical studies and as targets for developing novel and more efficient drugs.FGENTCARD is objective-driven research which develops along the following lines:

1) Characterization of CAD phenotypes, using classical physiological and biochemical methods in a large cohort of patients and in animal models;

2) Generation of functional genomic quantitative trait datasets using plasma and urine metabonomic profiling in animal models and humans, plasma proteomic profiling in animal models and humans and tissue transcriptomic, proteomic and metabonomic profiling in animal models;

3) Genetic studies which aim at testing the association between plasma biomarkers and CAD risk factors in humans, at testing the inheritance of plasma, urine and organ biomarkers in animal models and at identifying underlying gene variants in animal models and humans.

Close interactions with external international groups investigating related disorders in other models and human cohorts will provide resources for extension and validation of CAD biomar-kers. In addition, interactions with other EC funded programmes of research, including MOL-TOOLS and MOLPAGE, will maximize the scientific and technical outputs of FGENTCARD.

Expected Results: The consortium plans to deliver the following specific results:

1) Multimodal phenotyping in a novel collection of 5,000 CAD patients, and in mouse and rat models of spontaneous and experimentally-induced pathologies relevant to CAD risk factors;

2) A series of integrated functional genomic datasets defining biomarkers associated with CAD risk factors, through quantitative genetic studies in experimental crosses derived from animal models and further genetic association and linkage studies in humans;

3) CAD susceptibility loci and genes providing chromosomal targets for positional clon-ing experiments and entry points to the development of novel drugs designed for specific protein and metabolite disease biomarkers;


FGENTCARD

Project Type:SME-Specific Targeted Research ProjectContract number:LSHG-CT-2006-037683Starting date:1st January 2007Duration:36 monthsEC Funding:

3 000 000

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4) A set of standard operation procedures (SOPs) for the characterization of novel CAD quantitative biomarkers, applicable to genetic and clinical studies in other cohorts of patients and controls.

5) Data analysis using bioinformatics and statistical genetic tools developed in experi-mental populations and human cohorts, which will further strengthen the impact of comparative genomics in biomedical research.

Potential Impact: FGENTCARD brings together a comprehensive set of specific expertise in functional ge-nomic technologies (metabonomics, proteomics, transcriptomics), genotyping methods and statistical genetics in rodent models and humans. This multidisciplinary approach is neces-sary when undertaking an integrated functional genomic approach that addresses genetic variation, in the context of CAD risk factors.

Overall, the potential wealth of information that can be obtained on gene expression, from transcription to protein effects, is enormous. It represents novel challenges in quantitative genetics, and ultimately, significant advances for disease diagnosis and prevention as well. An important goal of this research in CAD patients and animal models lies in disease gene identification. Knowledge of the effects of genetic variations on metabolic processes and metabotype regulation will have a major impact in the field of polypharmacology, on the development of novel drugs designed to affect multiple targets simultaneously.

Keywords: metabonomics, quantitative genetics, diagnostics, coronary artery, cardiovascular disease

Project Coordinator: Dr. Dominique GauguierUniversity of OxfordWellcome Trust Centrefor Human GeneticsRoosevelt DriveOxford, OX3 7BN, [email protected]

Prof. Mark Lathrop, Dr. Ivo G. GutCentre National de Génotypage (CNG)Evry, France

Prof. Jeremy K. NicholsonImperial College Faculty of MedicineChemical and Molecular Systems BiologyLondon, UK

Dr. Pierre ZallouaLebanese American UniversitySchool of MedicineDepartment of Internal MedicineBeirut, Lebanon

Dr. Ulla Grove SidelmannNovoNordisk A/SMalov, Denmark

Dr. Jorg HagerIntegraGen SAEvry, France

Dr. Frank BonnerMetabometrix LtdLondon, UK

Partners


Functional GENomic diagnostic Tools for Coronary Artery Disease



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State-of-the-Art:The pharmaceutical industry is highly interested in using primary cells instead of cell lines for cell-based screening campaigns in drug development since primary cells are freshly isolated from the organism’s tissue, and have not gone through any transformations, which is the prerequisite for the unlimited growth of conventional cell lines. With more predictive screens in terms of both the relevance of a target and the pharmaco-kinetics/-dynamics of a drug compound, it becomes much easier to make adequate decisions as to which targets or compounds to focus on for further development. While conventional transfection methods, such as lipofection or electroporation, usually yield satisfactory results for standard cell lines, many other cell lines — as well as most primary cells — are difficult or even impossible to transfect with these methods. Viral vectors - as an alternative for DNA delivery - work well in some cases, but are labour-intensive, not versatile, and remain connected with significant safety issues. As a consequence, most primary cells are considered non-transfectable. This represents a tremendous disadvantage in highly relevant research areas, as primary cells are the ones that most closely resemble the situation of the living organism.

Besides the delivery of DNA, RNA or small molecules to primary cells, throughput of trans-fection experiments is of extreme importance. The emerging RNA interference (RNAi) tech-nology, continued growth of (drug) compound libraries, and the increasing number of po-tential targets to be screened, have resulted in the high pressure to increase the throughput of screening to higher formats, the so-called ultrahigh-throughput screening (uHTS). How-ever, cell-based assays still use the 96- or occasionally the 384-well format and screening of millions of compounds may take months instead of days.

Scientific/Technological Objectives: The principle objective of the MODEST project is the development and use of an ultrahigh-throughput device for nucleofection (uHTN device) as well as protocols for highly efficient, small volume ultrahigh-throughput screenings of primary cells, mainly in the areas of immunol-ogy, neurology and liver metastasis with the aim of accelerating basic research, target identi-fication and validation as well as drug development.

These uHTN device will represent a major breakthrough, since it would allow high-throughput screenings in efficiently transfected and differentiated networks of primary cells. In addition, the concept of disposable modular multi-well plates for transfection is perfectly suited for pre-plating substances, for storage and for later use, thus allowing flexible approaches, e.g. for high-throughput screening campaigns.

Application of these tools is planned in order to investigate medically highly relevant disor-ders. On the basis of the 96-well Nucleofector, which was launched by “amaxa” in 2006, the Consortium will develop ultrahigh-throughput devices. In parallel, protocols for cultivating, differentiation, nucleofection and functional screens of primary cells in very small volumes will be elaborated on and, furthermore, adapted to the devices.

Expected Results: Development of uHTS device is the main objective of this project. These devices will be dis-tributed by the coordinator, “amaxa”. In order to efficiently commercialise this platform with-in a well-balanced marketing and sales strategy, the coordinator will combine a top-notch sales force in key markets and alliances with quality strategic and distribution partners. The commercialisation strategy aims to optimise short- and medium-term revenues, secure broad market access and share, and provide crucial market feedback to the company.

Development of automated cell manipulation in the 384-well

format will add an important tool for biomedical research and drug

development.


MODEST

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2007-037291Starting date:1st April 2007Duration:36 monthsEC Funding:

2 755 356


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The scientific knowledge of the MODEST project shall be published in premium peer-re-viewed journals, and scientists involved in the project will present their data at national and international conferences.

Potential Impact: The partners of MODEST will employ the results of the project to service pharmaceutical customers who repeatedly have expressed the urgent need for devices, protocols and as-says for primary cells or differentiated human neuronal stem cells in target discovery and validation. The results of the project will give the partners a clear competitive advantage. The use of primary cells in preclinical R&D will positively impact attrition rates and reduce the significant time and capital involved in drug development. The proximity to European pharmaceutical research and the size of the international pharmaceutical research market strengthen the logic for the creation and implementation of the MODEST project.

Keywords:

nucleofection, primary cells, hard-to-transfect cell lines, RNAi, siRNA, ultra high throughput transfection, adult stem cells, neuronal cells, apoptosis, lead, gene silencing/knockdown, screening

PartnersProject Coordinator: Dr. Birgit Nelsen-Salz Amaxa AGNattermannallee 150935 Cologne, [email protected]

Dr. Alexander ScheffoldDeutsches Rheuma ForschungszentrumBerlin, Germany

Dr. Joerg PoetzschRNAx GmbHBerlin, Germany

Dr. Kaia PalmProtobios Ltd.Tallin, Estonia

Helmut LoiblFOTEC Forschungs- und Technologietransfer GmbHWiener Neustadt, Austria

Josef Anton PallanitsHTP High Tech Electronics GmbHNeudoerfl, Austria

Dr. Naiara TelleriaDominion Pharmakine S. L. Derio, Spain

Thomas SchaumannPrevas ABVästerås, Sweden


Modular Devices for Ultrahigh-throughput and Small-volume Transfection




TOOLS & TECHNOLOGIES FOR PROTEOMICS

1.2INTERACTION PROTEOME

NEUPROCF

CAMP

ProDac


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State-of-the-Art:The main objective of the INTERACTION PROTEOME project is the establishment of a broad-ly applicable platform of routine methods for the analysis of protein interaction networks in biomedical research. A multidisciplinary approach will address different aspects of the generation of protein-interaction data, their validation by cell biological, biochemical and biophysical methods, their collection in a new type of public database and their exploitation and use for in silico simulations of protein-interaction networks.

These goals represent substantial state-of-the-art advances in these technologies. The innova-tions generated in INTERACTION PROTEOME will thus provide the basis for an efficient analysis and systems modelling of fundamental biological processes in health and disease.

More specifically, INTERACTION PROTEOME will develop novel technologies, including a high-end mass spectrometer with an extremely large dynamic range, high-density peptide ar-rays and improved visualisation technology for light and electron microscopy. These technolo-gies will be validated through model systems of great relevance to medicine and biotechnol-ogy. In order to cope with the massive increase in experimental data on protein interactions obtained by using the novel technologies, extensive bioinformatics support will be a key element in facilitating this work. In particular, the efficient integration of disparate data sets represents a vital challenge in proteomics and functional genomics.

Within the context of interaction data already included within the scientific literature written by a community of ‘traditional biologists’, the analysis of the newly discovered interactions will represent an essential prerequisite for the success of the consortium. For this purpose, the consortium includes the creation of the only European protein-interactions database, called MINT.

Scientific/Technological Objectives: The aim of INTERACTION PRO-TEOME is to establish Europe as the international scientific leader in the field of functional proteomics, and in particular in the analysis of protein-protein interactions. One of the major objectives includes the establishment of a broadly applicable platform of routine methods for the analysis of protein interaction networks.

The interaction partners of more than 100 relevant protein domains and more than 3,000 peptides will be characterised using these novel

technologies, while the data obtained during the project will be collected in an improved version of the European MINT database. At the same time, novel bioinformatics tools for the prediction of protein interactions and their relation to post-translational modifications will be created. In addition, software for in silico modelling of protein interactions will be developed and validated with the projects’ model systems.

Localisation of proteins within a cell: Protein complexes (coloured) are depicted at various levels of

resolution in their cellular context (background). This technology

enables the visualisation of the 3-dimensional architecture and

supramolecular structure of cells.


INTERACTION PROTEOME

Project Type:Integrated ProjectContract number:LSHG-CT-2003-505520Starting date:1st January 2004Duration:66 monthsEC Funding:

11 999 527

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Expected Results: The aim of INTERACTION PROTEOME is to establish ground-breaking technology for the analysis of protein-protein inter-actions. During the first two years of the project, major goals have already been achieved.

In terms of technology, a major breakthrough by INTERAC-TION PROTEOME was the development of a novel mass spectrometer, the LTQ-Orbitrap, and its introduction to the market in June 2005 by the project partner Thermo Electron (Bremen). The Orbitrap is the first fundamentally new mass analyser in more than 20 years. Compared to a state-of-the-art high performance mass spectrometer (LTQ-FT), the Orbitrap exhibits a 10-fold increase in sensitivity along with a four-fold extension of the dynamic range. Based on highly accurate mass determination combined with high resolution and sensitivity, the novel instrument not only allows for routine analysis with high-throughput, but also for straight forward analysis of peptide mixtures without chemical or enzymatic modifications.

From a methodological point of view, the Orbitrap is the ideal instrument for the two novel “2D-Gel-free” proteomics approaches developed within the project, namely the “SILAC” (Stable Isotopic Labelling by Amino acids in Cell culture) technology developed by the team of Matthias Mann at the University of Odense/Max Planck Institute of Biochemistry, Mar-tinsried, and the “COFRADIC” (COmbined FRActional DIagonal Chromatography) created by the team of J. Vandekerckhove from Flanders Interuniversity Institute of Biotechnology, Ghent. Both technologies have been successfully applied to a number of the project’s model systems, including, among others, the analysis of protein processing in apoptosis by COF-RADIC, as well as the analysis of Chaperone-dependent protein folding and of signalling (de)differentiating stem cells by SILAC.In the first two years of its existence, INTERACTION PROTEOME has published over 30 peer-reviewed publications in internationally renowned journals. During the project’s mid-term review in December 2005, external experts evaluated INTERACTION PROTEOME as a clear “showcase project for EU research”. By the end of year four of the project, the number of publications issued has risen up to 120.

Potential Impact:

Visualisation of the cytoskeleton of a Dictyostelium cell. Colours were subjectively attributed to mark the actin filaments (reddish); other macromolecular complexes, mostly ribosomes (green); and membranes (blue).


Functional Proteomics: Towards defining the interaction proteome

Protein folding by the Chap-erone machinery: an unfolded substrate protein is inserted into the barrel-shaped GroEL cage, which is subsequently locked with the GroES lid. Folding proceeds within the secluded chaperonin cage, which finally releases either correctly folded functional protein (upper), or an incompletely folded protein which may undergo either an-other folding cycle or degrada-tion in the cytosol.


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The technology and methodology produced in INTERACTION PRO-TEOME will facilitate a large-scale analysis of protein interactions in various fields of bio-medicine. The interdis-ciplinary collaboration within the project will support the development of coherent standards in methodology and data formats, foster further horizontal integration of research centres and facilitate the exchange and comparison of data

obtained in different laboratories. Although this coherence will initially be observed only within the consortium, its scientific success will promote the spreading of its standards to European proteomics centres outside the partnership. The active contribution of individual partners to various other networks at national and international level will also facilitate the dissemination of standards and promote the coherence of the proteomics field in Europe.

In terms of human resources, the impact of INTERACTION PROTEOME in the many ex-panding areas of biomedicine will be considerable. Young scientists involved in the project will acquire multidisciplinary skills, including training in bioinformatics, and will thus rep-resent a valuable resource for the growing biomedical and biotechnological industry. In addition, highly qualified technical personnel in this novel interdisciplinary research field will become available through the project. Finally, administrative staff involved in the management of this large EU project will gain experience for future careers as managers of international projects.

Keywords: protein-protein interaction, signalling network, proteome

Clusters of phosphorylation sites assigned according to the tempo-

ral profiles of their modulation after EGF stimulation of the cells. Prominent members are indicated

above each cluster.


INTERACTION PROTEOME

Phototaxis in Halobacterium salinarum. A) Halobacteria are repelled by blue light (left) and

attracted by orange light (right). B) Components of the halobacte-

rial signal transduction chain modulating clockwise (CW) and

counterclockwise (CCW) rotation of the flagellar motor.


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PartnersProject Coordinator: Prof. F. Ulrich HartlMax-Planck-Institute of BiochemistryDepartment of Cellular BiochemistryAm Klopferspitz 1882152 Martinsried, [email protected]

Project Manager: Dr. Anne Katrin WerenskioldMax-Planck-Institute of BiochemistryEU Project Acquisition & ManagementAm Klopferspitz 1882152 Martinsried, [email protected]

Prof. Wolfgang Baumeister, Prof. Dieter Oesterhelt, Prof. Matthias MannMax-Planck -Institute of BiochemistryMartinsried, Germany

Prof. Joel VandekerckhoveFlanders Interuniversity Institute of BiotechnologyDepartment of Medical Protein ResearchGhent, Belgium

Prof. Gianni CesareniUniversity of Rome Tor VergataDepartment of BiologyLaboratory of Molecular GeneticsRome, Italy

Prof. Søren BrunakTechnical University of DenmarkCenter for Biological Sequence AnalysisLyngby, Denmark

Dr. Raymond WagnerFEI Electron Optics BVEindhoven, The Netherlands

Prof. Walter KolchBeatson Institute for Cancer Research Signalling & Proteomics LaboratoryGlasgow, UK

Dr. Marius UeffingGSF - National Research Center for Environment and HealthInstitute of Human GeneticsNeuherberg, Germany

Dr. Reinhold PeschThermoElectron (Bremen) GmbHBremen, Germany

Prof. Luis SerranoCentre De Regulació Genómica (CRG)Systems Biology Research unitBarcelona, Spain

Dr. Philippe BastiaensEuropean Molecular Biology Laboratory (EMBL)(EMBL)-HeidelbergCell Biology and Cell Biophysics ProgrammeHeidelberg, Germany

Dr. Mike SchutkowskiJT Peptide TechnologiesBerlin, Germany


Functional Proteomics: Towards defining the interaction proteome




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State-of-the-Art:In the search for new diagnostic and prognostic biomarkers for the development of new drugs for cystic fibrosis (CF), the identification of new low- and medium-abundance pro-teins involved in its pathophysiology is a very promising field. The characterisation of such markers requires the development of several high performance techniques and the crea-tion of standards for these new approaches. Several ways will be explored to bring new knowledge to the CF community, applying and developing state-of-the-art mass spectrom-etry, chromatography and electrophoresis methods to the inflammation mechanisms in CF, interaction between proteins, mainly the cystic fibrosis transmembrane regulator (CFTR), and other molecules, like DNA, other proteins or lipids. In addition to the biomarkers, this should bring a better understanding of CF pathophysiology with regard to transepithelial ion transport, inflammatory processes and the identification of factors responsible for the different CF phenotypes.

Scientific/Technological Objectives: The aim is to identify new low abundance protein biomarkers in serum. In the meantime, the project will generate new basic knowledge for inflammation, protein-, lipid- and DNA-interaction in all fields related to scientific fields, such as cancer, neurodegenerative dis-eases and asthma that are considered as priorities for EC science.Another strategic impact concerns prognostic biomarkers: the phenotype of CF is quite vari-able, even in patients bearing the most frequent mutation delta F508. To tackle the prob-lems posed by this disease and to try to decipher the underlying mechanisms, large-scale studies at the protein level would certainly accelerate discoveries, in particular by detecting low abundance proteins. This will imply new standard protocols for sample collection and technologies by:

which will be useful for the proteomic community;-

cation of lipid molecules which interact with CF-related proteins;

pathogenesis of CF;

Expected Results: Methodological improvements in mass spectrometry, to be patented if applicable, will maintain the very high level of skills in this field in Europe, and open new lipidomic-DNA-proteomic approaches.Here is a list of expected results:

CF patients;

Potential Impact: Through the NEUPROCF results and the ability to monitor low- and medium-abundance CF biomarkers, the objective is to give a better prognostic of the disease severity. The treat-


NEUPROCF

Project Type:Specific Targeted Research Project Contract number:LSHG-CT-2004-512044 Starting date:1st July 2005 Duration:36 months EC Funding:

2 355 000


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ments could be then adapted, being lighter for a less severe affection, hence improving the pa-tient’s quality of life.

In addition, the input of knowledge on the mechanisms underlying CF phenotypes in a da-tabase could prove to be a decisive asset in the perspective of transferring the knowledge to biotech or pharmaceutical groups, together with standard protocols for sample collection and high-tech technology.

Keywords: low abundance proteins, proteomics, cystic fibrosis

Project Coordinator: Dr. Aleksander EdelmanInstitut National de la Santé et de la Recherche MédicaleFaculte de Medecine Necker Inserm U467156, rue de Vaugirard75730 Paris, [email protected]

Dr. Michal DadlezPolish Academy of SciencesDepartment of BioinformaticsWarsaw, Poland

Dr. Peter BergstenUppsala UniversityDepartment of Medical Cell BiologyUppsala, Sweden

Prof. Jasminka Godovac-ZimmermannUniversity College LondonDepartment of Medicine Rayne InstituteLondon, UK

Dr. Robert DormerUniversity of WalesDepartment of Medical Biochemistry & Immunology School of Medicine Cardiff, United Kingdom

Prof. Gérard LenoirAssistance Publique - Hopitaux de ParisHôpital Necker Department of PediatricsParis, France

Dr. Dorota SandsInstitute of Mother and ChildCF CentreWarsaw, Poland

Dr. Lena HjelteKarolinska InstitutetHuddinge University HospitalStockholm Cystic Fibrosis Center Stockholm, Sweden

Dr. Laure-Emmanuelle BenhamouINSERM - TransfertEuropean Projects ManagementSaint-Beauzire, France

Dr. Michael CahillProteoSys AgMainz, Germany

Dr. Josef VogtUniversitätsklinikum UlmDepartment of Anaesthesiology Ulm, Germany

Prof. Margarida AmaraFundacao da Faculdade de Ciencias de Universidade de LisboaDepartment of Chemistry and Biochemistry - Laboratory of Molecular GeneticsLisbon, Portugal

Partners

One of the NEUPROCF strategies to identify biomarkers: high resolution MS/MS analysis peptide map. © Dr. M. Dadlez (IBB-MS)


Development of New Methodologies for Low Abundance Proteomics:

Application to Cystic Fibrosis



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State-of-the-Art:Proteases are key molecules in biological systems. They modify numerous proteins by hydro-lytic cleavage, thus controlling and executing many physiological processes. Their intricate networks require rigorous regulation to prevent fortuitous proteolysis. Where this regulation fails, proteases trigger pathologies such as neurodegeneration, inflammation, and cancer. Many therapeutic approaches are directed towards proteases or their natural inhibitors, and are already leading to drugs for life threatening diseases. However, the tight regulation of proteases by posttranslational modifications makes current functional genomics technologies unsuitable for fully establishing biological relevance. The project “Chemical Genomics by Ac-tivity Monitoring of Proteases” (CAMP) will lay the groundwork for the study and understand-ing of proteases through activity labelling and functional imaging in cells. Specifically, CAMP will investigate the substrate specificity of proteases by using large peptide libraries, derive fluorescent labelling molecules from the sequence information gathered, and use these mol-ecules to investigate proteolytic activities in cellular environments. Given the estimated number of 600 proteases to 1100 proteases in the human genome, the team’s selected set constitutes a significant representation and will establish the feasibility of the project’s approach to ad-dress the protease proteome. CAMP’s proteases will serve as prototypes to develop novel protease-specific technologies and probes for studying expression and folding, the activity state of proteases and their endogenous interaction partners in vitro and in vivo. The gathered information will be annotated in a public repository. The team expects the derived insights of CAMP to foster high-throughput approaches and research, leading to new avenues in drug discovery, using integrated data on the protease proteome.

Scientific/Technological Objectives: The CAMP project will develop and integrate novel technologies in the areas of recombinant protein production, High Throughput (HT) structure determination and bioinformatics, together with the development of specific chemical tools for functional annotation, localization and characterization. Ultimately, CAMP will provide the following: information on synthetic peptide substrates of proteases; chemical probes as tools to investigate the physiological role of proteases in cellular environment; identification of physiological substrates of proteases providing information about protease signalling pathways, essential for understanding bio-logical roles in health and disease, and an assessment of the tools developed in the project; and novel crystal structures of proteases in the activated form (either alone or in complex with inhibitors), as well as in the zymogen state. The team has selected a total of 45 targets from the cysteine proteases (papain-like lysosomal proteases and caspases) and metalloproteases (carboxypeptidases, matrix metalloproteases and ADAM-TS metalloproteases) to develop, implement and demonstrate the feasibility of the team’s proteomics-oriented approaches for proteases. The aim of CAMP is to establish the interdisciplinary core infrastructure and tech-nologies that will be required for a subsequent full-scale protease proteomics approach. The team’s choice of protease targets has been based on two criteria: implication in important physiological processes, as well as novelty with respect to function.

Expected Results: Besides the proteomics-focused technological aims, CAMP focuses on a selected and medi-cally highly relevant subset of human proteases. The team further expects to substantially increase the current knowledge (at the level of genomic annotation) of four selected clans of proteases, encompassing 45 prototypic representatives. Many of them are critically involved in medical problems and pathologies, such as those related to hormone and neuropeptide processing and maturation (i.e.N/E carboxypeptidases), inflammation and joint diseases (cathepsins, caspases, ADAM-TSs), stroke and cardiovascular arteriosclerosis (caspases, TAFI, MMPs, ADAM-TSs) andcancer (cathepsins, caspases, MMPs).


CAMP

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2006-018830Starting date:1st January 2006Duration:36 monthsEC Funding:

2 700 000

Structure of the LCI-CPA2 complex

Structure of Caspase 2

http://camp.bioinfo.cipf.es


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Potential Impact: The data resulting from CAMP will promote and stimulate novel applied research based on the enzyme targets, which have been poorly interconnected or neglected so far owing to the lack of an integrated and generally available platform for protease-specific proteomics. Within the present project, the selected proteases will be used as a training set to develop such proteomics technologies. Proteases have been recognized as valid drug targets, and many inhibitors of proteases have been designed that resulted in drugs, e.g. to treat HIV infec-tions, thrombosis, or hypertension. Therefore, a significant expansion of knowledge on these enzymes and on molecules controlling them (such as natural or artificial inhibitors) will have a direct impact on the landscape of biomedical sciences and technologies in Europe. The results and technologies of CAMP should facilitate the efficient generation of structural and functional data for this set at a full proteomic scale. Furthermore, the tools developed in CAMP should facilitate the future application of the developed technologies to other hydrolytic enzymes. By developing and integrating family-specific technologies for high-throughput expression, bio-chemistry, inhibitor design and structural proteomics, CAMP aims to enable a future functional and structural annotation of the entire protease proteome.

Keywords: chemogenomics, chemoproteomics, functional probing, proteolytic enzymes

Project Coordinator: Prof. Francesc Xavier AvilesUniversitat Autonoma de BarcelonaInstitut de Biotecnologia i de BiomedicinaProtein Engineering and Enzymology Unit08193 Bellaterra (Barcelona), [email protected]

Dr. Matthias WilmannsEuropean Molecular Biology Laboratory(EMBL) – Hamburg unitGerman Synchrotron Research CenterHamburg, Germany

Prof. Boris TurkJ. Stefan Institute ProteolysisResearch GroupDepartment of Biochemistry andMolecular BiologyLjubljana, Slovenia

Prof. Markus G. GruetterUniversity of ZurichDepartment of Biochemistryof the University of ZurichZurich, Switzerland

Dr. Ernst MeinjohannsArpida ASCopenhagen, Denmark

Dr. Ulrich WendtSanofi-AventisDeutschland GmbHValorisation & InnovationFrankfurt, Germany

Prof. Dr. Wolfram BodeMax-Planck Institute of BiochemistryMartinsried, Germany

Partners


Chemical Genomics by Activity Monitoring of Proteases

Complex between TIMP-1 and the catalytic domain of MMP-3



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State-of-the-Art:Based on the work of the Human Proteomics Organisation (HUPO), the Proteomics Standards Initiative (PSI) and the experience of the HUPO Brain Proteome Project (HUPO BPP), ProDaC aims to develop and implement international standards for the representation of high-per-formance proteomics data. The main focus of the project is standardised data collection as well as standardised data analysis of protein identification by mass spectrometry. In total, 12 core partners (European Bioinformatics groups and proteomics laboratories) and 31 associ-ated partners (non-EU laboratories, both academic and commercial) will participate in the 30-month project. Data providers from experienced European proteomics laboratories will provide appropriate data, derived from state-of-the-art proteomics technologies, for proof of concept; moreover, they will utilise the newly developed software tools. The project will be supported by a number of high-ranking scientific journals, which will be actively involved in the standards’ development, including the defining of mandatory supplementary information for submitting articles.

Scientific/Technological Objectives:In phase one, all ProDaC partners will contribute to the finalisation of the analysisXMLstandard for the representation of protein identifications; they will also contribute to the PSI GPS modules for the overall representation of a proteomics experiment, in particular the sample description, sample handling, and separation modules.In phase two, ProDaC core partners will establish submission pipelines from experimental data providers and data analysis centres to the PRIDE proteomics repository.In phase three, the strategies developed will be implemented by a much broader group of project participants, building on the previous project experience, and supported by dedi-cated technical advisors. At the end of phase three, it is expected that the PSI proteomics standards will be adopted by major European and worldwide proteomics data providers.To demonstrate the immediate benefit of central data collection to data producers, we will extend PRIDE functionality to allow for the comparison of submitted, but nonetheless pri-vate data in pre-publication status, to other, publicly available datasets. Through the data exchange between proteomics repositories, the scope of proteomics data integration into sequence databases will reach out to other repositories, such as Proteios, ProteinScape, and PeptideAtlas; ultimately, this may improve or validate (or both), or even sequence databases themselves.

Expected Results: ProDaC expects that the following results will be produced:

1. PSI standards finalised and tested;2. Implementation of mzData and analysisXML capabilities in ProteinScape;3. PROTEIOS, Phenyx and Mascot and PRIDE (and conversion of existing data);4. Identification of relevant proteomics tools used in the consortium, and of develop-

ment needs to ensure functional data submission pipelines from data producers to PSI-compatible repositories;

5. Tools for compiling raw data into standard file formats (mzData and analysisXML);6. Evaluation of existing data storage solutions at the participants’ sites;7. Elaboration, testing and optimising of the data submission pipeline;8. Elaboration and testing of submitted supplementary data sets for publications;9. Collection of data packages;10. Establishing of a steering committee and the network structure;11. Implementation of the intranet and other communication platforms;12. Coordination of software implementation


ProDac


1 000 000

www.fp6-prodac.eu


http://www.fp6-prodac.eu

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Potential Impact: Systematic coordination in the ProDaC context may boost proteomics data standardisation and collection on a global level, and may significantly reduce the timeframe in which these aims could otherwise be achieved, to boot. Moreover, the European core component of the ProDaC proposal will help to retain Europe’s strong position in the field of proteomics, while the significant global participation of associated partners will ensure broad acceptance of the project in the global proteomics community.

The ProDaC consortium comprises commercial and open source proteomics tool providers who will implement PSI standards in their products, thus minimising the effort necessary for data conversion and submission. Moreover, the participation of scientific publishers in Pro-DaC will ensure that the developed standards, tools and repositories meet the requirements of the publication process, and will in turn, promote the application of these standards on behalf of their authors, thus increasing the transparency, quality and public value of pro-teomics publications.

Keywords: proteomics, databases, standardisation

PartnersProject Coordinator: Prof. Helmut E. MeyerRuhr-Universitaet Bochum Medizinisches Proteom-CenterUniversitätsstrasse 15044801 Bochum, [email protected]

Dr. Rolf ApweilerEuropean Molecular Biology Laboratory (EMBL)European Bioinfomatics Institute (EBI)Hinxton, UK

Prof. Rudi AebersoldFederal Institute of TechnologyETH ZurichZurich, Switzerland

Prof. Joel VandekerckhoveUniversity of GhentDepartment of Medical Protein ResearchGhent, Belgium

Prof. Michael J. DunnUniversity College DublinConway Institute of Biomolecular and Biomedical ResearchDublin, Ireland

Dr. Frederique LisacekSwiss Institute of BioinformaticsProteome Informatics GroupGeneva, Switzerland

Dr. Jari HäkkinenLund UniversityDepartment of Theoretical PhysicsLund, Sweden

Dr. Simon HubbertManchester UniversitySchool of Biological SciencesManchester, UK

Dr. Pierre-Alain BinzGenebioGeneva, Switzerland

Martin BlüggelProtagen AGDortmund, Germany

Prof. Herbert ThieleBruker Daltonics GmbHBremen, Germany

Dr. John CottrellMatrix ScienceLondon, UK


Proteomics Data Collection




TOOLS & TECHNOLOGIESFOR MOLECULAR IMAGING

1.3MOLECULAR IMAGING

Tips4Cells

COMPUTIS


120

State-of-the-Art:Advances in molecular biology have provided considerable information concerning the sequence, structure and function of genes. This has opened new perspectives for the un-derstanding of fundamental biological processes underlying human disease and for the development of innovative diagnostic, prognostic and therapeutic tools. Strategies for ge-nomic research and therapeutic interventions at the genetic level will benefit from increased capability to monitor in vivo the effects of genetic manipulations in cells and living organ-isms. Ironically, although biology is fundamentally dynamic, most of the current knowledge on gene expression, regulation and delivery in mammalian systems relies on results from in vitro or ex vivo studies. This, coupled with our inability to easily monitor multiple molecu-lar species simultaneously, seriously limits our ability to study a wide range of biological processes. Furthermore, since empirical descriptions of the evolution of systems over time

are generally constructed from a series of data ob-tained from different specimens, they often fail to represent the true order of events accurately. Ad-ditionally, these invasive techniques tend to be time consuming and labour intensive, often leading to distortion or even destruction of native properties. Thus the current capacity to extract biological in-formation in intact microenvironments of living sys-tems is severely limited. MOLECULAR IMAGING aims at developing new tools that will enable moni-toring the dynamics of multiple molecules within living systems and will transform our understand-ing of biology, making experimental investigations much more efficient and accelerate the progress in life sciences.

Scientific/Technological Objectives:The goal of the Molecular Imaging Integrated Project is to generate and apply novel ad-vanced technology for non-invasive imaging of biomolecular function in living systems rang-ing from single cells to whole animals. The main areas for technological innovation are:

Single-molecule fluorescence close to an absorbing nanostructure.

The emission rate is strongly modified by the local-field enhancement and the non-

radiative coupling with the object.

Different imaging scales involved in the MOLECULAR IMAGING

Integrated Project

www.molimg.gr


MOLECULAR IMAGING

Project Type:Integrated ProjectContract number:LSHG-CT-2003-503259 Starting date:1st January 2004 Duration:60 months EC Funding:

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We will combine multidisciplinary research in biology, bioorganic chemistry, theoretical physics and biomedical optics with the objective of developing novel imaging tools that will enhance genomic and post genomic research, and biotechnological capabilities in Europe. It is expected that our combined effort will provide spectacular new opportunities for phe-notyping functional (molecular) analysis in cells and animal models.

Expected Results:The expected results are:

3D tomographic approaches-

proved microscopic molecular imaging techniques

probes and biosensors

become available to a variety of end-users in the scientific community.

The development of such tools will offer multilevel information, (spatial, temporal and rela-tive) so that reliable and complex conclusions can be reached faster. This proposal aims to coordinate the development of functional in vivo imaging capabilities in order to address fundamental biological questions. This will be achieved by partnering high-resolution im-aging with post-genomic molecular technology. Much of the technology and techniques to be developed under this integrated project will be directly applicable to high-throughput screening and genomic and proteomic microanalysis.

Non-invasive phenotyping will drastically reduce the number of sacrificed animals neces-sary for accurately addressing biological problems and will:

a) Visualisation of the intestinal lymphatic system

b) Flow chart of the different subprojects and work packages

a) b)


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Potential Impact:The proposed consortium of physicists, mathematicians, biologists and chemists offers a unique opportunity to address the challenge of in vivo molecular imaging in a concentrated but Europe-wide effort. We believe that this project will lead to the for-mation of centres of excellence in the near future that will attract scientists to join those countries and institutions that are able to provide this technology. Such research cen-tres would promote the commercialisation of this technology in partnership with high-end industry to make it widely available and widely deployed in the near future.

This will create many new jobs for highly educated scientific and technical personnel. Spe-cific innovation aspects include:

a) New probes. These will be engineered, taking into account the natural absorbance properties of tissue and will be suitable for imaging in organs and animals.

b) Simultaneous spatially and temporally resolved detection of multiple physiological events.

c) Novel theoretical tools to model light propagation and atomic-scale interactions.d) New optical instruments with improved depth detection that allows the identification

of fluorescent organs or structures within the animal body non-invasively in vivo.e) New optical instruments that allow the localisation of individual cells and their distribu-

tion and migration within organs.f) Novel multimodal nanometric imaging setups that will allow follow up of atomic inter-

actions in vivo.

Keywords: genetic engineering, applied optics, molecular chemistry, tomogra-phy, microscopy, fluorescence, inverse problem, functional genom-ics, phenotyping

Partners

Interaction between disciplines in the

MOLECULAR IMAGING Integrated Project

Fluorescence molecular tomography (FMT) imaging

of T-cell regulation. (A) FMT setup where the specimen rotates along an axis, an

excitation source (Ar+ laser) is scanned over the surface and

excitation and emission images are collected using appropriate

filters. (B) 3D reconstruction of GFP concentration in the spleen

for GFP-tagged T-cells in a F5 mouse. This figure indicates the potential that FMT has to image

biological processes in vivo.

Project Coordinator:Prof. Eleftherios EconomouFoundation for Research and Technology – HellasInstitute of Electronic Structure and Laser (IESL)Institute of molecular biology and biotechnology (IMBB)P.O Box 1385, Vassilika Vouton 71 110 Heraklion, [email protected]

Prof. Stefan Andersson-EngelsLund UniversityDepartment of PhysicsLund, Sweden

Prof. Simon ArridgeUniversity College LondonDepartment of Computer ScienceLondon, UK


MOLECULAR IMAGING



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Prof. Dr. Christoph BremerUniversity of MünsterDepartment of Clinical RadiologyMünster, Germany

Prof. Remi CarminatiCentrale Recherche SALaboratoire EM2CParis, France

Prof. Juan Jose SaenzUniversidad Autonoma de MadridDepartamento de Fisica dela Materia CondensadaMadrid, Spain

Prof. Maria Carmo-FonsecaInstitute of Molecular MedicineLaboratory of Cell BiologyLisbon, Portugal

Dr. Paul FrenchImperial College of Science Technology and MedicinePhysics DepartmentLondon, UK

Prof. Theodorus GadellaUniversity of AmsterdamSwammerdam Institute for Life SciencesAmsterdam, The Netherlands

Dr Dimitris Kioussis Medical Research CouncilDivision of Moleculer Immunology, National Institute for Medical ResearchLondon, UK

Dr. Carsten SchultzEuropean Molecular Biology Laboratory (EMBL)Gene Expression ProgrammeHeidelberg, Germany

Prof. Vahid SandoghdarSwiss Federal Institute of Technology (ETH)Department of ChemistryZurich, Switzerland

Dr. Konstantin LukyanovRussian Academy of SciencesInstitute of Bioorganic ChemistryMoscow, Russia

Dr. Oliver DornUniversidad Carlos III de MadridDepartment of MathematicsMadrid, Spain

Prof. Frank GrosveldErasmus Medical Centre RotterdamDepartment of Cell BiologyRotterdam, The Netherlands

Prof. Carlos Martinez, Prof. M. Nieto-Vesperinas, Prof. N. GarciaConsejo Superior de Investigaciones CientíficasMadrid, Spain

Prof. Cristoph CremerRuprecht-Karls-Universitat HeidelbergKirchhoff-Institute for PhysicsHeidelberg, Germany

Dr. Martin InglePhotek LtdSt Leonards-on-Sea, UK

Dr. Patrick CourtneyPerkinelmer Life andAnalytical ScienceCambridge, UK

Dr. Levin ShimonLenslet Labs LtdRamat-Gan, Israel

Dr. Paul WynnKentech Instruments LtdDidcot, UK

Dr. Jens SteinUniversity of BernTheodor Kocher InstituteBern, Switzerland

Dr. James SharpeCentre for Genomic Regulation (CRG)Barcelona, Spain

Dr. Miguel TorresCNIC Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadrid, Spain


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State-of-the-Art:High resolution imaging of living cells and subcellular components is essential for func-tional and structural genomics. Scanning Probe Microscopy (SPM) is currently the imaging method of choice, because it yields the greatest number of structural details of biological samples in their native, aqueous environment and at ambient conditions. Due to the high lat-eral resolution and sensitive force detection capability of SPM, it is now possible to measure intermolecular and intramolecular forces in biomolecules at the single molecule level. This, in turn, has made it possible to examine the physiological consequences of the interaction of a single ligand molecule with its cognate receptor. The Tips4Cells consortium proposes to develop SPM still further. New technologies, such as faster scanning force microscopy (SFM) at lower forces, improved tip chemistry and integration of optical imaging techniques will be used to analyse ligand-receptor interactions in the plasma membrane and in down-stream signalling events in living cells, and to study the structure, transport and dynamics of nuclear pore complexes (NPC) in functional nuclei.

Scientific/Technological Objectives:The general goal of the consortium is to develop new SPM technologies for functional and structural genomics. More specifically, its goals are as follows:

1) To develop new SFM hardware, including fast scanning hardware (scanner, mini-ature cantilevers) and electronics (high speed data acquisition, Q control);

2) To develop molecular recognition force microscopy (MRFM), via the intermediary development of the following: (i) Chemically functionalised tips/beads; (ii) The chem-istry of the drugs that are put on those tips/beads; (iii) Imaging and spectroscopy modes for recognition (pulsed force mode and recognition mode);

3) To integrate optical techniques into SFM, to improve detection of signalling after administering a chemical to a cell, by approaching it with a functionalised tip;

4) To validate the new technologies in the study of cell biology systems, such as the non-genomic effects of steroids (e.g. aldosterone), the Wnt signalling pathway and the structure, transport and dynamics of NPC in functional nuclei.

Expected Results:The consortium expects to achieve higher data acquisition rates through faster electron-ics, and faster sensors with higher force sensitivity through miniaturised cantilevers. Faster scanners will move more rapidly around the surfaces to be scanned, allowing for frame rates above 100 images per second. The consortium also expects to improve the speed of MRFM. More general functionalisation protocols will allow a wider range of chemicals to be attached to SFM tips. Through the use of linkers between tip and molecule that are optimised in length, a higher resolution will be achieved in molecular recognition imaging. Genomics knowledge will be advanced through high resolution imaging and docking site identification, the development of new tools for biomolecular analysis of drugs for orphan receptors, the introduction of new chemistries for drugs on tips, and new substitutes for map-ping receptor distribution in living cells. The commercialisation of novel imaging platforms will be managed by the consortium’s SME partners, thereby bringing these techniques within reach of a broad range of researchers.


Tips4Cells

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2005-512101Starting date:1st February 2005Duration:36 monthsEC Funding:

1 713 000

www.tips4cells.org


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Potential Impact:The project will generate improved research tools and insights in SPM. It is anticipated that the breakthroughs in nanoscience and technology will serve to stimulate industry, generating employment opportunities. The SMEs involved in Tips4cells specialise in hardware develop-ment, and will clearly benefit from the commercial opportunities generated by the research. The multinational, multidisciplinary nature of the consortium will facilitate broad dissemina-tion of new knowledge, both across Europe and across academia and industry. The consor-tium will also foster novel collaborations between research institutes and industry.

Keywords: scanning force microscopy, imaging techniques, high resolution, molecular recognition

Project Coordinator:Dr. Tjerk OosterkampLeiden Institute of PhysicsLeiden UniversityNiels Bohrweg 22333 CA Leiden, The [email protected]

Dr. Peter HinterdorferUniversity of LinzInstitute of BiophysicsLinz, Austria

Prof. Michael HortonUniversity College LondonDepartment of MedicineLondon, UK

Dr. Ziv ReichWeizmann Institute of ScienceDepartment of Biological ChemistryRehovot, Israel

Prof. Mervyn MilesUniversity of BristolH.H. Wills Physics LaboratoryBristol, UK

Prof. Hans OberleithnerUniversity Hospital MünsterDepartment of PhysicsInstitut für Physiologie IIMünster, Germany

Partners

Dr. Torsten JähnkeJPK Instruments AGBerlin, Germany

Dr. Gertjan van Baarle Leiden Probe MicroscopyLeiden, The Netherlands

Dr. Gerald KadaAgilent TechnologiesÖsterreich GmbHAustria


Scanning Probe Microscopy techniques for real time, high resolution imaging

and molecular recognition in functional and structural genomics



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State-of-the-Art:Significant improvements in desorption and ionisation techniques, such as SIMS (secondary ion mass spectrometry) or MALDI-MS (matrix-assisted laser desorption ionisation – mass spectrometry ) associated with TOF-MS (time of flight – mass spectrometers), offer levels of sensitivity and mass accuracy which allow detection, and analysis of large organic mol-ecules like peptides or proteins with very small sample amounts.Recent developments showed the possibility of extrapolating these techniques to produce actual molecular images of flat samples with a full mass spectrometry at each pixel down to micrometric scales.The growing interest of this approach and its high potential will lead to the development, optimisation, combination and correlation of these SIMS and MALDI-MS techniques.

Scientific/Technological Objectives:This project aims to develop new and improved technologies for molecular imaging mass spectrometry (MIMS), enabling innovative methods of investigation in functional genomics, proteomics and metabolomics, as well as investigation in cells and tissues. It is the goal of the project to develop, optimise, combine, correlate and apply methods of mass spectrometric molecular imaging, especially various specialised methods of SIMS and MALDI associated with various types of mass spectrometers.The three principal objectives of the project are:

novel desorption, ionisation and detection techniques

the study of molecular images

cells or tissue growth.

This project will provide innovative analytical capabilities for mapping a variety of biologi-cal compounds directly at the tissue or cell level by superposing information from different sources in the same image.MIMS needs further development to make it routinely accessible to users. Application of these methods to analytical problems requires appropriate instrumentation, sample prepa-ration methodology, and computerisation with high performance massive data acquisition and processing.

Expected Results:The objectives of the project will be achieved by significant improvements in desorption and ionisation techniques, leading to a new protocol of sample preparation for better matrix deposition control. Instrumentation developments include the setup of UV confocal microscopy integrated into the MALDI imaging instrument and the adaptation of new ion guns favouring secondary ion emission for SIMS analysis. Dedicated software tools will be implemented for high performance data acquisition and processing with, in particular, the realisation of the superposition of data from different analytical sources in the same image. The project will conclude with definition, implementation and testing of new analyti-cal concepts, as well as criteria for diagnostics of chosen pathologies or diseases, and the development of an industrial concept. In addition, a validation phase through the applica-


COMPUTIS

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2005-518194 Starting date:1st January 2006 Duration:42 months EC Funding:

2 200 000


127

tion of MIMS to the three selected biological problems is imperative for the acceptance of the methodology.

Potential Impact:MIMS techniques connected with proteomics and bioinformatics pave the way to in situ in-spection of cell and tissue physiology. They could be extended towards pathophysiological inspections of human tissues performed at the molecular level on a large-scale. Imaging MS eliminates the need to know in advance about the specific proteins that may have changed in a comparative study. So, these new analytical methods will be performed ideally with almost no a priori knowledge about markers and gene products expressed in normal and pathological specimens. Improved image acquisition, image processing and connectiv-ity with existing biological databases will have a critical impact for applications in human healthcare.

Keywords: bioanalytical chemistry, mass spectrometry, massive data processing and information treatment

Project Coordinator: Dr Haan Serge, Dr Robbe Marie-FranceCommissariat à l’Energie Atomique CEA)LIST/DETECSCentre de Saclay, Bat. 451P.O. Box 91191 CedexGif-sur-Yvette, [email protected]@cea.fr

Prof. Bernhard SpenglerJustus Liebig UniversityInstitute of Inorganic andAnalytical ChemistryGiessen, Germany

Prof. Ronald MA HeerenStichting FOM (FundamenteelOnderzoek der Materie)AMOLFAmsterdam, The Netherlands

Dr. Olivier LaprevoteCentre National de la RechercheScientifique (CNRS)Institute de Chimie des SubstancesNaturelles (ICSN)Gif-sur-Yvette, France

Partners

Dr. Ronald SchutPCC UvA BVAmsterdam, The Netherlands

Dr. Fedor SvinartchoukGénéthonDépartement Rechercheet DéveloppementEvry, France

Dr. Markus StoeckliNovartis Pharma AGDiscovery TechnologiesAnalytical and Imaging SciencesBasel, Switzerland


Molecular Imaging in Tissue and Cells by Computer-Assisted Innovative

Multimode Mass Spectrometry





TOOLS & TECHNOLOGIESFOR GENE INTEGRATION AND

RECOMBINATION

1.4GENINTEG

PLASTOMICS

TAGIP

MEGATOOLS


130

State-of-the-Art: Despite the enormous potential of using transgenesis for gene function analysis and gene therapy, little is known about the mechanism of gene integration in eukaryotic cells. Trans-gene integration into the chromosomes of living cells can occur either randomly or targeted by homologous recombination. The latter type of integration is the most useful, because it allows precisely sequences to be precisely deleted or modified at defined chromosomal po-sitions. The GENINTEG consortium was formed to study gene integration by recombination in a number of different model organisms. As DNA repair is conserved during evolution, a comparative genomics approach was proposed to discover evolutionary conserved princi-ples of gene integration.

Scientific/Technological Objectives: The main objective is to understand and enhance gene integration through interdiscipli-nary and comparative genome analysis in different model organisms. As DNA structure and DNA repair are conserved during evolution, the gained knowledge and resources will improve gene integration across plant and animal species and facilitate large-scale gene function analysis and transgene expression for biotech and medical applications. Other objectives are: (1) better insight into the genetics, the regulation and the mechanism of homologous recombination; (2) new protocols to increase targeted gene integration in primary cells and cell lines either by modification of gene constructs or the gene delivery mode; (3) adaptation of existing site specific recombination system for safe and stable gene expression and long range chromosome engineering; (4) use of improved gene integration for gene function analysis; (5) exploitation of the generated knowledge and resources for commercial application through the protection of intellectual property and product develop-ment; (6) new protocols for transgenesis of whole organisms.

Expected Results: Controlled gene integration and in particular targeted integration has to be considered a key technology for exploiting the wealth of recently obtained genome information. This is due to the fact that traditional transgenesis can only add bits of poorly controlled infor-mation to the genome, whereas targeted integration can be used to modify the genome precisely at any chosen position. The proposed work will therefore significantly reinforce genome research and support many of the activities envisioned for funding within FP6. Al-though successfully employed in yeast and murine embryonic stem cells, a major stumbling block for the widespread use of targeted integration is the tendency of most eukaryotic cells to insert transfected DNA at random chromosomal positions. More efficient gene targeting will expedite reverse genetics in a variety of cells and organisms enabling truly comparative genome function analysis across species boundaries. Targeted gene integration also fulfills a critical role for medical research, as it allows the experimental verification of the findings of human genetics and the establishment of animal disease models for further detailed re-search of pathogenesis and treatment.

Potential Impact: To realize the full potential of transgenesis for genome research, biotechnology and medical applications, only a concerted European initiative can bring together and focus the avail-able expertise in academia and industry. The GENINTEG consortium has recruited some of the best laboratories working on gene integration and also balances the work among different species to allow for a truly comparative genomics approach.

The availability of genome sequences helps traditional genetics approaches and it pro-motes reverse genetics as a means to modify the genotype in precisely defined terms.



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The clarification of gene function by transgenesis is paramount to our understanding of biological processes and disease pathogenesis. Consequently, investment in further devel-opment of controlled gene integration technology promises rich returns not only for basic research, but also for drug development.

Keywords: gene, homologous recombination, transformation, biotechnology, genomic function, transgenes, site-specific, integration

PartnersProject Coordinator:Prof. Dr. Jean-Marie BuersteddeGSF-Forschungszentrum fur Umwelt und Gesundheit GmbHInstitute of Molecular Radiation BiologyIngolstädter Landstraße 185764 Neuherberg, [email protected]

Dr. William Brown University of NottinghamQueen’s Medical CentreInstitute of GeneticsNottingham, UK

Prof. Ann DepickerFlanders Interuniversity Institute for Biotechnology (VIB)Ghent University TechnologieparkDepartment of Plant Systems BiologyGhent, Belgium

Dr. Francis FabreCommissariat à l’Energie Atomique (CEA)Fontenay-aux-Roses, France

Prof. Dr. Martin FusseneggerCistronics Cell Technology GmbHZurich, Switzerland

Dr. Andrzej M. KierzekUniversity of SurreySchool of Biomedical and Molecular SciencesGuildford, UK

Dr. Bernd ReissMax Planck Society for the Advancement of ScienceMax-Planck Institute for Plant Breeding Research MPIZCologne, Germany

Prof. Dr. Walter SchaffnerUniversity of Zurich-IrchelInstitute of Molecular Biology Zurich, Switzerland


Controlled gene integration: a requisite for genome analysis

and gene therapy



132

State-of-the-Art:Plastid transformation is the most precise method of integrating foreign genes in plants. It offers the possibility of cheap and large-scale production for therapeutic proteins, such as hormones and vaccines, and also for food of improved nutritional quality. Plastid transfor-mation and high level expression of foreign proteins in chloroplasts in tobacco leaves is well established. However, the commercial success of plastid transformation as a production platform, depends mainly on the successful high level expression in non-green plastids (such as chromoplasts and amyloplasts), using crops that are amenable to processing.

Scientific/Technological objectives:The aim of the project was to define the mechanisms and to improve the understanding of the genes and proteins involved in several key stages of plastid transformation and foreign gene expression, in different plastid types, in tobacco, tomato and potato. Genomics and proteomics approaches were used to identify genes and proteins involved in several proc-esses: 1) transgene integration and marker gene excision via homologous recombination; 2) regulated gene expression in chloroplasts, chromoplasts and amyloplasts; 3) protein degradation in different plastid types. The project was divided into 3 work packages (WPs). WP1 relates to transgene integra-tion and marker excision. WP2 relates to regulated plastid gene expression. WP3 relates to protein degradation in different plastid types. WP3 aimed to identify the proteolysis systems in plastids that may limit the expression of transgenes in plastids. It also aimed to develop cleavable protein-fusion systems that may protect foreign proteins from proteolysis and simplify protein purification.

Expected results:WP1’s achievements are as follows:

1. Identification (using database searches) of genes encoding putative components of the plastid recombination system in higher plants and isolation of tobacco cDNAs encod-ing some of these plastid recombination proteins.

2. Characterization of transgenic tobacco plants with altered expression of genes encod-ing plastid recombination proteins to examine the effects on transgene integration and marker excision

3. Optimization of plastid transformation vectors, with different amounts of flanking plastid DNA, and with foreign genes of different length, orientation and control sequences.

4. Proof-of-concept of an novel system of automatic marker excision, using transformation vectors with the selectable marker gene located outside the plastid sequences flanking the transgene.

WP2’s achievements are as follows:1. Determination of the complete nucleotide sequences of the plastid genomes of tomato

and potato.2. Use of DNA microarrays and macroarrays for examining transcripts of all plastid genes

and open reading frames in tomato fruits and in potato tubers.3. Characterization of nuclear-encoded RNA polymerases (NEP) and identification of

NEP-transcribed plastid genes.4. Production of improved plastid transformation vectors, with altered sequences in the

vicinity of the translation initiation codon.WP3’s achievements are as follows:

1. Identification by database searches of genes and cDNAs encoding components of plastid proteolysis systems in tobacco, tomato and potato, and production of trans-genic tobacco with alteration of levels of ClpC.

2. Production and introduction of gene constructs into the tobacco plastid genome for three cleavable protein-fusion systems.


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Potential impact:The PLASTOMICS team expects the project to result in improved understanding of processes involved in plastid transformation, and in improved efficiency of plastid trans-formation and transgene expression in tomato and potato. This has the potential to impact significantly on the area of plant biotechnology applied to human health, through the production of protein products of benefit to human health and food, with better nutritional value.

Keywords: gene integration, gene expression, protein degradation, plastid trans-formation, proteomics, plant models

PartnersProject Coordinator:Prof. John GrayUniversity of CambridgeDepartment of Plant SciencesDowning Street CB2 3EA Cambridge, [email protected]

Dr. Anil DayVictoria University of ManchesterSchool of Biological SciencesManchester, UK

Prof. Zach Adam Hebrew University of JerusalemDepartment of Agricultural BotanyJerusalem, Israel

Prof. Ralph BockMax-Planck Institute of Molecular Plant PhysiologyGolm, Germany

Dr. Janusz BujnickiInternational Institute of Molecular and Cell BiologyLaboratory of BioinformaticsWarsaw, Poland

Dr Teodoro CardiConsiglio Nazionale Delle RicercheCNR-IGV, Institute of Plant GeneticsResearch Division PorticiRome, Italy

Prof. Philip DixNational University ofIreland MaynoothBiology DepartmentMaynooth, Co Kildare, Ireland

Prof. Tony KavanaghTrinity College DublinSmurfit InstituteDepartment of GeneticsDublin, Ireland

Dr. Stefan HerzIcon Genetics AGResearch Centre FreisingMunich, Germany

Dr Silva Lerbs-MacheUniversité Joseph Fourier Grenoble 1Laboratoire Plastes et Differenciation CellulaireGrenoble, France


Mechanisms of transgene integration and expression in crop plant plastids,

underpinning a technology for improving human health



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State-of-the-Art:Plants can be considered as natural, solar energy powered, and environmentally friendly protein factories that can be genetically improved for the production of proteins with thera-peutic value. It is crucial that the production of target proteins is well controlled in terms of high and steady yield, and tissue-specific deposition allowing for easy harvest, extraction and purification. However, current transgenesis technologies are not accurate enough to secure a protein production scheme that demands such high reliability and precision.Random chromosomal integration of transgenic inserts often causes unpredictable misregula-tion of their transcription, including complete gene silencing. Therefore, the abilities to modify the plant genome in a precise manner and/or control the chromatin environment of transgen-ic inserts, are arguably the most important missing technologies in the toolkit of plant biolo-gists. DNA integration, via homologous recombination (Gene Targeting, or GT) has proved to be a powerful technology in many species. In particular, it enables not only targeted gene disruption or replacement of an endogenous locus by a modified or different gene, but also expression of a new protein in the genomic context of the native gene. GT enables a precise alteration of genomes, from single nucleotide modifications to gene replacement or knockout. It is an invaluable tool for functional genomics as well as for biotechnology. Despite its success in other organisms, GT has not yet become a routine technique in plants, owing to the natu-rally low frequencies of homologous, as compared to non-homologous, DNA integration.

Scientific/Technological Objectives: New findings, several of which originate from the TAGIP partners, as well as advances in functional genomics, suggest that the precise engineering of plant genomes structure by GT, via DNA integration at any locus or at specific sites, has recently become a realistic goal. Achieving this goal will involve the following activities: 1) gaining fundamental knowledge in the field of genome maintenance/modifications via DNA recombination; 2) applying this knowledge to develop new technologies for precise engineering of plant genomes in the model organism Arabidopsis and in selected crop plants; and 3) using this knowledge for the production of proteins of high value in the most suitable crop. There are three specific objectives:

1) Stimulation of GT via reduction of non-homologous DNA recombination pathways; 2) Enhancing the rate of GT in Arabidopsis via over-expression of GT-related proteins;3) Testing for synergistic interactions between partner proteins, to stimulate GT.

Expected Results:The exploitable products expected from this project include a technological platform for GT in crops and a technological platform for protein production in plants (based on GT). This project will speed up the acceptance of new GM corn in Europe. The Biogemma consor-tium, which includes key EU players for crop improvement, guarantees the preservation of EU Plant Biotech and Seed Business company competitiveness. This will ensure that in the future era of GM crops in Europe, EU companies will not have to pay large royalties to US competitors, to gain access to GT technologies necessary for the registration of GM traits.

Potential Impact: Industry competitiveness and societal problems:An important aspect of this project is that in the EU, public reluctance to consume GMO products has slowed down progress in agricultural biotechnology, while in other countries (such as the USA, China, Japan), this Agro-biotech revolution is taking place. A technol-


TAGIP

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2005-018785Starting date:1st December 2005Duration:36 monthsEC Funding:

1 980 972

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ogy such as GT, enables precise and controlled alteration of the genome. The European added-value:One reason to carry out this work at European level is that research in DNA recombination in plants is far more advanced in Europe than in the USA, and it should be further supported to maintain this competitive edge. The proposed TAGIP project brings together leading groups in the field of DNA recombination in plants, thus further increasing the competitiveness of the EU in this field.Innovation aspects:At a technological level, the project plans to turn GT into a routine tool in plants. This technol-ogy has a very high potential economic impact in the Agro-biotech industry, as well as on the pharma industry via “molecular farming” for protein production in plants. At a scientific level, the mechanism whereby GT occurs is still poorly understood in higher eukaryotes. The team will test several genes, working at different levels of the DNA recombination process (initiation, invasion, strand exchange, heteroduplex formation and resolution), for their effect on GT.

Keywords: homologous recombination, gene targeting, protein production, model organisms, Arabidopsis, genome structure and mainte-nance, functional genomics, plant technologies

Project Coordinator: Prof. Avi LevyWeizmann Institute of ScienceFaculty of BiochemistryDepartment of Plant SciencesHerzl St. 27600 Rehovot, [email protected]

Dr. Charles WhiteCentre National de la RechercheScientifique (CNRS)UMR47, Université Blaise PascalAubière, France

Prof. Holger PuchtaUniversity of KarlsruheBotanical InstituteKarlsruhe, Germany

Dr. Karel J. AngelisInstitute of ExperimentalBotany ASCRMolecular Farming andDNA Repair LaboratoryPrague, Czech Republic

Prof. Jerzy PaszkowskiUniversity of GenevaDépartement de BiologieVégétaleGeneva, Switzerland

Dr. Pascual PerezBiogemma SAS Les CrezauxAubière, France

Dr. Hagai KarchEvogene LtdRehovot, Israel

Prof. Barbara HohnNovartis ForschungsstiftungZweigniederlassungFriedrich MiescherInstitute for BiomedicalResearchBasel, Switzerland

Dr. Pnina DanOSM-Dan LtdRehovot, Israel

Partners


Targeted Gene Integration in Plants: Vectors, Mechanisms and

Applications for Protein Production

1247948

2538

1813

11

Size MarkerskDaA B

One single protein, Poly Phenol Oxydase (PPO), consitutes 60% of the proteins in trichomes (leaf hairs) of tomato. Trichome are thus ideally suited for protein production and purification. One of the goals of TAGIP is to replace PPO by a gene of interest for high and specific expression and for simple purification.



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State-of-the-Art:The genome sequence programmes have contributed a huge amount of information, and created many possibilities. An exhaustive catalogue of genes is now available for many organisms, but the real meaning of this information remains to be deciphered. Thus, the success of functional genomics definitively lies in the development of novel tools breaking through the practical limits it suffers today. Meganucleases-induced recombination could provide a practical alternative to current approaches. Meganucleases are, by definition, sequence-specific endonucleases with large (>14 bp) recognition sites. However, the inacti-vation or modification of any and all known genes, or genomic sequence, depends on the availability of Meganucleases that cleave within or in the vicinity of each gene sequences. This issue would be addressed if it was possible to rapidly engineer the specificity of natural Meganucleases.

Scientific/Technological Objectives: The first objective of the project is to provide the means to modify a large number of se-quence in rodent genomes. The second is to develop the tools to engineer a large number of rodent genes, for functional genomic purposes. Since meganuclease-induced recombina-tion represents an extremely powerful tool for gene alteration, we will focus on the genera-tion of four kinds of results:

1) A large collection of novel meganucleases. This collection of novel proteins should greatly enhance the repertoire of natural meganucleases and thus allow for the target-ing of a large number of genes in organisms whose genome has been sequenced, with a strong focus on rodent genomes.

2) The means to exponentially increase this collection. The collection of novel meganucle-ases should provide a unique database of characterised DNA binders. Structural and statistical studies should reveal the laws governing these interactions, and this data could in turn be used in a predictive way, for the design of novel meganucleases.

3) The methods, procedures and quality standards to make these meganucleases widely usable as research tools.

4) A refined method to use these mega-nucleases in cells. The focus will be on mouse cells for functional genom-ics, providing a direct validation.

Purpose of MEGATOOLS and strategy for meganuclease

engineering

Expected Results:1) Protein engineering: Partner 1 has

established the basis of a combina-torial process to assemble functional engineered meganucleases. We ex-pect this combinatorial strategy to provide a functional meganuclease for most chosen gene.

2) Computational biology: The FoldX al-gorithm can successfully predict the effect of protein mutation on the spe-cificity of protein-DNA recognition specificities. Subsequent versions of


MEGATOOLS

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2006-037226Starting date:1st October 2006 Duration:36 monthsEC Funding:

1 999 962

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Project Coordinator: Dr. Frédéric PâquesCELLECTIS SA102 Route de Noisy92 235 Romainville Cedex, [email protected]

Prof. Guillermo Montoya BlancoCentro Nacional de Investigaciones Oncologicas (CNIO)Structural Biology Macromolecular Cristolography GroupMadrid, Spain

Prof. Luis SerranoCentro de Regulacio GenomicaSystem Biology LaboratoryBarcelona, Spain

Dr. Arvydas LubysFermentas UABVilnius, Lithuania

Partners

FoldX should allow for more efficient design of meganucleases combinatorial process.3) Structural Biology: A continuous flow of novel structures that will contribute to the

computational steps is expected.4) Standardisation of protein storage and use: An efficient purification and characterisa-

tion process for each engineered protein is expected. 5) Validation of the general approach: The whole approach should eventually be vali-

dated by the use of engineered meganucleases on real chromosomal targets in rodent cells. A general, standard protocol for rodent cells is expected.

Potential Impact: The possibility of correcting errors in a genome through targeted homologous recombina-tion or modifying at will any DNA sequence is clearly enormously attractive to the scientific community. Although it is clearly valuable to understand how genomic information is trans-lated into function, rational modification of the DNA sequence of an organism has been limited by the time consuming process it requires, despite the development of new tools for the construction of targeting vectors. Thus, the possibility of having new tools that will al-low targeting of any DNA sequence for insertion, deletion or repair could introduce a new revolution in the field of functional genomics and could also bring a new paradigm and a new momentum to human gene therapy.

Keywords: genome engineering, protein engineering, meganucleases, gene targeting, homologous recombination, functional genomics, tools and technologies


New tools for Functional Genomics based on homologous recombination

induced by double-strand break and specific meganucleases




REGULATION OFGENE EXPRESSION2.



TRANSCRIPTIONREGULATION

2.1TRANS-REG

X-TRA-NET


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State-of-the-Art:In the pathways of gene expression, the first regulated and, in most cases, rate-limiting step is the process of transcription. Despite the detailed picture that is emerging, a great number of conceptual as well as mechanistic questions still need to be resolved. One of the main gaps in our knowledge is the limited insights we have on transcription regulation in the nu-clear environment. The general goal of the project is to obtain a comprehensive knowledge on the mechanism of regulation of model genes during cell differentiation, cell proliferation and signal transduction. The consortium will undertake concerted efforts to develop and apply fluorescent imaging techniques, coupled with genetic, proteomic and conventional molecular and cell biology approaches to study the molecular characteristics and functions of individual multiprotein complexes, and their dynamic interplay in the context of unique chromatin structures in living cells.

Scientific/Technological Objectives:The objectives of this project are:

-calisation studies by indirect immunofluorescence assays in vivo and in situ protein-protein interaction studies by FRET (fluorescence resonance energy transfer)

known nuclear structures under different conditions

course of assembly of complexes on model genes induced during cell differentiation, cell proliferation and signal transductionin situ analysis by FLIP (fluorescence loss in photobleaching) and FRAP (fluorescence recovery after photobleaching) of the time course of assembly of complexes on a model gene and its relationship with transcription initiation

-sponding to euchromatin and heterochromatin during gene activation/ repression

role in subnuclear targetingdrosophila and mice, and cross-species

comparisons of the individual complex components.

Expected Results:The successful execution of the project is expected to result in:

1. new knowledge on the in situ dynamics of the RNA polymerase-II machinery 2. new knowledge on the molecular mechanism of transcription regulation that leads to

pathway-specific gene expression programmes3. development of new technologies and research tools.

The results of the first 18-month period resulted in 4 joint publications and 27 individual publications in high impact scientific journals. These and other results of the research can be found on the project’s website.

Potential Impact:The consortium is developing and applying state-of-the-art in vivo imaging techniques based on FRET, with improved spatial and temporal resolution and mathematical tools to extract three-dimensional information from two-dimensional spatial images. Development of high sensitivity and quantitative assays for chromatin immunoprecipitation is also an important deliverable of the project. While the work focus is on transcription complexes, we be-


TRANS-REG

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2003-502950 Starting date:1st April 2004Duration:36 monthsEC Funding:

1 860 000

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lieve that the technologies and the research tools generated in parallel will be useful for a broader range of biological applications.The project combines and ex-pands individual activities with a more comprehensive collab-oration.

Keywords:

gene expression, transcription, RNA polymerase-II, transcrip-tion regulation, transcription factors, complex-complex in-teractions, signal transduction

PartnersProject Coordinator:Prof. Iannis TalianidisFoundation for Research and Technology – HellasInstitute of Molecular Biology and BiotechnologyVassilika Vouton P.O. Box 152771110 Heraklion, [email protected]

Prof. Imre BorosUniversity of SzegedFaculty of ScienceDepartment of Genetics and Molecular BiologySzeged, Hungary

Dr. Annick Harel-BellanCentre National de la Recherche Scientifique (CNRS)Institut André LwoffVillejuif, France

Prof. Dr. Michael MeisterernstGSF-Forschungszentrum für Umweltund GesundheitNational Department of Gene ExpressionMunich, Germany

Dr. Alexander PintzasNational Hellenic Research FoundationInstitute of Biological Research andBiotechnologyAthens, Greece

Dr. Marc TimmersUniversity Medical Centre – UtrechtLaboratory for Physiological ChemistryUtrecht, The Netherlands

Dr. Laszlo ToraInstitut de Génétique et deBiologie Moléculaire et CellulaireIllkirch, France

Localization of TBP and TBP2 (TBP-related factor 3) during mouse folliculogenesis. TBP and TBP2 exhibit different localization pattern. TBP expression is absent in the oocyte but present in surrounding follicular cells. TBP2 is detected exclusively in oocytes.


Transcription Complex Dynamics Controlling Specific Gene Expression Programmes



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State-of-the-Art:The majority of nuclear receptors signal as heterodimers with the promiscuous retinoid X receptors (RXRs). Heterodimerisation introduces several key regulatory features to the RXR family, as it specifies response element recognition and allows dual ligand input in an HD-specific manner. Together these features allow the large family of RXR heterodimerising nuclear receptors to establish a plethora of cognate ligand-dependent gene networks that regulate major aspects of cell and organ function during embryogenesis and in the adult. Importantly, nuclear receptors are “druggable” and play central roles in major diseases like cancer, diabetes and atherosclerosis. Hitherto, heterodimer target gene regulation has only been investigated by a gene-by-gene approach. Thus, key aspects of this regulatory network, such as the identity of primary targets and their response dynamics, sharing of targets by different heterodimers, nuclear receptor subtype and ligand dependency, are entirely unknown.

Scientific/Technological Objectives:The main objective of X-TRA-NET is to develop and employ chromatin-immunoprecipitation (ChIP) in combination high throughput sequencing (ChIP-seq) to explore the complex transcrip-tional network of RXR and its partners. X-TRA-NET will use this combination to investigate the impact of position and binding site diversity on the mechanisms of RXR target gene activation. The complex interplay between cellular context, target site diversity and receptor subtype specificity will also be addressed. Furthermore, the genome-wide ChIP analyses will be used to investigate how treatment of cell culture and animal models with different ligands targeting the heterodimerization partner, or RXR itself, differentially affects recruitment of the NRs and their associated co-factors to target sites. Thus, X-TRA-NET aims to provide the first “proof of concept” for the use of genome-wide ChIP technology in NR ligand profiling. This would rep-resent a major leap forward in NR pharmacogenomics by providing the missing link between in vitro ligand binding studies and testing these putative drugs in animals.

Expected Results:Global RXR target site profiles will be generated by ChIP-seq. These analyses will allow us to gain insight into several aspects of the RXR transcriptional network. These will include:

1) the impact of position and binding site diversity on the composition, kinetics and spatio-temporal action of transcription-factor/co-factor complexes recruited

2) molecular mechanisms underlying nuclear receptor subtype specific action3) molecular mechanisms of RXR agonists4) molecular mechanisms of selective nuclear receptor modulators, thereby providing

proof of concept that the ChIP-seq approach is suitable nuclear receptor profiling.

Potential Impact:The ChIP-seq approach pioneered by X-TRA-NET will serve as a model to tackle other transcription factor families. In addition, due to the central role of nuclear recepors in a number of major diseases, the new insight into the nuclear receptor field would significantly improve our understanding of the molecular mechanisms of the etiology and treatment of major diseases like cancer, insulin resistance and atherosclerosis. In addition, proof of con-


X-TRA-NET

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2005-018882Starting date:1st September 2005Duration:42 monthsEC Funding:

1 950 000

http://rxrnet.dk/


http://rxrnet.dk

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cept that ChIP-seq technology can be used in nuclear receptor drug discovery will provide companies with hitherto unsurpassed insight into the molecular mechanisms underlying the physiological effects of their drugs. Thus X-TRA-NET is likely to increase competitiveness of European biotechnology and pharmaceutical companies.

Keywords:

chromatin-IP, nuclear receptors, global target site array, ligand specific effects, co-factors, pharmacogenomics, transcription factors, high-throughput techniques, ChIP-chip

PartnersProject Coordinator:Prof. Susanne MandrupUniversity of Southern DenmarkDepartment of Biochemistry andMolecular BiologyCampusvej 555230 Odense M, [email protected]

Prof. Hendrik G. StunnenbergStichting Katholieke UniversiteitDeptartment of Molecular BiologyNijmegen, The Netherlands

Dr. Hinrich GronemeyerCentre Européen de Recherche en Biologieet Médecine - Groupement d’IntérêtEconomiqueInstitut de Génétique et de BiologieMoléculaire et Cellulaire (IGBMC)Illkirch, France

Prof. Bart StaelsUniversité de Lille 2 - Droit et SantéDepartment of AtherosclerosisInstitut Pasteur de LilleLille, France

Dr. Dean HumGENFITLoos, France


ChIP-Chip to DecipherTranscription Networks of RXR and Partners




EPIGENETIC REGULATION

2.2THE EPIGENOME

HEROIC

ChILL

SMARTER


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State-of-the-Art:In this “post-genomic” era, advances in epigenetic research represent a new frontier that is predicted to yield novel insights into gene regulation, cell differentiation, stem cell plastic-ity, development, human diseases, cancer, infertility and ageing. According to an impor-tant emerging concept, there is an “epigenetic code”, which greatly extends the potential information of the genetic code. Based on this concept, one genome can generate many “epigenomes”, as the fertilised egg progresses through development and translates its infor-mation into a multitude of cell fates. In general, epigenetic research covers many topics that are of key interest to the public and scientists alike, such as embryonic and adult stem cells. Epigenetic research is therefore anticipated to have far-reaching implications for medicine and for the understanding of the basic processes of cell fate determination. The developments of research in this field will therefore undoubtedly impact academic and industrial research communities and will form an important knowledge-base for policymakers and public bodies that contribute to the socio-economic future of our “post-genomic” society. Europe has many world-leading laboratories in epigenetic research. The Network of Excel-lence (NoE) project EPIGENOME, proposes to follow a progressively expanding strategy. In the initial phase of the project, 25 teams with a proven record as leaders in their field will combine their expertise and resources and will constitute the “virtual core centre” of the project.

During the course of the project, 22 additional “junior” researchers (newly established teams, or NETs) will be supported and integrated via the NET programme, which will pro-vide them with access to a world class epigenetic research platform.

Scientific/Technological Objectives: The EPIGENOME NoE aims at reinforcing existing synergies to build a strong base for sci-entific excellence. Furthermore, it seeks to promote the ERA not only by means of a strong research programme, but also by integrating and disseminating the project’s activities, including an efficient communication infrastructure to enable internal communication of geographically dispersed teams and to foster a dialogue with the public.

The NoE comprises around 25 of the leading European research groups to study epigenetic mechanisms. Together, they constitute the critical mass for an internationally competitive research programme. This programme is structured into 8 research topics to build on the current strengths of the NoE. Within this framework, the 8 sub-programmes will address a number of the ‘big questions’ in epigenetic research, thereby providing a coordinate ap-proach to establish a research force of world-class standard.There are 8 sub-programes:

1. Chromatin modification 2. Nuclear dynamics 3. Non-coding RNA & gene silencing 4. X-inactivation & imprinting

5. Transcriptional memory 6. Assembly & nuclear organisation 7. Cell fate & disease 8. Epigenomic maps

The major advantage of the NoE is that the common theme of chromatin modifications will ideally interconnect most of the projects carried out by the individual members. Thus, although there are progressively increasing layers of experimental approaches in different organisms to study the complex mechanisms of epigenetic control in regulating information of the chromatin template, all 8 research topics can be integrated into a logical platform, central to the unravelling of the many questions that will lead to a deeper understanding of stem cell plasticity and disease.


THE EPIGENOMEwww.epigenome-noe.net

Project Type:Network of ExcellenceContract number:LSHG-CT-2004-503433Starting date:1st June 2004Duration:60 monthsEC Funding:

12 500 000


http://www.epigenome-noe.net

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Based on the resources and expertises provided by this NoE, and fostered by the numerous collaborations even broader initiatives can be envisaged. These can include large-scale profiling for decipher-ing the epigenetic plasticity of the genetic information by genome-wide microarray analyses. The availability of genomic micro-arrays in genetically tractable organisms, together with the expertises of ChIP-on-chip technology and modification-specific histone antibod-ies places this NoE in a strong position to analyse the differences between stem cells versus committed cells and to map epigenetic transitions along entire chromosomes (chromosome landscaping). With respect to model organisms, THE EPIGENOME represents a multidisciplinary project covering S.cerevisiae, S.pombe, plants, Drosophila, mouse and human. It integrates high-end genetic, bio-chemical, cytological and micro-array approaches for a functional analysis of epigenetic control. The strength of this NoE is in its focus on molecular mechanisms rather than on descriptive analyses. In addition, thanks to the ex-pertise of the NoE members, some of the most important questions in modern epigenetic research may be addressed. The implications of epigenetic research are far-reaching and range from agriculture to human biology and disease, including our understanding of stem cells, cancer and ageing. The programme of EPIGENOME NoE rests on 5 pillars, namely, a joint research pro-gramme that is directed towards elucidating epigenetic mechanisms; a Newly Established Team (NET) programme to integrate ‘junior’ scientists into the NoE; measures ensuring network development and durability; communication platforms to address the needs of both scientific exchange, and public consulting and a management structure that will underpin the network.

Expected Results:Research into epigenetics represents the new frontier for addressing many questions that, despite a vast resource of existing genetic data, still remain unanswered. The importance of the “epigenetic code” concept explains why it is essential to have a better understanding of the processes of cell fate determination: better knowledge means better understanding of disease and development, and will therefore, improve intervention strategies for multifacto-rial disease. The recent discoveries related to an epigenetic “histone code” and the function of the RNAi machinery in epigenetic silencing only serve to highlight the emerging new concepts in epigenetic research. In this sense, the creation of a NoE will not only provide an important nucleation point for durable structure research, but will also overcome the problem of frag-mentation by promoting the longer-term aims of scientific progress, and by contributing to an expanding and dynamic community. Our increasing understanding of epigenetic control should therefore foster the development of innovative strategies for therapeutic intervention based on regulatory pathways of epi-genetic mechanisms. Epigenetics covers many topics of key interest to the general public, including embryonic and adult stem cells, their medical use and the cloning of whole animals. Advances in epi-genetic research are expected to have far-reaching implications for medicine and human health. By acknowledging its responsibility towards the public, the NoE is committed to ensuring the dissemination of knowledge regarding epigenetic research and its societal im-plications. With these measures the NoE aims to provide a benchmark for a new European partnership between science and society.

Genomes vs Epigenomes


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Project Coordinator:Prof. Thomas JenuweinResearch Institute for Molecular Pathology (IMP)Dr. Bohr-Gasse 71030 Vienna, [email protected]

Dr. Denise BarlowResearch Center for Molecular MedicineVienna, Austria

Prof. Ingrid GrummtDeutsches Krebsforschungszentrum HeidelbergDivision Molecular Biology of the Cell II / A030Heidelberg, Germany

Prof. Jörn WalterUniversität des SaarlandsDepartment of GeneticsSaarbrücken, Germany

Prof. Peter Becker, Philipp KorberLudwig-Maximilians-UniversitätAdolf-Butenandt-Institut MolekularbiologieMunich, Germany

Prof. Gunter ReuterMartin-Luther-Universität Halle-WittenbergInstitut fur GenetikHalle, Germany

Prof. Frank Grosveld, Peter VerrijzerErasmus Medical CenterRotterdam, The Netherlands

Prof. Robin Allshire, Dr. Adrian Bird, Dr. Irina StanchevaUniversity of Edinburgh Wellcome Trust Centre for Cell Biology Edinburgh, United Kingdom

Prof. Wendy Bickmore, Prof. Neil Brockdorff Prof. Amanda Fisher The Medical Research CouncilFaculty of MedicineMRC Clinical Sciences CenterLymphocyte Development GroupEdinburgh, United Kingdom

PartnersPotential Impact: In defining a coordinated joint programme of activities (JPA), this NoE will assimilate ex-isting synergies for building a structure that can feed three important needs: advance scientific discoveries, integrate European research and establish an open dialogue. The project’s main objectives will contribute to the long-lasting determination of a co-herent European Research Area (ERA) on epigenetic research. In the short term, THE EPIGENOME aims at constituting a frame-work for important discoveries in Europe, thus establishing the NoE as an internation-ally competitive research force. As a con-sequence, the NoE will provide a platform for the development of epigenetic research, benefiting not only the NET members, but also the wider scientific communityA major goal of THE EPIGENOME is to support post-doctoral research, thereby al-lowing the team to gain visibility at interna-tional meetings and to disseminate their re-sults. The NoE organises annual meetings, workshops and the ‘Alan Wolffe’ Epigenet-ics Conference, which provides a venue to effectively showcase the NoE’s excellence. The EPIGENOME also promotes initiatives for dialogue and disseminates information to the public via organised events, the media, and the World Wide Web. This will help the public keep pace with new developments in knowledge, technology and innovation, and facilitate a greater acceptance of sci-entific endeavours. As a consequence, the public could have a more informed role in scientific governance, particularly on impor-tant issues for society, which also raise ethi-cal questions.

Keywords:chromatin modification, RNA silencing, epi-genetic code, cell fate determination, repro-gramming

THE EPIGENOME group


THE EPIGENOME



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Prof. Bryan TurnerThe University of BirminghamSchool of MedicineDepartment of AnatomyBirmingham, UK

Dr. Wolf Reik, Dr. Patrick Varga-WeiszDr.Miguel Constancia The Babraham InstituteDevelopmental Genetics & Imprinting LaboratoryCambridge, United Kingdom

Prof. Azim Surani The University of Cambridge Gurdon InstituteCambridge, United Kingdom

Prof. Peter MeyerThe University of LeedsLeeds, UK

Dr. Genevieve Almouzni, Dr. Edith HeardCentre National de la Recherche Scientifique (CNRS)Institut CurieParis, France

Prof. Philip AvnerCentre National de la Recherche Scientifique (CNRS)Institut PasteurParis, France

Prof. Jerzy PaszkowskiUniversité de GenèveGeneva, Switzerland

Prof. Ueli GrossniklausUniversität ZürichInstitute of Plant BiologyDepartment of Plant Developmental BiologyZurich, Switzerland

Dr. Asifa Akhtar, Dr. Andreas LadurnerEuropean Molecular Biology Laboratory (EMBL)Heidelberg, Germany

Dr. Karl EkwallKarolinska InstitutetUniversity College SödertörnStockholm, Sweden

Dr. Vincent ColotCentre National de la Recherche Scientifique (CNRS)Plant Genomics Research UnitInstitut National de la Recherche Agronomique (INRA)Evry, France

Dr. Giacomo CavalliCentre National de la Recherche Scientifique (CNRS)Institut de Génétique HumaineMontpellier, France

Dr. Fred van Leeuwen, Dr. Bas van SteenselHet Nederlands Kanker InstituutAmsterdam, The Netherlands

Dr. Valerio OrlandoFondazione TelethonDulbecco Telethon InstituteNaples, Italy

Prof. Susan Gasser, Dr. Antoine PetersDr. Dirk SchübelerFriedrich Miescher Institute for Biomedical ResearchBasel, Switzerland

Dr. Ana Losada, Dr. Oskar Fernandez-CapetilloCentro Nacional de Investigaciones OncológicasMadrid, Spain

Dr. Ortrun Mittelsten ScheidGregor Mendel-InstitutVienna, Austria

Dr. Leonie RingroseInstitute of Molecular BiotechnologyVienna, Austria

Dr. Deborah Bourc’hisInstitut National de la Santé et de la RechercheMédicale (INSERM)Institut Jacques MonodParis, France

Dr. Wolfgang FischleMax Planck Institute for Biophysical ChemistryGoettingen, Germany

Dr. Robert SchneiderMax Planck Institute of ImmunobiologyFreiburg, Germany

Prof. Renato ParoEidgenössische Technische Hochschule ZürichBasel, Switzerland

The complete list of the 22 newly established groups integrated might not appear due to space limitations; see project web site for updated information


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State-of-the-Art:At last the completed genetic code of many organisms gives science the chance to under-stand how genes build organisms. Unfortunately, like all truly great codes, simply decoding the letters does not explain how life is manifest, since buried deep in the primary genetic code is a second regulatory code, which we need to decipher to understand how the ge-nome works. This regulatory code is encrypted in chromatin and 3D nuclear organisation, and functions to regulate the accessibility of the primary genetic information. We know that there is linear genome organisation and that genes subject to similar regulatory con-trols are adjacent to each other. What we do not yet know is the extent of these ‘genome domains’ – if domains operate between different chromosomes, or how domains are set up and maintained. Answers to these questions will depend upon global and long-range genome strategies that need the development of high-throughput technologies. HEROIC will take a two-pronged approach. First, it will develop global biochemical and high-throughput genomic tools and screens that will identify novel gene regulators and determine when and where transcription factors, histone modifying enzymes and chromatin remodelling proteins interact with the primary genetic code. Then well-characterised progenitor-differ-entiation systems, such as pluripotent mouse ES cells and paradigm silencing models from genomic imprinting and X-inactivation, will be studied using high-throughput ChIP-on-chip, chromosome interaction and whole genome nuclear localisation assays to provide basic information on linear and 3D genome organisation. HEROIC will provide knowledge that contributes to a functional understanding of gene regulation in a genome context. It will inject epigenetic research with high-throughput technology on a genome-wide scale, thus making a wider contribution to understanding the primary genetic code that will eventually allow society the full benefit expected from its decryption.

Scientific/Technological Objectives:The main objective of HEROIC is to make significant advances in the mechanistic ques-tions of epigenetic regulation, characterise the epigenetic modifications that occur, and then understand the implications for gene expression in different cell types. The approach focuses on the use of high-throughput enabling technologies on predominantly primary and established mouse cell lines, particularly ES cells.

To characterise the epigenome, high-throughput bisulphite sequencing, advanced mass spectrometry applied to histone post-translational modifications, ChIP-on-chip, and three dimensional interaction mapping and profiling DNA replication timing across the genome will be applied to ES cells, mutated ES cells and macrophages differentiated from these ES cell lines. This will allow a comparison of pluripotent to differentiated aspects and changes of the epigenome in a model case. As a complement, aspects of the epigenome will be mapped in the haematopoietic compartment in the mouse.

Expected Results:The histone codeHEROIC aims to unravel the meaning of the epigenetic code. This requires comprehensive documentation of coding combinations, the hierarchies and cross signalling within the code and understanding what the code means.


HEROIC

Project Type:Integrated ProjectContract number:LSHG-CT-2004-018883 Starting date:1st November 2005 Duration:52 months EC Funding:

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Whole genome epigenetic and transcription factor profilingHEROIC will screen whole ge-nome tile path arrays to identify and compile a definitive set of non-coding regulatory elements for the mouse genome yielding a TRR microarray. HEROIC will screen high-density oligonu-cleotide arrays at nucleosome resolution to study the epige-netic response of cells in cul-ture to short-term treatment with hormones in relevant regions of the genome. It will use the TRR microarrays to profile changes in gene expression and chro-matin structure that underlie the reprogramming of differentiated B-lymphocytes towards the my-eloid lineage by the enforced expression of the transcription factor CEBP.

In-depth DNA methylation and epigenetic profiling of mouse Chromosome 17HEROIC aims to provide a comprehensive map of epigenetic layers of chromosome 17 ranging from histone marks, factors that read, write and interpret the marks, DNA meth-ylation and parental imprinting to understand how transcription networks and epigenetic information contribute to the formation of specialised cell types in multicellular organisms. HEROIC will focus on two fundamental areas: pluripotency and lineage restriction.

The epigenetic dimension of global genome structure and nuclear organisationHEROIC addresses epigenetic aspects of nuclear architecture and its relevance to cell com-mitment and memory by exploiting well-defined cellular systems to examine how gene regulation is affected by global genome structure and nuclear organisation.

BioinformaticsHEROIC will accumulate all epigenetic data generated as well as public data. The accumu-lated datasets will be analysed for currently unknown patterns of epigenetic states.

Potential Impact:

The main impact of the HEROIC IP will be research into gene regulatory systems at the level of chromatin structure and nuclear organisation, with high-throughput tech-nology approaches in the context of the whole genome. Never before has such an extensive multidisciplinary consortium been assembled at European level.

The yield of cumulative joint research carried out in this IP will stimulate competitive-ness within Europe and between other developed countries, such as the US and Canada. HEROIC will also act as a focal point within Europe for the development of novel technology applied to chromatin and nuclear organisation studies.


High-Throughput Epigenetic Regulatory Organisation in Chromatin

Overview ofHEROIC’s scientific goals


154

The undertaking of proactive training will contribute to extending the widespread use of the technology employed by consortium members to address other research ques-tions.

HEEROIC aims to disseminate actively but also protect research results where com-mercial exploitation is a possibility. Dissemination will occur in the form of joint publi-cations and within the network through conferences and workshops.

Researchers of HEROIC will be called upon as expert voices in discussions within Europe on topics such as stem cell therapy, novel genetic and epigenetic diagnostic screening methods and gene therapies involving RNAi.

Keywords: epigenetics, chromatin, gene regulation, high-throughput techniques


HEROIC

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PartnersProject Coordinator:Prof. Henk StunnenbergStichting Katholieke UniversiteitDepartment of Molecular BiologyGeert Grooteplein 286500 HB Nijmegan, The [email protected]

Project Manager:Dr. Adrian CohenScientific ManagerNijmegen Centre for Molecular Life Sciences (NCMLS)P.O. Box 91016500 HB Nijmegen, The Netherlands

Prof. Denise BarlowCeMM - Forschungszentrum fürMolekulare Medizin GmbHInstitute of Microbiology and GeneticsVienna, Austria

Prof. Rolf OhlssonUppsala UniversityDepartment of Development & GeneticsUppsala, Sweden

Dr. Matthias MannMax-Planck Society for the Advancement of SciencesProteomics and Signal TransductionMartinsreid, Germany

Prof. Francis StewartTechnische Universität DresdenBiotec and GenomicsDresden, Germany

Dr. Stephan Beck, Dr. Dave VetrieGenome Research LtdWellcome Trust Sanger Institute, Immunogenomics LaboratoryCambridge, UK

Dr. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI) Hinxton, UK

Didier AllaerDiagenode SAScience DepartmentLiege, Belgium

Prof. Matthias MerkenschlagerMedical Research CouncilMRC Clinical Sciences CentreLymphocyte Development GroupLondon, UK

Dr. Miguel BeatoCentre de Regulació GenòmicaDepartment of Chromatin & Gene ExpressionBarcelona, Spain

Dr. Edith HeardInstitut Curie Paris Nuclear Dynamics and Plasticity of the GenomeParis, France

Dr. Kurt BerlinEpigenomics AGScience DepartmentBerlin, Germany


High-Throughput Epigenetic Regulatory Organisation in Chromatin



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State-of-the-Art:The sequence of an organism’s genome does not directly determine how the genome is used to build the organism. A second, more complex regulatory code - the epigenetic code - is encrypted in the chromatin structure and the 3D nuclear organisation of chromosomes. Epigenetic information is encoded in DNA modifications (namely methylation), chromatin composition and modification, and nuclear topology, or the dynamic organisation of the genome within the nucleus. Epigenetic information not only provides the first cue to allow a cell to interpret the genome, it can also be heritably transmitted through cell division to maintain cellular identity. Moreo-ver, while many heritable disorders in humans are caused by DNA sequence changes (mu-tations) that abolish gene expression, a number of diseases are caused by inappropriate gene silencing brought about by epigenetic modifications. Indeed, most cancers involve the epigenetic silencing of genes that normally control cell proliferation. The principal forms of epigenetic modification are DNA and histone methylation.A challenge that is central to modern biology is the identification of the spatial and tempo-ral dynamics of epigenetic factors in a number of physiological situations. The Chromatin Immuno-Precipitation (ChIP) assay has played a pivotal role in deciphering patterns of epigenetic marks that govern gene transcription. Besides ‘classical’ ChIP, several similar techniques have been described in the literature. Recently, new technologies designed to improve on the existing ChIP and native ChIP (NChIP) technologies, have emerged. In addition, low resolution and reproducibility problems are often encountered. These se-vere limitations of the ChIP method are overcome by the Chromatin Immuno-Linked Ligation (ChILL) method, , which could provide the foundation for a new generation of biotechnology tools and methods.

Scientific/Technological Objectives:The objective of this project is to develop and validate a new technology which has the potential to replace the various ChIP technologies, and to transform the way the molecular analysis of chromatin is performed. The ChILL technique has been patented by one of the partners of this project, leaving the consortium free to operate with regard to intellectual property rights. The ChILL method is based on specific ligations which occur between DNA stretches under diluted conditions. In this environment, ligation partners can only interact if they are in close proximity. This proximity is created by new oligonucleotide-antibody conjugates (nucleoproteic probes, or oligo-ab), which physically place the target DNA in contact with the oligonucleotide re-porter sequences. The ligation products are then amplified by the polymerase chain reac-tion and analysed with real-time instruments and/or classical gel electrophoresis.Due to the ligation step taking place under diluted conditions, the ChILL method will gen-erate data comparable to those obtained with ChIP, but with increased sensitivity and a simpler protocol that omits the tedious immuno-precipitation step. As a proof of principle, the ChILL method has already been shown to be at least 100 times more sensitive than the regular ChIP assay. ChILL will not only facilitate analysis of very small samples, such as early embryos or diag-nostic samples from patients, but will also radically improve the resolution of the epigenetic marks. In addition, strong detergents used in the ChILL assay open up the chromatin struc-ture, rendering it more accessible to antibodies than in conventional ChIP assays.Another major advantage of ChILL will be its ability to interrogate several parameters in a single sample. For this purpose, a variant of ChILL called combinatorial ChILL will be devel-oped. This will represent a major breakthrough, because it will mean that several epigenetic marks can be collected from a single tube, making it easier to build up what might be called an “epigenetic profile” of the biological material in question.


ChILL

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2006-037462Starting date:1st October 2006Duration:36 monthsEC Funding:

1 800 480


157

Expected Results:The Chromatin Immuno-Precipitation (ChIP) assay plays an absolutely pivotal role in deci-phering patterns of epigenetic marks that govern gene transcription. While the ChIP assay is a versatile tool, it suffers from low resolution and low sensitivity. These strong limitations of the ChIP method are overcome by the Chromatin Immuno-Linked Ligation (ChILL) meth-od. ChILL will not only facilitate analysis of very small sample sizes, such as early embryos or diagnostic samples from patients suffering from a range of diseases, but also radically improve the resolution of the epigenetic marks. The ChILL approach also offers opportuni-ties to examine simultaneous co localization of two or more factors on the same chromatin template, and the epigenetic marks will be resolved in unprecedented detail.

The expected results of the program would be to make ChILL technology accessible to all European research laboratories via validated procedures, reagents or kits. We also ex-pected to launch diagnostic kits using ChILL technology for the diagnosis of diseases linked to epigenetic disorders.

Potential Impact: The first impact of ChILL will be a better understanding of the epigenetic code. Of course, the commercial impact of the ChILL method might consequently also be very important for Diagenode with the possible development of tools for the research or diagnostic market.

Keywords:chromatin remodeling, transcription regulation, epigenetics, ChIP assay, histones, DNA methylation

Project Coordinator: Didier AllaerDiagenode SAAvenue de L’Hopital, 1 Tour Giga B344000 (Sart Tilman) Liège, [email protected] Prof. Dr. Rolf I. OhlssonUppsala UniversityDevelopment andGenetics Evolution CenterUppsala, Sweden

Prof. Dr. Henk G. Stunnenberg Radbout University NijmegenDepartment of Molecular BiologyNijmegen, The Netherlands

Dr. François FuksFree University of BrusselsFaculty of MedicineLaboratory of Molecular VirologyBrussels, Belgium

Dr. Duncan Clark GeneSys LtdCamberley, UK

Partners


Chromatin Immuno-linked ligation: A novel generation of biotechnological

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State-of-the-Art:The identity of a given cell within a metazoan organism is primarily defined by the expression pattern of its genes. The activation and repression of genes is tightly regulated by the con-certed action of transcription factors that recognise and bind specific DNA sequences within regulatory regions. Work done over the last 20 years established this basic regulatory mecha-nism of gene activation and repression, while recent experiments have exposed an additional layer of regulation involving modifications of DNA and bound histones. These modifications are involved in cellular inheritance of transcriptional states through cell division and develop-ment, and as they are not coupled to DNA sequence, are referred to as epigenetic.

Many factors that impact on epigenetic phenomena are clearly distinct from basic transcrip-tion factors and are involved in regulating chromatin structure. Modulation of chromatin structure is frequently achieved by intrinsic enzymatic activities that either mark particular regions within the genome for activity or repression, or use the hydrolysis of ATP to remodel nucleosomal arrays. This alteration of gene expression patterns in response to external and internal signals has a major influence on stem cell differentiation, the maintenance of tissue integrity, and the adaptation of organisms to environmental changes.

Recently, small molecules that target histone deacetylases (HDAC) have been used in the treatment of cancer, opening up new avenues in therapeutic research. However, small molecules targeting epigenetic regulators have so far not been the major focus of drug discovery efforts.

The SMARTER project aims to develop such compounds, and this is also the primary mis-sion of Chroma Therapeutics, the SME participating in the consortium. The interaction be-tween leading European chromatin labs and Chroma is expected to greatly strengthen the company’s knowledge base, and thus, have a powerful impact on its ability to enter drug candidates for clinical trials.

Scientific/Technological Objectives:The SMARTER project has the following goals:

1) Identification of small molecule inhibitors that target various histone-modifying en-zymes (SMARTERs);

2) Validation of these inhibitors through in vivo analysis of histone modification states; 3) Establishment of histone modification states as standard readouts for drugs that target

epigenetic modifiers; 4) Improvement of known epigenetic modulators through medicinal chemistry; 5) Identification of target genes that are regulated by the SMARTER molecules and 6) Application of the SMARTER molecules in standard animal model systems to verify

their activity in living organisms.

Expected Results:After 48 months, SMARTER will provide:

1) SMARTER molecules that are selective for specific histone deacetylases and two ad-ditional targets, with high potency;

2) An assay system for new epigenetic modifiers that is applicable to high throughput screen for small molecule inhibitors;

3) Definition of SMARTER effects on histone modification patterns and kinetic analysis of effects on chromatin;

4) Identification of one or several bona fide target genes for direct SMARTER effects;


Project Type:SME-Specific Targeted Research ProjectContract number:LSHG-CT-2006-037415Starting date:1st December 2006Duration:48 monthsEC Funding:

2 499 999

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5) Establishment of one or several SMARTER molecules for one or several targets that show an in vivo effect in mice;

6) Demonstration of global and gene-specific effects of SMARTERs on the epigenetic pattern of lymphomas in a model of radiation-induced lymphomagenesis, with a view to investigating the chemotherapeutic potential of SMARTERs.

Potential Impact:The SMARTER project is specifically designed to increase the knowledge base of Chroma Therapeutics, a SME located in the UK. Chroma will profit from the collaboration, because the consortium will greatly facilitate the analysis of SMARTER molecules that have been and will be discovered by the company. The project will also allow Chroma to direct improve-ment of the small molecules through medicinal chemistry, and to test them rapidly in various biological systems. Being a SME-targeted STREP, the project will contribute significantly to the Lisbon objective of Europe becoming the most competitive knowledge-based economy in the world by 2015.

The knowledge gained through this project will be disseminated and translated into new therapies and clinical practice. SMARTER will have a strategic impact on European R&D through facilitating the generation of small molecules that are cell-permeable and that dura-bly change chromatin modification states. In order to fully understand how the eukaryotic genome in general and the human genome in particular operate, knowledge about their DNA sequence, epigenetic control systems and dynamic structure in relation to gene ex-pression must be integrated.

Keywords: epigenetics, small molecules, gene regulation

Project Coordinator:Prof. Axel ImhofLudwig Maximilians University of MunichAdolf-Butenandt InstituteHistone Modifications GroupProtein Analysis Core FacilitySchillerstr. 4480336 Munich, [email protected]

Dr. Scott CuthillChroma Therapeutics LtdOxford, UK

Dr. Dirk SchübelerFriedrich Miescher Institute forBiomedical ResearchBasel, Switzerland

Dr. Manuel EstellerSpanish National Cancer CentreCancer Epigenetics LaboratoryMadrid, Spain

Prof. Tony KouzaridesUniversity of CambridgeThe Wellcome TrustCancer ResearchUK Gurdon InstituteCambridge, UK

Partners


Development of small modulators of gene activation and repression

by targeting epigenetic regulators




STRUCTURAL GENOMICS & STRUCTURALPROTEOMICS3.



STRUCTURAL GENOMICS

3.3DGENOME

BIOXHIT

3D-EM

GeneFun

E-MeP

FSG-V-RNA

VIZIER

UPMAN

NDDP

3D repertoire

FESP

E-MeP-Lab

HT3DEM

NMR-Life

Extend-NMR

IMPS

SPINE2-COMPLEXES

OptiCryst

TEACH-SG


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State-of-the-Art:

Understanding the molecular mechanisms that underlie the orchestration of many thousands of genes in higher eukaryotes is a key target in modern biomedical research. Our knowl-edge about gene regulation at the single gene is rapidly expanding. However, understand-ing of the coordination of gene regulation, for example during cell differentiation and dis-ease, is still remarkably limited. There is considerable evidence that the three-dimensional folding of the DNA chain, packaged as chromatin, plays an important role in gene control. The 3DGENOME project has the ambition to force a breakthrough in our understanding of the relationship between the functioning of the human genome and its 3D structure inside the cell nucleus. To this end we analyse the 3D folding of the human genome inside its natu-ral environment, i.e. the cell nucleus, and relate this to its transcriptional activity. This study combines 3D light microscopy with genome-wide information about gene activity.

Scientific/Technological Objectives:The 3DGENOME project is based on the systematic and large-scale combination of two main technologies:

in situ hybridisation (FISH) followed by 3D light microscopy

A major challenge is created by the large cell-to-cell variation of 3D chromatin structure in otherwise identical (cultured) human cells. Novel methods are developed to identify signifi-cant structural features that stand out against this ‘noisy’ background. At the same time it is essential to quantify and characterise this cell-to-cell variation precisely. Results will tell which aspects of chromatin structure are important for genome function and which are not.An integral part of this approach is the development of novel high-throughput 3D imag-ing routines in combination with automated 3D image processing and quantitative image analysis. Specific aspects of 3D chromatin structure will be analysed by high-resolution light microscopy, including 4Pi microscopy.Most of the work is carried out with primary human cells and cell lines. In addition, Dro-sophila is used as a system in which specific changes can be made in the genome, after which the effect of 3D chromatin structure can be analysed.

Expected Results:The 3DGENOME project is unveiling the link between the folding of the chromatin/chromo-some fibre inside the interphase nucleus and the functional (primarily transcriptional) proper-ties of the human genome. It builds on the human transcriptome, which shows genes of high transcriptional activity in a limited number of gene-dense clusters in the genome. Results of these studies will give new insight into how the eukaryotic genome in general, and the human genome in particular, operates inside the living cell. This project will lay the groundwork for understanding how, beyond the regulation at the individual gene level, a large-scale chromatin structure affects the complex gene regulation networks in normal and deceased cells.

Potential Impact:1. Fundamental insight into the relationship between gene regulation and 3D struc-

ture of the eukaryotic genome. To understand fully how the eukaryotic genome in general, and the human genome in particular, operate, knowledge about its DNA sequence, its epigenetic control systems and its dynamic 3D structure in relation to gene expression must be integrated.


3DGENOMEhttp://3dgenome.uva.sara.nl/3dg.html

Project Type:Specific Targeted Research projectContract number:LSHG-CT-2003-503441Starting date:1st December 2003Duration:42 monthsEC Funding:

2 173 803


http://3dgenome.uva.sara.nl/3dg.html

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2. High resolution 3D microscopy and related software tools 3DGENOME will bring forth new developments on the areas of high-resolution 3D light microscopy, 3D im-age processing and quantitative analysis of acquired images. Furthermore, we will develop methods to quantitatively compare and statistically analyse 3D structures and distribution in biological specimens.

Keywords: 3D structure, fluorescent in situ hybridization, gene expression, high throughput imaging analysis

PartnersProject Coordinator: Prof. Roeland Van DrielUniversiteit van AmsterdamScience FacultySwammerdam Institute for Life SciencesKruislaan 3181098 SM Amsterdam, The [email protected]

Prof. Dr. Thomas CremerLudwig-Maximilians-Universität München (LMU)Department of Biology IIMartinsried/Munich, Germany

Prof. Dr. Christoph CremerAngewandte Optik und InformationsverarbeitungKirchhoff Institut für PhysikHeidelberg, Germany

Prof. Dr. Roland EilsDeutsches Krebsforschungszentrum (DKFZ)Division of Theoretical BioinformaticsHeidelberg, Germany

Prof. Dr. Giacomo CavalliCentre National de la Recherche Scientifique (CNRS)-IHGInstitute of Human GeneticsMontpellier, France

Prof. Dr. Rogier VersteegUniversity of AmsterdamAcademisch Medisch CentrumAmsterdam, The Netherlands

Prof. Dr. Stanislav KozubekAcademy of Sciences of the Czech Republic Institute of BiophysicsBrno, Czech Republic

Dr. Hans van der VoortScientific Volume Imaging BVHilversum, The Netherlands


3D Genome Structure and Function



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State-of-the-Art:The recently acquired knowledge pertaining to numerous genome sequences provides a unique opportunity to quantitatively decipher the roles of biological molecules in complex processes within cells, organs and organisms. An essential step in accomplishing this task is to determine their atomic structures; this permits a more comprehensive description of the roles of molecules in living systems, in the context of both health and disease. The acquisi-tion of structural information on biological macromolecules on a genomic scale lies at the core of Structural Genomics (SG).

At present, the only techniques appropriate for determining three-dimensional (3D) struc-tures of biological macromolecules in atomic detail, and at a rate appropriate for SG, are biological X-ray crystallography (biocrystallography) and NMR-spectroscopy. Biocrystal-lography has been responsible for roughly 85% of all biomolecular structures (and for 95% of all the smallest proteins) deposited in the Protein Data Bank (http://www.rcsb.org/pdb) and the Molecular Structural Database (http://www.ebi.ac.uk/msd).

Biocrystallography has undergone a tremendous transitional period over the past decade. Formerly, determining a macromolecular crystal structure required years; today it would typically require a few weeks, if not days. And crucially, the potential for further improve-ment is far from exhausted. Furthermore, recent technological advances have made a wide range of new biological problems responsive to crystallographic study. Although obtaining large amounts of a protein in soluble form is still in many cases an important issue, bioc-rystallography is in principle applicable to the complete spectrum of biological macromol-ecules, derived from all organisms (from eubacteria and archeae, to human organisms), and of all sizes (from small domains to gigantic ribosome or virus particles).

Scientific/Technological Objectives: The central objective of the BIOXHIT project entails tackling the challenge posed by the Structural Genomics initiatives already underway in the USA and in Japan, and to de-velop, assemble, standardise and provide a highly integrated technology platform for High Throughput Structural Biology. This goal will be attained as a result of coordinated efforts with the present and future European synchrotron radiation facilities, and a team of inter-nationally recognised European leaders in hardware and software development, directly associated with high-throughput methodologies.

BOIXHIT Group


BIOXHIT

Project Type:Integrated ProjectContract number:LSHG-CT-2003-503420Starting date:1st January 2004 Duration:54 monthsEC Funding:

9 993 849

www.bioxhit.org


http://www.rcsb.org/pdb

http://www.ebi.ac.uk/msd

http://www.bioxhit.org

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Biocrystallography is the method of choice, and synchrotron radiation the principal source of X-rays, for data acquisition. This technology encompasses the components necessary to produce an efficient pipeline linking crystallisation to completed 3D-structure determination. It will operate with minimal user intervention, and will be fully accessible to the wider life sciences research community.

Expected Results: BIOXHIT aims to deliver the following results:

smaller crystallisation drops, with less protein consumption;

X-ray beam;

and easy-to-operate beamlines, providing high-quality stable X-rays, that are auto-matically delivered to the sample;

in order to optimally plan the actual diffraction experiment;

the success of the experiment at the earliest possible stage, and to allow direct feed-back for data collection and crystallisation;

control;-

tioned above, and high-level training in new hardware;

within and external to the BIOXHIT consortium.

Potential Impact: BIOXHIT provides a substantial component in scientific as well as technical innovation. The task of building such integrated platforms entails numerous developments in instrumentation and in hardware automation. Instances of this are the complete tracking of crystal samples during synchrotron experiments, and interaction with the project information management systems of the users; the automated handling of crystal samples by robots, their automatic recognition and centring on the goniometric hardware; and their automated screening.

The BIOXHIT project activities include innovative developments in many of these directions, (as exemplified in the mini-kappa goniometer and its control software), and therefore pro-vide access to new categories of data collection strategies hitherto inaccessible. Another prominent feature of BIOXHIT is the assembly of a computational crystallographic pipeline, which aims at automating the sequence of steps involved in determining macromolecular crystal structures. This requires a dramatic paradigm shift in X-ray crystallographic meth-odology, as compared to the old paradigm, whereby the successive steps of structure de-termination were performed by crystallographers running computer programs interactively through graphical interfaces, to a new pipeline operating with little or no human interven-tion. The immediate demand for such integration will be met by connecting these programs,


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thus emulating the actions of a crystallographer by the execution of suitable scripts. The complexity of this approach should not be underestimated; it will serve to deliver a first generation of integrated structure determination pipelines.

BIOXHIT ultimately proposes to achieve a genuine integration of all of the processes into a single, seamless computational scheme that will be structured around a conceptual uni-fication of the structure determination process. This demands a radical rethinking of X-ray crystallographic methods, and a profound reorganisation of their software implementation around the modern techniques of object-oriented programming. In return, it will deliver a markedly powerful second generation of integrated pipelines, as well as considerably im-proved software for general use. The combination of hardware and software innovations will in turn render new phasing techniques accessible, such as routine phasing by means of anomalous dispersion from sulphur and phosphorus.

The number of scientists from the structural biology community subsequently becoming new users of the synchrotron facilities has increased rapidly during recent years. Synchrotron radiation centres have had long experience in training users, but training of the increasing number of new users represents a challenge that would be impossible to meet by the hard-ware core-facilities alone. These efforts will be amplified throughout the BIOXHIT project lifetime. A number of Training, Implementation and Dissemination TID-centres will be estab-lished outside the participating laboratories as the vital tools for the dissemination of the developed know-how.

Keywords: synchrotrons, hardware and software pipeline, protein crystallisa-tion, X-ray crystallography, robotics, automation techniques, stand-ardisation, technology platform, structural genomics

BIOXHIT: Integration and Activity Areas

1Crystallisationtechnologies

2Synchrotrontechnologies

3Beamline end-

stations and datacollection

4Data processing and

structure determination

5Databases and

networking

Standardisation Samplepreparation

andmanipulation

Core hardwaredevelopments

Core softwaredevelopments

DiffractionExperiment

Logistics / remoteoperation / integration

Project Coordinator: Dr. Victor LamzinEuropean Molecular Biology Laboratory (EMBL)Outstation HamburgMacromolecular Crystallography22603 Hamburg, [email protected]

Project Research Director:Dr. Manfred WeissEuropean Molecular Biology Laboratory (EMBL)Outstation HamburgMacromolecular Crystallography22603 Hamburg, [email protected]

The BIOXHIT project: Relationship between activity areas, partner

contributions, workpackages and sections. Each link defines a

contribution of a Partner to a WP.


BIOXHIT

Partners




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Project Manager:Natalie SebastianEuropean Molecular Biology Laboratory (EMBL)Outstation Hamburgc/o DESYNotkestr. 85, building 25A22603 Hamburg, [email protected]

Dr. Raimond Ravelli (since 2008 replaced by Dr. Andrew McCarthy)European Molecular Biology Laboratory (EMBL)Outstation GrenobleGrenoble, France

Dr. Kim HenrickEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Dr. Sean McSweeneyEuropean Synchrotron FacilityGrenoble, France

Dr. C. Schulze-BrieseSwiss Light Source (SLS)Villigen, Switzerland

Dr. Gerard BricogneGlobal Phasing LtdCambridge, UK

Dr. Anastassis PerrakisHet Nederlands Kanker Instituut Antoni van LeeuwenhoekziekenhuisAmsterdam, The Netherlands

Dr. Roberto PuglieseELETTRA TriesteSincrotrone Trieste S.C.P.A.Trieste, Italy

Prof. Keith Sanderson WilsonUniversity of YorkStructural Biology LaboratoryDepartment of ChemistryYork, UK

Dr. Uwe MuellerFreie Universität BerlinProteinstrukturfabrik c/o BESSY GmbHBerlin, Germany

Dr. Peter John BriggsCouncil of the Central Laboratoryof Research CouncilsWarrington, UK

Prof. George SheldrickGeorg-August-Universität GöttingenGöttingen, Germany

Dr. Andrew ThompsonSociete Civile Synchrotron SOLEILGif-sur-Yvette, France

Dr. Thomas SchneiderFondazione Italiana per la Ricerca sul CancroMilan, Italy(Since 2007 at the project coordinator’s site)

Dr. Marjolein ThunnissenLund UniversityDepartment of Molecular BiophysicsLund, Sweden

Prof. Sine LarsenUniversity of CopenhagenDepartment of ChemistryCopenhagen, Denmark

Dr. Elizabeth Duke, Dr. Colin NaveDiamond Light Source LtdDidcot, UK

Dr. J. JuanhuixCampus Universitat Autònoma de BarcelonaConsorci Laboratori de Llum de SincrotóBarcelona, Spain

Dr. Edgar WeckertDeutsches Elektronen SynchrotronHamburg, Germany

Dr. Gábor Mihály LammEMBLEM Enterprise ManagementTechnology Transfer GmbHHeidelberg, Germany

Dr. Kristina Djinovic-CarugoUniversity of ViennaInsittute for BiomolecularStructural ChemistryVienna, Austria


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State-of-the-Art:Currently, the primary challenge for biological research lies in understanding the cellular function in molecular detail, based on genomic and proteomic information. Detailed knowl-edge of the structure of macromolecules and macromolecular complexes, and also of the interaction networks that underlie cellular function, allow for progress in the study of biologi-cal processes in health and disease. This project will specify potential targets for therapeutic intervention, as well as identify pharmaceutical lead structures.

Three-dimensional (3D) visualization is the best way to appreciate the complex interactions of macromolecules, such as proteins. Visual techniques, especially electron microscopy (EM), can complement and extend quantitative data obtained using other methods in this field.

EM is a powerful tool that derives 3D structural information from biological specimens. The specific EM technologies provide 3D projections in a wide spectrum of resolutions ranging from atomic to cellular. Electron crystallography is applied when studying symmetric 2D crystals of molecules, such as membrane proteins, showing the same structure and orienta-tion. Single particle analysis enables the 3D reconstruction of noncrystalline and asymmet-ric assemblies. The application of electron tomography reveals macromolecular interactions in native cellular contexts. A near physiological preservation of small cells and viruses is achieved by rapid freezing in vitreous ice.

The sectioning of these vitreous samples and subsequent cryo-electron tomography, as well as the 3D reconstruction based on low contrast 2D images, represent technical challenges. European laboratories and companies are taking the lead in different EM techniques, and also in their related aspects, like that of image processing. Such interdisciplinary coopera-tion is required to standardise, develop, improve and combine EM techniques.

Scientific/Technological Objectives: The 3D determination of macromolecular structures, such as proteins, will play an essential role in future life-science research. The 3D-EM network was initiated so as to create a forum for internationally recognised European manufacturers and institutions, in various fields of 3D structural research. The activities of the network focus on 3D imaging of macromolecules and molecular machines, as well as cells and cell organelles.

The main objectives of 3D-EM are the following: 1) Improvement and development: 3D-EM improves existing techniques, and also de-

velops novel techniques necessary for 3D visualization of macromolecules and their functions within cells.

2) Provision of training: The European Molecular Biology Organization (EMBO) annu-ally offers a continually oversubscribed training course on cryo-EM. A novel course programme has been established in close collaboration with EMBO. 3D-EM experts train advanced students and scientists in specific EM techniques, data analysis and image processing. The courses provide hands-on training, as well as lectures and seminars concerning the theoretical background of EM methods. Basic skills in state-of-the-art EM technologies will increase, since new knowledge is included in the ad-vanced training courses. The training programme, access to central registration and further details are available on the Internet (http://www.3dem-noe-training.org/).


3D-EM

Project Type:Network of ExcellenceContract number:LSHG-CT-2004-502828Starting date:1st March 2004 Duration:60 monthsEC Funding:

10 000 000

www.3dem-noe.org


http://www.3dem-noe-training.org

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3) Exchange of knowledge: Expertise gained in EM techniques, especially the inno-vative cryo-electron microscopy of vitreous sections (CEMOVIS), is disseminated to scientists both within and external to 3D-EM. In addition to the course programme, workshops have also been organised, intended to promote discussion and the aware-ness of new developments in electron microscopy.

4) Standardisation: the processing and comparison of data obtained with the different EM methods are extremely time-consuming. Standards for 3D image reconstruction must be identified, developed and tested. An EM data base and an optimal stand-ard software platform (based on these standards), will be established. User-friendly interfaces, operating between electron crystallography, single particle analysis and electron tomography, will reduce processing time. Knowledge and excellence are spread via collaborations, training courses, scientific meetings and publications.

The results achieved by 3D-EM have been presented at numerous conferences and work-shops. Furthermore, they have been published in over 65 scientific articles in peer-reviewed journals, and are listed in detail on the project web page, mentioned above.

Expected Results:Towards the end of its second year, 3D-EM was reviewed by external experts. These advi-sors rated the overall project performance as excellent. Over the full project duration, the following results are expected:

1) Improvement of methods and technologies related to electron microscopy, e.g. speci-men preparation and image processing

2) Integration of software packages and tools with instrumentation? User-friendly, uni-versal interfaces between electron crystallography, single particle analysis and elec-tron tomography

3) Development and use of standards for 3D image reconstruction Expansion of the network in the direction of Eastern Europe

Setting 3D-EM guidelines for software development and data exchange some highlights of the current results are:

240 participants, beginners and advanced, were trained in 21 courses

Scientists from several European labs have already been trained in the technology devel-oped by CEMOVIS. The outstanding results achieved thus far include the development of several software tools, packages and algorithms, such as the TOM Toolbox and the IPLT (Image processing library & toolbox) programme.


New Electron Microscopy Approaches for Studying Protein Complexes

and Cellular Supramolecular Architecture


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Potential Impact:In the field of electron microscopic technologies, 3D-EM provides a platform for the joint solution of issues. A standardised comparison and exchange of experimental data obtained with differing EM methods, will facilitate these efforts and contribute to the understanding of cellular function in molecular detail.

The close cooperation of individuals, respectively grounded in academic and applied re-search, guarantees an immediate transfer of knowledge and experience from the field of basic research to industrial application. In addition, the added benefit of improved tools or instrumentation, suitable for research requirements, strengthens the market position of European companies.

A growing market for structural biology in Europe generates novel employment opportuni-ties in this sector, associated with the need for experienced personnel. In collaboration with the European Molecular Biology Organization (EMBO), 3D-EM created a novel training programme covering specific aspects of electron microscopy, applicable to both beginners and experienced scientists.

3D-EM trains and supports groups with experience in electron microscopy to bring them to the state-of-the-art in terms of methodology and equipment. This strategy will generate a network of electron microscopy centres across Europe. The network defines future needs for research, standardisation and instrumentation.

Keywords:3D electron microscopy, protein complexes, cryoelectron microscopy, electron tomography, single particle, electron microscopy techniques, imaging, structural biology

Training Program WP 1

Setting 3D-EM GuidelinesWPs: 2, 3

Co-ordinationand NetworkManagement

WP 12

Electron TomographyWPs: 4, 5, 6, 8, 13

ElectronCrystallography

WP 7

Single ParticleAnalysis

WPs: 9, 10, 11


3D-EM


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Project Coordinator:Prof. Andreas EngelUniversity of BaselM.E. Miller Institute for Structural BiologyBiozentrumKlingelbergstrasse 70CH-4056 Basel, [email protected]

Project Manager:Dr. Urs MüllerUniversity of BaselM.E. Miller Institute for Structural BiologyBiozentrumKlingelbergstrasse 70CH-4056 Basel, [email protected]

Prof. Wolfgang BaumeisterMax-Planck Institute of BiochemistryDepartment of Molecular Structural Biology (MPIB)Martinsried, Germany

Prof. Werner KühlbrandtMax-Planck Institute of BiophysicsFrankfurt am Main, Germany

Prof. Jose CarrascosaConsejo Superior de Investigaciones CientificasCentro Nacional de Biotecnologia (CNB)Madrid, Spain

Dr. Kim HenrickEuropean Molecular Biology Laboratory (EMBL)European BioInformatics Institute (EBI)Hinxton, UK

Dr. Achilleas FrangakisEuropean Molecular Biology Laboratory (EMBL)Heidelberg, Germany

Dr. Werner HaxFEI CompanyEindhoven, The Netherlands

Prof. Bertil Daneholt, Prof. Hans Hebert,Prof. Oleg Shupliakov, Prof. Ulf SkoglundKarolinska InstitutetMedical Nobel InstituteStockholm, Sweden

Prof. Nicolas Boisset † , Dr. Eric Larquet Centre National de la Recherche Scientifique (CNRS)Paris, France

Prof. Arie VerkleijUniversity of UtrechtFaculty of BiologyUtrecht, The Netherlands

Prof. Stephen FullerUniversity of OxfordDivision of Structural BiologyOxford, UK

Prof. Marin van HeelImperial CollegeCentre for Biomolecular Electron MicroscopyCentre for Structural BiologyLondon, UK

Prof. Helen SaibilBirkbeck University of LondonDepartment of CrystallographyLondon, UK

Prof. Jacques DubochetUniversity of LausanneLaboratory of Ultrastructural AnalysisLausanne, Switzerland

Dr. Nicolas Boisset † , Dr. Slavica JonicUniversité Pierre et Marie CurieParis, France

Prof. A.J. (Bram) KosterLeiden University Medical CenterDepartment of Molecular Cell BiologyElectron Microscopy DivisionLeiden, The Netherlands

Prof. Christian SpahnCharité – Universitätsmedizin BerlinInstitut für Medizinische Physikund BiophysikBerlin, Germany

Dr. Sergio Marco Centre de Recherche Laboratoire Raymond LatarjetInstitut CurieCentre Universitaire d’Orsay Orsay, France


New Electron Microscopy Approaches for Studying Protein Complexes and Cellular Supramolecular Architecture

Partners




174

State-of-the-Art: Deciphering the information on genome sequences in terms of the biological function of genes and proteins is a major challenge of the post-genomic era. Most function assignments for new-ly sequenced genomes are performed using bioinformatics tools that infer the function of a gene on the basis of sequence similarity with other genes of known function. This approach is, however, error-prone. Continuing to use it without clearly defining the limits of its applicability would lead to an unmanageable propagation of errors. On the other hand, various novel bodies of data are being generated. These provide information on the physical and functional interactions between genes and proteins, and on whole networks and processes. In parallel, structural genomics efforts are providing much better coverage of proteins structures and in-teractions. This novel data offers an unprecedented opportunity for incorporating higher-level functional features into the annotation pipeline, and the GeneFun project addressed these important aspects. To limit error propagation, criteria will be developed for evaluating the reli-ability of the annotations currently available in databases, and derived reliability scores will be incorporated into standard annotation pipelines. To incorporate higher-level features into functional annotations, the project will combine sequence and structure information in order to identify non-linear functional features (eg. interaction sites), and will also integrate avail-able and newly developed methods for inferring function from information on protein domain architecture, protein-protein interaction, genomic context, etc.

Scientific/Technological Objectives: The main objective of the GeneFun project is to develop improved methods for reliably assign-ing function to genes. To that end it will pursue the following specific scientific and technical objectives: (1) Quantifying error rates (error baseline) for classical sequence similarity-based functional annotations from the analysis of meaningful descriptions of protein families and sub-families, and functional annotations currently available; (2) Developing automatic pro-cedures for deriving detailed functional descriptors for individual protein families by map-ping sequence family information onto the experimental or modelled 3D structure, then using this information to improve functional annotation from sequence; (3) Combining objective 1 and objective 2, in order to enable more efficient and reliable prediction of function from sequence; (4) Exploiting information on domain architecture to infer context-based function-al properties, including domain and protein interactions; (5) Developing new methods for identifying protein-protein interactions by combining information on sequence families, 3D structure, domain and genome architecture; (6) Benchmarking existing and newly developed methods for the prediction of interactions, which use context-based approaches, combine information on sequences families and 3D structure, and analyse various data sets on protein-protein interactions (obtained through experiments and automatic analyses of published lit-erature); (7) Integrating sequence similarity-based and context-based prediction methods, and applying them to verify and improve available annotations of eukaryotic genes and to infer function for the still important number of non-annotated regions of these genes; (8) Performing experimental validation of the predicted function and other related features, for a selected set of proteins of strategic importance for evaluating the performance of the various function prediction algorithms. Methods and data produced in this project will be made available to the scientific community through the Internet. This will include a web server for assessing ho-mology-based annotation reliability, a downloadable protocol for performing the assessment, and a comprehensive set of protein family trees with structure-annotated functional groups. Other tools will include an automated system for predicting enzyme function, sites for specific high affinity recognition, and interaction partners for peptide-binding modules.

Expected Results: The expected results of the GeneFun project are as follows: (1) improved procedures for inferring function on the basis of sequence similarity; (2) a set of procedures for predicting


GeneFunwww.genefun.org

Project Type:Specific Targeted Research projectContract number:LSHG-CT-2004-503567Starting date:1st March 2004Duration:52 monthsEC Funding:

1 500 000


http://www.genefun.org

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non-linear functional features from sequence and 3D structure in a more automated way; (3) benchmarked procedures for predicting context-based functional features. Major efforts will be devoted to devising protocols that optimally combine the results from several methods. In particular, web-based servers for the individual and combined procedures will be devel-oped and made available to the scientific community. The community will be introduced to these new tools through open workshops and training sessions.

Potential Impact: The developed function prediction methods should make a significant contribution towards improving the in silico annotation of gene function, and thereby have an important impact on the entire life-science sector, which heavily depends on these annotations.

Keywords: Function prediction, protein structure, protein-protein interactions, interaction networks, structural genomics

Project Coordinator:Prof. Shoshana WodakUniversité Libre de BruxellesService de Conformation de MacromoleculesBiolgiques et BioinformatiqueBiologie MoleculaireAvenue F Roosevelt CP 194/6 B-1050 Brussels, [email protected]

Dr. Alfonso ValenciaCentro Nacional de InvestigacionesOncologicasMadrid, Spain

Dr. Arne ElofssonStockholm UniversityStockholm Bioinformatics CenterStockholm, Sweden

Prof Peer BorkEuropean Molecular Biology Laboratory (EMBL)Heidelberg OutstationHeidelberg, Germany

Dr. Chen Ceasar. Prof. Daniel FischerBen-Gurion UniversityDepartment of Computer ScienceBeer Sheva, Israel

Dr. Leszek RychlewskiBioInfoBank InstitutePoznan, Poland

Prof. Cheryl ArrowsmithOntario Cancer InstituteUniversity Health NetworkToronto, Canada

Dr. Christian Blaschke Alma Bioinformatics SlMadrid, Spain

PartnersProf. Luis SerranoCenter for Genomic Regulation (CRG)Systems Biology LaboratoryBarcelona, Spain


Prediction of gene function



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State-of-the-Art:E-MeP’s research platform focuses on developing and implementing new technologies to solve the bottlenecks that preclude the determination, at high throughput, of high-resolution structures of membrane proteins and membrane protein complexes. This has been achieved by integrating the activities of many of the world leaders in membrane protein structural biology. The E-MeP consortium focuses on developing methods and exchanges laboratory and in silico tools, with the aim of solving the structures of membrane proteins, which com-prise more than 30% of known proteomes.

Specifically, the heterologous production, purification and crystallisation of a library of bioinformatically-selected membrane proteins are being streamlined by elucidating the pa-rameters responsible for success and failure at each of these key stages. In the process, new technologies are being developed and commercialised, to overcome existing bottlenecks peculiar to membrane protein structural genomics, which cannot be solved using existing methods. A mobilisation of European expertise to address this timely issue, will ultimately contribute to understanding membrane protein-related human diseases.

Scientific/Technological Objectives:E-MeP has several scientific objectives, including the following:

-taining milligram quantities;

pertinent data.

Crystal Structure of a Divalent Metal Ion Transporter CorA at 2.9

Angstrom Resolution.


E-MePwww.e-mep.org

Project Type:Integrated ProjectContract number:LSHG-CT-2004-504601Starting date:1st May 2004Duration:60 monthsEC Funding:

10 347 066


http://www.e-mep.org

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There are also several specific technological objectives, namely:

structural genomics platform. Overall, the aim is to build a European Membrane Pro-tein Structural Genomics Research Area.

Expected Results: The resolution of membrane protein (MP) structures is important for health. The findings of E-MeP will contribute to scientific communities’ understanding of key biological processes, and will also serve as templates for structure-based drug design.

Potential Impact: An increase in the number of membrane protein (MP) structures will help to understand many basic phenomena underlying the cellular functions essential to human health, and may lead

Structure of a LTC4 synthase; 2.15 Å. Published in Nature, 2007, 448: 613-616


The European Membrane Protein Consortium


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PartnersProject Coordinator: Dr. Roslyn BillAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham B4 7ET, [email protected]

Project Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, BA 7ET, [email protected]

Prof. So Iwata, Prof. Naomi ChayenImperial College of Science, Technology and MedicineDivision of Molecular Biosciencesand Division of Biomedical Sciences – Biological Structure and Function SectionLondon, UK

Prof. Peter Henderson, Prof. John FindlayThe University of LeedsAstbury Centre for Structural – Molecular Biology and Faculty of Biological Sciences Institute of Membrane and Systems BiologyLeeds, UK

Sir John Walker, Dr. Edmund R. S. KunjiMedical Research CouncilDunn Human Nutrition UnitCambridge, UK

Dr. Franc PattusCentre Européen de Recherche en Biologieet Médicine (CERBM)Groupement d’intérêt économiqueIllkirch, France

directly to products with both societal impact and commercial value. E-MeP will contribute to important social requirements related to health, because structural genomics, together with functional genomics, transcriptomics and proteomics, will open up new routes to fight disease and will explore new dimensions in biotechnology and bio-nanotechnology.

Keywords:membrane proteins, protein production, X-ray crystallography, structure determination, 3D structure, structural genomics


E-MeP




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Prof. Christian CambillauUniversité de la Mediterranée Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS-Université Aix-Marseille I & IIMarseille, France

Dr. Etienne L’HermiteBioXtal SAMundolsheim, France

Prof. Hartmut MichelMax-Planck-Institut für BiophysikMolecular Membrane BiologyFrankfurt am Main, Germany

Prof. Richard CogdellUniversity of GlasgowInstitute of Biomedical & Life Sciences - Division of Biochemistry & Molecular BiologyGlasgow, UK

Prof. Paula BoothUniversity of BristolDepartment of BiochemistryBristol, UK

Dr. Nicolas Le NovèreEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Prof. Horst VogelEcole Polytechnique Fédérale de LausanneLaboratoire de Chimie Physique des Polymèreset Membranes (LCPPM)Institut des Sciences et Ingénierie Chimiques (ISIC)Lausanne, Switzerland

Prof. Arnold Driessen, Prof. Bert PoolmanUniversity of GroningenGroningen Biomolecular Sciences and Biotechnology InstituteKerklaan, The Netherlands

Prof. Rainer RudolphMartin-Luther-Universität Halle-WittenbergInstitut fur BiotechnologieHalle, Germany

Prof. Wim de GripStichting Katolieke UniversiteitUniversity Medical Centre NijmegenNijmegen, The Netherlands

Prof. Lars-Oliver EssenPhillipps-Universität Marburg Department of ChemistryMarburg, Germany

Prof. Pär NordlundKarolinska InstituteMedical Biochemistry and BiophysicsStockholm, Sweden

Prof. Richard NeutzeGothenburg UniversityDepartment of ChemistryBiochemistry & BiophysicsGothenburg, Sweden


The European Membrane Protein Consortium


180

State-of-the-Art:We will develop and improve tools and approaches to facilitate the generation of new knowledge in functional and structural genomics of viral RNAs. The project exploits avail-able RNA sequence data but will also expand our knowledge of viral RNA sequence ele-ments and their variations.The biomedical importance of RNA as a research target is stressed by the fact that viral infections are global public health problems. The outcomes of the project can initiate the de-velopment of novel drugs that target viral RNA molecules and thus have strong implications for public health. The innovative tools developed will open the way for efficient analysis of a wide range of RNA-based processes extending far beyond the analysis of viral RNAs.

Scientific/Technological Objectives:RNA is a central molecule in all living organisms. They can adopt a wide variety of confor-mations ranging from single-stranded to complex tertiary structures tightly associated with their functions. To understand the function of RNAs, and to act on these functions with small molecules, it is essential to expand our knowledge of the structure of these molecules and of their interactions. A multidisciplinary research approach is taken in the project to address this need, by integrating the research facilities of a number of leading European labs as well as an SME. The main objectives of the consortium are:1. to develop new methods and tools for rapid and efficient structure determination of (large)

RNA and (large) RNA-protein complexes and RNA ligand screening, including:a) new and streamlined methods for site-specific and segmental 2H, 13C, 15N isotope

labelling of RNAs via in-vitro and/or in-vivo methodsb) to establish, experimentally and theoretically, chemical shift-structure relationships

(CSRs) for 1H, 13C, 15N, 31P of RNAsc) to implement these (CSRs) and other easily accessible NMR parameters, such as

RDCs and CSAs, in efficient NMR structure calculation protocolsd) to implement scanning probe microscopy (SPM) tools for morphology and interactions.

2. to apply these methods on key viral RNA targets (from HBV, HCV and HIV), which are currently considered major public health threats. The efforts will be three-fold: a) characterise the RNA sequences involvedb) perform structural analysis on key RNA elements and/or reconstituted viral RNA and

RNA-protein assemblies either by NMR or SPM for the larger objectsc) produce and identify new antiviral compounds (small molecules, siRNA, modified

oligonucleotides) capable of binding these RNAs. These compounds could provide the basis for developing new viral agents.

Expected Results: Novel tools will be developed and implemented, which will provide improved methods for structural analysis of RNA and RNA-protein complexes. The molecular details obtained by applying these tools to viral and other important RNA molecules will provide a basis for the identification and screening of small molecule inhibitors that target key RNA structures. The unique combination of technological platforms available within the consortium will add new fundamental knowledge on HCV translation and HBV replication by generating novel three-dimensional data on the corresponding RNAs and RNA-protein complexes. This will provide an opportunity to correlate RNA 3D structure with function, and to make the HCV, HBV and HIV RNA elements and their protein complexes new targets for the rational design of drug leads. The results of the project will allow a comparative analysis of small compounds targeting viral RNA elements and antiviral RNAs.


FSG-V-RNAwww.fsgvrna.nmr.ru.nl

Project Type:Specific Targeted Research projectContract number:LSHG-CT-2004-503455Starting date:1st July 2004Duration:51 monthsEC Funding:

2 400 000


http://www.fsgvrna.nmr.ru.nl

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Potential Impact:New and optimised research tools for the structure/function analysis of RNA and RNA-based processes will be generated. The potential of these tools in correlating structure and function of RNA molecules and the identification of inhibitors will enhance basic research on RNA splicing, translation and the recently discovered essential mechanisms for the post-transcriptional regulation of gene expression that involve non-coding RNAs. These tools are also expected to enhance our understanding of viral RNAs significantly and to further the development of new antiviral drugs. The consortium allows the setting up a multidisciplinary research-project that addresses biomedical questions in a unique way that extends beyond current research programmes.

Keywords: labelling, synthesis, NMR, screening, function, RNA structure, ge-nomics, RNA viruses, RNA, RNAi, HBV, HIV, HCV

Project Coordinator: Prof. Sybren Wijmenga Radboud University NijmegenIMM/Faculty of Science Mathematics and Informatics Toemooiveld 1 6525 ED Nijmegen, The Netherlands [email protected]

Project Manager:Susanna BicknellRadboud University NijmegenFaculty of ScienceFinance and Economic [email protected]

Prof. Dr. Michael SattlerHelmholtz Zentrum MünchenGerman Research Center for Environmental HealthAnd Lehrstuhl Biomolekulare NMR-SpektroskopieDepartment ChemieTechnische Universität MünchenGarching, Germany

Prof. Frédéric Dardel Centre National de la Recherche Scientifique (CNRS)Laboratory of Crystallography and Biological NMRParis, France

Prof. Vladimir SklenarMasaryk UniversityNational Center for Biomolecular ResearchBrno, Czech Republic

Prof. Michael NassalUniversitätsklinikum FreiburgDepartment of Internal Medicine Laboratory of Molecular BiologyUniversity Hospital FreiburgFreiburg, Germany

PartnersDr. Karin Kidd-LjunggrenLund UniversityDepartment of Medical Microbiology,Dermatology and Infectious DiseasesLund, Sweden

Dr. Richard BlaauwChiralix B.V.Nijmegen, The Netherlands


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www.vizier-europe.org

State-of-the-Art: This project aims to have a significant impact on the identification of potential new drug targets against RNA viruses through comprehensive structural characterisation of a diverse set of viruses. RNA viruses include more than 350 different major human pathogens and most of the etiological agents of emerging diseases: viruses of gastroenteritis (1 million deaths annually), measles (45 million cases and 0.6 million deaths annually), influenza (100 million cases annually), dengue fever (300 million cases annually), enteroviruses and encephalitis (several million cases of meningitis annually), and hepatitis C virus (170 million infected people in the world).

The SARS outbreak has dramatically demonstrated how high the economic cost of an epi-demic caused by an emerging virus could be. This possibility is growing every day as many governments are being forced to make costly arrangements to cope with the threat of bio-terrorism, which lists some deadly RNA viruses in its arsenal. To meet these challenges, science needs to look for new therapeutic and prophylactic substances active against RNA viruses since those currently available are scarce and of low potency. The common strate-gies used for the development of antiviral drugs are mainly based on the knowledge ac-cumulated through studies of virus genetics and structure. Yet, genomic and structural char-acterisation of RNA viruses was not accepted as a priority until very recently. The VIZIER project proposes to fill the existing gap between the necessary scientific characterisation of emerging viruses and pre-clinical drug design.

Scientific/Technological Objectives: To address society’s needs, scientists need to anticipate potential threats and be ready should they arise. The participants of the VIZIER project have created a team that brings together the leading authorities on RNA viruses in the EU and other countries as well as many leading European structural biologists. This team includes three partners with P4 facilities, as well as leaders in the field of structural genomics. The development of proto-cols for high-throughput (HTP) protein production means that a concerted programme of structure determination is now appropriate and feasible. The VIZIER consortium will char-acterise RNA viruses that do not include a DNA stage in their replicative cycle. These virus classes employ profoundly different replicative mechanisms driven by poorly characterised replication machineries. Although virus-specific, they are the most conserved and essential viral components and thus the most attractive targets for antiviral therapy. In the framework of this project the core enzymes/proteins of the replication machinery, carefully selected among 300 different RNA viruses, including strains of medical interest, will be character-ised. One unique feature of VIZIER, compared to other structural genomics projects, is the integration of major structural effort within a broad multidisciplinary study, having virology upstream and target validation (candidate drug design) downstream. As a result, the im-plementation plan of the VIZIER project is structured into five interacting scientific sections: (1) bioinformatics, for genome annotation, target selection and data integration (2) virus production and genome sequencing (3) HTP protein production (4) HTP crystallisation and structural determination (5) target validation to assess the function of enzymes and design strategies for virus inhibition (6) training, implementation and dissemination. This organisa-tion will allow in record time the full characterisation of a viral target that can quickly be used to design drugs, either by the pharmaceutical industry through the VIZIER industrial platform or by any research and development institution.

Crystal structure of the 3C proteinase of coxsackievirus B3


VIZIER

Project Type:Integrated ProjectContract number:LSHG-CT-2004-511960Starting date:1st November 2004Duration:48 monthsEC Funding:

12 905 986


http://www.vizier-europe.org

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Expected Results: VIZIER will produce an unprecedented wealth of data on replicases of RNA viruses with a window into the antiviral drug development. A representative set of RNA-based viruses that belong to three major classes which are profoundly different in their replicative strategies, will be characterised by a concerted and multidisciplinary effort unparalleled to date. At the end of this programme, the percentage of sequenced genomes of RNA virus species that infect vertebrates will virtually double from 30% to 55%. As a case example, the genomic characterisation of Flavivirus (ssRNA+) and Arenavirus (ssRNA-) genera, which include a large number of human pathogens, will be systematically executed. A dramatic advance is expected in the number and diversity of 3D structures of the replicative subunits, now in the one-digit range. VIZIER will aim to identify lead molecules inhibiting the replicative enzymes, but will not enter into the broad field of drug development. Offers of cooperation will be made on a contractual basis to the pharmaceutical and biotechnology industries for further drug development, and through the VIZIER industrial platform, which connects upfront scientific results to the pharmaceutical industry.

Potential Impact: With no equivalent integrated programme in the world, the VIZIER project will undoubt-edly have a profound impact on the field of structural genomics of emerging viruses. In particular, it is expected that VIZIER will contribute very significantly to the sequencing of new viruses (viral genomics) as well as to the deposition of new crystal structures of viral proteins in the Protein Data Bank. These viral proteins can then be considered as targets for drug design. There is expected to be considerable scientific impact on drug design through concepts and methods implemented up to the design stage. Indeed, current drug discov-ery still often relies on screening compounds in a blind manner. Thousands or millions of compounds are screened on infected cells or purified enzymes, and ‘hits’ are selected. This is followed by confirmation of the inhibitor activity and basic toxicology studies, which is a frequently tedious and uncertain phase for a project. It is widely believed that structural biology is capable of speeding up the whole process. HTP crystallography, coupled with a strong validation section such as that proposed in VIZIER, will undoubtedly reinforce this trend by leading the field. Indeed, the concept of finding a drug and its target together with the putative bottlenecks in further improvement can prove to be scientifically challenging, innovative, and promising.

VIZIER will develop new products, technologies and strategies. The products are RNA virus genomic sequences, soluble viral protein domains, their 3D structures, assigned protein functions, and inhibitors or ligands for selected protein targets (drug leads). All these prod-ucts will have a substantial impact on our (currently limited) understanding of the RNA viral replication machinery. They will also identify entirely new targets for the development of specific drugs, with a high level of detail. Collectively such information is seen as being of strong strategic value, not only for the health issues described, but also for the development of industrial enterprises. Although diverse DNA-based cellular and viral parasites are also responsible for a large fraction of human infections, none of them are so poorly controlled by drugs as the RNA viruses. Consequently, drug development against RNA viruses, the ultimate goal of the VIZIER project, is becoming a top priority for global health-care pro-grammes.


Comparative structural genomics on viral enzymes involved in replication


184

Keywords: RNA viruses, genomics, structural genomics, antiviral drugs, crys-tal structure, bioinformatics, protein production, high-throughput, screening

PartnersProject Coordinator:Dr. Bruno CanardUniversité de la MéditerranéeCentre National de la Recherche Scientifique (CNRS)Laboratoire Architecture et Fonction desMacromolecules Biologiques UMR 6098Marseille, [email protected]

Dr. Andrei M LeontovichMoscow State UniversityA N Belozersky Institute of Physico-Chemical BiologyDepartment of Mathematical Methods in BiologyGenebee GroupMoscow, Russia

Prof. Miguel Coll Consejo Superior De Investigaciones CientificasInstituto De Biologia Molecular De BarcelonaMadrid, Spain

Prof. Johan Neyts Katholieke Unversiteit LeuvenDepartment of Microbiology and Immunology Division of Virology and ChemotherapyLeuven, Belgium

Dr. Etienne L’HermiteBioXtal SAMundolsheim, France

3D Structure Drug-design


VIZIER



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Dr. Paul TuckerEuropean Molecular Biology Laboratory (EMBL)Hamburg OutstationHamburg, Germany

Dr. Segolene Arnoux Alma Consulting Group SasInnovation DepartmentHoulbec Cocherel, France

Dr. Herve Bourhy Institut PasteurLaboratoire de la RageParis, France

Dr. Gerard Bricogne, Global Phasing LtdCambridge, UK

Prof. Dave Stuart University of OxfordWellcome Trust Centre for Human GeneticsDivision of Structural Biology Oxford, UK

Prof. Martino Bolognesi National Institute for the Physics of Matter - GenovaUdr GenovaGenoa, Italy

Prof. Andrea MatteviUniversity of PaviaDepartment of Genetics and MicrobiologyLaboratory of BiocrystallographyPavia, Italy

Prof. Alwyn T. Jones Uppsala UniversitetUppsala, Sweden

Dr. Alexander Gorbalenya Leiden University Medical CenterDepartment of Medical MicrobiologyLeiden, The Netherlands

Prof. Ernest GouldNatural Environment Research CouncilCEH OxfordPolaris HouseSwindon, UK

Dr. Helene Norder Swedish Institute for Infectious Disease ControlVirological Department, Hepatitis Section Solna, Sweden

Dr. Boris KlempaSlovak Academy of SciencesInstitute Of ZoologyBratislava, Slovakia

Dr. Jacques Rohayem Technische Universität DresdenInstitut für Virologie - The Calcilab Medical Faculty Carl Gustav CarusDresden, Germany

Prof. Rolf Hilgenfeld Universität LübeckInstitute of BiochemistryLübeck, Germany

Prof. Paolo La Colla Università Degli Studi di CagliariDipartimento di Scienze E Tecnologie BiomedicheCagliari, Italy

Prof. Par Nordlund Stockholm UniversityDepartment of Biochemistry and Biophysics Stockholm, Sweden

Dr. Eric Leroy, Dr. Jean Paul GonzalesInstitut de recherche pour le développementParis, France

Dr. Stephan GüntherBernhard-Nocht-Institute (BNI)Centers for Disease Control and PreventionHamburg, Germany

Dr. Gerhard PuerstingerUniversität InnsbruckInnrain 52aInstitut für PharmazieInnsbruck, Austria


Comparative structural genomics on viral enzymes involved in replication


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State-of-the-Art:To gain biological function, polypeptide chains generally need to fold into specific 3D structures – their native states. Aberrant folding of proteins can lead to a range of other scenarios, including the development of highly organised and intractable aggregates that are deposited inside or outside cells. Such misfolding events are at the origins of a range of neurological and systemic diseases that increasingly compromise the quality and ex-pectancy of life and the health resources of advanced societies. The focus of this applica-tion is the development of novel methods to study the structural states of proteins that are particularly relevant to understanding protein misfolding and aggregation. In most of these states, polypeptide chains acquire structures that differ substantially from those of the native proteins, which are accessible from conventional approaches of structural biology or from structural genomics procedures.

Scientific/Technological Objectives:In this STREP, a range of complementary NMR approaches will be developed. These ap-proaches include a variety of NMR techniques, which will be coupled with novel computa-tional approaches able to define even the disorganised ensembles characteristic of some of the most interesting and biologically relevant species. These techniques will then be applied to representative examples of the various types of proteins that are associated with misfold-ing diseases. These range from native unfolded species (such as a-synuclein associated with Parkinson’s disease) and partially unfolded intermediates (such as forms of superoxide dis-mutase associated with motor neuron disease), to the precursors of aggregation prone frag-ments (such as the Alzheimer precursor protein) and the prion proteins, which are uniquely associated with transmissible conditions. One of the major aims of this project is to provide a novel unified view of the conformational behaviour of protein molecules, which will have a broad significance for understanding important aspects of functional genomics, includ-ing the fundamental links between genetic mutations and disease, and the mechanisms by which normally soluble proteins can sporadically misfold, giving rise to a wide range of disorders associated with diet, medical and agricultural practices and ageing.NMR is able to provide both dynamic and structural information about proteins in a variety of different states at atomic resolution. It has the potential for probing residual structure, the size of aggregating molecules and variation in the internal dynamical properties based on diffusion-weighted NMR spectroscopy, heteronuclear relaxation measurements, paramag-netic enhancement of relaxation induced by paramagnetic spin labels, and residual dipolar couplings.

Expected Results: Fundamental Research, Structural Studies:

1) Structure of protein-folding intermediates2) Time course of the folding process3) Structure of protein aggregates4) New technologies to characterise protein folding and aggregation at atomic resolution5) Common factors underlying the development of protein-folding diseases.

Potential Impact:By generating structural information about prefibrillar states that are currently assumed to be the most toxic states of protein folding diseases, this STREP research project would help to develop pharmaceutical products against some of the most debilitating conditions in mod-


UPMANhttp://schwalbe.org.chemie.uni-frankfurt.de/upman

Project Type:Specific Targeted Research projectContract number:LSHG-CT-2004-512052Starting date:1st November 2004Duration:42 monthsEC Funding:

1 900 000


http://schwalbe.org.chemie.uni-frankfurt.de/upman

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ern society. However, in contrast to many other major diseases, the fundamental mechanism of protein misfolding and aggregation is less well studied. Therefore, studies aiming at providing a structural basis for protein misfolding and aggregation are not only at the forefront of innovative research but are also important assets for the Life Science and Health priority area of the European Commission.

Keywords: mutation genetics, protein deposition disorders, molecular evolution

The different states a protein molecule can attain

Project Coordinator: Prof. Harald SchwalbeJohann Wolfgang Goethe-UniversitätCenter for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry and Chemical BiologyMarie-Curie-Atr. 1160439 Frankfurt am Main, [email protected]

Prof. Lucia BanciUniversity of FlorencePolo ScientificoCentro Risonanze Magnetiche (CERM)Sesto Fiorentino, Italy

Prof. Rolf BoelensUtrecht UniversityBijvoet Center for Biomolecular ResearchNMR Spectroscopy Research GroupUtrecht, The Netherlands

Prof. Chris DobsonUniversity of CambridgeThe University Chemical LaboratoryCambridge, UK

Prof. Astrid GräslundStockholm UniversityThe Arrhenius Laboratories for Natural SciencesDepartment of Biochemistry and BiophysicsStockholm, Sweden

Prof. Flemming Martin PoulsenUniversity of CopenhagenDepartment of Molecular BiologyStructural Biology and NMR LaboratoryCopenhagen, Denmark

PartnersDr. Ago SamosonNational Institute of ChemicalPhysics and BiophysicsTallinn, Estonia

Prof. Kurt WüthrichETH ZurichInstitute of MolecularBiology and BiophysicsZurich, Switzerland

Dr. Jesús ZurdoZyentia LtdBabraham Research CampusCambridge, UK


Understanding Protein Misfolding and Aggregation by NMR



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State-of-the-Art:The instruments for drug discovery include high-throughput synthesis and subsequent screen-ing, biological assays, molecular biology, computational modelling, electron microscopy, X-ray crystallography, and NMR spectroscopy. Only NMR and X-ray diffraction provide high-resolution information about the protein-ligand interactions at atomic resolution.

While the technology for high-throughput X-ray crystallography of protein-ligand complexes has been optimised such that it is now routinely used in all major pharmaceutical compa-nies, this is not the case for NMR spectroscopy, despite its tremendous potential, relative to and complementary to X-ray crystallography. NMR can provide both structural and dy-namic information on the protein-ligand complex at atomic resolution, information that is highly desirable for efficient drug design. Potentially, NMR can provide such information very rapidly and without the constraints of co-crystallization.

Scientific/Technological Objectives:This structure-based drug design will use cutting-edge nuclear magnetic resonance (NMR) techniques. The NDDP project will speed up drug design efforts for typical drug targets and will shorten the lead time for new drugs.

Fast, reliable and robust NMR techniques will be developed by the team, for an exact structural and dynamic characterisation of drug-receptor interactions at atomic resolution, thus enabling and/or improving the directed development of drugs by demonstrating the maximum desired interaction characteristics in a relatively short time.

Protocols for obtaining the NMR parameters needed for the characterisation of proteins, inhibitors and protein-inhibitor complexes will be developed, starting from known X-ray structures. These parameters will establish a tight connection between NMR and X-ray tech-

nology, enabling the optimal exploitation of the complementary strengths of the two techniques.The NMR technologies to be developed will be complemented by new, fast computer modelling approaches for protein-inhibitor complexes, and also by specific advanced tailored protein expres-sion methods.

X-ray structures of unknown phosphatases will be determined, and these structures will be used as molecular models to provide a highly detailed picture of the proteins in question. Knowing the X-ray structure of the protein target, the NDDP consortium will be able to provide a streamlined protocol for the rapid identification of its protein-lig-and complexes. Such a protocol will boost the impact of NMR technology on structure-based drug discovery. It is the intention of this consortium to provide the means to de-termine protein-ligand complexes, with a turnaround of three structures per high-field instrument per week.

Schematic project presentation. The NDDP project aims to de-

velop an efficient screening pro-tocol using high-field NMR and advanced modelling techniques

that allows to dock lead targets to pharmaceutical receptors such

as phosphatases.


NDDP

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-512077 Starting date:1st November 2004Duration:42 monthsEC Funding:

1 000 000

www.projects.bijvoet-center.nl/nddp


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Expected Results:In order to show the potential impact of NMR techniques on drug development, NMR pro-tocols will be developed and tested using phosphatases, a major class of drug targets for a broad range of medical indications. The majority of cellular functions depend on phos-phorylation by kinases and dephosphorylation by phosphatases. High eukaryotes encode approximately 500 protein kinase and 100 protein phosphatase schemes, corresponding to three percent of their genome. While the importance of kinases in cellular regulation has led to substantial drug design activities, the importance of phosphatases has only recently become appreciated.

Potential Impact:Protein phosphatases regulate insulin signalling, cell growth and the cell cycle. The inhibi-tion of phosphatases is therefore relevant NDDP to the treatment of diabetes, obesity and various types of cancer, for instance. The availability of the human genome provides re-searchers with access to a wide variety of phosphatases, and allows systematic drug design using sophisticated techniques to identify potential inhibitors.

Keywords: NMR spectroscopy, phosphatases, drug design, structural genomics

PartnersProject Coordinator:Prof. Rolf BoelensUtrecht UniversityBijvoet Center for Biomolecular ResearchFaculty of SciencesHeidelberglaan 83584 CS Utrecht, The [email protected]

Prof. Harald SchwalbeJohann Wolfgang Goethe-UniversitätCenter for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry andChemical BiologyFrankfurt am Main, Germany

Prof. Ivano BertiniConsorzio Interuniversitario di Risonanze Magnetichedi Metalloproteine ParamagneticheMagnetic Resonance Centre (CERM)Sesto Fiorentino, Italy

Prof. David BarfordInstitute of Cancer Research Section ofStructural BiologyChester Beatty LaboratoriesLondon, UK

Prof. Egon OgrisUniversity of ViennaDepartment of Medical BiochemistryVienna, Austria

Dr. Wolfgang StirnerSynthacon GmbHFrankfurt am Main, Germany


NMR Tools for Drug Design Validated on Phosphatases



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State-of-the-Art:The major current initiatives in structural biology can be divided into two general types. Re-searchers are channelling their efforts into structural genomics, with the aim of determining structures for all individual protein structures in an organism or system. At the same time, efforts have been intensified to obtain structures of individual large complexes. Despite all the efforts that have been made, an initiative aimed at the structural resolution of all protein complexes in a living organism, has not yet been formulated. Such an initiative, if combined with other EU-oriented initiatives such as BIO-XHIT or SPINE, would give Europe the edge over all non-European competitors.

Recent proteomics studies with the budding yeast Saccharomyces cerevisiae have indicated that the number of complexes that exist, transiently at least, in a cell, has been largely underes-timated. The techniques of isolation and purification that are traditionally used in biochemistry often include many steps, and due to this, the most robust and abundant complexes tend to be selected. This is especially true as many complexes are transient, occurring, for example, only during a certain stage of the cell cycle, or in the presence of a specific co-factor, such as GTP, calcium or phosphorylated subunits. More recent technologies, including the Tandem Affinity Purification (TAP), which has been developed at the EMBL and commercialised by the Euro-pean company Cellzome, allow purification of weaker complexes. There are also a number of means to identify both new components of complexes, or entirely new assemblies, through the use of other sources of protein interaction data (experimental and in silico). Such methods are currently being developed by members of the consortium project 3D Repertoire.

Large-scale proteomic approaches suggest that single proteins interact, on average, with seven other proteins. Even if this is an overestimation, it is clear that many more complex struc-tures are needed, in order to complete the structural view of the cell. Analysis of proteins in the context of complexes has the advantage of revealing new protein folds, to help complete the known repertoire in nature, as well as adding to the set of protein-protein interaction surfaces. The latter advantage cannot emerge from an analysis of single proteins or domains. The aim of 3D-Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate toponomic and dynamic analyses of protein complexes in a cell.

Scientific/Technological Objectives:3D Repertoire will develop novel approaches and technologies for the expression and isolation of protein complexes, as well as for the analysis of their constituents by mass spectrometry. New methods for the production of yeast protein complexes will be tested and validated, to become part of the standard technology for the production of protein complexes from any source of biochemical characterisation and structural analysis. In par-ticular, 3D-Repertoire will focus on the development of combined Free Flow Electrophoresis (FFE) separation techniques, specifically for the separation of protein complexes, and on the development and production of a prototype instrument. The performance of the prototype-instrument and the underlying separation techniques will be tested in the case of the enrich-ment and isolation of complexes of interest. 3D-Repertoire will develop new tools for faster and more accurate image processing in single particle electron cryomicroscopy, which should help to speed up 3D structure determination at increasingly higher resolution.


Project Type:Integrated ProjectContract number:LSHG-CT-2005-512028Starting date:1st February 2005Duration:54 monthsEC Funding:

12 997 641

3D repertoirewww.3drepertoire.org


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The instrumentation of electron microscopes will be improved to allow for automated data collection. Improved sample preparation techniques will also be developed to make even the most difficult complexes accessible to structural studies by cryo-EM. Furthermore, 3D Repertoire will develop X-ray crystallography and electron microscopy technologies, par-ticularly suited for the structural analysis of large macromolecular assemblies. In particular, automated crystal screening procedures to detect optimally diffracting crystals and to im-prove initial crystal diffraction by systematically applying shrinking, annealing or derivatisa-tion protocols will be developed.

Moreover, major technological advances are expected in the automation of single-particle electron microscopy data collection, which will considerably speed up data acquisition. Special emphasis will be placed on the development of technologies at the interface be-tween X-ray crystallography and electron microscopy, where improved docking procedures and validation of these fits are required, to allow such hybrid approaches to become stand-ard procedure in structural biology. In addition, the collaboration of a leading laboratory in electron tomography will stimulate the development of new technologies suited to the analysis of protein complexes within the cell. It will provide a unique platform for the subcel-lular localisation of protein complexes.

Expected Results: The project’s deliverables include a series of high and medium resolution structures of the yeast complexes as well as improved protocols and vectors, for expression and purification of large complexes. Furthermore, the partners aim to develop software to automatically build protein complexes using structural information regarding the complex components, or related proteins as well as innovative software to automatically fit modelled complexes into low resolution structures. Within the 3D Repertoire consortium, partners will create a data-base resource containing structural, functional and experimental information on all protein complexes of S. cerevisiae, as well as on homologues in other organisms. Finally, training in new protein expression, and purification and software technologies, will be provided to researchers both within and outside the 3D-Repertoire consortium.

Potential Impact:The era of post-genomic research is characterised by the necessity to develop high through-put procedures, in order to exploit the vast amount of information generated by the large number of genome projects. This is of particular relevance for the health sector, where the effective identification of functional protein-protein interactions in multiprotein complexes, e.g. in cell signalling, provides the basis for the development of novel diagnostics and therapeutics. Recently, some 50 biologists and officials from government-funding agencies met at the NIH campus in Bethesda, Maryland, to explore the interdisciplinary science and organisation of the emerging field of structural proteomics. This field aims to discover mac-romolecular complexes and characterise their three-dimensional structures and functional mechanisms, in space and time.

The goal of structural proteomics may appear daunting, but the consensus is that the pre-dictable outcome is well worth the effort invested, especially given the importance of mo-lecular machines and functional networks in biology and medicine. Identification of assem-blies and transient complexes combined with their structural and functional characterisation

The RNA Polymerase III: protein purification and composition (left), negatively stained particles (middle) and cryo-EM structure (right).


A Multidisciplinary Approach to Determine the Structures of Protein

Complexes in a Model Organism


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Project Coordinator:Prof. Luis SerranoCentre de Regulació Genòmica (CRG)Systems Biology Laboratory Dr. Aiguader 8808003 Barcelona, [email protected]

Project Manager:Dr. Michela BerteroCentre de Regulació Genòmica (CRG)Dr. Aiguader 8808003 Barcelona, [email protected]

Prof. Alfred Wittinghofer, Dr. Susanne EschenburgMax-Planck Institute for Molecular PhysiologyDortmund, Germany

Prof. Wolfgang Baumeister, Dr. Stephan Nickel,Prof. Elena ContiMax-Planck Institute of BiochemistryAbteilung Molekulare StrukturbiologieMartinsried, Germany

Dr. Holger StarkMax-Planck Institute for Biophysical ChemistryResearch Group 3D Electron Cryo-MicroscopyGoettingen, Germany

Prof. Herman van TilbeurghInstitut de Biochimie et de Biophysique Moléculaire et Cellulaire (IBBMC)Centre National de la Recherche Scientifique (CNRS) UMR8619Université Paris-Sud Orsay, France

Prof. Bertrand SéraphinCentre National de la RechercheScientifique (CNRS)Center for Molecular GeneticsGif-sur-Yvette, France

Prof. Patrick CramerLudwig-Maximilians-Universität MünchenGene Center MunichDepartment of Chemistry and BiochemistryMunich, Germany

Dr. Anastassis Perrakis, Dr. Titia SixmaNetherlands Cancer InstituteMolecular CarcinogenesisAmsterdam, The Netherlands

Dr. Andrea MusacchioEuropean Institute of OncologyMilan, Italy

Dr. Guillermo Montoya, Dr. Jeronimo BravoSpanish National Cancer Research CentreMadrid, Spain

Partners

will allow us to understand, control, design and change the functioning of larger biological systems, and to contribute to drug target discovery, lead discovery, and lead optimisation for treatment of human disease.

To maintain Europe’s international competitiveness in this field, it is essential to promote interdisciplinary cooperation of the continent’s most innovative research centres. Europe playing a leading role in the structure genomics field will also yield economic benefits, since the number of drugs developed or improved using 3D structures is growing every year. In addition, it will allow Europe to be well positioned for the next challenge in biology, namely the quantitative understanding of the cell.

3D Repertoire will contribute to rendering this task feasible, through the establishment of suitable technological platforms. The project’s main contribution comprises large data sets and material for protein complexes, which will be produced for biomedically relevant com-ponents of the cell.

Keywords: protein complexes, 3D-electron microscopy, electron tomography, X-ray crystallography, structural genomics, yeast, bioinformatics


3D repertoire




193

Prof. Helen SaibilBirkbeck College LondonDepartment of CrystallographyBloomsbury Centre for Structural BiologyLondon, UK

Prof. Jose L. CarrascosaCentro Nacional de BiotecnologiaMadrid, Spain

Prof. Miquel CollInstitute for Research in Biomedicine(IRB Barcelona)Barcelona, Spain

Prof. Hanah MargalitThe Hebrew UniversityFaculty of MedicineThe Institute of MicrobiologyJerusalem, Israel

Prof. Carol RobinsonUniversity of CambridgeChurchill CollegeCambridge, UK

Dr. Gordana ApicCambridge Cell Networks LtdSt. John’s Innovation CentreCambridge, UK

Dr. Hervé GinistyGTP TechnologyImmeuble BiostepLabège, France

Dr. Joan AymamiCrystax LtdBarcelona, Spain

Dr. Rob Russell, Dr. Elena Conti, Dr. Bettina Boettcher, Dr. Klaus Scheffzeck, Dr. Dietrich Suck, Dr. Peer Bork, Dr. Anne-Claude Gavin, Dr. Christoph MuellerEuropean MolecularBiology Laboratory (EMBL)Heidelberg OutstationHeidelberg, Germany(*Dr. Sattler moved to GSF as of 01/10/2007)

Dr. Darren HartEuropean MolecularBiology Laboratory (EMBL)Grenoble OutstationGrenoble, France

Dr. Matthias WilmannsEuropean MolecularBiology Laboratory (EMBL)Hamburg OustationHamburg, Germany

Dr. Patrick AloyInstitute for Research inBiomedicineBarcelona, Spain

Dr. Andrzej DziembowskiWarsaw UniversityInstitute of Geneticsand BiotechnologyWarsaw, Poland

Dr. Michael SattlerHelmholtz Zentrum Muenchen (HMGU)Neuherberg, Germany

Dr. Francisco BlancoCentro de Investigación Cooperativa en BiocienciasCICBioGUNEBilbao, Spain


A Multidisciplinary Approach to Determine the Structures of Protein Complexes in a Model Organism


194

State-of-the-Art:The main goal of the project is to perform a thorough assessment of the existing structural genomics (SG) and structural proteomics (SP) projects throughout the world. This will in-clude the assessment of the existing infrastructures in Europe relevant to SG and SP, and their comparison with those active in the rest of the world. The requirements, in terms of thematic areas and infrastructures, will also be evaluated. This SSA will result in staged pub-lications, a complete register of the structural genomics and structural proteomics projects worldwide, and a position paper on strategic plans for a European policy in the area of structural genomics and proteomics.

Scientific/Technological Objectives:The objectives are:

1) an assessment of the existing infrastructures relevant to SG and SP projects in Europe in comparison with the rest of the world, and the evaluation of EU requirements, especially for new EU members

2) an assessment and analysis of existing SG and SP projects at national and EU levels and worldwide, and a comparison with respect to their strategic objectives, organi-sation, budgetary aspects, their outcomes (i.e. structures determined, contribution to data banks, etc.) and their impact on academia and industry

3) an assessment of industrial needs for SG and SP and of their impact on health and the economy in the EU

4) establishing of a database resource to serve as a complete register of structural genomics and structural proteomics projects worldwide

5) drafting a series of staged publications based on the as-sessment and compilation of a position paper that will in-clude an assessment of SG and SP activities in the EU, and a strategic road map to guide future directions of structural genomics and structural proteomics initiatives in Europe.

Expected Results:A database will be established and it will serve as a complete register of the structural genomics/proteomics projects worldwide.A position paper will be compiled which will include an assessment of structural genom-ics/proteomics, and the infrastructures and activities in Europe and the rest of the world. A strategic road map will be prepared to guide future directions of SG and SP initia-tives in the EU.

hAChe-FAS-II

Nuclear pore particle

NMR Structure


FESP

Project Type:Specific Support ActionContract number:LSSG-CT-2005-018750Starting date:1st July 2005Duration:30 monthsEC Funding:

300 000

www.ec-fesp.org


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195

Potential Impact:1) The open discussion that we plan to stimulate and

direct within the SG/SP European community should raise the awareness of structural biology centres among high-throughput SG/SP research-ers in healthcare and academia, and in big phar-macological and biotech companies throughout the EU.

2) The staged documents, based on our assessments and discussions with a wide spectrum of scientists and national scientific officers worldwide, should help the EC in formulating policies for future scientific calls in Life Sciences, in general, and in SG/SP in particular.

3) The position paper will provide guidelines for an overall strategic direction that the EC can consider adopting for future directions for European research in the SG/SP area.

Keywords: structural proteomics, structural genomics, research policies

Project Coordinator: Prof. Joel L. Sussman Weizmann Institute of ScienceDepartment of Structural Biology Herzel Street P.O. Box 26 76100 Rehovot, Israel [email protected]

Project Manager:Bracha VakninWeizmann Institute of ScienceIsrael Structural Proteomics CenterDepartment of Structural Biology 100 Herzel Street P.O. Box 26 76100 Rehovot, [email protected]

Prof. Lucia BanciUniversity of Florence Centro Risonanze Magnetiche (CERM) Sesto Fiorentino, Italy

Prof. Udo HeinemannMax-Delbrück-Center for Molecular Medicine Department of CrystallographyBerlin, Germany

Prof. Gunter SchneiderKarolinska InstitutetDivision of Molecular Structural Biology Department of Medical Biochemistry and BiophysicsStockholm, Sweden

Prof. Wolfgang BaumeisterMax-Planck Institut für BiochemieAbteilung Molekulare StrukturbiologieMartinsried, Germany

Partners


Forum for European Structural Proteomics




196

State-of-the-Art:E-MeP is an EC funded FP6 integrated project. Its research will develop new technologies to solve the bottlenecks that preclude the determination, at high throughput, of high-resolution structures of membrane proteins and their complexes. This will be achieved by integrat-ing the activities of world leaders in membrane protein structural biology. E-MeP-Lab is a proposal for a Specific Support Action to exploit this confluence of talent. For the first time, Europe’s membrane protein structural biology community will converge as teachers and demonstrators in a Master Class and five Advanced Practical Courses in the best equipped laboratories in their fields in Europe. This research field is important because membrane proteins comprise the major target area of study within modern structural genomics. Moreo-ver, the field of membrane protein study involves approximately 70 percent of human pa-tients that qualify for therapeutic intervention.

Scientific/Technological Objectives:E-MeP-Lab’s objectives are to:

1) Increase the pool of appropriately skilled young researchers in membrane protein structural genomics;

2) Provide access for all European researchers to training programmes; 3) Integrate with other Structural Genomics programmes to facilitate a coherent Euro-

pean Structural genomics strategy on membrane and soluble proteins.

Expected Results:In addition to working with researchers from European member states, the project aims to harness the considerable scientific talent in the new Member States to ensure their full participation within the European Structural Genomics community, through the provision of ring-fenced funding. Together with an analysis provided by an expert in gender and mobil-ity issues, this will provide an excellent opportunity to evaluate the potential impact of an increase in scientific mobility and more equal gender participation. Thus, achievement of balanced growth in the wider ERA will be achieved with a particular focus on the transfer of knowledge in the structural genomics of membrane proteins.

E-MeP-Lab Training workshop


E-MeP-Lab

Project Type:Specific Support ActionContract number:LSHG-CT-2005-512011Starting date:1st July 2005Duration:48 monthsEC Funding:

250 000

www.e-mep.org/?rub=lab


http://www.e-mep.org/?rub=lab

197

Project Coordinator:Dr. Roslyn BillAston University Department of Life and Health Sciences Aston TriangleBirmingham, B4 7ET, UK [email protected]

Project Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, [email protected]

Prof. Peter Henderson University of LeedsAstbury Centre for Structural - Molecular BiologyLeeds, UK

Partners

Potential Impact:By providing training to eliminate bottlenecks that preclude the structural determination of membrane proteins and membrane protein complexes to atomic resolution, the E-MeP-Lab project addresses this issue head-on. Intelligent, structure-based drug design will short-cir-cuit current brute force random screening of drugs and will therefore save pharmaceutical companies time and money. Even in the absence of structures, the provision of the skill set to produce functional eukaryotic membrane proteins for targeted drug screening by high-tech SMEs will be an important outcome from E-MeP-Lab. This will give Europe a competitive edge in the pharmaceutical and biotechnology markets.

Keywords: structural proteomics, structural genomics, research policies


E-MeP-Lab Training events in membrane protein structural biology




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State-of-the-Art: Membrane proteins, unlike soluble proteins, are generally not easily amenable to 3D crys-tallization. The most regular organization of a membrane protein amenable to crystallogra-phy is a 2D crystal (2DX). It comprises only a single layer of the regularly packed protein, which is reconstituted in a lipid bilayer. Electrons must be used for the diffraction analyses. The availability of membrane proteins suitable for electron crystallography is of high impor-tance for rational drug design since about 70% of all drug targets are membrane proteins. The potential of this approach has long been recognized, and the first structure of a human channel protein, aquaporin-1, has been solved to a 3.8 Å resolution. An innovative technol-ogy platform for high throughput screening and analysis of native protein complexes and protein crystals by EM would reduce processing time and cost and greatly increase the probability of obtaining high quality 2D crystals of membrane proteins.

Scientific/Technological Objectives: The objective of the HT3DEM project is to develop an automated pipeline for sample prepa-ration and analysis by electron microscopy. The novel hardware and software under devel-opment includes: (1) a 2D crystallisation robot: Membrane protein reconstitution is critically dependent on lipid mixtures, lipid-to-protein ratio and cofactors such as divalent cations, ionic strength and pH. Such a multi-parameter optimisation for each protein investigated can only be satisfyingly screened using a high-throughput approach; (2) a sample prepa-ration robot. This robot is designed to prepare negatively stained samples from cytosolic fractions or 2D crystallisation experiments. The robot will be compatible with the 96 well plate format and the autoloader of the EM; (3) An automated grid loader (AutoLoader) and a cassette revolver fitting on the EM and the corresponding software are in develop-ment. These robots will enable the automatic loading of up to 96 samples and thus be fully compatible with the sample preparation robot; (4) development of software for instrumental control and screening acquisition schemes. Automatic acquisition and screening software, involving novel developments and improvement of existing routines will allow a first quality assessment and the selection of suitable sample areas for further in-depth investigations; (5) development of a versatile, self-learning image analysis and pattern recognition system for the automated identification of interesting sample areas and directing the pertinent image acquisition at different magnifications; (6) design of a versatile, user friendly database to allow storage and analysis of all pertinent experimental data.

Expected Results:

1) A fully integrated high throughput system for screening and analysis of native protein complexes and protein crystals by electron microscopy is expected. Good progress has been achieved in all parts of the project.

2) 2D-Cryrsallisation Robot: The alpha version of the robot (96 well plate) has been working reliably for a few months. Proteins have already been processed to yield high quality crystals. (Picture).

3) Sample Preparation Robot: A first version of a robot has been used with encouraging results. New developments to improve the automated staining are in progress.

4) Autoloader and Cassette Revolver: Both robots are in a well advanced state of devel-opment and will be ready in six to nine months.

5) Software for instrumental control and screening acquisition: The software to control the automatic grid loading hardware (AutoLoader) has been tested and will be inte-grated as soon as the EM is ready. The software design of the screening and acquisi-tion process suitable for crystalline objects and particles is well advanced.

6) Image analysis and pattern recognition software for crystal detection and analysis

Regions Of Interest (ROI) identification at medium

magnification: after an edge detection of the membranes (B), the ROI (red squares) are placed around the detected edges. Then,

a selection process retains the more significant ones (C).


HT3DEMwww.ht3dem.org

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018811Starting date:1st October 2005Duration:42 monthsEC Funding:

1 802 501


http://www.ht3dem.org

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has been developed for low, medium and high magnification.

7) Database: A first version of the database is ready for data entry. The statistical analysis of data is in development.

Potential Impact: The development of a versatile platform enabling the automated screening and analysis of various types of samples by electron microscopy closes a gap in the gen-eral use of this technology. It will speed up the structural analysis of several classes of fundamentally important specimens, such as macromolecular complexes, and, most importantly, membrane proteins. 2D crystals can provide 3D structural information of membrane proteins in their native environment by EM analysis and on surface properties by AFM analysis, including molecular interactions. This development thus fits in with the European effort to advance leadership in electron microscopy and with the enhance-ment of European competitiveness in the field of structural genomics. In the greater context, the project will also aid competitiveness in life sciences and the European pharma industry.

Keywords: high throughput, three-dimensional electron microscopy, membrane proteins, 2D crystallisation

Alpha version of the 2D-crystal-lisation robot at Partner BIOZ (Right). High quality crystals of Aeromonas hydrophila Aerolysin obtained with the cy-clodextrin method. Scale bars represent 100 nm. (Left)(Prof. Gisou van der Goot and Ioan Iacovache are acknowledged for kindly provid-ing us with Aero-lysin).

Project Coordinator:Prof. Andreas EngelUniversity of Basel M E Mueller Institute for Structural BiologyBiozentrumNadelberg 64054 Basel, [email protected]

Project Manager:Dr. Urs MuellerUniversity of Basel M E Mueller Institute for Structural BiologyBiozentrumNadelberg 64054 Basel, [email protected]

Prof. Wolfgang BaumeisterMax-Planck Institute of BiochemistryDepartment of Molecular Structural BiologyMartinsried, Germany

Dr. Werner Hax, Dr. Marc StormsFEI Electron Optics BV Eindoven, The Netherlands

Dr. Bart van der SchootSeyonic SANeuchatel, Switzerland

Prof. Jean-Philippe UrbanUniversité de Haute Alsace Faculté des Sciences etTechniquesMulhouse, France

Partners


High throughput Three-dimensional Electron Microscopy




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State-of-the-Art:Structural genomics originally aimed at the full structural coverage of the proteome. In the meantime, the investigation of the whole network of interacting proteins produced by a living organism (the ‘interactome’), and of how these interactions are being modulated by changing concentrations of small molecules, has become an emerging field of research providing information on the biochemical processes which occur through protein-protein and protein-DNA/RNA interactions. NMR spectroscopy is particularly suited for the study of weak and/or transient intermolecular interactions.The present project will implement coordination activities focused on the scientific areas of protein-protein, protein-DNA/RNA, and protein-ligand interactions, and membrane pro-teins. These scientific areas share common technical and methodological aspects, which represent crucial issues for the development of the whole field of biological NMR. The project will contribute to standardising and disseminating best practices.

Scientific/Technological Objectives:Coordination activities will be developed to achieve the following main goals:

focuses, mainly through the common vertical aspects

methodological approaches

the spreading of innovative methods and tools-

net by maintaining a common virtual laboratory

The above coordination activities will be crucial in guaranteeing that on-going research and methodological innovation in Europe, such as the development of new software tools, are carried out by promptly tackling the needs of the European scientific community. This will be achieved by guaranteeing the awareness of the potential stakeholders, and by avoiding both the duplication and exclusion of efforts (as much as possible), which may later become bottlenecks for the evolution of the whole field of biological NMR.

Expected Results:Actions to be taken within the project are planned by the managing committee (MC) on a yearly basis. Actions will involve:

-tions of high potential impact, unprecedented scientific challenges and opportunities, proposition of new standards, etc.

demonstrations or road shows presenting new advances, etc.

These actions are complemented by an annual meeting involving all participants in the project, organised by the coordinator in collaboration with all MC members.

Potential Impact:The impact of this Coordination Action is that it brings together scientists, creating a com-

Endothelin-1 bound to Endothelin-B receptor

www.postgenomicnmr.net


NMR-Life

Project Type:Co-ordination Action Contract number:LSHG-CT-2005-018758Starting date:1st December 2005 Duration:39 months EC Funding:

1 070 000


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mon reference basis in terms of experimental approaches, data elaboration and analysis through exchanges of good practices and/or by sharing procedures and results. The coordination of research activities is important when making breakthroughs or advanc-ing technologies achieved by the various scientists in the field, by avoiding needless duplication of efforts, thus enhancing and allowing the extensive scientific productivity of European researchers. This will help reinforce the European lead in the field of biologi-cal NMR, and the interaction with pharmacological and biotech companies will lead to industrial applications.

Keywords: protein interactions, protein ligand interactions, membrane pro-teins, immobilised proteins, NMR

Structure of a protein: single-stranded DNA complex

NMR Structure of the yeast Atx1: Copper(I): Ccc2a adduct

Project Coordinator: Prof. Ivano Bertini Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine Paramagnetiche, Magnetic Resonance Center (CERM) Via Luigi Sacconi, 6 50019 Sesto Fiorentino, Italy [email protected]

Project Manager:Kathleen McGreevyConsorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine Paramagnetiche, Magnetic Resonance Center (CERM) Via Luigi Sacconi, 6 50019 Sesto Fiorentino, Italy [email protected]

Dr. Michael SattlerGSF – National Research Center for Environment and HealthLehrstuhl Biomolekulare NMR-SpektroskopieDepartment ChemieTechnische Universität MünchenGarching, Germany

Prof. Rolf BoelensUtrecht University Bijvoet Center for Biomolecular Research NMR Spectroscopy Research Group Utrecht, The Netherlands

Prof. Harald Schwalbe Johann Wolfgang Goethe-Universität Center for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry and Chemical Biology Frankfurt am Main, Germany

Prof. Hartmunt OschkinatLeibniz-Institut für Molekulare Pharmakologie (FMP)Berlin, Germany

Prof. Geoffrey BodenhausenEcole Normale Supérieure de ParisDépartement de chimieLaboratoire de Resonance Magnetique BiomoleculaireParis, France

PartnersProf. Ernest D. LaueUniversity of CambridgeCambridge, UK

Prof. Iain CampbellUniversity of OxfordDepartment of Biochemistry Oxford, UK

Prof. Flemming Martin PoulsenUniversity of Copenhagen Structural Biology andNMR Laboratory the Institute of Molecular BiologyCopenhagen, Denmark

Prof. Vladimir SklenarMasaryk UniversityNational Center for Biomolecular ResearchBrno, Czech Republic


Focusing NMR on the Machinery of Life




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State-of-the-Art:In comparison with better-established methods like X-ray crystallography, computational tools for the extraction of information from NMR spectra of large proteins and complexes, and its analysis and interpretation, are much less well developed. As a result, the full power of the method cannot be exploited at present. Novel tools that allow the identification of signals in crowded NMR spectra of larger proteins and complexes, and their quantification, are urgently needed. The resulting information will, in turn, provide the starting point for the development of novel algorithms that facilitate structure determination of protein complexes in situations where NMR can play a key role; for example, where one or more components are only partly structured, or for solid-state studies of membrane proteins.

Scientific/Technological Objectives:The objectives of the project are:

1. the development of novel computational tools that allow rapid assignment of NMR spectra for studies of interactions and dynamics by making optimal use of existing (in particular structural) information, i.e. the NMR equivalent of molecular replacement in X-ray crystallography,

2. extending the scope of NMR spectroscopy by developing novel tools that allow the calculation of structures without the need for prior spectral assignment,

3. the development of improved tools for the identification and quantification of signals from NMR data.

These three objectives will be facilitated by the development and implementation of a series of computational algorithms involving Bayesian analysis, maximum entropy reconstruction, multi-dimensional decomposition, principle component analysis, and statistical and expert system-based analysis tools. These algorithms will be implemented within a common soft-ware framework developed by the CCPN project, so that they can be flexibly employed in the development of the different tools. We will develop novel tools for the validation of structures and experimental results and mine databases for NMR and structural information crucial to the aims of the project.

Expected Results:The expected result is the development of a highly integrated set of computational tools, which will extend the scope of NMR spectroscopy and allow researchers to carry out studies flexibly in functional and structural genomics, as well as NMR-based drug design.

Potential Impact:An integrated system allowing the extrac-tion of information from raw NMR data and the direct calculation of the final 3D structure, without the need for assignment of that information to specific atoms in the


Extend-NMRwww.ccpn.ac.uk/ccpn/projects/extendnmr/extend-nmr-project-information

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018988Starting date:1st January 2006Duration:42 monthsEC Funding:

2 000 000


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molecule, would be highly desirable and make a significant impact in NMR programmes of functional/structural genomics. In a similar vein, a method that allowed one to obtain assignments with the aid of a structure of a homologous protein would be extremely useful for functional studies. The development of novel algorithms will therefore greatly stimu-late the use and usefulness of NMR in functional/structural genomics, having a crucial impact on increasing the potential of NMR for studies in biology and medicine in the post-genomic era.

Keywords: nuclear magnetic resonance, NMR, structural genomics, functional genomics, biomolecular complexes, spectrum assignment, structure calculation, high-throughput techniques

Project Coordinator: Professor Ernest D. LaueUniversity of Cambridge80 Tennis Court RoadCambridge, CB2 1GA, [email protected]

Project Manager:Charles Shannon Research Services Division 16 Mill LaneCambridge, CB2 1SB, [email protected]

Dr. Kim Henrick European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI), Hinxton, UK

Dr. Michael NilgesCentre National de la Recherche Scientifique (CNRS) -Institut Pasteur Unité de Recherche Associeé (URA)Unité de Bioinformatique Structurale, Paris, France

Dr. Gert VriendRadboud University Nijmegen Medical Centre Nijmegen Centre for Molecular Life Sciences (NCMLS) Centre for Molecular and Biomolecular Informatics (CMBI)Nijmegen, The Netherlands

Dr. Martin BilleterGothenburg University Biochemistry and Biophysics Department of Chemistry Gothenburg, Sweden

Dr. Hans-Robert KalbitzerUniversity of Regensburg Institute of Biophysics Regensburg, Germany

Dr. Bruno Guigas Bruker BioSpin GmbHMagnet DivisionKarlsruhe, Germany

Dr. Alexandre BonvinUtrecht UniversityNMR Research Group Bijvoet Center for Biomolecular ResearchUtrecht, The Netherlands

Partners


Extending NMR for Functional and Structural Genomics




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State-of-the-Art: The objective of IMPS is to explore innovative approaches to membrane protein (MP) over-expression, stabilization and crystallography. Establishing the structure of MPs is of major importance in basic life sciences as well as drug development. Yet fewer than 1% of protein structures currently available correspond to MPs, most of them devoid of pharmacological interest. The reason for the paucity of crystallographic structures can be traced mainly to the following factors: (1) most MPs purified from natural sources are in short supply, hence the need for overexpression; (2) most MPs become unstable once extracted from their natural membrane environment, hence the need for improved handling conditions; (3) MPs do not crystallize easily, hence the need for alternative crystallization approaches to improving crystal quality and for specialized methods to deal with microcrystals. IMPS is an integrated attempt to develop novel, original ways of circumventing these three bottlenecks.

Scientific/Technological Objectives: MPs play key roles in innumerable biological processes. Even though their genes are now accessible, solving their structure remains time-consuming and most often unsuccessful. Given their physiological and biomedical importance, this constitutes a major problem in basic life sciences as well as public health care. Tools have been developed to overexpress, solubilize, stabilize, purify and crystallize MPs, and they are currently being used in large-scale initiatives for structure determination. Unfortunately, most MPs resist one or more of these steps.

The objective of IMPS is to develop imaginative, broad-range tools for membrane structural proteomics. The project brings together experts in chemistry, biochemistry, molecular genetics, electron microscopy and X-ray crystallography, and aims at developing original, innovative tools to attack each of these stumbling blocks. A strong core of crystallographers with dem-onstrated expertise in MP structure determination will apply these novel techniques to a rep-resentative test set of MPs. The approaches to be developed include original overexpression systems (insect photoreceptor cells and the chloroplast), unconventional surfactants (amphip-athic polymers, fluorinated surfactants, novel detergents and additives) and unconventional crystallization systems (lipid cubic phase crystallization, other non-detergent environments, molecular scaffolding). As the project progresses, some of these objectives are being adapted, extended, or, in some cases, superseded by alternative novel approaches that have yielded particularly promising results. These novel methodologies will be made available to the scien-tific community through a distributed technological platform including workshops, hands-on training, and dissemination of the new molecules, whose large-scale synthesis and distribution will be carried out by a participant SME. The circulation of scientists between IMPS laborato-ries and the organization of workshops ensures the rapid spread of know-how.

Expected Results: The general philosophy of the project has been outlined above. The resources and experi-ence brought by the eight partners and four associated laboratories are highly complemen-tary. Thirteen MPs have been selected either as models for technological development and/or as pharmacologically important targets. At the onset of the project, some proteins were already available in mg amounts, either from natural sources or following overexpression, while others were at the stage of setting up overexpression systems. As methodologies de-velop, new proteins are being chosen to further explore their domain of applicability, a rule of the game being the sharing among IMPS laboratories of plasmids, novel molecules and know-how. The main results to be expected are the following:

1) validation and dissemination of the most promising of the novel approaches to MP overexpression, stabilization and crystallization;

2) solving, or making significant steps towards solving, the structure of some of the tar-get MPs;

3) training the members of IMPS and other laboratories and creating the basis for col-laborations extending beyond the end of the project.


IMPS


1 900 000


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Potential Impact: Solving the structure of MPs that constitute important pharmacological targets is currently a high-risk endeavor, calling for long-term work-intensive investments. Providing new tools to-wards this goal will speed up structure resolution and cut down on its cost, which can have a significant economic impact in a field where research investments represent hundreds of millions of dollars. Most of the innovative approaches developed by IMPS partners origi-nated in Europe. IMPS provides an opportunity to consolidate the leadership that European laboratories currently hold in these new developments and speed up their optimization and the definition of their field of applicability. Once validated, the novel methods will be disseminated throughout European laboratories, thanks, in particular, to workshops and collaborations involving both IMPS and external laboratories.

Keywords: membrane proteins, overexpression, crystallization, stabilization, novel surfactants, microcrystallography, lipid cubic phases, am-phipols, Drosophila, yeast

Project Coordinator:Dr. Jean-Luc PopotCentre National de la Recherche Scientifique (CNRS)/Université Paris-7 UMR 7099Institut de Biologie Physico-Chimique13, rue Pierre-et-Marie-Curie75005 Paris, [email protected]

Prof. Eva Pebay-PeyroulaCentre National de la Recherche Scientifique (CNRS)CEA/Université Joseph FourierInstitut de Biologie StructuraleGrenoble, France

Dr. Isabelle Mus-VeteauCentre National de la Recherche Scientifique (CNRS)Université de Nice-Sophia AntipolisNice, France

Prof. Irmgard SinningRuprecht-Karls-UniversitätHeidelberg, Germany

Prof. Bernard PucciUniversité d’Avignon et des Pays du VaucluseAvignon, France

Prof. Wolfram WelteUniversität Konstanz, F R GMathematisch-Naturwissenschaftliche SektionFachbereich BiologieLehrstuhl BiophysikKonstanz, Germany

Dr. Jean-Pierre SallesTargeting System PharmaEguilles, France

Prof. Kaspar HegetschweilerUniversität des SaarlandesFakultaet 8 Chemie PharmazieBiowissenschaftenWerkstoffwissenschaftenSaarbrücken, Germany

Dr. Gebhard SchertlerMRC-LMBMedical Research CouncilCambridge, UK

Partners


Innovative tools for membrane structural proteomics



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State-of-the-Art:SPINE2-COMPLEXES builds on the technological developments in structural genomics/pro-teomics of the last decade and aims to break new territory in this field. The concept of struc-tural genomics arose in the USA at the end of the 1990s, as a response to the availability of whole genome information, and also as a response to the success of high throughput (HTP) methods in genome sequencing. At that time, it was foreseen that similar HTP methods could be applied to obtain 3-D structures of all the proteins (the proteome) of an organism, thus generating an efficient way of filling in the gaps in observed fold-space. This vision led to the investment of immense sums of money into large-scale structural genomics projects. Instances of this are noted both in Japan, e.g. the massive RIKEN project, (http://www.rsgi.riken.go.jp/), and in the USA, e.g. nine multi-million dollar projects funded by the NIH/NIGMS Protein Structure Initiative, costing around $270 million and stretching over a 5 year period, ending in June 2005 (http://www.nigms.nih.gov/psi/ ).

These projects were characterised by the following elements: the concentration of resources into a small number of large centres, the development of novel, automated technologies per-mitting a high-throughput, a pipeline approach to structure determination, a focus on novel folds as the major target criterion, and immediate public deposition of structural data. Europe has been slower off the mark in implementing structural genomics. The Protein Structure Factory in Berlin, Germany (http://www.proteinstrukturfabrik.de/) first made the move, followed by the OPPF in Oxford, England (http://www.oppf.ox.ac.uk/), and the Genopoles in France (notably Gif, Marseille and Strasbourg, http://rng.cnrg.fr/). How-ever, it was not until October 2002 that the first Europe-wide project began. This was a three-year project funded by the EU FP5 programme called SPINE: Structural Proteomics in Europe (http://www.spineurope.org). SPINE, a second generation structural genomics project, made some radical departures from previously funded initiatives, and has benefited from the experience and developments in technology arising from previous findings in this field. SPINE2-COMPLEXES plans to push developments beyond the previous limits.

Scientific/Technological Objectives: SPINE2-COMPLEXES’ aim is to investigate challenging biological systems by combining knowledge of genomes with HTP methods for structural proteomics. The project targets the development and application of HTP methods, for an efficient determination of atomic resolution structures of protein-protein and protein-ligand complexes. These complexes, which are extremely important with respect to human health, are drawn from the common theme of signalling pathways from receptor to gene. Overall, the success of SPINE2-COMPLEXES will be assessed on the scientific impact of its output.

The project work is divided into 3 sections: Section 1 involves 3-D structure determination of complexes within the target focus of

signalling pathways from receptor to gene. This is the major section of SPINE2-COM-PLEXES, both in terms of allocation of manpower, and in terms of scientific impor-tance. Targets are drawn from key areas of biology, including cell cycle, neurobiol-ogy, cancer and immunology, as well as pathogen proteins that modulate or subvert human signalling pathways. This section has been subdivided into a set of WPs which

www.spine2.eu


Project Type:Integrated ProjectContract number:LSHG-CT-2005-031220Starting date:1st July 2006Duration:42 months EC Funding:

12 000 000

SPINE2-COMPLEXES


http://www.spine2.eu

http://www.rsgi.riken.go.jp

http://www.rsgi.riken.go.jp

http://www.nigms.nih.gov/psi

http://www.proteinstrukturfabrik.de

http://www.oppf.ox.ac.uk

http://rng.cnrg.fr


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bring together Partners working in specific areas. Since the apparently diverse cel-lular processes often involve the same components and pathways, this will provide wide opportunities for inter-Partner synergies.

Section 2 involves the development of technologies addressing the difficult problems associated with the production of human protein complexes in quantities sufficient for structural studies, and also with the provision of an interdisciplinary approach for determining protein complex structures. This will build on and extend the HTP protein expression and crystallisation technologies initiated and implemented within the SPINE project.

Section 3 deals with the dissemination and organization of the emerging data and knowledge, through a series of training session and symposia on an annual basis.

Expected Results: To date, the SPINE2-COMPLEXES project has made progress in several areas, as detailed below:

1) Significant progress has been made towards the development of protein complex-specific target tracking software, to enable the rigorous capture, storage and analysis of protein expression and structure determination data. This tracking software will be PIMS compatible and will utilise a similar interface for data acquisition and retrieval.

2) A SPINE2-COMPLEXES website (http://www.spine2.eu) has been set up and will be further developed over the next months, after which it will form the centre of the consor-tium communication strategy.

3) A planned timetable of training workshops, demonstrating the state-of-the-art technolo-gies relevant to protein structure determination, will be implemented in the first twelve-month reporting period of the project.

4) All Partners have started work on the structure determination of their nominated protein components. These component proteins have been identified as members of the cell signalling pathways, which in turn, form the biological focus of the project. Some pro-tein structures are expected to be delivered in the first twelve-month reporting period.

Potential Impact: SPINE2-COMPLEXES has several deliverables, and they are as follows: 1) high value 3D structures of complexes of fundamental and biomedical importance; 2) novel methods for the production, characterisation and structure determination of eukaryotic proteins and complexes; 3) new bioinformatics tools; and 4) an interactive and co-ordinated Europe-wide network of laboratories engaged in training and research in structural proteomics. These deliverables will ensure the profound impact of this project both in Europe and be-yond. SPINE2-COMPLEXES intends to further develop and streamline the high through-put technologies, so as to tackle not only individual proteins, but also more challenging protein/protein and protein/nucleic acid complexes. The success of the consortium will demand technological innovation, resulting in new and/or improved HTP procedures at all stages, from cloning, expression and purification, through biophysical and biochemical characterization of individual proteins and complexes, to crystallization, data collection, and solution of their structures, as well as solution of smaller protein structures by NMR, and electron microscopy (EM) studies on complexes.


From Receptor to Gene: Structures of Complexes from Signalling

Pathways linking Immunology, Neurobiology and Cancer


http://www.spine2.eu

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The SPINE2-COMPLEXES project goes far beyond the capacities of individual laboratories, which work in isolation, lacking both the infrastructure and the critical mass to tackle such a far-reaching and ambitious project. At European level, the added value of the project will find expression in several ways. Firstly, consortium members will be able to take advantage of infrastructures and expertise, especially in protein production, bioinformatics and LIMS, NMR and synchrotron facilities that are offered by consortium partners. The training and mobility programme of SPINE2-COMPLEXES will facilitate interactions and dissemination. Secondly, major emphasis will be placed on Internal Networking. This will utilize a website, with adjunct internal databases, linked to LIMS systems in the member laboratories.

Keywords: crystallography, protein expression, nanodrop technology, protein complexes, ligand interfaces, signalling pathways, protein structure, structural genomics, high-throughput techniques

PartnersProject Coordinator: Prof. David Stuart Wellcome Trust Centre for Human GeneticsDivision of Structural BiologyRoosevelt Drive, HeadingtonOxford, OX3 7BN, [email protected]

Project Manager:Dr. Susan DaenkeScientific Program ManagerEuropean ProjectsWellcome Trust Centre for Human GeneticsRoosevelt Drive, Headington Oxford, OX3 7BN, [email protected]

Prof. Joel SussmannWeizmann Institute of Science The Israel Structural Proteomics CenterDepartment of Structural BiologyRehovot, Israel

Dr. Stephen CusackEuropean Molecular Biology Laboratory (EMBL)Grenoble Outstation Grenoble, France

Dr. Matthias WilmannsEuropean Molecular Biology Laboratory (EMBL)Hamburg OutstationHamburg, Germany

Dr. Dino Moras Centre Européen de Recherche en Biologie et en Médecine – Groupement d’Intérêt Économique UPR9004/CERBM G.I.E.Illkirch, France


SPINE2-COMPLEXES




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Prof. Gunter SchneiderKarolinska Institutet Department of Medical Biochemistry and BiophysicsStockholm, Sweden

Prof. Keith Wilson University of York Department of Chemistry Structural Biology LaboratoryYork, UK Dr. Rolf Boelens University of UtrechtBijvoet Center for Biomolecular ResearchNMR Spectroscopy Utrecht, The Netherlands Prof. Titia Sixma Netherlands Cancer Institute (NKI) Division of Molecular CarcinogenesisAmsterdam, The Netherlands

Prof. Ivano Bertini Magnetic Resonance Center (CERM)SestoFiorentino (FI), Italy

Prof. Sine Larsen European Synchrotron Radiation Facility(Installation Européenne de Rayonnement Synchrotron)Grenoble, France Prof. Udo HeinemannMax-Delbruck-Center for Molecular MedicineDepartment of CrystallographyBerlin, Germany Prof. Miquel Coll Consejo Superior de Investigaciones CientíficasInstitut de Biologia Molecular de Barcelona Barcelona, Spain

Dr. Yves Bourne Institute de Biologie Structurale et Microbiologie Architecture et Fonction desMacromolecules Biologiques Marseille, France Dr. Herman van TilbeurghUniversité Paris-SudIBBMC-Institut de Biochemie et de Biophysique Moleculaire et CellulaireCentre National de la Recherche Scientifique (CNRS) UMR 8619Orsay, France

Dr. Beata Vertessy Hungarian Academy of SciencesMetabolism and Repair Department Institute of EnzymologyBudapest, Hungary

Dr. Jan Dohnalek Ustav makromolekularnii chemie Akademie ved Ceske republikyDepartment of Structure AnalysisGroup of Analysis of Molecular StructurePrague, Czech Republic

Prof. Maria Armenia Carrondo Instituto de Technolgie Quimica e BiologicaProtein crystallography laboratoryOeiras, Portugal

Dr. Renos Savva Domainex LimitedBirkbeck College, University of LondonRosalend Franklin LaboratoryLondon, UK


From Receptor to Gene: Structures of Complexes from Signalling Pathways linking Immunology, Neurobiology and Cancer


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State-of-the-Art:The wealth of information obtained by Structural Genomics has allowed protein structure-based drug design to complement screening and combinatorial chemistry to provide more efficient drug development. Ultimately, this approach will reduce the time of production cycles and therefore cost per drug.

Structural Genomics has coincided with the era of high-throughput, resulting in major ad-vances in the automation of protein preparation and X-ray crystallographic analysis, and in automating and miniaturising crystallisation trials (thousands per day). Despite this, the suc-cess rate in going from cloned gene to high-resolution protein structure is still relatively low in all current Structural Genomics projects, with a major bottleneck situation from purified protein to diffracting crystals. This problem clearly needs to be addressed. This can be done through the production of a design that will offer new and improved optimisation methods, in order to turn crystal leads into useful diffracting crystals.

Scientific/Technological Objectives: The key objective of the OptiCryst project is to address the critical post-protein production bottleneck area in the field of Structural Genomics. To date, this area has been consistently ignored by initiatives worldwide. We propose to enhance the state-of-the-art in protein crystal optimisation by increasing the success rate of the production of diffraction-quality crystals from the current rate of 21 percent to at least 40 percent.

Expected Results:Moving away from current approaches, and applying methods based on understanding the fundamental principles of crystallisation, the OptiCryst project will focus on designing tech-niques to actively control the crystallisation environment as the project progresses through its stages.

Potential Impact:Structural Genomics is a key discipline in post-genomic biology, and today the pressure to produce diffraction-quality crystals that can yield new protein structures is greater than ever. As a result, the science of crystallisation is becoming a rapidly developing field and it is gathering new momentum. The work being carried out by the Opticryst project will go a sig-nificantly long way towards addressing the outstanding needs within that research area.

Masterclass Opticryst 2007

www.opticryst.org


OptiCryst

Project Type:SME- Specific Targeted Research Project Contract number:LSHG-CT-2006-037793Starting date:1st December 2006Duration:36 monthsEC Funding:

2 270 000


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PartnersProject Coordinator:Dr. Roslyn BillAston University Department of Life and Health Sciences Aston TriangleBirmingham, B4 7ET, UK [email protected]

Project Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, [email protected]

Prof. Naomi Chayen Imperial College of Science, Technology and MedicineBiomedical Sciences Biological Structure and Function London, UK

Dr. Patrick Shaw Stewart Douglas Instruments LtdHungerford, UK

Dr. Flip Hoedemaeker Key Drug PrototypingAmsterdam, The Netherlands

Dr. Anthony Savill Molecular Dimensions Ltd Newmarket, UK

Dr. Rafael Rubio Cruz Triana Science & TechnologyArmilla, Spain Prof. Rolf Hilgenfeld University of Lübeck Institute of Biochemistry Lübeck, Germany

Keywords: protein crystallization, phase diagrams, nucleation, robotics, high throughput, structural genomics

Dr. Marcus J. SwannFairfield Scientific LtdCrewe, UK

Prof. Juan Manuel Garcia-RuizConsejo Superior de Investigaciones Cientificas (CSIC)Laboratorio de Estudios CristalograficosArmilla, Spain

Prof. Christian BetzelPLS Design GmbHHamburg, Germany

Prof. Lena GustafsonGothia Yeast Solutions ABGothenburg, Sweden


Optimisation of Protein Crystallisationfor European Structural Genomics




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State-of-the-Art: Since 2002, momentum has been gathering in European structural genomics. EU funding for six major projects, along with other initiatives in Europe (SGC, PSF, OPPF, Genopoles and PSB) has provided a broad base to build a comprehensive and competitive European structural genomics research effort. These early programmes have excelled in the development and im-plementation of automated, computational and high throughput methods for protein structure determination in a number of organisms. The challenge is to broadcast this knowledge to Eu-ropean laboratories as the scientific and strategic goals of structural genomics are expanded and refined to address important issues for human health. TEACH-SG provides a focus for training in all the main methodological areas of structural genomics, bringing together exper-tise from each programme to provide an integrated skill resource for researchers in the field.

Scientific/Technological objectives: The principal objective of TEACH-SG is to institute a programme to train and educate the next generation of biomedical and computational scientists in the methods and technologies of high throughput and high value structural proteomics. TEACH-SG will provide training in several formats:

1) Practical workshops on state-of-the-art structural genomics/proteomics methodology. 2) Networking meetings bringing together several projects under the European struc-

tural genomics umbrella, TEACH-SG, will host joint meetings with representatives from other structural genomics programmes.

3) Unrestricted web-based training information: All workshop and conference pro-grammes will be published on a dedicated TEACH-SG website.

4) European Structural Genomics Newsletter: As part of the information dissemination, a newsletter will be established

5) Visits from world-class scientific researchers in SG.

Expected results:TEACH-SG will provide a platform for training young scientists and those from smaller labo-ratories and new EU member states in the technologies developed in Structural Genomics, particularly in high throughput techniques. Training will be provided in: i) bioinformatics approaches to target selection and data handling; ii) high throughput automated methods in cloning and protein expression in prokaryotic and eukaryotic systems; iii) automated protein characterization iv) high volume crystallogenesis and evaluation; v) computational structural determination methods. The programme of networking meetings will have a spe-cific Structural Genomics/Proteomics theme, presenting recent technological and methodo-logical advances in the field with the aim of fostering a constructive dialog between devel-opers of similar or complementary technologies.

Potential impact: TEACH-SG will provide essential focus for training in all the main methodological areas of high throughput structural biology, bringing together expertise from each programme to provide integrated skills resource for researchers. Productive associations with the commer-cial and industrial sector will also identify and support the transfer of developmental work into the highly focused area of new drug design. TEACH-SG will provide a scale of training and opportunity that is not always met with a limited budget available within a multidi-mensional but largely research-driven programme. TEACH-SG will be able to concentrate on providing these resources, particularly practical hands-on experience of emerging and fast-moving technologies and will be in an excellent position to monitor the impact of this programme in subsequent years.

www.teach-sg.eu


TEACH-SG

Project Type:Specific Support ActionContract number:LSSG-CT-2004-503468Starting date:1st January 2007Duration:30 monthsEC Funding:

490 000


http://www.teach-sg.eu

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Keywords:

structural proteomics, training, work-shops, website, networking, crystal-lography, structure determination

Project Coordinator:Prof. David StuartUniversity of Oxford Wellcome Trust Centre for Human GeneticsDivision of Structural BiologyRoosevelt DriveHeadington, OX3 7BN, [email protected]

Project Manager:Dr. Susan DaenkeUniversity of Oxford Wellcome Trust Centre for Human GeneticsRoosevelt DriveHeadington, OX3 7BN, [email protected]

Prof. Joel L. SussmanWeizmann Institute of ScienceDepartment of Structural BiologyFaculty of Chemistry Rehovot, Israel

Dr. Stephen Cusack European Molecular BiologyLaboratory (EMBL) Grenoble Outstation Grenoble, France

Prof. Dino MorasCentre Européen de Recherche en Biologie et en Médecine – Groupement d’Intérêt Economique UPR9004/CERBM G.I.E.Illkirch, France

Prof. Keith WilsonUniversity of YorkDepartment of ChemistryStructural Biology LaboratoryYork, UK

Dr. Anastassis Perrakis Netherlands Cancer Institute (NKI)Division of Molecular Carcinogenesis Amsterdam, The Netherlands

Dr. Beata Vertessy Hungarian Academy of SciencesMetabolism and Repair DepartmentInstitute of EnzymologyBudapest, Hungary

Dr. Jan DohnalekUstav makromolekularnii chemie Akademie vedCeske republikyDepartment of Structure AnalysisGroup of Analysis of Molecular StructurePrague, Czech Republic

PartnersDr. Maria Armenia CarrondoInstituto de Technolgie Quimica e BiologicaProtein crystallography laboratoryOeiras, Portugal

Prof. Miquel CollInstitute for Research in Biomedicine (IRB Barcelona)Barcelona, Spain

Prof. Lucia BanciUniversity of Florence Polo Scientifico Centro Risonanze Magnetiche (CERM) Sesto Fiorentino, Italy


Training and Education in High Volume and High Value Structural Genomics





COMPARATIVE GENOMICS & MODEL ORGANISMS4.



MOUSE4.1

EURExpress

MUGEN

PRIME

FLPFLEX

EUCOMM

EUMODIC

CASIMIR


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State-of-the-Art: This EURExpress integrated project responds to the priority topic “Global in situ gene ex-pression analysis in rodent models and human tissues”. EURExpress integrates European skills, efforts, resources and information in the field of systematic gene expression analysis. Expression data of approximately 20 000 genes will be generated by RNA in situ hybridi-sation (ISH) on E14.5 wild type murine embryos which will result in detailed description (at a cellular level) of gene expression patterns. A ‘transcriptome atlas’ will be generated using a newly developed automated RNA ISH system. Automated scanning microscopes will collect image data which will be electronically sent out in a digital format for annota-tion. The latter will be performed using a web-based ‘virtual’ microscope and entered in a hierarchical database designed to hold large amounts of image data and display them in a user-friendly format. For a subset of genes, mainly those directly involved in human diseases, expression data will also be generated by using human and murine tissue arrays. This will offer the opportunity to compare human and mouse expression patterns in adult tissues. This project builds up a strong European concentration of skills in gene expression analysis and mouse genomics. It will allow integration with existing European projects, such as mouse mutagenesis and mouse phenotyping projects, which critically depend on detailed information on gene expression patterns. Integration of the efforts of several Eu-ropean laboratories will result in the standardisation of methods to generate, collect and display gene expression data. Furthermore, technological expertise will be disseminated by training and exchange programmes. All expression data will be made readily avail-able to the scientific community via the EURExpress web-linked database, advancing our knowledge of gene function and having a significant impact on the identification of gene expression markers of disease processes.

Scientific/Technological Objectives:The scientific and technological objectives of this grant proposal are:

represent the major source for the transcriptome atlas. Additional priorities include disease genes and genes subject to alternative splicing

of approximately 20 000 genes-

man tissues using tissue microarray analysis with medically relevant genes

and synergistically integrate with other European mouse functional genomics efforts such as EUMORPHIA.

Expected Results:EURExpress proposes a transcriptome-wide acquisition of expression patterns chiefly by means of in situ hybridisation (ISH) with non-radioactive probes and will use this data to establish a web-linked, interactive digital transcriptome atlas of embryonic mouse. In addi-


EURExpress

Project Type:Integrated ProjectContract number:LSHG-CT-2004-512003 Starting date:1st January 2005Duration:48 months EC Funding:

10 800 000

www.eurexpress.org/ee/


http://www.eurexpress.org/ee

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tion to generating large sets of embryonic expression data in mouse, EURExpress will take a detailed look at expression in human tissues. Over >1000 disease-related genes will be analysed using tissue microarrays containing several hundred mouse and adult human tissues. A publicly accessible transcriptome atlas database will be created to store and retrieve all image, experimental and annotation data. The consortium will undertake an integrated approach to create a web-based gene expres-sion atlas by RNA in situ hybridisation. The direct results at the end of the project will be:The establishment of a tracking database that will allow monitoring and integrating data flow. This database will be accessible across the project, facilitating the management of data production.

The establishment of high-throughput ISH technology in Europe.Eurexpress will contribute to setting up a structure in which scientists can be trained in the field of gene expression and database management. The generation and management of approximately 20 000 murine templates.The implementation of simple search interfaces to the transcriptome database and of an initial set of programmatic interfaces to other bio-informatics resources to support functional genomics analyses.High-resolution expression data throughout brain development for a subset of brain-specific genes.

Clone Selection

TemplateGeneration

EURExpressTranscriptomeAtals

TrackingDatabase

Image Annotation

Automated Microscopy

AUTOMATED in situ

Work Flow. In Situ Hybridization (ISH)


A European Consortium to Generate a Web-Based Gene Expression Atlas

by RNA in situ Hybridisation


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The gene expression data for approximately 20 000 genes. The generation of ISH data for tissue microarray sections. The implementation of user interfaces, which will provide public access to EURExpress data and will facilitate its application in functional genomics. The generation of a web-based gene expression atlas.

Potential Impact:The era of ‘post-genomic research’ is characterised by the requirement of high-throughput procedures to exploit the vast amount of information generated in genome projects. High-resolution analysis of gene expression can be performed by RNA in situ hybridisation, which allows definition of gene expression with great accuracy. Europe is not only at the leading edge in studies in mammalian genetics and the use of mouse models to elucidate the genetic bases of disease, but has undertaken the lead in a number of new research and development areas in the field of mouse functional genomics. EURExpress intends to add to this European effort by creating an atlas of mouse gene expression in the form of a searchable database that will be available to the scientific community. The expression pattern of a gene in a multicellular organism is a basic feature of the biological function of any gene. The mouse is strategic for this type of study because the mouse genome encodes an experimentally tractable organism and has emerged as a pre-eminent organism for the study of human diseases and gene function. More than 98% of human genes are present in the mouse.The potential impact on the study of human development and disease is enormous:

phenotypes

evaluate disease prognosis and to measure therapeutic benefits.

Keywords:

RNA in situ hybridisation, mouse, gene expression analysis, functional genomics, transcrip-tome atlas, automated RNA ISH system, web-based virtual microscope, web-linked gene expression database


EURExpress

left: Saggittal section of an E14.5 embryo showing the

expression pattern of Fgfb3 (Fibroblast binding protein 3) in

the developing CNS.

middle: Expression of an uncharacterized gene in the CNS, in the sympathetic ganglion and

in the dorsal root ganglia

right: Example of a gene (Otx2) with strong expression in the

developing retina


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PartnersProject Coordinator:Prof. Andrea BallabioFondazione TelethonTIGEM-Telethon Institute of Genetics and MedicineVia Pietro Castellino 11180131 Naples, [email protected]

Prof. Gregor EicheleMax-Planck Institute of Biophysical ChemistryGöttingen, Germany

Dr. Marie-Laure YaspoMax-Planck Institute for Molecular GeneticsBerlin, Germany

Dr. Duncan DavidsonMedical Research CouncilMRC Human Genetics UnitEdinburgh, UK

Prof. Stylianos AntonarakisUniversity of GenevaFaculty of Medicine/ Division of Medical GeneticsGeneva, Switzerland

Prof. Salvador Martinez PerezUniversidad Miguel HernandezInstituto de Neurociencias -Laboratorio deEmbriología ExperimentalAlicante, Spain

Dr. Pascal DolleCentre Européen pour la Recherche en Biologieet MédecineMouse Clinic InstituteIllkirch, France

Dr. David TannahillWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, UK

Prof. Pier Paolo Di FioreIFOM, The FIRC Institute for Molecular OncologyMilan, Italy

Dr. Stefan KruseOrgarat GmbHEssen, Germany

Dr. Paolo SarmientosPRIMM SrlMilan, Italy

Dr. Uwe RadelofRZPD German Resource Center for Genome ResearchBerlin, Germany


A European Consortium to Generate a Web-Based Gene Expression Atlas by RNA in situ Hybridisation



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State-of-the-Art: Immunological diseases are complex diseases. They encompass a wide variety of disor-ders, affecting a steadily increasing proportion of people living in modern societies. During the past decade, dramatic advances have been made in understanding the mechanisms regulating the immune system, its pathological processes and the processes of immune de-viation. Central to this was the ability of studying individual genes in the immune system of live animals using gene-targeting technologies. At the same time, this allowed the develop-ment of models of immune diseases.

Life Sciences have entered the post-genomic era. A surprisingly small number of 30 000 or less genes comprise our genome. Thus, it is feasible to apply technologies such as DNA microarrays and proteomics to analyse almost all genes and proteins simultaneously. This provides the unprecedented opportunity to map genes and gene networks systematically. By applying functional genomics to models for immunological diseases, gene-networks can be mapped and genes underpinning immune deviations and diseases can be identified. This will unlock a huge potential for generating novel diagnostic tools and identifying novel pharmacological targets. The next major contribution to our understanding of the immune system is expected to come from a systematic coordinated application of functional genom-ics approaches to animal models for immune disorders or processes.

Scientific/Technological Objectives:MUGEN aims to structure and shape a world-class network of European scientific and tech-nological excellence in the field of murine models of human immunological diseases that will advance understanding of the genetic basis of disease and enhance the innovation and translatability of research efforts. The network is pursuing three parallel approaches:

-mum use of the common resources to identify new target genes for immune processes and diseases

expertise able to provide all MUGEN participants with the services necessary for an efficient application of post-genomic protocols

relational database for the integration and management of knowledge and informa-tion in the area of immunological research.

Expected Results:MUGEN aims to bridge the gaps in immunological research by assembling, coordinating and exploiting the animal model resources of its participants, and employing a unifying functional genomics approach to efficiently predict and validate dominant gene function with pathogenic relevance for human immunological disease. In the first phase, the project is as-similating expertise in key areas of immunological research that can be divided roughly into the three categories: basic immunological processes, immunological diseases and immuno-genetics. Following this assimilation, a selective functional genomics strategy will lead to the identification of putative genetic networks in human immunological diseases. A comparative analysis of the data produced by the first phase will allow us to decide on key genetic targets


MUGEN

Project Type:Integrated ProjectContract number:LSHG-CT-2004-005203 Starting date:1st January 2005Duration:60 months EC Funding:

11 000 000

www.mugen-noe.org


http://www.mugen-noe.org

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for immune diseases. Integrating functional genomic platforms will be implemented to validate the genetic targets in animal model systems and allow for the devel-opment of biotechnological prod-ucts targeting pathological proc-esses. This will produce new basic knowledge on immune processes and additional targets for human immunological diseases.

Through the integration of this knowledge into the MKE, the re-sults from this network will help formulate new concepts for clinical applications. Besides the scientific and technological components, the network is keen on spreading its scientific and technological excel-lence. The primary objective is to promote training-through-research to a new generation of scientists. MUGEN also wants to create an impact on the public awareness of the pan-European dimension of re-search efforts into immunological problems.

MUGEN is dedicated to extending every effort to promote the exploi-tation, dissemination and commu-nication of its scientific and tech-nological excellence to key stakeholders in the area of immunological diseases, including physicians, patients, policy-makers, the industry, academia and the public at large.

Potential Impact:Immune pathologies encompass a wide variety of disorders with epidemiological relevance, hence the discovery of therapeutic targets is a major priority in European health policies. Previous work in immunological research resulted in independent knowledge, complemen-tary expertise and resources. The benefit of the consortium lies in the integration of labora-tories that are expert in the modelling of immunological processes or disease, state-of-the-art technologies in genome research and functional genomics, with the aim of enhancing our understanding of mechanisms in immunity and disease.

The coordinated application of functional genomics approaches to existing mouse models and the integration of the research results into a common knowledge environment is expect-ed to have a significant impact on our understanding of pathways and gene networks un-derlying immunological diseases. With the notion that the major drug candidates in clinical

TNFRI positive Follicular Dendritic Cells

TNFRI deficient Follicular Dendritic Cells


Integrated Functional Genomics in Mutant Mouse Models as Tools to Investigate the Complexity of Human Immunological Disease


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PartnersProject Coordinator:Dr. George KolliasBiomedical Sciences Research Center34 Al. Fleming Street16672 Vari, [email protected]

Prof. James DisantoInstitut PasteurUnité des Cytokines et Developpement LymphoideParis, France

Dr. Günter HaemmerlingDeutsches Krebsforschungszentrum (DKFZ)Molekulare ImmunologieHeidelberg, Germany

Prof. Bernard MalissenCentre National de la Recherche Scientifique (CNRS),Delegation ProvenceMarseille, France

development were either predicted or validated in mouse models, this approach promises to add significantly to future diagnostic and treatment options of immune related diseases.

Thus, the successful implementation of the network will have a major structural impact for biomedical research in Europe, which will persist well after the end of the duration of the project. MUGEN’s achievements and deliverables are expected to benefit research beyond its borders and will therefore be of broad scientific and socioeconomic value.

Keywords: functional biology, molecular genetics, animal immunology, targeted mutagenesis, animal models, molecular pathways, exploratory drug discovery, functional genomics

Prof. Paola Ricciardi-CastagnoliUniversity of Milano-BicoccaDepartment of Biotechnology and BioscienceMilan, Italy

Prof. Maries Van Den Broek, Prof. Rolf ZinkernagelUniversity of ZurichInstitute of Experimental ImmunologyZurich, Switzerland

Dr. Werner MüllerGBF Gesellschaft für Biotechnologishe Forschung mbHDepartment of Experimental ImmunologyBraunschweig, Germany

Prof. Anton BernsNetherlands Cancer InstituteAntoni van Leeuwenhoek HospitalDivision of Molecular GeneticsAmsterdam, The Netherlands

Project FlyerThis is the first project flyer describing participation and

activities throughout the first Joint Programme of Activities,

running from month 1-18. © BSRC Al. Fleming


MUGEN



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Prof. Alvis BrazmaEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Microarray Informatics TeamOutstation HinxtonHinxton, UK

Prof. Lars Fugger, Prof. Dimitris KioussisMedical Research CouncilHuman Immunology UnitOxford, UK

Prof. Rikard HolmdahlLunds Universitet – Medical Inflammation ResearchDepartment of Cell and Molecular BiologyLund, Sweden

Prof. Paola Ricciardi-CastagnoliGenopolis ConsortiumUniversity of Milano-BicoccaDepartment of Bioscience and Biotechnology/U4Milan, Italy

Dr. Antonio LanzavecchiaInstitute for Research in BiomedicineBellinzona, Switzerland

Prof. Klaus PfefferHeinrich-Heine-Universitat DüsseldorfInstitut für Medizinische MikrobiologieDüsseldorf, Germany

Prof. Andreas RadbruchDeutsches Rheuma-Forschungszentrum Berlin, Germany

Prof. Glauco Tocchini-ValentiniConsiglio Nazionale delle Richerche Istituto di Biologia CellulareRome, Italy

Prof. Jurg TschoppUniversity of LausanneInstitute of BiochemistryEpalinges, Switzerland

Dr. Klaus RajewskyThe CBR Institute for Biomedical Research IncHarvard Medical SchoolBoston, USA

Dr. Andreas PersidisBiovista – A. Persidis & Sia O.E.Elliniko, Athens, Greece

Dr. François RomagneInnate Pharma SASMarseille, France

Dr. Martin BachmannCytos Biotechnology AGZurich-Schlieren, Switzerland

Jesper ZeuthenBiomedical Venture, Bankinvest GroupCopenhagen, Denmark

Dr. Alberto MantovaniInstituto Clinico HumanitasRozzano, Italy

Dr. Bjorn LowenadlerBiovitrum ABGothenburg, Sweden

Dr. Manolis PasparakisUniversity of CologneInstitute of GeneticsDepartment for Mouse Genetics and InflammationCologne, Germany

Dr. Lefteris ZachariaBioMedCode Hellas SAVari, Athens, Greece


Integrated Functional Genomics in Mutant Mouse Models as Tools to Investigate the Complexity of Human Immunological Disease


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State-of-the-Art:At present, the genetic make-up or genome of the mouse is familiar to scientists. The next chal-lenge for biomedical science is to determine the function of these genes, and the manner in which their alterations can cause disease. This is what is referred to as functional genomics.

The mouse model plays a pivotal role in the investigation of human diseases and their diagno-sis and treatment. Most EU member states perform research into mouse functional genomics. This research is funded at two levels: nationally, and by the European Commission. Mouse functional genomics research in Europe would benefit significantly from a pan-European ap-proach, which would integrate both national and EU programmes. Greater interaction be-tween research scientists and national policymakers would in fact allow for research priorities to be formulated.

The European Commission provides support for infrastructures, such as the development of databases of anatomy, or the European Mutant Mouse Archive (EMMA). Collaboration amongst policy makers within the member states may promote the development of new strate-gies, which would secure funding to support these essential infrastructures.

Scientific/Technological Objectives: In delivering a new coordinating action to improve the structure and integration of Euro-pean mouse functional genomics, we propose 3 phases for PRIME, namely:

1. Benchmarking, mapping and assessment of European activities committed to mouse functional genomics;

2. Exploring methods for convergence of policy, communality of research and commu-nication;

3. Extending and consolidating the new coordination activities.

The aim is to ensure that Europe delivers research of outstanding quality, by employing more integrated approaches and by more effectively harnessing existing resources (both biologi-cal and informational); the development of new resource and infrastructure opportunities will likewise further this cause. Achieving these goals will allow us to more advantageously compete for funding, utilise available opportunities, and ultimately acquire financial back-ing from both national and European sources.

Networking meetings will be held, with the intention of determining how far Europe is already integrated in terms of research policy, and how the means for achieving such convergence might be enhanced. It is also important to assess how communication and informational resources can assist in this matter. Following networking meetings, dialogue between expert groups of scientists and policy makers will establish new means for im-proved convergence of policy, communality of research and communication. The following key areas will be addressed:

Convergence of research policy1. Initiation of dialogue between key research funders and policy makers;2. Exploration of research policies and mechanisms of research support.

Communality of research currency1. Determination of current resource centres (including infrastructures), inclusive of those

under development, and those requiring assistance; 2. Determination of informatics currently used to keep records, and provide access to

these resource centres;


PRIMEwww.prime-eu.org

Project Type:Coordination ActionContract number:LSHG-CT-2005-005283Starting date:1st June 2005Duration:48 monthsEC Funding:

799 417


http://www.prime-eu.org

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3. Determination of areas with standard protocols in place, and areas lacking such protocols;

4. Determination of the presence and absence of quality control.

Improved communication1. Determination of websites and databases cur-

rently available, and of means to improve their inter-communication;

2. Exploration of training needs, and means to fund training;

3. Determination of available expertise at indi-vidual institutes within the project, and poten-tial for training provision.

Potential Impact: The Eumorphia programme of mouse phenotyping delivered pan-European standards for a mouse phenotyping platform (www.empress.har.mrc.ac.uk). PRIME will investigate stand-ardisation in other areas of mouse functional genomics, by investigating means of produc-ing common and standardised information systems for mouse resources, as well as improv-ing integration and common data standards.

PRIME will find ways to avoid duplication in research, by facilitating interaction between research groups working in common research areas; improve access to resources and da-tabases, ensuring that data can be shared and avoiding duplication; and work to common standards and protocols, allowing data to be directly compared by laboratories, reducing the need to duplicate the research. In addition, the project will genuinely benefit the cause of animal welfare, by reducing the number of animals used for research purposes.

Keywords: mouse functional genomics, animal models, integrating research, resources, infrastructures, research policies

Project Coordinator:Prof. Steve BrownMedical Research Council Mammalian Genetics Unit MRC HarwellOxfordshire, OX11 0RD, [email protected]

Prof. Martin Hrabé de AngelisGSF-National Research Center for Environment and Health GmbHInstitute of Experimental GeneticsNeuherberg, Germany

Prof. Andrea BallabioTIGEM, Telethon Institute of Genetic MedicineNaples, Italy

Prof. Johan AuwerxInstitut Clinique de la SourisIllkirch, France

Prof. Philip AvnerInstitut PasteurParis, France

Partners


Priorities for mouse functional genomics research across Europe: integrating and

strengthening research in Europe


http://www.empress.har.mrc.ac.uk


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State-of-the-Art: The aim of FLPFLEX is to develop a novel genetic approach to the manipulation of gene expression in the mouse in order to dissect complex genetic pathways and to provide more accurate models of human disease. Most major human diseases are caused by small cumulative changes in cell function that are often related to inherited susceptibility to differ-ent diseases. Recapitulating these multiple genetic susceptibilities in an animal model has remained a major challenge to modern medical research. The FLFPLEX system engages the cell’s own gene regulatory circuits to capture subtle gene expression patterns, and at the same time provides a means to target different small changes to specific genes, allowing rapid assessment of the effect of gene mutations that cause human disease. This novel tech-nology provides powerful and adaptable tools for designing increasingly complex genetic models of human physiology and pathology.

Scientific/Technological Objectives:The project will develop readout vector technologies, establish the FLPFLEX cell library and develop flexible genomic insertion cassettes carrying modifications to allow recombinase-mediated cassette exchange of effector genes of interest. The FLPFLEX vector carrying a mul-tifunctional tag will be randomly incorporated into the genome of embryonic stem (ES) cells. The team will also sequence and identify 10 000 FLPFLEX cassette integration sites using mouse genomic information. Fifty FLPFLEX clones will be selected for further characterisation and focused studies in vivo. Different effector genes will be introduced in selected FLPFLEX cell clones. The consortium will engage and refine the FLPFLEX system in a series of proof-of-concept experiments that focus on genes whose disease relevance is well documented, but mutations which have yet to be modelled in the mouse

Expected Results: Once proven, the system can be scaled to produce the desired change in virtually any gene of clinical interest. The project also intends to provide an efficient mechanism for gen-erating, characterising and disseminating these models. FLPFLEX is strategically designed to provide an efficient mechanism for generating, characterising and disseminating these models. Information and reagents generated will be disseminated on a publicly accessible database.

Potential Impact:These studies will be correlated with work in related EU-funded projects on mouse gene ex-pression patterns and mutagenesis and the models will be disseminated to the international scientific community for further analysis and testing, broadening the knowledge base of gene expression in mice for future testing.

Keywords: medical genetics, molecular genetics, genetic engineering, animal models


FLPFLEX

Project Type:Specific Targeted Research Project Contract number:LSHG-CT-2005-513769Starting date:1st July 2005Duration:42 monthsEC Funding:

1 698 000


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Project Coordinator:Prof. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)Mouse Biology UnitMonterotondo OutstationCampus “A Buzzati-Traverso”Via Ramarini 3200016 Monterotondo, [email protected]

Prof. Andrea BallabioTIGEM, Telethon Institute of Genetics and MedicineRome, Italy

Prof. Dr. Wolgang WurstHelmholtz-Zentrum MuenchenGerman Research Center for Environmental HealthInstitute of Developmental GeneticsNeuherberg, Germany

Prof. Riccardo Cortese(Partner until project month 24) Istituto Di Ricerca Di Biologia Molecolare P AngelettiPomezia, Italy

Dr. Hansjorg HauserHelmholz Center for Infection ResearchDepartment of Molecular BiologyBraunschweig, Germany

Partners


A Flexible Toolkit for Controlling Gene Expression in the Mouse

b

a The transgene has the same pattern of expression of the endogenous SPNR gene, as visualized by in situ hybridization with both SPNR and GFP probes and by direct GFP fluorescence (a) Diagram of direct ( geo) and flipped (hygro-GFP) insertions in the third intron of the SPNR locus (b) Sagittal sections of whole embryos at 13.5 d.p.c. of heterozygous SPNR +/GFP mice, hybridized with a DIG-labeled probe of the endogenous SPNR gene and the GFP gene, indicate a specific signal in the telencephalon, mesencephalon and spinal cord. Direct GFP visualization of the adjacent sections shows the same pattern of expression of the transgene.



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State-of-the-Art:The EUCOMM project responds to the most important topic defined by Priority 1, Life Sciences and Biotechnology for Health, Genome-wide Mutagenesis in Mouse. EUCOMM integrates European skills, efforts, resources and infrastructure to produce, in a systematic high-throughput way, mutations throughout the mouse genome. A collection of up to 20 000 mutated genes will be generated in mouse embryonic stem (ES) cells using conditional gene trapping and gene targeting approaches. This library will enable mouse mutants to be established worldwide in a standardised and cost-effective manner, making mouse mu-tants available to a much wider biomedical research community than has been previously possible. For a subset of genes relevant for human disease, mutant mice will be estab-lished, archived and analysed. This will offer an opportunity to decipher molecular disease mechanisms and, in some cases, provide a foundation for the development of diagnostic, prognostic and therapeutic strategies. This project is built on exceptionally strong European expertise in mouse molecular genetics, genomics and bioinformatics, and enables automa-tion of targeting vector production and professional dissemination of material. EUCOMM fosters integration with existing European consortia which address mouse gene expression analysis, mutant phenotyping, imaging and archiving. Progress of all of these projects will be enhanced by EUCOMM mouse mutants. All targeting vectors, mutant ES cells, mouse resources and standard operating procedures generated by EUCOMM are displayed to the scientific community via the EUCOMM web-linked database, other EU consortia databases and the Ensembl browser, and distributed by two professional distribution units. Taken to-gether, EUCOMM will make a major contribution to the analysis of gene function. Finally, EUCOMM resources will represent major opportunities for exploitation by SMEs and the pharmaceutical industry.

Scientific/Technological Objectives:EUCOMM presents a work plan for a pan-European effort in mouse mutagenesis that builds on existing resources in mutagenesis, gene expression analysis, phenotyping, archiving and bioinformatics to move towards a comprehensive annotation of gene function in the mouse genome. EUCOMM aims at making a significant contribution to the international

effort to establish a library of condi-tionally mutated mouse ES cells which are available to the scientific com-munity. An ES cell library containing up to 20 000 independently mutated genes will be created using condi-tional gene trapping and conditional gene targeting approaches. From the mutant ES cell resource, by EUCO-MM itself, up to 320 mutant mouse lines will be established focusing on disease-relevant gene mutations. EU-COMM’s mutant ES cells, vectors and mouse models are publicly accessible via an interactive website, and mate-rial is disseminated via two profes-sional distributing units. Chimeric mice © GSF - IDG

Photo: Ralf Kuehn


Project Type:Integrated ProjectContract number:LSHM-CT-2005-018931 Starting date:1st January 2006Duration:48 months EC Funding:

13 000 000

EUCOMMwww.eucomm.org


http://www.eucomm.org

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Expected Results:The expected EUCOMM results after the end of the funding period will be:

conditional gene targeting mutations in mouse ES cells, including mutations associated with human disease

archiving of up to 320 mutant mouse lines

20 ligand-inducible Cre-recombinase expressing transgenic mouse lines which differ in their expression characteristics

an online database to disseminate EUCOMM material worldwide

Schematic presentation of EUCOMM organisation

Mouse embryonic stem (ES) cell colonies ©GSF - IDG Photo: Ralf Kuehn


The European Conditional Mouse Mutagenesis Programme


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integration of EURExpress, FLPFLEX, EMAGE, PRIME, FunGenES, EUMODIC, EMMA, and others.

Potential Impact:EUCOMM’s repository of conditionally mutated ES cells will allow the establishment of sophisticated mouse models for a wide range of human diseases including neurological and psychiatric diseases, cardiovascular diseases, cancer and diseases related to ageing processes. EUCOMM’s deliverables will also be very useful for target identification and validation in the development process of human disease diagnostics and therapeutics, im-plemented by companies. EUCOMM will secure intellectual property rights and the benefit for the European industry, especially SMEs, in exploiting the respective results. Altogether, EUCOMM will have a great impact on societal needs as well as on the strengthening of the European biotech industry. Furthermore, EUCOMM will contribute to the establishment of a European Research Area:

1) EUCOMM’s repository of conditionally mutated mouse ES cells will allow the estab-lishment of mouse models in a systematic, standardised, and non-redundant manner across the European scientific community, thus helping to overcome fragmentation of research efforts.

2) EUCOMM will establish a close interaction with several other EU research consortia, including the integration of all the projects’ databases, thereby supporting the estab-lishment of a European Research Area in web area terms. In addition, EUCOMM co-operates with complementary mouse functional genomics initiatives at the global level (KOMP, TIGM in the United States, and NorCOMM in Canada) in the frame-work of the International Knockout Mouse Consortium (IKMC).

Keywords: functional analysis of the mouse genome, mouse disease models, conditionally mutated mouse ES cell library

Cell culture robot (HAMILTON MICROLAB STAR)

Detail of a HAMILTON MICROLAB STAR, showing the independently

spreadable channels and a 96-channel pipetting head in

the background. ©Hamilton Life Science Robotics allowed the use

of the picture for this purpose. Photo: Alexander Starcevic


EUCOMM


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PartnersProject Coordinator: Prof. Wolfgang WurstHelmholtz Zentrum München, German Research Centerfor Environmental Health GmbHInstitute of Developmental GeneticsIngolstaedter Landstrasse 185764 Neuherberg, [email protected]

Project Co-Coordinator:Prof. Allan BradleyGenome Research LtdWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, CB10 1SA, [email protected]

Project Manager:Dr. Cornelia KaloffHelmholtz Zentrum München, German Research Centerfor Environmental Health GmbHInstitute of Developmental GeneticsIngolstaedter Landstrasse 185764 Neuherberg, [email protected]

Prof. Martin Hrabé de AngelisHelmholtz Zentrum München,German Research Center for Environmental Health (GmbH)Institute of Experimental GeneticsNeuherberg, Germany

Prof. Harald von Melchner University Hospital of the Johann Wolfgang Goethe University FrankfurtDepartment of HaematologyFrankfurt am Main, Germany

Prof. Patricia RuizCharité Universitaetsmedizin BerlinCenter for Cardiovascular ResearchBerlin, Germany

Prof. Francis StewartTechnische Universitaet DresdenDepartment of Biotec, GenomicsDresden, Germany

Prof. Johan AuwerxCentre Européen de Recherche en Biologie et Médecine - Groupement d’Intérêt EconomiqueInstitut Clinique de la SourisIllkirch, France

Prof. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)EMBL Monterotondo OutstationMouse Biology Unit Monterotondo, Italy

Prof. Steve BrownMedical Research CouncilMammalian Genetics UnitHarwell, UK

Prof. Glauco Tocchini-ValentiniConsiglio Nazionale delle RicercheIstituto di Biologia Cellulare (CNR-IBC)Monterotondo Scalo, Italy


The European Conditional Mouse Mutagenesis Programme





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State-of-the-Art:The major challenge for genetics in the 21st century is the determination of the function of all the proteins encoded by the human genome and, moreover, the role of these proteins in disease. Model organisms will be the key to this endeavour as the EUMODIC team are able to manipulate the genes and investigate the consequences for the organism. The EUMODIC (http://www.eumodic.eu) consortium is made up of 18 laboratories across Europe and in-cludes leading experts in the field of mouse functional genomics and phenotyping who have a track record of successful collaborative research in the FP5 EUMORPHIA project.

The mouse occupies a unique position in determining the genetics of disease for a number of reasons. Firstly, it demonstrates a remarkably similar development, physiology and bio-chemistry to the human. Secondly, mouse geneticists have developed a very extensive ge-netic toolkit that enables defined targeted alteration of genes in the mouse genome. Thirdly, previous research has revealed the complete sequence of the mouse genome.

As a first step towards a functional annotation of the mouse genome, EUMODIC will under-take a primary phenotype assessment of up to 650 mouse mutant lines. In addition, a number of these mutant lines will be subject to a more in-depth secondary phenotype assessment.

Scientific/Technological Objectives: The EUMODIC project will provide the tools to determine the function of the genes, by pass-ing the mice through a series of screens that will fully identify the characteristics (or pheno-type) of a mouse that has had its genes altered. These screens are designed to identify a broad range of characteristics to determine the function of the gene. The screens will give reproducible results so information from different groups of mice with different alterations to their genes can be compared.

The EUMODIC consortium will build on the findings of the EUMORPHIA project, which delivered a comprehensive database EMPReSS (European Mouse Phenotyping Resource of Standardised Screens) of Standard Operating Procedures (SOPs) that can be used to determine the phenotype of a mouse (http://www.empress.har.mrc.ac.uk). EUMODIC has developed a selection of screens, EMPReSSslim, which is structured for comprehensive, primary, high-throughput phenotyping of large numbers of mice. Primary phenotype assess-ment using EMPReSSslim will be undertaken in four large-scale phenotyping centres. They are: GSF (Germany), ICS (France), MRC Harwell (UK) and the Sanger Institute (UK). Pheno-type data from these mice will be made publicly available to the wider scientific community via the EuroPhenome database (http://www.europhenome.eu).

Mutant lines will be made available from another EU initiative, the EUCOMM (European Conditional Mouse Mutagenesis) project which aims to produce conditional mutations in 20,000 mouse genes (www.eucomm.org). EUMODIC will undertake a comprehensive pri-mary phenotype assessment of up to 650 mouse mutant lines generated by the EUCOMM consortium in the null configuration.. A distributed network of centres with in-depth expertise in phenotyping domains will undertake more complex, secondary phenotyping screens and apply them to a subset of the mice which have shown interesting phenotypes in the primary screen. Phenome data on the mouse lines will be disseminated to the wider biomedical sci-ences community via the EuroPhenome database (www.europhenome.eu). EUMODIC will



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EUMODICwww.eumodic.org


http://www.eumodic.eu

http://www.empress.har.mrc.ac.uk

http://www.europhenome.eu

http://www.eucomm.org

http://www.europhenome.eu

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also undertake further refinement of a number of phe-notyping approaches to speed mouse phenotyping.

Overall, EUMODIC is a first step towards tackling the need for large-scale phenotyping in the mouse and the comprehensive study of mammalian gene function and its role in disease.

Expected Results: The aim of the EUMODIC project is to generate com-prehensive phenotype data covering most body sys-tems on a large number of mouse mutants.

Moreover, EUMODIC plans a major discovery phase of the programme where many of the most interesting mutants will undergo more detailed secondary phenotyping. The secondary data recovered will add considerable value to the primary phenome data on many of the mutant lines. Each virtual centre will deliver a set capacity to analyse a number of mutant lines for one or more secondary screens. In addition, EUMODIC may direct particular lines of high interest directly to the secondary phenotyping centres, depending on a variety of factors such as the putative functional domains of the relevant gene, its expression patterns or interactions with other genes of known function.

Potential Impact: One of the key objectives of the LifeSciHealth priority has been to translate genomic in-formation into an improved understanding of the role of genes in disease. Research on the determination of the gene function has been supported by the availability of complete sequences of both human and a number of model organism genomes. The provision of well annotated complete sequences of the mouse genome is an important starting-point for the determination of the function of mammalian genes and the role they play in disease.

With the extensive toolkit that is available to generate mutants, this team is now in a position to generate mutations for all of the genes in the mouse genome and to examine the pheno-typic outcome for each mutant allele. The information provided would bolster and underpin many of the projects in both human and mouse genetics that are at the core of European funding and objectives of the LifeSciHealth Priority. The EUMODIC project will ensure that Europe will remain competitive in the development of phenotyping tools and approaches.

The EUMODIC project is crucial for increasing momentum in the key goals of mouse func-tional genomics by applying phenotyping platforms to the mouse mutant resources that are being developed. Moreover, the proposed links with disease genetics groups across Europe in the selection of mutants to be phenotyped will underpin the competitiveness of European functional genomics programmes.

Identifying the genetic bases for human disease is a fundamental goal of biomedical sci-ences programmes. The investigation of gene function through mouse mutagenesis and phenotyping is a central element in achieving this goal and we can expect that the iden-tification of the many disease models that will arise from the EUMODIC programme will


The European Mouse Disease Clinic:A distributed phenotyping resource

for studying human disease


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considerably inform our understanding of disease genetics. The EUCOMM programme will be complemented by a major effort in the US to develop a knock-out mouse mutant re-source (the KOMP initiative). A large-scale gene trap initiative has been recently announced (NorCOMM) in Canada as well. An international Complex Trait Consortium (CTC) is also progressing with the generation of recombinant inbred mice strains which would comple-ment the mutants created on both sides of the Atlantic.

Keywords:

phenotyping, mouse disease models, animal models, human disease models

PartnersProject Coordinator: Prof. Steve BrownMedical Research Council Mammalian Genetics Unit MRC HarwellHarwell, OX11 0RD, [email protected]

Prof Johan Auwerx Centre Européen de Recherche en Biologie et en Médecine GIE Institut Clinique de la SourisIllkirch, France

Prof. Dr. Martin Hrabé de AngelisHelmholtz Zentrum München German Research Center for Environmental HealthInstitute of Experimental GeneticsNeuherberg, Germany

Prof. Karen SteelWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, UK

Dr. Werner MuellerHelmholtz-Zentrum für Infektionsforschung GmbHHelmholtz Centre for Infection Research Braunschweig, Germany

Prof. Glauco Tocchini-ValentiniConsiglio Nazionale delle RicercheIstituto di Biologia CelluareMonterotondo Scalo, Italy

Prof. Ludwig NeysesUniversity of Manchester Heart Failure GroupManchester, UK


EUMODIC



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Prof. Nadia RosenthalEuropean Molecular Laboratory (EMBL)EMBL Monterotondo OutstationMouse Biology UnitMonterotondo, Italy

Prof. Mariano Barbacid Centro Nacional de Investigaciones Oncológicas (CNIO) Spanish National Cancer Research Centre Madrid, Spain

Dr. Jacqueline MarvelEcole normale supérieure de Lyon Ani.Rhône-AlpesDR2 Centre National de la Recherche Scientifique (CNRS)Lyon, France

Prof. Karen B. Avraham Tel Aviv UniversitySackler School of MedicineDepartment of Human Molecular Genetics and BiochemistryTel Aviv, Israel

Prof. Fatima BoschUniversitat Autònoma de BarcelonaCenter of animal biotechnology and genetic therapy (CBATG)Bellaterra, Spain

Prof. Walter WahliUniversité de LausanneCentre Integratif de GénomiqueLe Génopode Lausanne, Switzerland

Dr. Yann HeraultCentre National de Recherche Scientifique (CNRS) Institut de Transgenose, Laboratoire d’Immunologie et Embryologie Moléculaires (IEM)Orléans, France

Dr. Paul SchofieldUniversity of CambridgeDepartment of Physiology,Development and NeuroscienceCambridge, UK

Prof. Andrea BallabioTelethon Insitute of Genetic and Medicine (TIGEM)Naples, Italy

Prof. George KolliasAlexander Fleming Biomedical Sciences Research CenterVari, Greece


The European Mouse Disease Clinic: A distributed phenotyping resource for studying human disease


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State-of-the-Art:In Europe, much of the current effort in functional genomics, as well as knowledge of the biology of human disease, is underpinned by a scattered collection of databases. Failure to sustain and integrate these databases will ultimately damage Europe’s competitiveness in these areas of research. CASIMIR is designed to coordinate and integrate databases that have been set up in support of the Fifth, Sixth and Seventh Framework Programmes for the storage of experimental data, including sequences; and of material resources, such as bio-logical collections, that are relevant to the mouse as a model for human disease. Ensuring that databases are inter-operable will generate enormous synergy in the provision, integra-tion and analysis of data, significantly enhancing the value of research.

Scientific/Technological Objectives:CASIMIR will deliver a series of scientific meetings, reports and papers addressing the cur-rent state of databases supporting mouse functional genomics in Europe, and will recom-mend a feasible and widely applicable model for their inter-operability and sustainability. It will also address the mobilisation of national resources, where databases are funded solely or partly by Member States. The consortium’s specific objectives are set out below:

1) Standardisation of data representation and its semantics; 2) Standardisation of data transfer and database-querying protocols; 3) Creation of the modes of database use that are required by the community, and

provision of appropriate interfaces; 4) Dissemination of information regarding the existence of, and means of accessing,

databases throughout Europe; 5) Consideration of legal issues surrounding the deposition of data in public databases.

Failure to address these issues could damage European research in future, if data resources remain fragmented. CASIMIR will also, therefore, address three aspects of the sustainability of databases and informatics infrastructures: (1) Scientific sustainability, as measured by the willingness of scientists to use them and to deposit their data in them, for the benefit of the whole scientific community; (2) Financial sustainability, measured mainly in terms of the provision of curators, database developers and informaticians; (3) Technical sustainability, i.e. the need to accommodate innovations in database and (semantic) web technologies, to keep databases compatible with evolving worldwide standards, once they have been established.

Expected Results:In the first phase of the project, which will last nine months, the consortium will gather information concerning interested parties with a stake in informatics infrastructures and da-tabases, beyond the consortium itself, and establish a presence on the world wide web, in order to inform the community of its existence and to invite external views. It will make use of reports from an existing European project known as PRIME, to obtain information about the current state-of-the-art, in mouse databases in Europe.

In the second phase of the project, the consortium will prepare a set of recommendations for data standards and semantics, together with reports on strategies for financial sustain-ability and an assessment of the impact of legal considerations on data deposition. An annual public meeting will be held, which, along with scientific publications, will contribute towards the dissemination of the project’s findings.


CASIMIR

Project Type:Co-ordination ActionContract number:LSHG-CT-2006-037811Starting date:1st February 2007Duration:36 monthsEC Funding:

1 300 000

www.casimir.org.uk


http://www.casimir.org.uk

239

Potential Impact:CASIMIR will produce a coherent strategy for the technical integration and scientific sus-tainability of the database infrastructure required for mouse functional genomics and re-lated investigations into human disease. It will lay the foundations for a coherent and sus-tainable informatics infrastructure, which will produce added value for both the European Commission and for funding agencies of the EU Member States. In doing so, it will support the following activities: (1) The functional analysis of mammalian genes; (2) The develop-ment of animal models of human disorders; (3) The development of widely applicable resources for the understanding of gene function and the dissection of genetic networks, which, in turn, will aid comparison of conserved and species-specific functions between various model organisms and man.Europe currently has a competitive edge over the rest of the world, in terms of academic and industrial research using the mouse as a model. If that advantage is to be retained, a coherent strategy must be settled for maintaining and developing the existing database infrastructure. To this end, CASIMIR will drive integration, the free flow of information and ultimately, innovation in the health sciences.

Keywords: bioinformatics, databases, mouse, animal models

Project Coordinator:Dr. Paul SchofieldUniversity of CambridgeDepartment of PhysiologyDevelopment and NeuroscienceDowning StreetCambridge, [email protected]

Dr. John HancockMedical Research CouncilMammalian Genetics UnitHarwell, UK

Dr. Duncan DavidsonMedical Research CouncilHuman Genetics UnitEdinburgh, UK

Prof. Rudi BallingHelmholtz-Zentrum für InfektionsforschungBraunschweig, Germany

Prof. Martin Hrabé de AngelisHelmholtz Zentrum München German Research Center for Environmental Health (GmbH)Institute of Experimental GeneticsNeuherberg, Germany

Prof. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)EMBL Monterotondo OustationMouse Biology Unit,Monterotondo, Italy

Dr. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Prof. George KolliasInstitute of ImmunologyBiomedical Sciences ResearchCentre ‘Alexander Fleming’Vari, Greece

Prof. Glauco Tocchini-ValentiniIstituto di Biologia CellulareConsiglio Nazionale della RicercheMonterotondo Scalo, Italy

Dr. Tom WeaverGeneservice LtdCambridge, UK

Partners


Co-ordination And Sustainability of International Mouse Informatics Resources




RAT4.2

STAR

EURATools

Med-Rat


242

State-of-the-Art:The rat is an important model organism for systems biology, providing the most relevant models of common multifactorial human disease, and is by far the leading model species in pharmacology and toxicology. Decades of exquisite phenotyping and detailed analysis of crosses of inbred rats have resulted in initial localisation of hundreds of loci involved in complex disease and quantitative phenotypes, but with very few eventual gene identifica-tions to date. A clear understanding of the origin and structure of the genetic variation in the rat will provide a missing key piece of this puzzle. The proposed SNP-based haplotype map provides a valuable tool for functional genomics, specifically by focusing positional cloning of QTLs through the reduction of regions obtained through linkage analysis, the selection of ideal strain combinations for further reduction of critical regions, and the use of correlation across many inbred strains to identify very short gene-harbouring regions.

Scientific/Technological Objectives:Taking advantage of the access to novel gene functions promised by mouse and rat QTL studies, there is a need for new innovative and straightforward approaches that provide strategic support for QTL research in the rat in Europe. The proposed haplotype map will be represented to the genetics community to facilitate QTL gene identification. The develop-ment of a set of 150 000 high-quality candidate SNPs is a prerequisite for the construction of a detailed haplotype map across the rat genome. Ancestral segments of rats representing the most commonly used rat strains in life science will be used to identify very short genomic regions, which are most likely to harbour the corresponding disease genes. A clear under-standing of the haplotype structure and origin of genetic variation in these strains will be a key progress in biology and will have deep impact on understanding disease development and health.

Expected Results:STAR will lead a comparative molecular analysis across many disease relevant strains. It will provide essential tools that will be immediately useful to focus positional cloning of QTLs through the reduction of regions obtained through linkage analysis via identification of seg-ments shared by the strains used for the cross, and the selection of ideal strain combinations for further reduction of critical regions through simple intercross/backcross experiments. Also, the use of correlation between phenotype and ancestral sequence origin across many inbred strains will help to identify the very short genomic regions most likely to harbour responsible genes. The research will be objective-driven and carried out in the following steps:

1. identification of sufficiently large sets of sequence variation throughout the rat ge-nome within transcribed sequences and within genomic sequences

2. establishment of a haplotype map 3. display of results to integrate into existing databases.


STAR

Project Type:Specific Targeted Research Project Contract number:LSHG-CT-2004-005235 Starting date:1st January 2005 Duration:24 months EC Funding:

2 400 000

www.mdc-berlin.de


http://www.mdc-berlin.de

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Potential Impact:STAR’s focus is to gather fundamental knowledge and basic tools for functional genomics by conducting research on sequence variation across the rat genome to define the ancestral haplotype blocks. It has strong innovative aspects and will contribute towards strengthen-ing the competitive position of European research, but it has also a potentially very signifi-cant societal impact in the mid to longer term regarding the improvement of healthcare. The STAR consortium will internally generate standard operational procedures for defining haplotype blocks and widely applicable genotyping panels, which will provide a valuable basis for the creation of standards in SNP typing and validation.

Keywords: rat model, SNP, haplotype map, genetic variation, positional clon-ing, phenotyping

PartnersDr. Richard ReinhardtMax-Planck-Institute for Molecular GeneticsHigh Throughput Technology and Service UnitBerlin, Germany

Dr. Roderic GuigóCentre de Regulació GenòmicaResearch Group on BiomedicalInformatics (GRIB-IMIM)Barcelona, Spain

Project Coordinator: Dr. Norbert HübnerMax-Delbrück-Center for Molecular MedicineExperimental Genetics of Cardiovascular DiseasesRobert-Rössle-Strasse 1013092 Berlin, [email protected]

Dr. Ivo Glynne GutConsortium National de Rechercheen Génomique (CNRG)Technology DepartmentEvry, France

Dr. Dominique GauguierUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UK

Dr. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Dr. Roderic GuigóInstitut Municipal d’Assitència SanitariaGenome Bioinformatics Research LabBarcelona, Spain

Dr. Edwin CuppenHubrecht Laboratory Netherlands Institute for Developmental BiologyFunctional Genomics GroupUtrecht, The Netherlands


A SNP and Haplotype Map for the Rat



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State-of-the-Art:The EURATools Consortium will address fundamental issues of genetic and phenotypic varia-tion in mammalian biology. The project will be carried out in an integrated manner by using a number of innovative approaches. EURATools methodology is credited with making it possible to anticipate that progress will be clearly demonstrable against the state-of-the-art.

The use of whole-genome scans to identify Quantitative Trait Locus (QTL) is a powerful way to investigate the genetic basis of susceptibility to complex human diseases. Although QTL map-ping has become easier with the availability of many genetic markers, identifying the genes that underlie the QTL that are associated with common phenotypes has proved to be a chal-lenge. The new genome data generated by EURATools will build on, and markedly improve, the recently assembled draft rat genome sequence, thus improving gene models as well as the utility of the sequence for rat genetics.

Genome projects are, by nature, highly collabora-tive, as it is unusual for any single centre (or even a single country) to em-bark on genome projects alone. This makes the EURATools proposal very suited to EU funding, and will place the EU in an extremely competitive po-sition. Collaborative work with the USA, Canada and Japan will give the EU a strong place in ne-

gotiations on future resources and initiatives in these countries, and will build on the signifi-cant investment already made by the EU in the area of rat biology and genetics.

Moreover, the advancement in knowledge and associated reagents and resources will con-tribute significantly to the scientific communities’ understanding of the genetic programmes that underpin multifactorial diseases. Progress in this area will play a key role in providing the essential tools for the development of future strategies. The main goals of these strategies are to identify susceptibility genes for epidemiologically important disorders; to optimise strate-gies for new drug design; and to identify new targets for therapies for treatment of common human diseases.

Scientific/Technological Objectives: The main scientific and technological objectives of the EURATools project are the following:

1) Development of high-throughput genomic tools for annotation and identification of complex trait disease genes in the rat;

2) Optimization and facilitation of germline modification procedures, refinement and adaptation of nuclear transfer protocols;

Optimisation of nuclear transfer techniques for standardised

creation of cloned rats


EURATools

Project Type:Integrated ProjectContract number:LSHG-CT-2005-019015Starting date:1st March 2006Duration:48 monthsEC Funding:

11 000 000

www.euratools.eu


http://www.euratools.eu

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3) Provision of a resource for depos-iting, exchanging, preserving and distributing inbred, congenic and mutant rat strains, mapping of mul-tiple physiological phenotypes;

4) Coordination of genome sequence, gene models, mapping resources and expression data, development of data mining resources and train-ing of bioinformatics expertise;

5) Definition of genes and regulatory pathways underlying control of gene expression and protein abundance in relation to disease phenotypes, integra-tion of expression profiling and linkage analysis;

6) Positional cloning of genes in minimal congenic strains representing cardiovascular and inflammatory diseases as models for human diseases, dissection of the complex-ity of pathway controls.

Expected Results: After 4 years, the EURATools programme plans to deliver the positional cloning of several rat complex trait genes. Presently, two have been definitively identified, but several more have tantalising results based on very small, minimal congenic regions and strong positional candidates. Given the development of proposed genome re-sources and tools, the development of this is likely to accelerate to such an extent that the team could anticipate entering an exponential phase of QTL gene discovery and characterisation.

Based on past successful progress and existing ex-pertise of EURATools Partners in the field of nuclear transfer and oocyte biology; achieving robust pro-tocols for rat cloning and homologous recombina-tion by the end of the project is anticipated. Results from the project would potentially give rise to a quantum leap in the research on rat genetics and would lead to mechanistic experiments of test hy-potheses that, through observational phenotyping experiments in the rat, have arisen in hundreds of laboratories world-wide over the past 50 years.

EURATools programme plans to offer very signifi-cant opportunities for translating investment in ba-sic scientific discovery to improvements in health and opportunities for wealth generation. The tools to be put in place under these proposals will pro-vide the stimulus for an exciting period of discovery in biomedical science and translational research.

Computerised measurement of blood pressure by radio telemetry in conscious, free-moving rats

Development of a rat congenic strain for genetic analysis of rat arthritis


European Rat Tools for Functional Genomics


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Project Coordinator: Prof. Timothy J. AitmanMedical Research Council Physiological Genomics and MedicineMRC Clinical Sciences CentreHammersmith HospitalDu Cane RoadLondon, W12 0NN, [email protected]

Project Manager:Dr. Erik WernerMedical Research Council Physiological Genomics and MedicineMRC Clinical Sciences CentreHammersmith CampusDu Cane RoadLondon, W12 0NN, [email protected]

Potential Impact: The project has strong innovative aspects that will contribute to strengthening the competi-tive position of European research. Specifically, EURATools will merge European research resources and, most importantly, will use and consolidate common tools and protocols that will allow genomics data to be effectively used to understand the biology of the genome for a large number of inbred strains. The Consortium will also develop a collection of novel molecular tools to mark and select disease specific inbred strains.

EURATools has a potentially significant societal impact regarding the improvement of health-care. Its integrative and multidisciplinary approach will considerably contribute to the re-

structuring and strengthening of European R&D activities. Comparative and functional genomics studies are likely to provide data for annotating the human genome sequence, for building better animal models, for assist-ing in the development of new therapeutic agents, and for understanding gene regula-tion. As the genomic sequence is annotated

with more and more function, it will become increasingly easy to formulate testable hypoth-eses for common diseases. In addition, the project will have a broad stimulating effect on gene target validation and drug development in pharmaceutical industries.

Keywords:complex traits, drug development, disease mechanisms, informatics, gene targeting

Nuclear donor cell in the pipette prior to transfer – a preparation for rat cloning

PartnersDr. Laurence GameMedical Research CouncilMicroarray CentreLondon, UK

Prof. Norbert Hübner, Prof. Michael BaderMax-Delbrück-Centrum für Molekulare Medizin (MDC) Berlin, Germany

Prof. John Mullins, Sir Ian Wilmut University of Edinburgh (UEDIN) Edinburgh, UK

Dr. Michal Pravenec, Dr. Vladimír Landa,Prof. Vladimír KrenCzech Academy of Sciences (CAS) Prague, Czech Republic

Dr. Ewan Birney, Dr. Xosé M. FernándezEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI) Hinxton, UK


EURATools




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Prof. Anna F Dominiczak, Prof. Walter KolchUniversity of Glasgow (UGL)Glasgow, UK

Prof. Rikard HolmdahlLund University Medical Inflammation ResearchLund, Sweden

Prof. Claude Szpirer Université Libre de Bruxelles Institut de Biologie et de Medecine Moleculaires (IBMM)Brussels, Belgium

Prof. Mark Lathrop, Dr. Ivo Gut,Dr. Jean WeissenbachCommissariat à l’Energie Atomique Centre National de Séquençage (CNS), Centre National de Génotypage (CNG)Evry, France

Prof. Dominique GauguierProf. Jonathan FlintUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UK

Prof. Alberto Fernández-TeruelUniversitat Autònoma de BarcelonaDept. of Psychiatry and Forensic MedicineBellaterra (Cerdanyola del Vallès), Spain

Prof. Tomas OlssonKarolinska InstituteNeuroimmunology UnitCenter for Molecular Medicine (CMM) Stockholm, Sweden

Prof. Qi Zhou Chinese Academy of Sciences (IOZ CAS)Institute of ZoologyState Key Lab of Reproductive BiologyBeijing, Peoples Republic of China

Dr. Richard ReinhardtMax-Planck-Institute for Molecular Genetics (MPIMG)Berlin, Germany

Prof. Jean-Paul RenardInstitut National de la Recherche Agronomique (INRA)Unité de Biologie du DéveloppementJouy en Josas, France

Dr. Alexandre FraichardgenOway SA Lyon, France

Prof. Roland WolfCXR Biosciences Ltd. (CXR)Dundee TechnopoleDundee, UK


European Rat Tools for Functional Genomics


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State-of-the-Art: The post-genomic era offers opportunities to improve the quality of life in Europe. Whilst projects involving mice and human genome have revealed the basic genomic information, complex modelling systems are now required to transfer knowledge into functional biology and medicine. Transgenic (TG) animal models play an important role in the attempt to dis-cover the genetic basis of human disease. In particular, there is a need for animal models instead of cell culture because of the complexity of the biological processes that form the ba-sis of most diseases. To date, most information on genomics has been generated through the mouse model. However, the potential of this is limited because the anatomy and physiology of mice are not always adequate for studying human disease. In addition, the sophisticated techniques used for the mouse model have, through the procedure of nuclear replacement, now become available for studies in non-murine species.

The MED-RAT project aims to exploit these advances, and, by generating transgenic models in other species, bridge the gap between mouse models and treatment of human diseases. Many species have metabolism and organs more similar to humans than to mice. However, the lack of stable stem cell lines in animal species other than mice has impeded the use of refined genetic tools for specific targeted genetic models.

Scientific/Technological Objectives: The aim of the MED-RAT project is to establish Europe as a leader in animal models for compar-ative functional genetic research by 2008. The establishment of transgenic laboratory animal models will reveal the correlation between the genetic code and the biological functions and this approach will potentially clarify the genetic base of many diseases including Alzheimer’s, cardiovascular diseases, diabetes and cancer.As part of the 6th Framework Programme, the primary objective of MED-RAT is to produce a technological platform for the generation of novel targeted genetic animal models, thus provid-ing a powerful tool for European functional genomics with great potential for medical research. Additional objectives include: 1) validating the nuclear replacement as a technical platform to produce transgenic mouse models; 2) clarifying the role of mitochondrial inheritance in nuclear replacement; 3) improving gene targeting methods in somatic cells cultures; 4) developing an improved system for banking and distributing the newly generated model animals.

Expected Results: The examples reported above demonstrate the need to understand gene function differences in various species. The aim of MED-RAT is to create models in rats with targeted genetic modi-fications. This will result in the creation of new models to compare the functional genomics

of rats with those of mice. The application of these conclusions will create new or improved methods for somatic cell gene targeting, gam-ete and embryo cryopreservation, and new knowledge on the role of mitochondria in nu-clear replacement, Activation of mitochondrial and ribosomal RNA genes following nuclear replacement will altogether contribute to the creation of a novel technological platform. The safety and reliability of this platform will be validated in the mouse model, by apply-ing an already existing state-of-the-art mouse geno- and phenotyping system. Mouse clones


Med-Rat

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2006-518240Starting date:1st March 2006Duration:36 monthsEC Funding:

1 575 000


249

Potential Impact: The development of novel and more efficient animal nuclear replacement techniques for mammalian animal models in mouse and rat with targeted genetic modifications, is crucial for the generation of precisely defined transgene conditions and defined genomic back-grounds. This is an important prerequisite for the standardised and reproducible appraisal of transgene-induced phenotypic variations. The parallel animal nuclear replacement and phenotype studies within this consortium will allow the standardisation of animal nuclear replacement procedures and result in interpretation. Development and dissemination of ani-mal models are fundamental for making them accessible for the wider scientific community. A separate work package focuses on the cryopreservation of gametes of newly generated animal models in mouse and rat. Banking of such gametes and their international exchange will allow the laboratories involved to study a standardized genetic background model.

Forecasts in different countries point out that in 2020, close to 40 percent of the population will be older than 65 years. The ageing population is prone to various diseases, causing immense social and economic problems. Gene medicines will be effective in primary pre-vention and in the treatment of chronic diseases as they interfere with their molecular cause, and will thus provide better treatment at lower cost.

Keywords: gene targeting, somatic cell, nuclear replacement, mouse, rat, com-parative functional genomics, animal models

Project Coordinator: Dr. Andras DinnyesAgricultural Biotechnology Center Genetic Reprogramming GroupSzent-Gyorgyi A. u. 42100 Godollo, [email protected]

Project Manager:Nora BurgmannAgricultural Biotechnology Center Genetic Reprogramming GroupSzent-Gyorgyi A. u. 42100 Godollo, [email protected]

Dr. Johannes BeckersHelmholtz Zentrum MünchenDeutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) (former GSF)Neuherberg, Germany

Prof. Mathias MüllerUniversity of Veterinary MedicineInstitute of Animal Breedingand GeneticsVienna, Austria

Prof. Poul Maddox-HyttelUniversity of CopenhagenDepartment of Basic Animaland Veterinary Sciences Frederiksberg, Denmark

Prof. Keith CampbellUniversity of NottinghamDivision of Animal PhysiologySchool of BiosciencesNottingham, UK

Dr. Andras DinnyesBioTalentum LtdGodollo, Hungary

Partners


New Tools to Generate Transgenic and Knock-out Mouse and Rat Models





ZEBRAFISH4.3ZF-MODELS

ZF-TOOLS


252

State-of-the-Art:In recent years, model organisms have played an increasingly important role in genome research, both in addressing basic biological questions and in making the best possible use of sequence information for human health (drug design and diagnostics). While Drosophila and have yielded valuable information, many aspects of human develop-ment and gene regulation require a vertebrate model. In this context, the zebrafish has several unique advantages, such as transparent, easily accessible embryos, simple breed-ing and a short generation time. It has therefore become the pre-eminent, non-mammalian vertebrate model organism, complementing the most widely used mammalian organism, the mouse.

Zebrafish mutants have been characterised, that affect a large number of developmental processes, such as early embryogenesis, organ formation and simple behaviour. The func-tions of most zebrafish genes have been shown to be conserved in other vertebrate groups, and a large proportion of the known zebrafish mutations are candidates for human disease genes. The importance of the zebrafish for functional genomics is illustrated by the recent establishment of several SMEs that focus on zebrafish research. To provide a systematic basis for the cloning of zebrafish mutations, increasingly powerful genomic tools have been developed, both in Europe and in the USA. The Fishman lab in Boston, for example, has produced 4,000 microsatellite markers, while the zebrafish genomics group currently led by Robert Geisler, in Tübingen, Germany, has mapped several hundred mutations and cre-ated a radiation hybrid map for the zebrafish.

Scientific/Technological Objectives:The ZF-MODELS consortium will produce new insights into how genes control development and ageing in vertebrates, insights that could potentially lead to the development of new or improved therapies for human diseases. Its targets include common pathologies such as cancer, neurodegenerative diseases, muscular dystrophies and eye diseases, as well as resistance to infections, the process of wound-healing and behavioural disorders.

Zebrafish development


ZF-MODELSwww.zf-models.org


12 000 000


http://www.zf-models.org

253

The specific, scientific objectives of the project can be described as follows: (1) Two large-scale mutagenesis projects, offering scientists the opportunity to examine zebrafish carrying genetic mutations. The first such screen, organised by the Max-Planck Institute for Develop-mental Biology, was initiated in January 2005; the second, organised by the University of Freiburg, got underway in mid-2005. In contrast to previous zebrafish mutagenesis screens, the ZF-MODELS project places an emphasis on the genes relevant to human disease, and on mutations affecting the adult as well as the developing fish; (2) Analysis of gene expres-sion patterns. Thousands of fish are being generated, in which the expression of green fluorescent protein is under the control of enhancer sequences of specific genes (enhancer detection screening). Under blue light, the tissues of these fish light up where the gene in question is being expressed. Three-dimensional patterns of gene expression will also be analysed during development, on a large scale, using in situ hybridisation; (3) Expression profiling and proteomics. The activity (expression) of tens of thousands of zebrafish genes is being analysed on gene chips (microarrays), in an effort to discover how genes regulate each other’s activity during normal development, and how this regulation is disturbed in mu-tants. In addition, proteins expressed in normal and mutant zebrafish are being analysed, to elucidate how protein expression is affected.

Expected Results:The expected results of the ZF-MODELS project are as follows: (1) Disease models. Fish with genetic disorders corresponding to human diseases will be produced by chemical muta-genesis (forward genetics) and targeted knockout (reverse genetics), and characterised by the consortium. These disease models will aid clinical researchers and the European phar-maceutical industry in developing new therapies; (2) Drug targets. The vast majority of ze-brafish genes are orthologues to human genes, over half of which have yet to be assigned a function in the Human Genome Project. ZF-MODELS will discover novel candidate genes for regulatory pathways by their expression patterns and mutant phenotypes. These genes will be made available to the European pharmaceutical industry for evaluation as potential drug targets, in small molecule screens, for instance; (3) Analysis of regulatory pathways. The consortium will elucidate previously unknown pathways of gene regulation that are relevant to human development. This information will be obtained by expression profiling

Zebrafish adult


Zebrafish Models for Human Development and Disease


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and proteomics, in combination with more traditional approaches in developmental genet-ics, such as phenotypic and functional analysis of mutants. Improving basic knowledge of human development is central to understanding the causes of many congenital diseases and cancers.

Potential Impact:ZF-MODELS will provide new tools and large data sets for functional genomics of the ze-brafish, allowing European researchers to access genomic data from the ongoing sequenc-ing project in novel ways. There are currently estimated to be nearly 300 research groups using zebrafish data and screening methods, of which almost 200 are located in the USA. The American research groups are focusing on the development and deployment of new functional genomics tools, in anticipation of sequencing information to be generated by the UK’s Wellcome Trust Sanger Institute. It is important that European groups also have the tools to use this resource, in order to compete on an international level, and to strengthen the European science base in comparative genomics, and its applications in understanding the basis of human diseases.

The geographical distribution of zebrafish research groups in Europe reflects past invest-ments in research as well as the historical development of the field. One of ZF-MODELS’ main goals is to spread expertise and to encourage the use of the zebrafish as a non-mam-malian vertebrate model in groups emerging beyond the traditional centres of strength — in particular, in groups in EU Candidate States, which lack the large-scale facilities required for genome sequencing and high-throughput functional genomics, but which could benefit greatly from use of the zebrafish model, in addressing their specific research questions. The ZF-MODELS consortium will therefore encourage the participation of researchers from emerging groups across the EU and the Candidate States in its training programmes and workshops. Arrangements will be made for the training of technicians, and advice will be offered on means of setting up new laboratories and screening facilities. There will also be opportunities for emerging groups to join the consortium — opportunities that will be announced publicly as and when they rise, through mailing lists, websites and international meetings, as well as through direct contact with those emerging European groups known to the consortium. With its strong focus on human disease, ZF-MODELS expects to advance basic, early clinical and translational research.

Keywords:functional genomics, model organisms, animal models, disease mechanisms, drug targets, bioinformatics, zebrafish, human development

PartnersProject Coordinator:Dr. Robert GeislerMax Planck Institute for Developmental BiologyDepartment of GeneticsTübingen, [email protected]

Prof. Christiane Nüsslein-VolhardMax Planck Institute for Developmental BiologyTübingen, Germany

Carl-Philipp HeisenbergMax Planck Institut of Molecular CellBiology and GeneticsDresden, Germany

Dr. Matthias HammerschmidtMax-Planck-Institut für ImmunbiologieFreiburg, Germany


ZF-MODELS



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Prof. Jane RogersGenome Research LtdWellcome Trust Sanger InstituteCambridge, UK

Dr. Christine ThisseCentre Européen de Recherche en Biologieet en Médecine (CERBM)Institut de Génétique et de Biologie Moléculaireet Cellulaire (IGBMC)Illkirch, France

Prof. Ronald H. A. PlasterkHubrecht LaboratoryNetherlands Institute for Developmental BiologyUtrecht, The Netherlands

Prof. Philip W. InghamThe University of SheffieldCentre for Developmental GeneticsSheffield, UK

Prof. Stephen WilsonUniversity College LondonDepartment of Anatomy and Developmental BiologyLondon, UK

Dr. Frédéric RosaInstitut National de la Santé et de la RechercheMédicale (INSERM)U368 INSERM: “Biologie Moléculaire duDeveloppement”Paris, France

Prof. Wolfgang DrieverAlbert-Ludwigs-Universität FreiburgLaboratory of Developmental BiologyFreiburg, Germany

Dr. Thomas BeckerUniversity of BergenSars Centre for Marine BiologyBergen, Norway

Dr. Francesco ArgentonUniversita’ degli Studi di PadovaDipartimento di BiologíaPadova, Italy

Dr. Laure Bally-CuifGSF-Research Center for Environment and HealthInstitute of Developmental GeneticsNeuherberg, Germany

Dr. Philippe HerbomelInstitut PasteurDépartement de Biologie du DéveloppementUnité Macrophages et Développement de l’ImmunitéParis, France

Prof. Herman SpainkLeiden UniversityInstitute of BiologyLeiden, The Netherlands

Prof. Uwe SträhleForschungszentrum Karlsruhe GmbHInstitut für Toxikologie und GenetikKarlsruhe, Germany

Dr. Michael BrandTechnische Universitaet DresdenBIOTEChnologisches ZentrumDresden, Germany

Prof. Stephan C. F. NeuhaussUniversität ZürichInstitute of ZoologyZurich, Switzerland


Zebrafish Models for Human Development and Disease


256

State-of-the-Art:Human disease research and drug development rely heavily on the use of animal models. Among these, the mouse model is the most intensively studied. However, over the last dec-ade the zebrafish has emerged as an attractive alternative model and has progressively gained importance. This is due to the fact that the zebrafish offers exciting novel research opportunities because of the optical transparency of its embryos and its amenability to genetics. To date, the value of zebrafish in pharmacological studies has not yet been exten-sively explored and exploited. However, findings emphasise the potential of using zebrafish in several phases of drug discovery processes and in toxicological screens.

Scientific/Technological Objectives: The ZF-TOOLS project comprises the coordinated effort of three research laboratories and three SMEs aimed at achieving the following two main objectives: Firstly, a genomic-based marker discovery for biomedical screens in zebrafish and, secondly, the use of high-through-put marker analysis and tumour cell implants for the identification of tumour growth and metastasis factors and organismal defence factors.

More specifically, the project aims to develop a case study for an anti-tumour drug screen-ing system, based on the implantation of fluorescently labelled tumour cells into zebrafish embryos. This innovative tumour cell implantation system is currently being developed by one of the SME partners and has the major advantage that it does not involve the use of transgenic animals. Growth and metastasis properties of implanted tumour cells can be ef-ficiently monitored by fluorescence microscopy during the development of the transparent zebrafish embryos. This system resembles the natural situation of tumour growth, as the tumour cells are derived from zebrafish cell cultures of embryonic origin and implanted back into zebrafish embryos. It is envisaged that a powerful screening system can arise by combining high-throughput marker analysis with the possibility to visualise tumour growth and metastasis in an optically transparent vertebrate model organism.

However, for the realisation of this complex screening system, the identification of relevant disease marker genes in zebrafish represents a crucial step. In ZF-TOOLS, different ge-nomics approaches will be used to discover novel markers, which will be suitable for ap-plication in the ZF-TOOLS tumour screening system and will also have a broader utility for disease research in the zebrafish model.

Expected Results: The strategic aim of ZF-TOOLS is the development of a zebrafish embryo screening system as an innovative genomics tool. This system will be employed for high-throughput effective-ness testing of pharmaceutical compounds that have the potential to influence disease proc-esses, including tumour growth, metastasis and immune defence responses. This zebrafish screening tool offers some unique features that make it very attractive in comparison with existing tools. In order to establish the zebrafish screening tools, the project will undertake a multidiscipli-nary functional genomics approach which integrates different global expression profiling techniques and bioinformatics. Based on this approach, the ZF-TOOLS project expects to achieve the following results:

1) Knowledge of tumour growth and metastasis factors and organismal defence factors; 2) High-throughput tools for quantitative analysis of disease marker sets; 3) A collection of constitutive and inducible, oncogenic and non-oncogenic reporter Transparent zebrafish embryo


ZF-TOOLS


1 739 000


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cell lines useful for basic disease research and for application in screening systems;

4) Case study results of a novel anti-tumour drug screening system, based on the implantation of fluorescently labelled tumour cells into zebrafish embryos.

Potential Impact: The ZF-TOOLS project aims to reinforce European competitiveness by generating strategic knowledge thanks to its multidisciplinary research approach. The developed tools and technology will be exploited for basic research on vertebrate disease and for strategic research and service activities on behalf of three high-tech SMEs.

The lack of basic knowledge of disease marker genes is the current bottleneck for biomedical research in zebrafish and for genomics-based compound screens in this model organism. The ZF-TOOLS project uses multidisciplinary functional genomics approaches to discover novel disease markers. The expected identification of factors important for tumour growth and metastasis and organismal defence responses will generate fundamental knowledge relevant to human health and will open the door to the establishment of zebrafish-based biomedical research and screening tools.

Keywords: zebrafish, animal models, zebrafish embryo model, oncogenic cell implants, anti-tumor drug discovery, reporter cell lines, tumor mark-ers, immune response markers, expression profiling, screens, high-throughput techniques

Project Coordinator: Dr. Annemarie H. MeijerLeiden UniversityInstitute of BiologyMolecular Cell BiologyWassenaarseweg 642333 AL Leiden, The [email protected]

Prof. Dr. Herman P. SpainkZF-screens BVLeiden, The Netherlands

Dr. Nicholas Simon FoulkesForschungszentrum Karlsruhe GmbHInstitute for Toxicology and GeneticsEggenstein-Leopoldshafen, Germany

Dr. Bas ReichertBaseClear BVLeiden, The Netherlands

Dr. Tamás ForraiZenon Bio LtdSzeged, Hungary

Dr. Mátyás MinkSzeged UniversityDepartment of Geneticsand Molecular BiologySzeged, Hungary

Partners

Tumour screening system


High-throughput Tools for Biomedical Screens in Zebrafish




OTHER MODELS

4.4NemaGENETAG

TP Plants and Health

X-OMICS


260

State-of-the-Art:The nematode Caenorhabditis elegans is a widely appreciated, powerful platform on which to study important biological mechanisms related to human health. Numerous human disease genes have homologues in C. elegans, and essential aspects of mammalian cell biology, neurobiology and development are faithfully recapitulated in this worm. We aim to develop cutting-edge tools and resources that will facilitate the modelling of human patholo-gies in C. elegans, and advance our understanding of animal development and physiology. The final product of our focused project – a comprehensive collection of transposon-tagged alleles – together with the acquisition of efficient transposon-based tools for mutagenesis and transgenesis in C. elegans, should be of great value to the European and international scientific community.

Scientific/Technological Objectives:Our initiative has three clear objectives.

1. Optimisation/automation of the Mos1-based system for large-scale mutagenesis. The Mos1 system has already been established as an efficient tool for gene tagging

in C. elegans. We will further characterise this system in terms of insertion bias and mutagenicity. Through such detailed characterisation, we will seek to optimise Mos1 tools and reagents for high-throughput screenings.

2. Development of novel transposon-based systems for mutagenesis, transgenesis and genome engineering in C. elegans.

Development of other transposon systems is important for two reasons. First, all trans-posons have preferential insertion sites in genomes. Second, transposons can be used to introduce foreign sequences into the host genome and can accommodate exogenous DNA, but the frequency of transposition decreases exponentially with the size of the insert. We plan to develop alternative transposon systems in C. el-egans based on the well-characterised and widely used Minos transposable element. Transposon insertions represent an entry point to further manipulate the locus where they were inserted. We aim to develop and optimise transposon-based tools for transgene-instructed gene conversion as an alternative to homologous recombination techniques that are not available in C. elegans.

3. Construction of an ordered library of transposon-tagged alleles covering at least 85% of the C. elegans gene complement.Our aim is to use the tools and technologies described above to generate a compre-hensive collection of transposon-tagged nematode genes. Such a mutant collection will provide an extremely valuable resource because it will accelerate our under-standing of gene function, which is a major challenge in biology.

Expected Results:The expected results of our activities are categorised into two major types.Research results:

1. Optimisation/automation of Mos1 transposon-based technologies2. Development of alternative systems for mutagenesis and transgenesis in C. elegans

based on the Minos transposon3. Generation of a comprehensive, ordered library of tagged nematode genes4. Case-studies/evaluation of the resource. Technological development, innovation and demonstration-related results:5. Platform technology development/deployment.


NemaGENETAG

Project Type:Specific Targeted Research Project Contract number:LSHG-CT-2003-503334 Starting date:1st January 2004 Duration:36 months EC Funding:

1 782 474

http://elegans.imbb.forth.gr/nemagenetag


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261

Potential Impact:The massive amount of raw data generated by genome sequencing projects worldwide presents the scientific community with the stag-gering task of making sense of the information. Upon completion of our programme, we will have generated a comprehensive resource, highly valuable for functional genomics as well as for individual case studies. This resource, to-gether with the acquisition of cutting-edge func-tional genomics tools, will transform the field of nematode functional genomics and allow straightforward modelling of human patholo-gies in C. elegans, in addition to greatly accel-erating research on important biological areas, ultimately interfacing with approaches aiming to improve human health and quality of life.

Keywords: nematode, Caenorhabditis elegans, functional genomics, trans-poson-mediated mutagenesis, transposable elements, transpo-son-tagged mutants, gene knock-out, heterologous transposition

Project Coordinator:Dr. Nektarios TavernarakisFoundation for Research and Technology – HellasInstitute of Molecular Biology and BiotechnologyVassilika VoutonP.O. Box 138571110 Heraklion, [email protected]

Dr. Jean-Louis BessereauInstitut National de la Santé et de la Recherche Médicale (INSERM)Paris, France

Dr. Jonathan EwbankCentre National de la Recherche Scientifique (CNRS)Institut National de la Santé etde la Recherche Médicale (INSERM)Centre d’Immunologie de Marseille-LuminyMarseille, France

Dr. Johan GeysenMAIA ScientificGeel, Belgium

Prof. Patricia KuwabaraUniversity of BristolDepartment of BiochemistryBristol, UK

Dr. Laurent SegalatCentre National de la Recherche ScientifiqueUniversité Claude BernardLyon, France

Partners

Procedure for generation of transposon-insertion

mutants


Nematode Gene-Tagging Tools and Resources



262

State-of-the-Art:In the 1970s and 80s plant science had a solid research base in Europe, but European plant biotechnology activities have declined over the past decade. The Eurobarometer sur-vey “Europeans and Biotechnology” in 2002 showed that most Europeans are in favour of biotechnology if it is related to medical research, but many remain sceptical of agricultural and food-related biotechnology. The academic sector and plant biotechnology industry has severely curtailed biotechnology field research programmes in the EU in favour of third country trials. Also, at European universities the number of students interested in pursuing careers in plant science, genomics and biotechnology has declined. This was recognised as a matter of concern by the 2003 EU Council with a recommendation that the matter be addressed.

Scientific/Technological Objectives:The key objectives of the TP Plants and Health project were to:

until 2025;

based on the long term strategic plan;

the development of plants and products offering a healthy, balanced diet.

Expected Results:The project’s main result will be publication of the Plant Genomics and Biotechnology Action Plan in 2010. Other results will be: 1) a common vision for plant genomics and biotechnol-ogy research in the EU and a discussion of this amongst policy makers to develop coherent

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TP Plants and Health

Project Type:Specific Support ActionContract number:LSSB-CT-2004-512149Starting date:1st June 2004Duration:32 monthsEC Funding:

555 840


263

research policy measures; 2) an increased interaction between the public and private plant genomics and biotechnology research sectors with the aim of stimulating knowledge to be turned into innovation leading to increased productivity and competitiveness in Europe; 3) a more balanced public debate recognising plant genomics, biotechnology, classical agri-cultural practices and organic farming all as natural and valid components of both research and application.

Potential Impact:The publications of TP Plants and Health will be used in meetings and consultations with different stakeholders including academic institutions, industry, farmers, consumers, etc). The project will also have a long-term impact on policy makers at European level (European Commission and European Parliament) and at national level (Member State consultations and several meetings organised by individual countries, for example by the UK during its EU-presidency). This will continue and increase in the future, creating an impact on science and research policy at European level (the European Commission’sproposal for FP7) and at national level (ERA-PG, 1st National Research Programmes).

Keywords:European technology platform, policy recommendations, genomics, plant models, stake-holder forum

PartnersProject Coordinator:Dr. Karin MetzlaffEuropean Plant Science OrganisationTechnologiepark 927Ghent, [email protected]

Simon BarberEUROPABIOThe European Association of BioindustriesPlant Biotechnology UnitBrussels, Belgium


The European Technology Platform on Plant Genomics and Biotechnology:

Plants for healthy lifestyles and for sustainable development



264

State-of-the-Art:Elucidation of the function of the 25 000 genes in the human genome will be significant-ly accelerated by exploiting comparative genomic approaches in an integrative manner. The international community will soon have access to the complete genome sequence of several organisms, already validated as excellent experimental models of developmental biology. European scientists need to coordinate an efficient interfacing in their strengths in comparative bioinformatics and functional genomic approaches. Comparisons across several vertebrate and invertebrate systems allow us, by bioinformatics analysis, to identify sequenced-conserved orthologous genes with important biological roles which will most likely have conserved functions in mammals, including humans. The aim of the proposal is to organise the coordination of the research of several recognised European laboratories using the amphibian Xenopus as a model to identify vertebrate genes of medical and de-velopmental interest.

Scientific/Technological Objectives:Our overall aim is to strengthen the coordination in functional genomics research in the EU in order to understand the genetic basis of human pathologies better. We will apply a comprehensive comparative functional genomics strategy, based on the amphibian Xeno-pus model organism, with the goal of identifying and assessing the function for conserved genes during early and late development. This objective will be reached through a strong coordination between European experts in several scientific areas: bioinformatics, genom-ics and developmental genetics, using the vertebrate amphibian models Xenopus laevis and Xenopus tropicalis. The consortium will coordinate the ‘vertical’ studies from in silico defini-tion of orthologous genes (comparisons across all available genomic models) down to gene expression and function studies. Analyses of many genes by high-throughput techniques will be followed by in-depth analysis of gene sets selected for their importance in human health. This project will be integrative through the generation of interactive databases linked to mouse and human electronic resources. More precisely, the objectives of the coordination action in Xenopus genomics are to coordinate:

identified by genomic sequencing and those of other model organisms: Drosophila, Ciona, zebrafish, chick, mouse and human

thousands of orthologous genes

genes playing a role in development and differentiation

amphibian

well as general and specialised meetings and workshops.

Expected Results:The first and central aspect of this project is to coordinate the use of integrated tools which means that we go beyond the classical way of doing our science, and use and develop tools for functional genomics. The functionally characterised genes will permit development of databases directly providing comparative information between all model organisms includ-ing man. They will also provide seamless integration with downstream applications, such as


X-OMICS

Project Type:Co-ordination Action Contract number:LSHG-CT-2004-512065 Starting date:1st January 2005 Duration:48 months EC Funding:

800 000


265

high-throughput screening of drug candidates and provide information for developing animal models of human diseases. Another side-product of our action is the dissemination of the im-provements of biotechnological techniques made by some of us for modulating gene function in Xenopus. The end result of X-OMICS will be the disposal of comparative functional genom-ics data as alternative and complementary information with other organisms.

Potential Impact:Novel gene functions and technological development resulting from Xenopus genomics will give fuel to innovation activities and help in understanding human development and diseas-es. X-OMICS will facilitate efficient comparative genomics, the generation and comparison across species of gene expression data, the improvement of techniques for gene expression analysis, the development of accessible gene expression and function databases, compatible with human databases and the expansion of bioinformatic tools.Moreover, the in-depth functional analyses carried out within the consortium framework will link genomic data to development and to several human diseases, thereby guaranteeing the medical impact of the project.

Keywords: vertebrate models, Xenopus, zebrafish, mouse, systematic high-throughput gene expression studies, conserved genes, functional in vivo studies, bioinformatics, genomics, developmental genetics, interactive databases

Project Coordinator:Dr. Andre MazabraudCentre National de la RechercheScientifique (CNRS)UMR 8080 Développement et EvolutionRue Michel-Ange 375794 Orsay, [email protected]

Dr. Nancy PapalopuluUniversity of CambridgeWellcome Trust Cancer ResearchCancer Gurdon InstituteCambridge, UK

Dr. Eric BellefroidUniversité Libre de BruxellesIBMM Laboratory of MolecularEmbryologyBrussels, Belgium

Prof. Christoph NiehrsDeutsches KrebsforschungszentrumDepartment of MolecularEmbryologyHeidelberg, Germany

Partners

Dr. Tim MohunMedical Research CouncilThe National Institute forMedical ResearchDivision of Development BiologyLondon, UK

Prof. Tomas PielerUniversity of Göttingen,Center of Molecular BiologyDepartment ofDevelopmental BiochemistryGoettingen, Germany


Xenopus Comparative Genomics: Coordinating Integrated and Comparative

Functional Genomics for Understanding Normal and Pathologic Development




POPULATION GENETICS & BIOBANKS5.



POPULATION GENETICS & BIOBANKS

5.HUMGERI

MolPAGE

GENOSEPT

MICROSAT workshop

EUHEALTHGEN

PHOEBE

EUROSPAN

DanuBiobank

Impacts

EpiGenChlamydia


270

State-of-the-Art:The morbidity and mortality statistics of the Hungarian population are among the worst in Europe and it is assumed that genetic as well as epigenetic factors play a significant role in this phenomenon. Genomic research is very likely to provide a new framework to approach this problem. However, Hungarian genomic research is in its infancy, rather fragmented and unfocused. The main objective of the project is to obtain specific support for changing this unfortunate situation. A consortium of Genomic Research for Human Health in Hungary has been formed, which starts organising genomic research within this action by pulling together all the related activities in the country and providing an umbrella for medically orientated genomic research.

Scientific/Technological Objectives:Based on studies and comparisons of European human genome projects, the objectives of this action are:

-nostic works carried out in Hungary and making it available to the public and of-ficials of the healthcare system.

1) explore and integrate existing, genome-specific bioinformatics resources of the members of the consortium

2) develop a common website for the consortium including links to local activities of the partners, to their national and international collaborations, and to other genome research networks

3) organise an international workshop with experts from several existing European genome research networks with the purpose of integrating the activities of the consortium with European partners.

1) collect and provide information about the various, existing human tissue and DNA/RNA collections, their content and medical background or research project, and rules for access

2) establish a nationwide quality assurance system for collecting, handling, storing and documenting human biological samples in Hungary

3) establish the framework for sample collections from large volunteer cohorts, and move towards a centralised national biobank.

projects. Establish an, as yet, non-existing, integrated, non-profit network of biotech-nology orientated, primarily Hungarian-based SMEs.

legal framework of R&D activity, the existing official network and procedure of the ethical assessment of research protocols, and in particular genomic research pro-grammes have to conform to high European standards and regulations.

Expected Results:

proposition on the required computing environment


HUMGERI www.humangenom.hu

Project Type:Specific Support Action Contract number:LSSG-CT-2003-503405 Starting date:1st April 2004 Duration:30 months EC Funding:

285 000


http://www.humangenom.hu

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Group

sub-domains and partner pages (SME partnering, bioethics, genetic tests, projects, etc.)

in Disease Development)

questionnaires are on the website. There is a standard database and information management system for Hungarian biobanks.

legislation.

Potential Impact:

will stimulate: a) further uncovering of inherited

risk factors and identify candidate genes/SNPs for major disease groups

b) identification of genetic features/markers unique to the Middle European region

c) characterisation of the MHC (HLA) gene pool in Hungary

-work, the EC will have access to all of the potential facets of the Hungarian genome-related SMEs.

-wards neighbouring candidate coun-tries will help integration of the region into the ERA.

-cial impact on decision-makers to start a new funding system, providing the appropriate framework for a long-term genomic programme in Hungary.

Keywords:human genomics, research policies

PartnersProject Coordinator:Dr. László FésüsUniversity of DebrecenMedical and Health Science CenterDepartment of Biochemistry andMolecular BiologyEgyetem Ter 14032 Debrecen, [email protected]


Human Genomic Research Integration



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State-of-the-Art:It is widely recognised that large-scale phenotyping studies are required in order to identify biomarkers that will translate from bench to bedside. More specifically, such studies are necessary for an examination of the influence of many environmental and genetic deter-minants of disease. Because of the molecular heterogeneity that contributes to most of the major common disease phenotypes studied in large populations, these studies must aim to analyse large numbers of cases and controls.

Currently, a number of biobank efforts are being carried out, not exclusively in the UK, but worldwide. These efforts will soon produce an unprecedented number of samples for molecular phenotyping. As a consequence, epidemiologists, clinical trial workers and ex-perimental scientists will potentially soon be presented with numerous opportunities for the molecular phenotyping of large numbers of biological samples obtained from these biobank cohorts, patients or animal models.

Although the development of genotyping technologies for the analysis of DNA markers has, to a degree, matured enough to allow for their use on an epidemiological scale, it is not yet clear how the application of post-genomic technologies such as metabonomics and proteomics, (where standardisation of procedures and high throughput approaches are less well established), will be tackled.

The MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) project aims to design a programme to bridge this gap. The four-year project MolPAGE brings together a consortium of 18 leading academic institutions, and biotechnology and pharmaceutical companies, with expertise from a wide variety of ‘omics’ technologies and computational methods, as well as from the biology of metabolic disease.

The consortium partners are working to upscale and optimise a range of genomic, metabo-nomic and proteomic tools. In addition, the consortium is seeking to develop novel technical data analysis and integration protocols, to facilitate biomarker discovery and validation studies conducted on an epidemiological scale (“genomic epidemiology”).

Post-genomic technologies deriving from the project will be applied to biomarker discovery and typing in metabolic diseases such as diabetes and its associated vascular complica-tions, which constitute major causes of ill health and premature death, and which are reach-ing epidemic proportions in Europe and worldwide.

Scientific/Technological Objectives: A major goal of the MolPAGE consortium, is to develop and upscale a range of ‘omic’ technology platform tools (metabonomic, genomic, proteomic), and to apply these identify-ing biomarkers in predicting disease, determining risk and relating to disease activity or response to therapy.

The programme is divided into three component parts. Firstly, the project aims to evaluate sample collection and storage methodologies, understand sources of technical and biologi-cal variation and explore issues of analyte stability, so as to inform ongoing and future endeavours in biobanking and biomarker discovery.

Secondly, MolPAGE seeks to develop, upscale and validate tools that will allow molecular phenotyping at an epidemiologic scale. This includes the capacity to undertake analysis of (a) small molecules (metabonomics); (b) mRNA (transcript profiling); (c) proteins and pep-tides; (d) DNA methylation patterns; and (e) genome sequence variation.


MolPAGE

Project Type:Integrated ProjectContract number:LSHG-CT-2004-512066Starting date:1st October 2004 Duration:48 monthsEC Funding:

12 000 000

www.molpage.org


http://www.molpage.org

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The third part of the project entails the development of bioinformatic tools and statistical methods to support the storage, interrogation and analysis of the large complex data sets produced. The analysis of longitudinal cohorts from Biobank projects will be used for the validation (and large-scale phenotyping) of risk biomarkers. A number of technologies in-ternal to the consortium will be utilised for these tasks.

The MolPAGE project is using two separate approaches to biomarker discovery and valida-tion, namely a genome wide, systematic methodology (for example, transcriptomics, NMR and MS based metabonomics, and ms based proteomics) and a limited analysis which uses sets of candidate biomarkers (methylation, affinity arrays, and tissue arrays).

The MolPAGE consortium, which is coordinated by the University of Oxford, comprises 18 partners from 5 SMEs, 2 international pharmaceutical organisations and 11 public bodies. The project is organized into work packages (WPs); from an operational point of view, these work packages fall into four main areas: sample-related (1); technology-related (2); informatics and analysis (3); and training and management (4).

Expected Results:The MolPAGE project will significantly contribute to the development of international sci-entific standards in molecular phenotyping. During the project the consortium will de-velop, establish and disseminate standards for the collection, processing and storage of biological samples that are firstly, suitable for use in large sets of individuals, secondly, applicable to blood, urine and solid tissue samples, and thirdly, optimised for future ‘omic’ platform analysis of DNA, RNA, protein and other biological analytes.

Another crucial aspect of the project is the development of standardised data handling and analysis methods, which will be applicable to future molecular phenotyping efforts performed on an epidemiological scale. The consortium has released an open source version of our novel web-based sample management system (http://passim.sourceforge.net) for use by other projects. Furthermore, by the end of the project, the consortium will have completed the development of a data warehouse, optimised for the submission, stor-age and integration of both raw and analysed data from a wide range of the MolPAGE technology platforms.

Similarly MolPAGE is actively working to improve the statistical tools available for analy-sis of many of these types of data, and to develop approaches for deriving an integrated view of the transcriptional, proteomic and metabonomic changes which associate with and/or predict disease. Towards MolPAGE standard setting goals, the consortium and the EU co-hosted an international workshop on ‘Standards and Norms in Population Genomics’, to establish a roadmap for developments standard setting and obtaining ac-ceptance by the wider scientific community.

Significant efforts to upscale the enabling metabonomic and proteomic technology plat-forms were made in the first two years of the project; these efforts will continue on a select-ed subset of the most promising technology platforms for the remainder of the project.

A medium-term goal of the MolPAGE consortium was to apply the methods developed in the initial phase, to proof-of-principle biomarker discovery efforts. These studies are now underway, focused on metabolic and cardiovascular disease in samples from MolPAGE and from selected European longitudinal cohort projects. By the end of the funding pe-riod, we propose to make our recommendations regarding the most suitable technology platforms for application to molecular phenotyping of biobank samples, in a broad range of disease areas.


Molecular Phenotyping to Accelerate Genomic Epidemiology


http://passim.sourceforge.net

http://passim.sourceforge.net

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Potential Impact:With MolPAGE’s initial focus on biomarker dis-covery and validation in metabolic disease (type 2 diabetes and cardiovas-cular disease), the team will be addressing a ma-jor public health problem in the EU community — a problem of considerable health and economic pro-portions even now, and one expected to escalate in the decades to come.

The methodology to be developed, however, will have applications in eve-ry form of common human disease, including cancer, inflammatory diseases and degenerative diseas-es. The involvement of five industrial partners in the

consortium, has provided the power necessary for the distribution of the project’s results and experience, to corporate institutions. These corporate institutions are capable of con-verting the knowledge generated by the project into new drug opportunities and treatment modalities, which will benefit patient groups worldwide, and increase the competitiveness of the EU-based pharmaceutical industry.

This project will therefore influence economic development in the EU in several distinct ways. By establishing successful technology platforms, we expect to stimulate the technol-ogy and diagnostic section of the health-care related economy. In addition, by addressing the single largest causes of ill health and premature death, and through their direct health benefits as well as indirectly through facilitating discovery in the pharmaceutical sector, these studies have the potential to enhance economic development.

Keywords: phenotyping, epidemiology, molecular phenotyping, genomics

Differential gene expression analysis of adipose

tissue RNA comparing obese and lean subjects from

a rat model of diabetes.


MolPAGE


275

Prof. Vladimir StichCharles UniversityDepartment of Sports Medicine Prague, Czech Republic

Dr. Alvis BrazmaEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Microarray GroupHinxton, UK

Dr. Juris ViksnaInstitute of Mathematics and Computer ScienceRiga, Latvia

Prof. Jeremy NicholsonImperial College LondonDepartment of Biological ChemistryLondon, UK

Prof. Luisa BernardinelliUniversity of PaviaDepartment of Health SciencesPavia, Italy

Dr. Stephan HoffmanGyros ABUppsala, Sweden

Joint Project Coordinators: Prof. John Bell University of OxfordRichard Doll Building, Roosevelt DriveHeadington, Oxford, OX3 7DG, [email protected]

Prof. Mark McCarthyUniversity of Oxford Oxford Centre for Diabetes Endocrinology and Metabolism (OCDEM)Churchill Hospital SiteOld Road, HeadingtonOxford, OX3 7LJ, [email protected]

Project Manager:Dr. Maxine AllenUniversity of OxfordOxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Churchill Hospital SiteOld Road, HeadingtonOxford, OX3 7LJ, [email protected]

Prof. Peter Donnelly, Prof. Lon CardonUniversity of Oxford Oxford, UK

Prof. Sir Edwin SouthernOxford Gene TechnologyOxford, UK

Dr. Ivo GutCentre National de Genotypage (CNG)Evry, France

Dr. Kurt BerlinEpigenomics AGBerlin, Germany

Dr. Rainer VoegeliDigilab BioVisioN GmbHHannover, Germany

Dr. Esper BoelNovo Nordisk A/SNovo Alle, Denmark

Prof. Mathias UhlenKTH BiotechnologyRoyal Institute of TechnologyAlbaNova University CenterStockholm, Sweden

Dr. Thomas BergmanAffibody ABBromma, Sweden

PartnersProf. Tim SpectorKings College London Twin Research Unit London, UK

Dr. Dominique LanginInstitut National de la Santé et de la Recherche Médicale (INSERM)Obesity Research UnitToulouse, France

Dr. Fredrik PontenUppsala UniversityDepartment of Genetics and PathologyHuman Proteome ResearchUppsala, Sweden

Dr. Hanno LangenF. Hoffman-La Roche AGProtemics InitiativeBasel, Switzerland


Molecular Phenotyping to Accelerate Genomic Epidemiology





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State-of-the-Art:GenOSept is a STREP which uses a multidisciplinary fundamental genomics approach (gene expression, structural genomics and population genetics) to examine genetic predisposition to sepsis. Sepsis (a life-threatening infection) is a major public health problem throughout Europe. In the USA, in 1995, it cost $17 billion to treat 751 000 patients with severe sep-sis, of whom 28.6% died. The Centre for Disease Control suggests that sepsis-attributable mortality rates are rising. We hypothesise that susceptibility to expensive new treatments and fatal outcomes from severe sepsis are, in part, genetically determined. The GenOSept project will test this hypothesis. It will standardise protocols for genotyping, facilitate application of new knowledge in functional and structural genomics, harmonise high-throughput genotyping and quality control between major European centres, and con-tribute to reducing sepsis-related mortality in European healthcare.

Scientific/Technological Objectives:Genetic predisposition for the incidence and outcome of sepsis has been recognised and suggested as a possible powerful tool for future risk stratification and even as inclusion cri-teria for therapeutic trials. GenOSept also contains a module which links patterns of gene expression with patterns of genomic variation in corresponding genes. Genomic variants may influence the individual phenotype including gene expression levels and patterns, as well as protein levels and protein structure. A possible result is that future intensive care physicians may have access to readily available genetic risk patterns includ-ing pharmacogenetics of their patients which not only allows for better risk stratification, but may also help tailor individual patient care and drug therapy.The major milestones of GenOSept are:

-base;

(ICUs);

Expected Results:The expected results of GenOSept are that it will:

-flammation, and of programmed cell death.

The novel genes identified by expression studies will add to a set of candidate genes used in a subsequent epidemiologic study which will:

functional and structural genomics;

by coordinating major European genotyping centres;

First project achievement: the diseases to be included in the study were refined and four will be examined. The inclusion and exclusion criteria database have been developed.

Potential Impact:The GenOSept findings will contribute to reducing sepsis-mortality and morbidity in Euro-


Project Type:Specific Targeted Research Project Contract number:LSHG-CT-2004-512155Starting date:1st January 2005 Duration:48 months EC Funding:

2 000 000

GenOSept https://www.genosept.eu


https://www.genosept.eu

277

pean ICUs. The project will link fundamental genomics to sepsis, a major European public health issue. The application of gene expression studies and structural genome analysis detecting genomic variation will generate novel data on relevant genes as well as novel genomic variations involved in the genetic predisposition of incidence and outcome from sepsis. The evaluation and use of novel techniques, including the gene chip technology and the establishment of a European network of clinical and laboratory groups working in the field of critical care medicine, will strengthen European biotech industry.

Keywords: intensive care medicine, sepsis, mortality, epidemiology, genetic testing, genetic predisposition

PartnersProject Coordinator:Prof. Julian Bion, Dr. Nathalie MathyEuropean Society of Intensive Care MedicineResearch Activities40 avenue Joseph Wybran1070 Brussels, [email protected]

Prof. Dr. Frank StüberRheinische Friedrich-Wilhelms-Universität BonnKlinik und Poliklinik für Anästhesiologie und spezielleIntensivmedizin UniversitätsklinikumBonn, Germany

Prof. Jean-Daniel ChicheInstitut National de la Santé et de la Recherche Médicale (INSERM)Institut Cochin- Réanimation médicaleParis, France

Prof. Adrian HillUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UK

Prof. Vito Marco RanieriUniversita degli Studi di TorinoSezione di Anestesiologica e RianimazioneTurin, Italy

Prof. Jordi RelloUniversity Rovira & Virgili Hospital Universitari Joan XXIIICritical Care Department Tarragona, Spain

Prof. Thomas MeitingerHelmholtz Zentrum MünchenInstitute of Human GeneticsNeuherberg, Germany

Dr. Yoram WeissHadassah Medical OrganisationDepartment of Anaesthesia and Critical Care MedicineJerusalem, Israel

Prof. Dr. Stefan RusswurmSIRS-Lab GmbHR&D DepartmentJena, Germany

Prof. Marion SchneiderUniversity Ulm Medical FacultySektion Experimentelle AnästhesiologieUniversitätsklinikum UlmUlm, Germany

Prof. Konrad ReinhartKlinikum der Friedrich-Schiller-Universität JenaDepartment for Anaesthesiology and Intensive Care MedicineJena, Germany

Dr. Vladimir SramekMasaryk University Brno Medical FacultySt Ann’s University Hospital Department of Anaesthesiology and Intensive CareBrno, Czech Republic

Dr. Ilona BobekNational Medical CenterDepartment of Anaesthesia and Intensive CareBudapest, Hungary

Dr. Silver SarapuuTartu University ClinicsIntensive Care UnitTartu, Estonia


Genetics of Sepsis in Europe



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State-of-the-Art: Tandem repeats are repeat sequences in the human genome. They occur in all genomes, including bacteria, yeast, plants and humans. Tandem repeats have been widely used in linkage analysis in many organisms, where they are used as non-functional markers for inheritance of genetic loci. They have also been implicated in human disease, with micros-atellites such as CAG triplet repeats causing a variety of neurological disorders and higher order motifs such as the insulin gene VNTR influencing complex diseases such as diabetes. VNTRs affect gene expression and are useful for genetic fine mapping of complex disease loci; for example they were used to identify the neuregulin 1 gene which predisposes to schizophrenia. However, despite their clear importance, in recent years far more emphasis has been placed on single nucleotide polymorphisms (SNPs) than tandem repeats because of the unproven perception that SNPs are the major cause of complex diseases. The SNP Consortium Ltd is a non-profit foundation that was developed for the purpose of provid-ing public genomic data. Its mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make the information related to these SNPs available to the public.

Scientific/Technological Objectives:

1) To stimulate international cooperation in functional genomics in Europe by bringing together researchers to examine microsatellite and variable number of tandem re-peat (VNTR) markers in human and non-human genetics and genomics.

2) To promote and facilitate international co-operation in microsatellite research by net-working scientists for a research consortium.

3) To develop microsatellite and VNTR markers as tools for genomic and genetic analy-sis with the potential to develop long term research funding and be a catalyst for cooperation, especially with SMEs and third world countries.

4) To develop web-based resources to facilitate the use of microsatellite markers in ge-nomic and genetic analysis.

Expected Results:The consortium ran two workshops, one in the UK at the Institute of Psychiatry and one in Hungary at the Hungarian Academy of Sciences (Institute of Enzymology) to train research-ers to use microsatellites in genomic and genetic analysis, which will lead to self-financing workshops in future years. The first workshop established the consortium and the second provided training in the field and allowed the dissemination of research findings and trans-fer of knowledge and technologies which developed as a result of the first workshop. SMEs participated directly in two workshops and were encouraged to develop technology that can be commercially exploited. Researchers from China and Brazil played a direct role in the consortium, and training and knowledge were transferred to other developing nations in addition to European states. The fist self-funded microsatellite workshop will be held in Colorado in February 2009.


MICROSAT workshop


112 000

www.microsatellites.org


http://www.microsatellites.org

279

Potential Impact: Microsat-SSA was focused on stimulating research into microsatellites and VNTRs as basic tools for genome research, and as candidate polymorphisms for human and animal dis-ease. A team working in a neglected area of genomics will have a significant impact on genetic and genomics, including the areas of human and animal disease, by increasing the variety of tools available to the scientists. This will improve our understanding of the basic biology of the genome, as well as the ability to locate disease-causing genes and the underlying variants, and to understand population genetics from a different perspective. Microsat-SSA will contribute to economic competitiveness by promoting the involvement of SMEs in activities related to microsatellite markers, including the provision of contract genotyping and other intellectual property related research services.

Keywords:

microsatellite, VNTR, tandem repeat, population, genetics, mapping, association, compar-ative, linkage

PartnersProject Coordinator:Prof. David CollierKing’s College, University of LondonDepartment of SocialGenetic and Developmental PsychiatryInstitute of PsychiatryDe Crespigny ParkLondon, SE5 8AF, [email protected]


Microsatellites and VNTRs: workshop on bioinformatics, genomics and functionality



280

State-of-the-Art:Member and Associated States across the European Research Area are supporting re-search on population genetics in order to build upon the significant investments made in sequencing the human genome. Significant added value can be obtained if the objectives and protocols involved in human population genetics research at a national level can be harmonised to become representative of the entire EU population. The EU would thereby develop and maintain a leading global position in genetic epidemiology and population genetics. Project coordination will be by a steering committee, which will meet twice dur-ing the planning phase of the proposed conference. It will then meet twice following the conference to agree the report and to lay the foundations for implementing the developed strategy. The conference will be held at the Wellcome Trust Conference Centre, Cambridge, United Kingdom on 21-23 September 2005.

Scientific/Technological Objectives: EUHEALTHGEN has been established to:

across the ERA and restrict fragmentation-

tabase infrastructure needed for major population genetic studies in Europe

-care professionals, policy-makers and funders about human population genetics

adoption of a joined-up and fully integrated strategy from basic research, through clinical studies to the treatment of individual patients

treatment to the identification of personal disease risk and the development of appro-priate personalised prevention strategies.

Expected Results: Some of the expected results are:

-ing technology and proteomic analysis for clinical research, thereby enhancing data generation, standardisation, acquisition and analysis

so achieve the better targeting of limited health resources


Project Type:Specific Support ActionContract number:LSHG-CT-2005-518144Starting date:1st September 2005Duration:12 monthsEC Funding:

245 000

EUHEALTHGEN


281

to the large data sets needed to integrate biological data with clinical need thus pro-moting translational research for improved human health

in this area and help improve the efficiency of translating the outcomes of clinical research into clinical practice.

Potential Impact:Human population genetics will play an important role in analysing the complex inter-actions that occur in determining susceptibility and cause of the priority disease areas. However, for this to be realised it will be necessary to ensure that the biobanks operating across Europe are compatible so that validated reagents, samples and information can be exchanged in a safe and ethically acceptable way. This provides further justification for the main aim of EUEALTHGEN, namely to develop a forward-looking strategy for translating the outputs of population genetics research into clinically useful and health enhancing initia-tives, whilst improving EU industrial competitiveness in this area.

Keywords: health sciences, population genetics, biobanks, human genetics

PartnersProject CoordinatorDr. Alan DoyleThe Wellcome TrustDepartment of Biomedical Resourcesand Functional Genomics215 Euston RoadLondon, NW1 2BE, [email protected]


Harnessing the Potentialof Human Population Genetics Research to Improve the Quality of the EU Citizen



282

State-of-the-Art:This coordination action aims to help create a harmonised network of population-based biobanks across Europe and Canada. The main purpose is to maximize the use of Europe’s population-based biobanks in the study of complex disease etiology.

Scientific/Technological Objectives: The objectives can be categorized accord-ing to the following harmonization areas: Epidemiology:

-tion-based biobanks and longitudinal cohort studies in Europe

to coordinated investigations of the ge-netic and environmental determinants of complex diseases

Isolated populations:

in Europe, with a focus on genetically isolated populations

-lection and collection of data and samples from these populations

Biobank information management:

Information Management Systems-

ed to the management of large and complex databases for biobanks

level programming and development

of flexible communication engines sup-porting reliable, efficient and secure communication between biobanks

Genotyping:

the evaluation of large-scale genotyp-ing efforts in population cohorts,

Phenotypes and environmental exposures:

approach to the assessment of a range of complex phenotypes and life-style exposures

Ethical, legal and governance issues: establish ethical, legal and governance criteria consistent with the international norms and European practices that will enable data and sample sharing for re-search purposes

Statistics:-

nadian expertise related to statistical challenges

-derpinning the design, analysis and harmonization of population-based

Expected Results: cohorts in Europe, and information on the accessibility of data and status of the studies;

isolates;

and storage strategy and report on standards in European biobanks;

population biobanks, genotyping quality and cost reports, a web-based SNP selection tool, and procedures for collection and storage of genotyping data;

phenotypes and exposures for future European biobanks;

platform;

Potential Impact:-

come existing fragmentation of European population genomic research.

sample sizes, and will help to promote collaborative international genetic epidemio-logical research.

biobanks.


Project Type:Co-ordination ActionContract number:LSHG-CT-2006-518148Starting date:1st March 2006Duration:36 monthsEC Funding:

800 870

PHOEBEwww.phoebe-eu.org


http://www.phoebe-eu.org

283

Keywords: epidemiology, genetic epidemiology, biobanks, population-based co-horts, complex disease, isolated populations, bioethics, phenotyping, genotyping, GenomEUtwin, COGENE, P3G, data management

Project Coordinator: Dr. Jennifer HarrisNorwegian Institute of Public HealthDivision of EpidemiologyOslo, [email protected]

Prof. George Davey-SmithUniversity of BristolDepartment of Social MedicineBristol, UK

Prof. Max BauerUniversity of BonnInstitute of Medical BiometryInformatics and EpidemiologyBonn, Germany

Prof. Paolo GaspariniUniversita degli Studi di TriesteFacolta di Medicina e ChirurgiaTrieste, Italy

Prof. Jaume Bertranpetit Universitat Pompeu FabraDepartment de Ciencies Experimentals i de la Salut Barcelona, Spain

Prof. Jan-Eric LittonKarolinska InstitutetDepartment of Medical Epidemiology and Biostatistics Stockholm, Sweden

Andy Harris UK Biobank LtdManchester Incubator BuildingManchester, UK

Prof. Leena Peltonen National Public Health InstituteDepartment of Molecular MedicineHelsinki, Finland

Dr. Thomas J. HudsonMcGill UniversityMcGill University and QuebecInnovation CentreMontreal, Canada

Prof. Dorret Boomsma Vrije UniversiteitDepartment of Biological PsychologyAmsterdam, The Netherlands

Prof. Anne Cambon-Thomsen INSERM U 558 Faculté de MédecineToulouse, France

Prof. Bartha Maria Knoppers Université de Montreal Faculté de Droit, Centre de Recherche en Droit PublicMontreal, Canada

Prof. Paul BurtonUniversity of LeicesterDepartment Epidemiologyand Public HealthLeicester, UK

Prof.. Cornelia van Duijn Erasmus Medical CenterDepartment of Epidemiology and BiostatisticsRotterdam, The Netherlands

Prof. Andres Metspalu University of Tartu, IMCBEstonian BiocentreTartu, Estonia

Prof. Milan MacekCharles University Prague Institute of Biology and Medical Genetics - Cystic Fibrosis CentrePrague, Czech Republic

Prof. Pagona LagiouUniversity of Athens Medical SchoolDepartment of Hygiene and EpidemiologyAthens, Greece

Prof. Paul ElliottImperial College of ScienceTechnology and MedicineDepartment of Epidemiology and Public HealthLondon, UK

Partners


Promoting harmonisationof epidemiological biobanks in Europe



284

State-of-the-Art:This project will study five special populations throughout Europe which represent a unique resource for genomic research. It will quantify genetic variation in genes known to be involved in health and disease and will harness this variation to identify novel variants. The project will build on the achievements of substantial existing investment in these special populations and will pool expertise across Europe in phenotyping, genotyping, statistical genetics and social and ethical aspects of genomic research. A common database of health and disease-related phenotypes will be established and cores of expertise established in the major project areas. This will create the largest database of phenotypic and genotypic data from genetic isolate populations and will thus improve European competitiveness in gene discovery. The project will also provide the platform for the evaluation of a novel gene discovery approach (hybrid identity profiling) which has been developed by a European SME.

Scientific/Technological Objectives:The objectives regarding genetic variation in established disease genes are:

(genetic isolate) populations in five European countries and in three outbred European populations

-ods across five special populations

-ly 40 QTs influenced by these genes across five diverse environmental backgrounds.

The objectives regarding employing genetic variation to identify novel genetic variants are:-

netic loci underlying traits (QTs) of public health importance in Europe and to employ cross population mapping and high density SNP association approaches to fine-map these loci

-ing shared chromosomal regions that show IBD sharing by genome hybrid identity profiling (HIP)

values and high-density chip genotyping

these special populations

develop a statement of best practice for interaction with study populations in terms of consent, sharing of benefits, and communication with individuals and communities

-duced in response to research findings, where this is appropriate.

Expected Results:New Knowledge:

-tions and three outbred populations in Europe will be described.

-ease-related phenotypes (QTs) will be described.

identify new genetic loci related to these QTs will be performed.


EUROSPAN

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2006-018947 Starting date:1st March 2006Duration:36 months EC Funding:

2 400 000


285

Tools:

extreme QT values will also be assessed.

Resources:-

put SNP genotyping and statistical genetics; ethical and social aspects of genomic research; phenotyping to serve the project partners.

Potential Impact:EUROSPAN will give new information on genetic variations in traits underlying conditions of public health importance in Europe and how this is related to disease risk. The project will result in greater efficiency of effort, application of state-of-the art methods, pooling of intellec-tual resources to tackle scientific problems and, ultimately, more internationally competitive research. The approach draws on genetic diversity across Europe and is distinct from exist-ing investments in national biobanks and international twin studies. The social and ethical issues raised, explored and resolved before and during the research process will have wider relevance for genetic epidemiology and the meaning of research participation.

Keywords: genomics, genetic variation, gene discovery, quantitative traits, endophenotypes, genetic isolate

Project Coordinator:Prof. Harry CampbellUniversity of EdinburghPublic Health SciencesTeviot PlaceEdinburgh, EH8 9AG, [email protected]

Prof. Alan WrightMedical Research CouncilHuman Genetics UnitEdinburgh, UK

Prof. Cornelia Van DuijnErasmus Medical CenterEpidemiology & BiostatisticsRotterdam, The Netherlands

Prof. Ulf GyllenstenUniversity of UppsalaDepartment of Genetics and PathologyUppsala, Sweden

Prof. Thomas MeitingerGSF - Forschungszentrum für Umwelt und GesundheitInstitute of Human Genetics Munich-Neuherberg, Germany

Prof. Igor RudanUniversity of ZagrebDeptarment of Medical StatisticsEpidemiology and Medical InformaticsZagreb, Croatia

Dr. Jorg HagerIntegraGen SAEvry, France

Dr. Peter Pramstaller EURAC - European Academy of BolzanoDepartment of Genetic MedicineBolzano, Italy

Partners

Pulse wave


EUROpean Special Populations Research Network: Quantifying and Harnessing Genetic Variation for Gene Discovery



286

State-of-the-Art:Public healthcare systems in Europe are facing the challenge of a rapidly ageing population which is susceptible to a wide variety of ageing-related disorders, such as heart disease and strokes, and metabolic disorders such as diabetes. People over 65 use 3 to 5 times more healthcare facilities than young people, and even though death rates from heart dis-ease and strokes have decreased in recent years, these illnesses are making an increasing financial demand on health services. Setting up a comprehensive healthcare strategy for dealing with this problem is imperative.

Scientific/Technological Objectives:The aim of Danubiobank is to establish a biobank foundation in molecular medicine for ageing disorders in order to identify risk factors in population studies. Large clinical trials of new medications can then take place. The project aims to connect universities, teaching hospitals, prevention programmes and clinics along the Danube River and in neighbouring areas. Danubiobank will study the field of ageing disorders, focusing mainly on diabetes-related endpoints including vascular disease and neuro-degenerative disorders. The project also aims to integrate biobanking into local and regional health care systems’ e-health structures and IT-based strategies along the Danube.

Expected Results:The formulation of regional networks will help to realise a biobank model providing access to the latest information and data concerning ageing-related disorders. Scientific meetings, networking, policy meetings and the publication of papers will bring attention to this field and encourage scientists and researchers to establish working alliances. A series of work-shops and a concluding conference will be organised to this effect. An interactive website will also be available with access for the general public. The project team hopes that other consortia will grow out of Danubiobank and will undertake research activities with national or international funding. The project also hopes to collaborate with self-help communities such as Weight Watchers, and public health groups.

Potential Impact:The project’s aim is to impact positively on the treatment of ageing-related disorders in European health services through the biobank foundation and through its networks of researchers disseminating information through workshops, meetings, research and poli-cymaking activities.

Keywords: metabolic disorder, ageing disorder, biobank, vascular disease, neuro-degenerative disorder


DanuBiobank


480 000


287

Project Coordinator:Prof. Gerd SchmitzUniversity Hospital RegensburgInstitute of Clinical Chemistry and Laboratory MedicineFranz-Josef-Straub-Allee 1193053 Regensburg, [email protected]

Prof. Oswald WagnerMedical University of ViennaClinical Institute for Medical and ChemicalLaboratory DiagnosticsVienna, Austria

Prof. Gyorgy KeriSemmelweis University BudapestCooperative Research CenterRational Drug Design LaboratoriesBudapest, Hungary

Dr. Jaroslav HubacekInstitute for Clinical and Experimental MedicineLaboratory of Molecular GeneticsPrague, Czech Republic

Prof. Iwar KlimešSlovak Academy of SciencesInstitute of Experimental EndocrinologyDiabetes and Nutrition GroupBratislava, Slovakia

Dr. Vita DolzanUniversity of LjubljanaFaculty of MedicineInstitute for BiochemistryLjubljana, Slovenia

Prof. Wolfgang König, Prof. Bernhard BoehmUniversity of UlmUlm, Germany

Dr. Jaako Tuomilehto, Prof. Michael BraininDanube University KremsKrems, Austria

Partners


The Danubian Biobank Initiative — Towards Information-based Medicine



288

State-of-the-Art: Today, most of the molecular research is carried out on cell culture and animal models, but it is possible also to apply it directly to human clinical tissues. A very important tool for translational research is represented by the large number of human archive tissues (AT) that are stored in hospitals all over Europe. Tissue specimens removed from patients for diagnosis or surgical therapy are fixed and paraffin-embedded in order to obtain a conclusive diagnosis. After a few sections are cut, the tissues are stored in archives for many decades. For each hospital an average of between 10 000 and 30 000 tissue samples are collected each year. We already have the technology that allows a molecular research at DNA and RNA level on fixed and paraffin embedded tissues, and new possibilities for proteomics analysis are emerging. In Europe, many laboratories are working with archive tissues at molecular level. DNA genomic analysis is already widely spread in research and diagnostics (lymphomas and leukaemia etc). Less diffused and validated are the techniques for studying DNA methylation, comparative ge-nomic hybridization (CGH) or single nucleotide polymorphisms (SNP) in archive tissues. Many laboratories also perform analysis at RNA level in order to detect RNA virus persistence or to study gene expression for functional genomics or micro-RNAs.

Scientific/Technological Objectives: The project is capable of overcoming some of the major obstacles and limitations in the devel-opment of clinical molecular medicine, obstacles created by insufficient expertise at clinical level in the use of molecular methods and the collection of appropriate clinical materials. The objectives of IMPACTS are:

1) to analyse the present knowledge and use of molecular analysis in archive human tis-sues in Europe and to propose methods of validation and standardisation;

2) to explore the range of technical availability and reproducibility of these new methods for research in functional genomics and clinical application;

3) to establish a more organised European research effort. There are uncommon protocols for some of the molecular analysis in AT and every laboratory has its own experience.

4) to compare methods and results by organising meetings and inter-laboratory compari-sons for a proposal of method validation and standardisation.

Expected Results: 1) organisation of meetings2) publication of technical guidelines3) definition of future research proposals on archive tissues4) standardised protocols and guidelines diffusion5) validation of new tissue fixation procedures with better molecular preservation6) proposal of bioethics guidelines for human archive tissue multicentric research7) guidelines for archive tissue multicentric collection8) proteomic analysis protocols in archive tissues for research and clinical applications

Potential Impact: This project will make a positive impact on the health of European citizens. Among the pro-ponents of the project are the scientists who first developed this type of molecular analysis. IMPACTS aims to integrate this expertise with others for the final goal of better management of research. The project will also have an impact on research and development in European industry. Collaboration with pharmaceutical and biotechnological enterprises may stimulate industrial activities with evident economic advantages. Preparing technological innovation is a basic aim of IMPACTS with the development of new procedures (new fixatives, standard-ised molecular methods and diagnostic kits) and suggestion of new devices for molecular analysis. The project has also developed a network of laboratories and pathology archives with a very large number of tissues to validate new methods and clinical biomarkers.


Impactswww.impactsnetwork.eu

Project Type:Co-ordination ActionContract number:LSHG-CT-2007-037211Starting date:1st February 2007Duration:24 monthsEC Funding:

600 000


http://www.impactsnetwork.eu

289

Keywords: pathological anatomy, ethics in health sciences, molecular biology, molecular medicine, functional genomics, personalised medicine, biobanks

Project Coordinator:Prof. Giorgio StantaUniversity of TriesteDepartment of ClinicalMorphological and Technological Sciencesc/o Ospedale di CattinaraStrada di Fiume 44734149 TriesteandInternational Centre for Genetic Engineering and BiotechnologyMolecular Histopathology LaboratoryPadriciano 99 34012 Trieste, [email protected]

Prof. J.H.J.M. Van KriekenRadboud UniversityNijmegen Medical CentrePO Box 9010 6500 GL Nijmegen, The Netherlands

Prof. Fatima CarneiroUniversity of PortoInstitute of Molecular Pathology and ImmunologyPorto, Portugal

Prof. Fred BosmanUniversity of LausanneLausanne, Switzerland

Prof. Generoso BevilacquaUniversity of PisaDepartment of OncologyPisa, Italy

Prof. Gregor MikuzMedical University InnsbruckInstitute of PathologyInnsbruck, Austria

Prof. Heinz HoeflerTechnical University MunichInstitute of PathologyMunich, Germany

Prof. Manfred DietelCharite – Universitatsmedizin BerlinInstitut for Pathologie CCMBerlin, Germany

Prof. Aldo Scarpa University of VeronaDepartment of PathologyVerona, Italy

Prof. Gianni Bussolati University of TorinoDepartment of Biomedical Sciences and Human OncologyTurin, Italy

Marco Bellini Milestone SrlSorisole- Bergamo, Italy

Prof. Mladen Belicza University Hospital “Sestre milosrdnice”University Department of Pathology “Ljudevit Jurak”Zagreb, Croatia

Prof. Nina GaleUniversity of LjubljanaInstitute of PathologyLjubljana, Slovenia

Prof. Pierre Bedossa Centre National de la RechercheScientifique (CNRS) UMR 8149 - Université Paris VHôpital BeaujonClichy, France

Prof. Maciej Zabel Medical University of Wroclaw Department of Histology and EmbryologyWroclaw, Poland

Prof. Helmut PopperMedical University of GrazInstitute for PathologyGraz, Austria

Prof. Thomas KirchnerLudwig-Maximilians-Universitaet München Department of PathologyMunich, Germany

Dr. Serena BoninInternational Centre for Genetic Engineering and BiotechnologyMolecular Histopathology LaboratoryTrieste, Italy

Prof. Samuel NavarroUniversity of ValenciaDepartment of PathologyValencia, Spain

Prof. Elias Campo Hospital Clinico Provincial de BarcelonaDepartment of PathologyBarcelona, Spain

Prof. Gerald HoeflerMedical University of GrazInstitute for PathologyGraz, Austria

Prof. Jaime PratHospital de la Santa Creu i Sant PauBarcelona, Spain

Partners


Archive tissues: improving molecular medicine research and clinical practice



290

State-of-the-Art: The preliminary findings of members of EpiGenChlamydia estimate that there is a 40 per-cent genetic predisposition to Chlamydia trachomatis (CT) infections. To allow full exploita-tion of this knowledge, it is essential to know which part of a person’s genetic make-up pre-disposes them to CT infections. Therefore, genomic analysis on a large number of unrelated individuals needs to be performed.

As no single entity has access to all the information, nor the necessary expertise to process all samples and data, a collaborative effort is required. This Coordination Action gives the consortium the opportunity to thoroughly define the requirements for successful collabora-tions on this issue.

Scientific/Technological Objectives: 1) To provide state-of-the-art reports on the epidemiology of both ocular and sexually

transmitted CT infections; 2) To define and provide an approach based on the host-pathogen interaction for large-

scale genetic typing; 3) To generate a validated and integrated large biobank and efficient data warehouse; 4) To integrate ongoing immunogenetic CT research lines in three European centres in

which several participants are involved; 5) To apply for research grants; 6) To disseminate the EpiGenChlamydia consortium’s activities.

Expected Results:1) A validated central biobank; 2) Validated data warehouses; 3) A validated EpiGenChlamydia website for the data warehouse; 4) Research integration; 5) Enhanced collaboration between partners and potential new partners; 6) Dissemination of results; 7) Media coverage, including publications and meetings. Reports and reviews will be

produced to keep the partners, the EC and the general public aware of the consor-tium’s achievements.

Potential Impact: By the end of this CA, an integrated network of all key players for the genetic epidemiologi-cal study to determine the genetic predisposition to CT infection will have been formed. The collective knowledge acquired in this CA will allow for the development of tools for the early detection of a predisposition to CT infection and diagnostics to detect CT infections indicative of non-regular treatment (persistent infections).

Keywords: genetic epidemiology and standardisation, SNP-Chip, Chlamydia trachomatis, screening-cohorts, sample collections, host factors, bac-terial factors, environmental factors, datawarehouse development


EpiGenChlamydia

Project Type:Co-ordination ActionContract number:LSHG-CT-2007-037637Starting date:1st July 2007 Duration:24 monthsEC Funding:

450 000

www.epigenchlamydia.eu


http://www.epigenchlamydia.eu

291

Project Coordinator:Dr. Servaas A. MorréVU University Medical CenterImmunogenetics of Infectious DiseasesDepartment of PathologyLaboratory of ImmunogeneticsDe Boelelaan 11171081 HV Amsterdam, The [email protected]

Prof. Chris Meijer, Prof. Salvador Peña,Bart CrusiusVU University Medical CenterDepartment of PathologyAmsterdam, The Netherlands

Prof. David Mabey, Prof. Robin BaileyUniversity of LondonSchool of Hygiene and Tropical MedicineLondon, UK

Dr. Ioannis Ragoussis, Richard Mott, Prof. Michael Parker, Prof. Dominic KwiatkowskiUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UK

Prof. Jorma PaavonenUniversity of HelsinkiUniversity HospitalDepartment of Obstetrics and GynaecologyHelsinki, Finland

Dr. Helj-Marja SurcelNational Public Health InstituteHelsinki, Finland Dr. Han Fennema, Dr. Henry de VriesMunicipal Health ServiceAmsterdam, The Netherlands

Dr. James Ito, Dr. Joe LyonsCity of Hope National Medical Center and Beckman Research Institute Department of Infectious DiseasesDuarte, California, USA

Dr. Jean-Francois SchemannL’Institut de Recherche pour le Developpement (IRD)Paris, France

Dr. Ansumana SillahThe Gambia International Centre for Eye HealthMinistry of HealthBanjul, Gambia

Dr. Björn HerrmannSwedish Institute of Infectious Disease ControlSection of Sexually Transmitted InfectionsUppsala, Sweden

Dr. Björn Buan, Dr. Inger BakkenStiftelsen for Industriell og TekniskForskning ved Norges Tekniske HogskoleTrondheim, Norway

Prof. Lars Ostergaard,Dr. Berit AndersenAahus University HospitalDepartment of Clinical MicrobiologyArhus, Denmark

Dr. Tjaco OssewaardeErasmus UniversityDepartment of Medical Molecular MicrobiologyRotterdam, The Netherlands

Dr. Yvonne PannekoekAcademic Medical CentreDepartment of Medical MicrobiologyAmsterdam, The Netherlands

Dr. Jan van BergenSTI AIDSAmsterdam, The Netherlands

Prof. Jolande LandUniversity of MaastrichtMaastricht, The Netherlands

Dr. Marianne van der Sande National Institute of Public Health and the EnvironmentDepartment of Infectious Diseases EpidemiologyBilthoven, The Netherlands

Prof. Joseph IgietsemeMorehouse School of MedicineAtlanta, USA

Prof. Paul SavelkoulMicrobiome LtdHouten, The Netherlands

Prof. Cathy Ison, Dr. Mary MacintoshHealth Protection AgencyCentre for InfectionSexually Transmitted Bacterial Reference LaboratoryLondon, UK

Partners


Contribution of molecular epidemiology and host-pathogen genomics to understand

Chlamydia trachomatis disease




BIOINFORMATICS6.



BIOINFORMATICS6.

BIOSAPIENS

ATD

EMBRACE

ENFIN

EUROFUNGBASE


296

State-of-the-Art:The genome projects have revealed for the first time the “blue-print” of life. The first draft of the human sequence was published in 2001, and there are now over 100 completed and 70 draft genome sequences in the public domain. This explosion in genomic information has been achieved in a remarkably short period of time, and the flood of new sequence data is likely to continue for the next decade. However, DNA sequence is merely a string of letters; it must be interpreted in terms of the RNA and proteins that it encodes and the promoter and regulatory regions that control transcription and translation.

Annotation can be described as the process of “defining the biological role of a molecule in all its complexity” and mapping this knowledge onto the relevant gene products encoded by genomes. This involves both experimental and computational approaches and, indeed, absolutely requires their integration. The BioSapiens network provides the necessary exper-tise and European infrastructure to allow distributed annotation, from both computational and experimental laboratories. These expert annotations will be made available to every-one over the web. To date, European scientists have been very active in the field of genome and protein annotation, with Ensembl and SWISS-PROT being the primary resources in use worldwide. Many of the tools used in genome and protein sequence and structure annota-tion, prediction and validation, as well as in pathway analysis were developed in Europe. Many of the secondary resources derived from protein sequences and structures are also European.

However, the groups that develop the methods for improving genome annotation are widely distributed throughout Europe and the best methods are often not incorporated into publicly available genome annotations. Furthermore, these methods are continually changing and improving, so keeping up to date becomes problematic. The fragmentation of currently available resources for genome annotation means that only a few bioinformatics experts know where to look for them. Consequently, most experimentalists cannot access all the best information about a genome. This problem will only get worse as annotation methods become more sophisticated and more bioinformatics laboratories are established to handle all the new data.

Scientific/Technological Objectives:The objective of the BIOSAPIENS Network of Excellence is to provide a large-scale, con-certed effort to annotate genome data by laboratories distributed around Europe, using both informatics tools and input from experimentalists. The Network will create a European Virtual Institute for Genome Annotation, bringing together many of the best laboratories in Europe. The institute will help to improve bioinformatics research in Europe, by providing a focus for annotation and through the organisation of European meetings and workshops to encourage cooperation, rather than duplication of effort.

An important aspect of the network activities is to try and achieve closer integration be-tween experimentalists and bioinformaticians, through a directed programme of genome analysis, focused on specific biological problems. The annotations generated by the Insti-tute will be available in the public domain and easily accessible on the web. This will be achieved initially through a distributed annotation system (DAS), which will evolve to take advantage of new developments in the GRID. European scientists have traditionally been


BioSapiens

Project Type:Network of ExcellenceContract number:LSHG-CT-2003-503265Starting date:1st January 2004Duration:60 monthsEC Funding:

12 000 000

www.biosapiens.info


http://www.biosapiens.info

297

very active in the field of protein and genome annotation, and Ensembl and SWISS-PROT (now part of UniProt) are the primary resources in use worldwide.

Many of the tools used in genome and protein sequence and structure annotation, predic-tion and validation, and pathway analysis have been developed in Europe. The BioSapiens NoE will further increase European competitiveness, through new discoveries, increased integration, expert training and improved tools and services, and enhance Europe’s role in the academic and industrial exploitation of genomics.

A further objective of the Network of Excellence is the establishment of a permanent Euro-pean School of Bioinformatics, to train bioinformaticians and to encourage best practice in the exploitation of genome annotation data for biologists. The courses and meetings will be open to all scientists throughout Europe, and available at all levels, from basic courses for experimentalists to more advanced training for experts.

Expected Results:Some of the main results expected from the project will be the development of an integrated approach to genome annotation from gene to function, and the establishment of an inte-grated and distributed website for Genome Annotation. The team expects a stimulation of cooperation between experimental scientists and computational biologists for genome annotation, in the form of meetings and joint collaborations. Experimental validation of predictions made in silico will form part of these col-laborations. The team will also focus on the develop-ment of improved computational methods for annota-tion through cooperation: new methods will be made available via the web. Annotations from new methods will be available on the BioSapiens website.

Potential Impact:The BioSapiens Network of Excellence will have an impact on the establishment of a European research structure that will support the coordination of bioinfor-

BIOSAPIENS School


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Project Coordinator:Prof. Janet ThorntonEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, [email protected]

Project Manager: Dr. Kerstin Nyberg European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI) Wellcome Trust Genome CampusHinxton, CB10 1SD, [email protected]

Prof. Peer Bork European Molecular Biology Laboratory,(EMBL)Heidelberg, Germany

Prof. Dmitrij FrishmanHelmholz ZentrumNeuherberg, Germany

Prof; Jacques van HeldenUniversité Libre de Bruxelles, Service de Conformation de Macromolécules Biologiques et BioinformatiqueBrussels, Belgium

Partners

matics research activities across different sub-areas, and across different areas of medical and biotechnological application. It will promote the development of the required level of critical mass, which is essential if Europe should be able to compete with the major invest-ments made in this area in the USA, Canada and Japan.

The integration between the groups in the BioSapiens Network of Excellence will have a lasting impact on the European bioinformatics infrastructure, and on the sharing of human resources, infrastructure databases and tools. Through cutting-edge research, high-level training, and vigorous European interaction, the BioSapiens Network of Excellence will make a substantial contribution to improving Europe’s knowledge base, and increase the potential for creating new industries, new knowledge, and new employment.

DNAAnnotation

ProteomeAnnotation

FunctionalAnnotation

Gene Definition (alternative splicing) Protein FamiliesProtein Structure & Modelling Sequence & Structure to Function

Regulators & PromotersExpressionVariation (haplotypes & SNP’s)

Membrane Proteins & LigandsPost Translation Modification

& Localisation

Protein-Protein ComplexesPathways and Networks

The exploitation of the biological informa-tion enabled by the BioSapiens Network of Excellence will in some cases be rela-tively direct: e.g., improved health-care through better drugs, new vaccines, and personalised medicines for individuals and sub-populations, and by improved understanding of diet and health.

Keywords:genome annotation, data integration, databases


BIOSAPIENS




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Prof. Alfonso ValenciaSpanish National Cancer Research Centre (CNIO)Madrid, Spain

Dr. Roderic GuigoCentre for Genomic RegulationBarcelona, Spain

Dr. Tim HubbardGenome Research Ltd Wellcome Trust Sanger InstituteHinxton, UK

Prof. Thomas LengauerMax-Planck Institute for Informatics Saarbrücken, Germany

Prof. Michal LinialHebrew University of Jerusalem Department of Biological ChemistryJerusalem, Israel

Prof. Anna TramontanoUniversity of Rome ‘La Sapienza’Department of Biochemical Sciences Rome, Italy

Prof. Gunnar von HeijneUniversity of Stockholm Department of Biochemistry and BiophysicsStockholm, Sweden

Dr. Richard MottUniversity of Oxford Wellcome Trust Centre for Human GeneticsOxford, UK

Prof. Christine Orengo, Prof. David Jones University College LondonDepartment of Biochemistry and Molecular BiologyLondon, UK

Prof. Gert VriendRadboud University Nijmegen Medical Centre Centre for Molecular and Biomolecular InformaticsNijmegen, The Netherlands

Dr. Anne-Lise VeutheySwiss Institute of Bioinformatics Geneva, Switzerland

Prof. Søren BrunakTechnical University of Denmark Center for Biological Sequence Analysis (CBS)Lyngby, Denmark

Prof. Esko UkkonenUniversity of Helsinki Department of Computer ScienceHelsinki, Finland

Prof. Stylianos AntonarakisUniversity of Geneva Division of Medical GeneticsGeneva, Switzerland

Prof. László PatthyInstitute of EnzymologyBiological Research CenterHungarian Academy of SciencesBudapest, Hungary

Dietmar SchomburgTechnical University of BraunschweigDepartment of Bioinformatics and BiochemistryBraunschweig, Germany

Antoine DanchinInstitut Pasteur Department Structure and Dynamics of GenomesParis, France

Dr; Leszek RychlewskiBioInfo Bank Institute Bioinformatics LaboratoryPoznan, Poland

Prof. Martin VingronMax-Planck Institute for Molecular Genetics Berlin, Germany

Dr. Vincent SchachterGenoscopeEvry, France

Prof. Rita CasadioUniversity of Bologna Department of BiologyBologna, Italy

Dr. Christos OuzounisInstitute of AgrobiotechnologyCentre for Research and Technology Hellas (CERTH)Thessaloniki, Greece


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State-of-the-Art:A single human gene can produce a variety of alternative transcripts (ATs or mRNA iso-forms), which differ in terms of their transcription initiation, splicing or polyadenylation pat-terns. Expression of alternative transcripts has been observed to be specific to tissue-type or developmental stage. Disruptions in AT expression have serious consequences for an organism and are associated with numerous diseases, including cancer, multiple sclerosis, heart failure and neurodegenerative disorders.

The ATD project aims to understand the mechanisms responsible for the formation of dif-ferent ATs. It is anticipated that studies in the field of ATs will develop into a significant research area, with direct applications for pharmaceutical industries. These applications are inclusive of disease diagnosis or prognosis of risk patients, as well as identification of new drug targets.

Scientific/Technological Objectives: The ATD project is a collaborative multi-disciplinary project. It aims to comprehensively characterise alternative tran-script (AT) forms throughout the human genome, and also to assess the differential expression of these forms in time and space, in normal and disease-related tissues. This is ac-companied by adequate quality control procedures, such as research for evolutionary proof through comparative se-quence data analysis, between human and mouse. Further characterisation of the AT is implemented through activities such as identification of regulatory patterns, and deriva-tion of expression states (i.e. expression specificity in terms of association with diseases, developmental stages, or tis-sue-specificity). The project also aims to develop standard vocabularies and models that will represent gene structures and their expression patterns.

The validity of the bioinformatics prediction of disease-specific ATs is being examined through the execution of RT-PCR experiments on selected tissues. The AT discovery effort is accompanied by database integration, and also by dissemination to the scientific community.

Expected Results: The principal end results being targeted are as follows:

gene, feature variants, transcript variants, annotations, derived expression states, pro-tein functionalities, results of experimental validations and associations with diseases. Fully developed query interfaces and toolboxes are available in the database, which is accessible at: http://www.ebi.ac.uk/atd/;

of vocabularies for the representation of annotations;

human and mouse;



2 000 000

www.atdproject.orgATD


http://www.ebi.ac.uk/atd

http://www.atdproject.org

301

Potential Impact: Alternative transcription has such a strong impact on gene products, that any disruption of ATs is potentially linked to fatal diseases. Diseases that have been linked to AT disruption include cancer, multiple sclerosis, heart failure and neurodegenerative diseases; ATD has the capacity to facilitate and support those areas.

Traditional molecular biology approaches founded on a “one gene at a time” basis, are no longer practical when detecting new disease-specific ATs. There is currently a need for the execution of genome-wide AT detection, followed by high-throughput analysis of transcript expression. It is predicted that these studies on alternative transcripts will develop into a major research area, with direct applications for pharmaceutical industries.

Keywords: transcriptome, gene expression regulation, splicing, diagnosis, disease markers, microarrays, basic biological processes, transcript

Project Coordinator: Prof. Daniel GautheretERM-0206 TAGCInstitut National de la Santé et de laRecherche Médicale (INSERM)75654 Marseille, [email protected]

Prof. Peer BorkEuropean Molecular Biology Laboratory (EMBL)Structural and Computational Biology UnitHeidelberg, Germany

Dr. Eleanor WhitfieldEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Prof. Winston HideUniversity of the Western CapeSouth African National Bioinformatics InstituteCape Town, South Africa

Dr Roderic GuigoCentre de Regualci Genmica Bioinformatics and Genomics UnitBarcelona, Spain

Dr. Jaak ViloEstonian BiocenterBioinformatics GroupTartu, Estonia

Prof. Magnus von Knebel DoeberitzUniversity of HeidelbergDepartment of Applied Tumor BiologyHeidelberg, Germany

Dr. Christiane Dascher-NadelInserm Transfert SAEuropean Project Management Department Marseille, France

Prof. Jens ReichMax-Delbruck-Centrum für Molekulare Medizin Berlin-BuchBioinformatics Unit Berlin-Buch, Germany

Partners


The Alternate Transcript Diversity Project



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State-of-the-Art: The EMBRACE project addresses the need for integration of data and analysis resources for biological and biomolecular information. The many publicly available collections of biomo-lecular information do a reasonable job for a given domain. Software tools to organise and analyse this information are available both from the public domain, and commercially. In principle, cross-references in these databases allow inter-database navigation; however, the links are sparse and coarse-grained, and their exploitation requires biological knowledge and expert programming. As a result, every serious bioinformatics centre is burdened not only with the task of maintaining local data and software, but also of supporting users in the substantial task of exploring the natural biological connections between data. This requires considerable human effort. Current trends in systems biology demand greatly improved connections between different domains of knowledge, and the weaknesses in information integration are becoming an intolerable hindrance. This network will address these weak-nesses by enabling data providers and tool builders to standardise their data access and software tools, using the new grid computing technologies that are ideally adapted to the task. The use of these standard methods will allow data resources to be essentially self-describing, allowing software to work out the structure of the data, in large part automati-cally. Apart from facilitating widespread integration of software and data, this will make the interacting systems easy to update; for example, it will reflect changes to the internal representation of the data.

Scientific/Technological Objectives: The objective of the EMBRACE Network of Excellence is to draw together a wide group of experts throughout Europe who are involved in the use of information technology in the biomolecular sciences. The EMBRACE network will optimize informatics and information ex-ploitation by pure and applied biological scientists, in both the academic and commercial sectors. The result will be highly integrated access to a broad range of biomolecular data and software packages. Groups in the network are involved in the following activities:

1) collection, curation and provision of biomolecular information; 2) development of tools and programming interfaces to exploit that information; and 3) tracking and exploiting advances in information technology, with a view to applying

them in bioinformatics training and also to reaching out to groups who can benefit from the work of the network.


Project Type:Network of Excellence Contract number:LHSG-CT-2004-512092Starting date:1st February 2005Duration:60 monthsEC Funding:

8 280 000

EMBRACEwww.embracegrid.info


http://www.embracegrid.info

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These groups work together to enable highly functional interactive access to a wide range of biomolecular data (sequence, structure, annotation, etc.), and tools with which to ex-ploit the data. This naturally includes many core databases and tools available from the European Bioinformatics Institute (EBI), but, crucially, the methods used will support the integration of dispersed, autonomous information. As a result, groups throughout Europe will be expected to integrate their own local or proprietary databases and tools into the collaborative “information space” which constitutes the EMBRACEgrid — a ‘data grid’ allowing integrated exploitation of data, analogous to a ‘compute grid’, which enables unified exploitation of dispersed computer resources. EMBRACEgrid will serve as a com-prehensive virtual information source: virtual in the sense that it will have no single physi-cal location, being rather a dispersed set of tightly coupled resources. EMBRACEgrid will be a permanent product of the project.

Expected Results: The results expected are as follows:

1) Standardized application programming interfaces (APIs) with all the core biological databases at the EBI, as well as with several wide-ranging sources of other information distributed throughout Europe.

2) Software tools that exploit the data through the new APIs, to provide a working environment in which to access and analyze the data, and also to facilitate the development of further tools in a consistent programming environment.

3) Technological standards for finding and describing the data and application services mentioned above.

4) Training and outreach to enable biologists to get the best out of the resulting tools and data, and bioinformaticians to develop ever better tools, in the knowledge that they are firmly connected to all the data.

Potential Impact: There is currently a great deal of investment in post-genomics projects. About once a week the sequence of an entire species becomes available. Transcriptomics and proteomics projects are producing data avalanche after data avalanche. Each time that (bio)informati-cians have dealt with the data flow of one type of project, two new types of high throughput experiment have been developed. All this data is finding its way to the biosciences, and fields such as pharma, health, food and agriculture are all likely to undergo major revolu-tions, that are expected to improve the quality of life for all, from infants to the elderly. This project sits in the context of existing integration projects such as Integr8 and BioMart. These projects, and information resources like Ensembl will exploit the standards developed in EMBRACE to provide common interfaces to data and tools across Europe, targeted to the needs of experimental research.

Keywords: bioinformatics, standards, web services, integration


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Project Coordinator:Dr. Graham Cameron European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UK [email protected]

Project Manager: Dr. Kerstin NybergEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UK [email protected]

Dr. Andreas Gisel Institute of Biomedical TechnologiesSection BariConsiglio Nazionale della Ricerche (CNR) Bari, Italy

Prof. Terri AttwoodUniversity of ManchesterSchool of Biological SciencesManchester, UK

Marco PagniSwiss Institute of BioinformaticsLausanne, Switzerland

Dr. Erik Bongcam-Rudloff Swedish University of Agricultural SciencesLinnaeus Centre for Bioinformatics Uppsala, Sweden

Dr. Vincent Breton, Dr Christophe BlanchetCentre National de la Recherche Scientifique (CNRS)Clermont-Ferrand and Lyon, France

Prof. Søren BrunakTechnical University of DenmarkCenter for Biological Sequence Analysis (CBS)BioCentrum-DTULyngby, Denmark

Jose-Maria Carazo Garcia Spanish National Research Council (CSIC)Madrid, Spain

Partners


EMBRACE




305

Prof. Arne Elofsson University of StockholmStockholm Bioinformatics CentreStockholm, Sweden

Dr. Daniel KahnINRIA-UCBLInstitut National de la Recherche Agronomique (INRA) Toulouse, France

Dr. Ralf HerwigMax-Planck Institute for Molecular GeneticsDepartment of Vertebrate GenomicsBerlin, Germany

Dr. Eija Korpelainen CSC – Scientific Computing LtdEspoo, Finland

Prof. Christine OrengoUniversity College LondonDepartment of Biochemistry and Molecular BiologyLondon, UK

Dr. Yitzhak Pilpel Weizmann Institute of ScienceDepartment of Molecular Genetics/BiochemistryRehovot, Israel

Dr. Gert VriendRadboud University Nijmegen Medical CentreCentre for Molecular and Biomolecular Informatics Nijmegen, The Netherlands

Prof. Alfonso ValenciaInstituto Nacional De Tecnica Aeroespacial (Centro De Astrobiologia)Laboratory of BionformaticsCABMadrid, Spain

Prof. Inge JonassenBergen Center for Computational ScienceBergen, Norway


A European Model for Bioinformatics Research and Community Education


306

State-of-the-Art:Despite the progress made in bioinformatics methods and databases to date, even the best experimental laboratories use only a small number of computational tools in their work, and they rarely exploit the potential of multiple datasets. The ENFIN network will transform the way computational analysis is used in the laboratory. The infrastructure will be entirely open, in the same way that genome information is accessible to all.

To achieve its goals, the network will encourage close internal collaboration between experi-mental and computational research groups, and will have a specific consumables budget for testing predictions experimentally. The computational work includes the development of a distributed database infrastructure appropriate for small laboratories, and the development of analysis methods, including Bayesian networks, metabolite flux modelling and correlations of protein modifications to pathways.

The experimental techniques used to test this system include mass spectroscopy, synthetic peptide biochemistry and RNA interference knockdown. Where appropriate, the network has chosen experimental areas related to intracellular signalling, associated with the cell cycle.

Scientific/Technological Objectives:ENFIN’s network’s specific objectives can be summarised as follows:

1) Development of the ENFIN Core (EnCORE), by taking a number of pre-existing database packages and providing a unified installation which can be used in laboratories worldwide;

2) Curation of appropriate pathway knowledge and hypotheses;3) Development and management of new experimental data standards;4) Discrete function prediction;5) Network reconstruction;6) Systems level modelling. (Objectives 4, 5 and 6 comprise the ENFIN analysis

layer. Cycling between computational predictions and experimental validation feedback will be used, to improve the accuracy of bioinformatics tools for predict-ing biological features in this layer);

7) Critical assessment and integration, i.e. bringing together groups across the analy-sis layer, both to critically assess the methods and also to uncover new synergies between computational and experimental groups;

8) Provision of graduate level training, coordinated with the European School of Bio-informatics, so as to arrange a short course for graduate level students;

9) Documentation from a wet laboratory perspective, enabling the consortium to de-velop a multi-authored resource, which is kept as current as possible through direct editing by appropriate researchers within the network;

10) Facilitating SME outreach, to raise awareness of ENFIN in the biotechnology com-munity, and to increase the understanding of SMEs’ needs.


Project Type:Network of ExcellenceContract number:LSHG-CT-2005-518254Starting date:15 November 2005Duration:60 monthsEC Funding:

8 967 500

www.enfin.orgENFIN


http://www.enfin.org

307

Expected Results:EnCore, the network, will develop a set of existing databases for the storage and integra-tion of public and local data, such as microarray data, protein-protein interaction data and pathway information. This core will be available by all nodes of the ENFIN network, and will form the backbone for the communication of datasets.

The ENFIN analysis layer will work with EnCore as a series of computer programs to pro-vide analysis of the data stored in EnCore. Interaction between experimental and computa-tional researchers is crucial in the development of these programs. There will be a critical assessment of the computational tools using experimental information as a challenge.

A truly multidisciplinary set of investigators will be gathered across Europe, spanning ex-perimental research in mitogenic signalling through to algorithm development in machine-learning techniques. ENFIN will use a variety of experimental techniques to test and inform computational work. This work will also provide insights into cancer, since the bulk of the network’s experimental research concerns regulation of the cell cycle. These biological results will prove the effectiveness of the network’s products and provide insights that could be used to enhance human health.

ENFIN’s products will be disseminated, not principally as scientific results, but rather as a technical solution for how to coordinate computational and experimental work. The produc-tive interactions between computational and experimental researchers will be as important as the technical programming aspect of the work. Through its dissemination programme, ENFIN will reach the post-doctoral student in the lab, the SME researcher, and biological and bioinformatics graduate students. The project will pass on developments in bioinfor-

Systems Modeling Methods


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308

matics best practice and software deployment to core biological labs, and will benefit from feedback on their use.

Potential Impact:The main tangible benefit of ENFIN will be the development of a set of scientific procedures for understanding multi-component systems using computational techniques. The ENFIN infrastructure will be distributed firstly to all the network’s partners, and then to various iden-tified collaborators and other interested laboratories. Local installation of ENFIN will allow on-site processing of information, access to public archived data as well as local informa-tion, access to specific, designed analysis methods which have been tested experimentally, and access to documentation written from the wet laboratory perspective.

ENFIN will have an impact on the understanding of complex human diseases such as can-cer and diabetes. The systems-level vision of ENFIN is applicable to many other complex diseases and biological processes in other fields. As well as mammalian cells, systems biology could potentially impact the understanding of many pathogenic organisms - both eubacteria and eukaryotes.

In addition to the network’s research being fully integrated with that of leading molecular biology laboratories, it will organise a public, highly visible conference to explicitly test the outputs of systems biology predictions. The scientific approach taken by ENFIN will be of great interest to many industrial groups. Through the industry programme at the European Bioinformatics Institute (EBI), whose members include all the main life science companies, the network will be able to educate these industrial partners in new approaches.

Keywords:systems biology, functional genomics, pathways, computational predictions

PartnersDr. Jan EllenbergEuropean Molecular Biology Laboratory (EMBL)Heidelberg, Germany

Dr. Henning Hermjakob European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Prof. Geoffrey J. BartonUniversity of DundeeDivision of Biological Chemistry and Molecular MicrobiologySchool of Life Sciences Dundee, UK

Prof. Søren BrunakTechnical University of DenmarkCentre for Biological Sequence AnalysisLyngby, Denmark

Project Coordinator:Prof. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome Campus Hinxton, CB10 1SD, [email protected]

Project ManagerDr. Pascal Kahlem European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome Campus Hinxton, CB10 1SD, [email protected]


ENFIN




309

Prof. Gianni CesareniUniversity of Rome Tor VergataDepartment of BiologyLaboratory of Molecular GeneticsRome, Italy

Dr. John HancockMedical Research Council Mammalian Genetics UnitHarwell, UK

Prof. Carl-Henrik HeldinLudwig Institute for Cancer ResearchUppsala, Sweden

Dr. Edda Klipp, Dr. James AdjayeMax-Planck Institute for Molecular GeneticsBerlin, Germany

Prof. Erich NiggMax-Planck Institute of BiochemistryDepartment of Cell BiologyMartinsried, Germany

Prof.Tomi MäkeläUniversity of HelsinkiFaculty of Medicine Molecular and Cancer Biology Research ProgramHelnsinki, Finland

Prof. Christine OrengoUniversity College LondonDepartment of Biochemistry and Molecular BiologyLondon, UK

Dr. Christos OuzounisNational Center for Research and TechnologyInstitute of AgrobiotechnologyThessaloniki Greece

Dr. Dietmar SchomburgTechnical University BraunschweigBioinformatics & BiochemistryBraunschweig, Germany

Dr. Vincent SchachterConsortium national de recherche en Genomique (Genoscope)Evry, France

Dr. Eran SegalWeizmann Institute of Science Department of Computer Science and Applied MathematicsRehovot, Israel

Dr. Jaak ViloOÜ QureTecTartu, Estonia

Ioannis XenariosSerono Pharmaceutical Research InstituteGeneva, Switzerland

Prof. Alfonso ValenciaSpanish National Cancer Research Centre (CNIO)S-CompBioStructural Biology and Biocomputing ProgrammeMadrid, Spain

Dr. Jaap HeringaCentre for Integrative Bioinformatics VUAmsterdam, The Netherlands


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State-of-the-Art:The biotechnology industries that exploit filamentous fungi are strong within Europe. Large companies and SMEs have participated in EUROFUNG projects within FP4 and FP5, and this is a major strength. Similarly, European research into the pathogenesis of A. fumiga-tus is strong. On the other hand, genomic resources for filamentous fungi have not been a strong European feature. The sequencing efforts have been carried out largely outside Europe (in the USA and Japan) although Europe has made modest contributions to sequenc-ing of fungal genomes and ESTs. Genome sequence information has only recently become publicly available for the fungi to be used within this project. There are no gene arrays currently available for any of these fungal species that cover the entire genome, although partial genome coverage has been achieved on slides in some cases. The international Aspergillus Genomes Research Policy Committee, which was founded in 2004, concluded that fabrication of A. nidulans microarrays is a top community priority

There is no bioinformatics resource available that makes it possible to store and inter-connect transcriptomic and proteomic data, for filamentous fungi. The current state of the art for yeast-based data repositories is that platforms have been developed and will serve as the model for the filamentous fungi. Integration of the yeast data will provide the model for the fungal equivalent. European scientists within the consortium are international lead-ers in many areas of science that will exploit the filamentous fungal genome sequence information.

Scientific/Technological Objectives: The EUROFUNGBASE project is a Coordination Action. The objectives of the project are to develop the tools and technologies necessary, so as to enable innovative functional genomic research of hyphal fungi. In that context it is also essential, as a community, to develop a strategy to set up and maintain a sustainable database. The project focuses on several filamentous fungi for different reasons. Aspergillus nidulans has a long record of use as a fungal model organism. Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum are important cell factories used for the production of enzymes and metabolites including compounds such as β-lactams with benefits to human health. The human pathogen Aspergillus fumigatus not only serves as a model pathogen, but is becoming more and more of a serious threat to human health. This new genomics information will thus be beneficial to Europe’s biotechnology industries, and will help to improve the prevention and treatment of fungal disease.

Expected results: The main results expected from this project are set out below:

-notation jamborees.

-laboration with bioinformatics centres, and incorporation of the consortium’s data.

-munity and the European fungal biotech industry through meetings, workshops and web-based information.


EUROFUNGBASEwww.eurofung.net

Project Type:Co-ordination ActionContract number:LSSG-CT-2005-018964Starting date:1st November 2005Duration:36 monthsEC Funding:

486 000


http://www.eurofung.net

311

Project Coordinator: Prof. Cees van den HondelLeiden UniversityClusius LaboratoryWassenaarseweg 642333 AL Leiden, The [email protected]

Dr. Dave UsseryTechnical University of DenmarkLyngby, Denmark

Prof. Steve Oliver, Dr. Geoffrey RobsonUniversity of Manchester,School of Biological SciencesManchester, UK

Partners

-pating industries, thus strengthening infrastructure for high quality fungal genomics research in Europe and determining joint research targets for the future.

and biotechnological research.

Potential impact: Enlarging and maintaining genomic databases is of paramount importance in order to further develop systems biology for model organisms, including relevant filamentous fungi. Therefore, bioinformatics tools must become progressively more sophisticated, to allow for the interpretation of the enormous amounts of data that already have been generated, and are increasing every day. In the end, not only the EUROFUNGBASE community but also other research communities will profit from the effort put in to maintaining a sustainable database. The EUROFUNGBASE project will illustrate the impact described above.

Keywords: fungal pathogenicity, fungal health applications, genomic databases


Strategy to build up and maintain an integrated sustainable European fungal genomic database

required for innovative genomics research on , important for

biotechnology and human health




FUNCTIONAL GENOMICS APPROACHES FOR BASICBIOLOGICAL PROCESSES7.



BIOLOGICAL PATHWAYS AND SIGNALLING

7.1MAIN

WOUND

MITOCHECK

SIGNALLING & TRAFFIC

TransDeath

PEROXISOMES

DNA REPAIR

STEROLTALK

RUBICON

EndoTrack

AnEUploidy


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State-of-the-Art:Chronic inflammation is a systemic disorder resulting from the dysregulation of multiple, mechanistically unrelated higher order biological processes. This consortium will promote the integration of multi-disciplinary research groups to achieve a thorough understanding of

directed inflammatory cell migration towards and across injured tissues. To achieve its goals, the MAIN consortium will be based on four developmental research programmes, three support facilities and one core facility. The research programmes are tightly inter-connected in a logical sequence of highly integrated activities. The tool development programme (TDP) will develop technologi-cal tools that are instrumental in making ad-vancements in the field of cell migration. The target identification programme (TIP) will identify signalling pathways and/or molecu-lar networks involved in defined aspects of inflammatory cell migration. The target vali-dation programme (TVP) will validate targets emerging from the TIP by testing them across in vitro and in vivo models, different inducing stimuli and manipulating conditions. The TVP combines the products of the TDP and the TIP to provide a unified explanation on how mul-tiple ‘inputs’ received by inflammatory cells result in spatially and temporally coordinated ‘outputs’, affecting the migratory behaviour of such cells. The drug development pro-gramme (DDP) will transfer selected targets into a pipeline of drug development, through the SMEs of the consortium. The support fa-cilities (imaging, microarrays and proteom-ics) and the bioinformatics core will provide technological and bio-computational support

to the programmes. To spread excellence through education and training, MAIN will imple-ment a training and education programme (TEP), with practical courses and workshops for graduate students and technicians.

Scientific/Technological Objectives:The scientific goal of MAIN is to identify and characterise the molecular mechanisms under-lying chronic inflammatory responses, with emphasis on a crucial step in such responses, namely the transmigration of leukocytes (white blood cells) from the bloodstream into in-flamed tissues and their local activation by inflammatory substances and pathogens. MAIN has gathered over 150 researchers and graduate students from 13 research institutes and two biotechnology companies of five EU Member States, and Switzerland and Israel. The international dimension of MAIN is emphasised by the strong connection between MAIN


MAINhttp://main-noe.org

Project Type:Network of ExcellenceContract number:LSHG-CT-2003-502935 Starting date:1st January 2004Duration:48 months EC Funding:

10 000 000

TNF-a stimulated HUVECs and T-lymphoblast, 12 min

coincubation. The projection of a z-stack of 8 images.

Acknowledgement: Jaime Millan


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scientists and the US Cell Migration Consortium’s (CMC) goal of exploring the complex mechanisms underlying cell migration in embryonic development, wound healing and can-cer. MAIN and CMC share information/technology platforms and will develop a coordi-nated agenda of scientific events to communicate their scientific achievements to a wider scientific audience and the public.

Expected Results:Bioinformatic databases on the website: integrated suite of MAIN’s resources, bioinformat-ics software tools, application databases enabling rapid data retrieval/analysis and cross-correlation of functional genomic/proteomic data facilitating biological hypothesis-making and ‘systems’ level investigations. It includes MAIN’s deliverables (public access) detail-ing work packages, publications, patents, training, meetings and workshops, experimental tools (main members’ access only)including a database of antibody, cell lines, peptides, plasmids, vectors, cDNA and transgenic organisms.Tutorials (the cell migration and inflammation section of website) explain the process to a non-expert public audience.

‘Deciphering the Cell Migration Code’: students meeting held 30 April-3 May 2005, Switzerland. The format was a combination of poster presentations, 20 student presentations and guest speakers/partners from the MAIN con-sortium. It was a unique opportunity to meet other students from the consor-tium, encouraging mobility and ena-bling an exchange of scientific/tech-nology transfer expertise between the consortium members via their young scientists.

MAIN published papers: Prof. B. Mo-ser: ‘Follicular B Helper T Cells in An-tibody Responses and Autoimmunity’ and ‘Professional Antigen-Presentation Function by Human gamma-delta T Cells’, (Nature Reviews Immunology November 2005/Science Express 2 June 2005); Prof. R. Alon: ‘How do rolling immune cells use their integrins to arrest on inflamed blood vessels?’ and ‘Immune Cell Migration in Inflam-mation: present and future therapeutic targets’, Nature Immunology May/De-cember 2005.

Tracking of leucocyte (white) transmigration through IL-1β-stimulated cremasteric venules immunostained with an anti-PECAM-1 mAb (red)

Endothelial cell junctions delineated in a mouse cremasteric venule by the use of an anti-PECAM-1 mAb


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Potential Impact:The bioinformatics core facility will or-ganise/disseminate MAIN’s informa-tion inside and outside its boundaries. It is hoped that the TDP will produce cutting-edge technological approaches for widespread use in the cell migration research community and refine existing technologies to make them appropriate for use in the cell migration field. The TIP will promote identification and charac-terisation of signalling pathways and/or molecular networks involved in defined aspects of inflammatory cell migration, achieved by the implementation of joint research projects. The TVP aims at com-bining the TDP and TIP results to provide a unified explanation of how multiple ‘inputs’ received by inflammatory cells result in spatially and temporally co-ordinated ‘outputs’, as applied to cell migration and related biological proc-esses occurring in chronically inflamed tissues. The TVP aims to identify the most promising targets for further analysis/potential use in drug development. The DDP will focus on selected target path-ways/networks emerging from the TVP and will transfer them into a pipeline of drug development, using biotechnologi-

cal/pharmaceutical SMEs participating in the network. The TEP aims to develop PhDs with top quality, up-to-date education in biotechnology/technology transfer. Training in different European institutions will encourage mobility and enable an exchange of scientific/technol-ogy transfer expertise.

Keywords: general pathology, immunology, medicine, cell migration, inflamma-tion, signal transduction


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Inflamed mouse cremasteric venule stained for pericytes

(a-SMA; red) and neutrophils (MRP-14; green)

Inflamed mouse cremasteric venule stained for pericytes

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PartnersProject Coordinator:Prof. Ruggero PardiFondazione Centro San Raffaele Del Monte TaborDepartment of Molecular Biology andFunctional GenomicsVia Olgettina 5820132 Milan, [email protected]

Prof. Francisco Sanchez-MadridUniversidad Autonoma de MadridHospital De La PrincesaDepartamento De MedicinaMadrid, Spain

Prof. Anne RidleyKing’s College LondonRandall Division of Cell & Molecular BiophysicsLondon, UK

Prof. Dietmar VestweberMax-Planck-Institute of Molecular BiomedicineDepartment of Cell BiologyMuenster, Germany

Dr. Jochen WittbrodtEuropean Molecular BiologyLaboratory (EMBL)Department of Molecular BiologyHeidelberg, Germany

Dr. Christina CaschettoIFOM-Istituto FIRC di Oncologia MolecolareInstitute for Molecular OncologyMilan, Italy

Prof. Antonio LanzavecchiaInstitute for Research in BiomedicineImmune Regulation LaboratoryBellinzona, Switzerland

Dr. Marlene WolfUniversity of BernTheodor-Kocher InstituteBern, Switzerland

Prof. Fritz KrombachLudwig-Maximilians-Universität MünchenInstitute for Surgical ResearchMunich, Germany

Prof. Ronen AlonWeizmann Institute of ScienceDepartment of ImmunologyRehovot, Israel

Prof. Dorian HaskardImperial College LondonNational Heart and Lung InstituteLondon, UK

Dr. Matthias P. WymannUniversity of BaselDepartment of Clinical & Biological Sciences Basel, Switzerland

Dr. Jean-Philippe GirardInstitut de Pharmacologie etde Biologie (IPBS)-Centre National de laRecherche Scientifique (CNRS)UMR 5089Department of Cancer BiologyToulouse, France

Dr. Daniele D’AmbrosioBIOXELL SpAResearch DepartmentMilan, Italy

Dr Françoise Cailler Endocube SASProloque BiotechLabege, France

Dr. Marco BaccantiScience Park Raf SpABiotechnology Transfer CentreMilan, Italy


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State-of-the-Art: Understanding the properties of the signalling mechanisms involved in epithelial fusion and wound healing is of central importance for basic science and in clinical applications. A func-tional genomics approach has been chosen to unravel the signalling pathways involved in these processes. It can provide direct information on the coordination of the cell communica-tion systems directing these events and on the molecules and cellular activities that implement them. Thus, the wealth of information and resources generated by efforts in genomics can be directly translated into understanding the functioning of cells and tissues in vivo and to clinical applications. To achieve these goals, a multiorganism approach will be developed to analyse the control of gene expression during wound healing and related morphogenetic programmes. The result will be a truly comparable genomic description of a basic biological mechanism conserved throughout evolution. It is important to emphasise that this multiorgan-ism analysis will be performed in organisms which have had their genomes sequenced.

Scientific/Technological Objectives: Wound healing disorders are major health problems that demand the development of effective therapeutics. This, however, requires a thorough understanding of the molecular mechanisms underlying healing. The goal of this project is to identify evolutionary conserved genes and major signalling pathways that orchestrate the healing process, and to use model systems to help define their function. Previous studies demonstrated a strong conservation of the genes involved in murine and human wound repair and epithelial movement and fusion in Dro-sophila and C. elegans. Therefore, we are performing a multi-organism functional genomics approach to identify genes that are under- or over-expressed during wound healing or that are required during epithelial morphogenesis. Our first objective is to identify genes regulat-ed in more than one system. The second objective is to analyse their expression in situations of impaired fusion/repair. The third objective is to use invertebrate models and monocultures and organotypic mammalian culture systems to examine the function of the most highly conserved genes. Finally, for a few selected genes, transgenic/knockout mouse studies and studies using skin-humanised mice shall be performed to identify their in vivo function in re-

pair. The ultimate goal is to identify and inves-tigate selected genes as targets for the develop-ment of innovative ther-apeutics.

Expected Results: The objective of this project is to define the conserved acting elements of the biomolecular networks involved in epithelial fusion/wound healing, to analyse their functions and to explore their use as targets for the development of innovative therapeutics. Major specific goals as identified below will be tackled in a logical sequential fashion. Each of them cor-responds to independent subprojects with recognised deliverables:

1) To identify the common pathways directing epithelial fusion both during morphogen-esis and in the process of wound healing.

2) To identify those conserved genes whose expression is altered in models of impaired epithelial fusion and wound healing.

The process of dorsal closure initiales at 10 hours after

egg laying and is completed after 13 hours


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3) The functional characterisation of the relevant genes/pathways in different organ-isms by defining the expression pattern of selected genes and interfering with their function.

4) Translational research and preclinical studies.

Potential Impact: In most cases, skin wounds heal without obvious problems. However, wound repair in the postnatal mammalian organism does not lead to perfect regeneration, but to the formation of a scar that lacks the elasticity of the normal dermis and all appendages. Therefore, pa-tients with large wounds, for example. extended burn wounds, suffer from severe cosmetic and functional impairments. The identification of genes that are regulated in different wound healing models in Drosophila, , mice and men using GeneChip hybridisation ap-proaches will help to define major conserved signalling pathways that are important for the healing response. In the long run, this project will help to define new therapeutic targets to alleviate and eventually perhaps cure major wound healing disorders and thus improve the quality of life for the patients concerned.

Keywords: wound healing, morphogenesis, skin, signalling pathways, con-served genes.

Project Coordinator: Dr. Enrique Martin-BlancoConsejo Superior de Investigaciones Cientificas (CSIC) Instituto de BiologiaMolecular de BarcelonaC/ Josep Samitier 1-508028 Barcelona, [email protected]

Prof. Sabine WernerSwiss Federal Institute of TechnologyDepartment of Biology, Institute of Cell BiologyZurich, Switzerland

Dr. Petra BoukampDeutsches Krebsforschungszentrum Genetics of Skin CarcinogenesisHeidelberg, Germany

Dr. Michel LabouesseInstitut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)Illkirch Graffenstaden, France

Dr. Jose Luis JorcanoCentro de Investigaciones Energeticas y MedioambientalesEpithelial Damage, Repair and Tissue Engineering DepartmentMadrid, Spain

Dr. Osvaldo PodhajcerGene Therapy LaboratoryBuenos Aires, Argentina

Partners


A multi-organism functional genomics approach to study signalling pathways

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State-of-the-Art:The proliferation of cells depends on the duplication and segregation of their genomes. The latter is an immensely complex process that remains poorly understood at a molecular level. Mistakes during mitosis contribute to cancer, whereas mistakes during meiosis, causing aneuploidy, are the leading cause of infertility and mental retardation.

During mitosis, sister DNA molecules are dragged towards opposite poles of the cell due to their prior attachment to microtubules with opposite orientations (bi-orientation). Bi-orien-tation involves dissolution of the nuclear membrane, changes in chromosome organisation and reorganisation of the spindle apparatus. How mitotic cells coordinate these disparate but interlocking processes is poorly understood.

Protein kinases like Cdk1 have fundamental roles during cell division. However, Cdk1’s actual function remains mysterious despite recognition of its importance with a Nobel Prize. The same is true for other mitotic kinases, such as Plk1 and Aurora A and B. We need to know which set of proteins are phosphorylated, what their functions are, and how phospho-rylation changes their activity. Identification of kinase substrates has been hampered by dif-ficulties in mapping phosphorylation sites, in experimentally controlling protein kinase activ-ity, and in evaluating the physiological consequences of defined phosphorylation sites. The premise behind MitoCheck is that all three hurdles can be overcome by new technologies, namely the use of RNA interference to identify in systematic (functional genomics) manner potential substrates, iTAP-tagging to purify protein complexes, small molecules to inhibit specific kinases in a controlled fashion and mass spectrometry to identify phosphorylation sites on complex subunits. As the concept behind MitoCheck’s project could be applied to other areas, the projects outcomes have the potential to impact on European cell biology far beyond the cell cycle community.

Scientific/Technological Objectives:The main objective for the MitoCheck team is to understand how mitotic kinases orchestrate the many events of mitosis.

MitoCheck is carrying out genome-wide RNAi screens in human cells to systematically search for potential substrates of mitotic kinases. A genome-wide collection of synthetic small interfering RNAs (siRNAs) is introduced into human cells to deplete the entire 22, 000 human genes one- by- one. The behaviour of the cells after transfection is then recorded by live cell video microscopy. Genes whose depletion causes mitosis to go awry are crucial for mitosis.


Project Type:Integrated ProjectContract number:LSHG-CT-2004-503464Starting date:1st April 2004Duration:48 monthsEC Funding:

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A subset of the proteins crucial for mitosis is currently being tagged with green fluorescent protein (GFP) and with an affinity purification tag. The GFP tag will allow visualisation of the subcellular localisation of these proteins during cell cycle, whereas the affinity tag will en-able the identification of binding partners of these proteins via affinity purification followed by mass spectrometry. Since the phosphorylation state of these proteins and their binding partners are thought to be crucial for their function during mitosis, much of MitoCheck’s efforts will be devoted to identifying the mitosis-specific phosphorylation sites on them by mass spectrometry and the mitotic kinases responsible for these phosphorylation events.Some mitotic kinases are over-expressed in human tumours. One important objective of Mi-toCheck is to develop assays to systematically evaluate the clinical utility of mitotic kinases as diagnostic or prognostic markers.

Expected Results:1) A list of mammalian proteins that have important roles during mitosis: This list will be

compiled based on knowledge in the published literature, knowledge obtained in the MitoCheck labs and, most importantly, data from our genome-wide RNAi screens.

2) Subunit composition of the mitotic protein complexes and their mitosis-specific phos-phorylation sites: MitoCheck will employ mass spectrometry methods to identify the binding partners of the selected mitotic proteins, and to map the mitosis-specific phos-phorylation sites on them. We will further link particular mitotic kinases with specific phosphorylation sites.

3) Expression profiles of mitotic kinases in tumour samples and the potential of the mi-totic kinases as diagnostic or prognostic markers in clinical oncology

4) A web-based database: This database will contain important information such as a list of genes required for mitosis, subunit composition of mitotic complexes and their phosphorylation sites. Furthermore, the dataset from the genome-wide RNAi screens will also be displayed in the future. This dataset includes a wide range of cellular phenotypes, mitotic and non-mitotic. The MitoCheck database will therefore be a unique and highly valuable source of information, not only for the cell cycle field but also for many other areas in the life sciences.

Potential Impact:In order to gain insight into how cell division is controlled by phosphorylation, MitoCheck is developing a variety of genomic, proteomic and chemical approaches. Besides cell division, protein phosphorylation is also essential in many other biological processes such as


Regulation of Mitosis by Phosphorylation- A Combined Functional Genomics,

Proteomics and Chemical Biology Approach

Normal rat kidney cells in different stages of cell division stained for chromosomes (blue) microtubules (green) and actin (red). (Courtesy of Dr. Jan Ellenberg, EMBL/Heidelberg)© Dr. Jan Ellenberg, EMBL/Heidelberg


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signal transduction, gene expression and cellular differentiation. Abnormalities in protein phosphorylation pathways can contribute to human diseases such as cancer. The technologies MitoCheck is establishing will therefore have an impact on other research areas, far beyond cell cycle field.

Although MitoCheck focuses on basic research, it will also foster innovations in applied research. In some cases it may lead to new commercial products. For example, MitoCheck is developing biological assays for measuring both the amount and the activity of protein kinases in human biopsy material. These methods may be useful as diagnostic

and prognostic assays in cancer therapy, where novel “biomarker” assays are urgently needed to tailor therapies to the specific needs of patients.

The potential impact of MitoCheck in the area of product development is reflected by the participation of both a small biotech company (Gene Bridges GmbH) and a large company (Leica Microsystems CMS GmbH). Leica is one of the world’s leading bio-optical manufacturers. It is expected that novel software tools developed by Leica as part of the MitoCheck project will be introduced to the market soon.

Last, but not least, a unique strength of MitoCheck is its integration of leading experts from many disciplines ranging from optical engineering to high throughput genomics, from chemical biology to protein crystallography, and from bioinformatics to human pathology. This unusual diversity of expertise helps to foster innovation in technology development. It also creates opportunities for basic research that may lead to unforeseen important discoveries.


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Project Coordinator:Dr. Jan-Michael PetersForschungsinstitut für Molekulare Pathologie GmbHDr. Bohrgasse 71030 Vienna, [email protected]

Project Manager:Dr. Yan SunForschungsinstitut für Molekulare Pathologie GmbHDr. Bohrgasse 71030 Vienna, [email protected]

Dr. Jan EllenbergGene Expression and Cell BiologyBiophysics ProgrammesEuropean Molecular Biology LaboratoryHeidelberg, Germany

Prof. Dr. Roland EilsTheoretical BioinformaticsDeutsches KrebsforschungszentrumHeidelberg, Germany

Frank SieckmannLeica Microsystems CMS GmbH Mannheim, Germany

Prof. Dr. Tony Hyman Max Planck Institute of Molecular Cell Biology and Genetics (CBG)Dresden, Germany

Gary StevensGene Bridges GmbHHeidelberg, Germany

Dr. Andrea MusacchioEuropean Institute of OncologyDepartment of Experimental Oncology Milan, Italy

Dr. Ariane Abrieu Centre de Recherche de Biochimie Macromoléculaire (CRBM) Centre National de la Recherche Scientifique (CNRS)Montpellier, France

Prof. Tim HuntCell Cycle Control LaboratoryClare Hall Laboratories, Cancer Research UKSouth Mimms, UK

Dr. Kai StoeberUniversity College LondonWolfson Institute for Biomedical ResearchLondon, UK

Dr. Richard DurbinWellcome Trust Sanger InstituteHinxton, UK

Partners

Keywords: mitosis, phosphorylation, RNAi, mass spectrometry, chemical inhibitors, cancer, chemical biology, proteomics, functional genomics, regulation, cell cycle


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State-of-the-art:Intracellular communication in eukaryotes is largely achieved by the trafficking of mem-branes carrying membrane-bound and/or intravesicular signalling molecules. Inside cells, vesicles circulate from one intracellular compartment to another thus facilitating vectorial transport of signals. Between cells, membrane anchored and secreted soluble molecules mediate extracellular signalling. Exocytosis and endocytosis of receptors control the re-sponse of sensitive cells to extracellular signals. The routes of membrane trafficking are controlled by cell signalling pathways but the underlying molecular machinery is scarcely characterised. Moreover, membrane trafficking has been studied mainly in differentiated cells and rarely in cells changing phenotype during differentiation or dedifferentiation. Such drastic phenotypic changes occur during development when cells mature to differentiated cells as complex as neurons, and during malignant transformation.

Scientific/Technological Objectives:The goal of this STREP is to establish the connections between signalling pathways and mem-brane trafficking in the context of migrating, dividing and adhering mammalian cells. Through the study of membrane traffic in the course of cell differentiation, dedifferentiation, and dur-ing mitosis, we aim to unravel how important signalling pathways remodel the intracellular trafficking routes and conversely, how membrane traffic can influence signalling cascades. We will take advantage of several cellular models including neurons differentiating in culture and cancer cells dividing and migrating. We will investigate proteins that play central roles in membrane trafficking and secretion such as rabs, SNAREs and their partners. We will focus on the trafficking of signalling molecules including cell-cell and cell-substrate adhesion molecules, growth factors and their receptors, and also investigate the role of glycosylation. Through these approaches we will define the connections between Signalling and Traffic.Using modern cell biological approaches, the SIGNALLING & TRAFFIC consortium will study several cellular models, including neurons differentiating and establishing contacts in culture, and cancer cells dividing and migrating. It will investigate proteins that play central roles in membrane trafficking and secretion — such as Rabs, SNAREs and their partners — some of which have already been linked to cancer and brain related diseases. It will also focus on the trafficking of signalling molecules, including cell-cell and cell-substrate adhesion molecules, growth factors and their receptors.

In the case of cancer, the goal is to shift the therapeutic emphasis (at least for some tumours) from surgical to pharmacological interventions, thereby reducing hospitalisation costs as well as the financial, psychological and physical burden on patients and their families. In the case of neurodegenerative diseases such as Alzheimer’s and Huntington’s diseases and neuropa-thies, there is an urgent need to identify effective therapies. This will depend on advances in knowledge concerning the physiopathological links between gene defects and symptoms.

The project’s results will be disseminated through congresses, workshops and publications, and in classes in the partners’ universities. Its website will represent the hub of a communica-tion network, intended to attract both students working in relevant academic fields, and the general public.

Expected Results:A number of results have already been reported by members of the consortium: (1) Tetanus neurotoxin-mediated cleavage of cellubrevin impairs epithelial cell migration and cell adhe-sion; (2) Expression of the cell adhesion molecule L1 augments cell motility, invasiveness and tumour growth in vivo; (3) Recycling of pro-transforming growth factor alpha regulates the activation of the epidermal growth factor receptor (EGFR), opening up the possibility that defects in trafficking may contribute to the development of tumours; (4) Two different


Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-503228Starting date:1st May 2004Duration:43 monthsEC Funding:

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pathways exist for the internalisation of the EGFR; (5) The Rab6A’ GTPase enzyme is re-quired for the metaphase/anaphase transition in mitosis; (6) Crosstalk exists between the actin-remodelling signalling pathway, activated by platelet-derived growth factor stimula-tion of cells, and endocytosis.

Potential Impact:The intention of SIGNALLING & TRAFFIC is to open up new avenues in the development of molecular diagnostic and therapeutic tools for diseases demonstrating a membrane trafficking and/or signalling component. This will be relevant to a range of pathologies, from cancer and proliferative non-neoplastic diseases, to neurodegenerative diseases and neuropathies.Cancer and brain-related diseases are major causes of death in Europe and they represent a large socioeconomic burden and an increasing challenge in Europe’s increasingly ageing population. SIGNALLING & TRAFFIC is designed to develop new therapies and new diag-nostic tools, ultimately leading to improvements in health and quality of life for the European population.

Keywords: Signalling, membrane trafficking, cell division, cell migration, cell adhesion

Project Coordinator:Prof. Thierry GalliInstitut Jacques MonodTeam ‘Avenir’ INSERM2 Place Jussieu75005 Paris, [email protected]

Prof. Peter AltevogtGerman Cancer Research CentreTumour Immunology ProgrammeHeidelberg, Germany

Dr. Joaquín ArribasUniversity Hospital Research InstituteMedical Oncology Research ProgrammeBarcelona, Spain

Dr. Júlia CostaInstituto de Tecnologia Químicae BiológicaLaboratory of GlycobiologyOeiras, Portugal

Prof. Pier Paolo Di FioreFIRC Institute of Molecular OncologyFoundationMilan, Italy

Dr. Bruno GoudCentre National de laRecherche Scientifique (CNRS)Institut CurieUMR 144Paris, France

Prof. Jacqueline TrotterJohannesGutenberg-UniversitätInterdisciplinary Centrefor NeurosciencesMainz, Germany

Dr. Letizia LanzettiInstitute for CancerResearch and TreatmentDivision of MolecularAngiogenesisTurin, Italy

PartnersDr Jonathan DandoInserm-TransfertDept International and European AffairsParis, France


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State-of-the-art:Apoptosis is controlled by multiple pathways, which include extrinsic signalling via death receptors, and by intrinsic pathways involving the mitochondria and endoplasmatic reticu-lum. These inputs activate proteolytic caspase cascades and subsequent cell death. Pro- and anti-apoptotic Bcl-2 family members are important in controlling mitochondrial signals, in-cluding cytochrome c, whose association with the downstream regulator Apaf-1 and pro-caspase-9 forms the apoptosome that mediates caspase activation. Although homologs of the apoptotic machinery are not found in plants and lower eukaryotes, comparative phylo-genetic analysis of the domains conserved in these proteins indicates that they existed in the common ancestor of animals, plants, and fungi. These ancient domains were, and in some cases still are, components of ancestral signalling pathways for responses to pathogens and stresses, including starvation and DNA damage. A goal of the Transdeath program is to understand the mechanistic relations between extant PCD programmes in different organisms. For example, plant leaves senesce at the end of growth seasons. How is this developmental form of PCD related to the more rapid PCD induced during the plant hypersensitive response to pathogens?

Scientific/Technological Objectives: Transdeath aims to define (phenomenologically and molecularly) dis-tinct types of cell death by using models appropriate for each type of death. A main focus of the project is the research on the less studied cell death types, which are caspase-independent and non-apoptotic. These mechanisms will then be used to understand corresponding types of cell death in mammals, in particular humans. The general lines of inquiry followed in the WorkPackages (WPs) in-clude: analysing distinct types of cell death in their respective optimal model(s); comparing cell death types within and between these models; and extending the study to corresponding cell death types in humans.

The project has five scientific WPs. WP1 (Bioinformatics & Database) identifies genes of interest for experimental WPs, and provides a hub for data used to develop gene-silencing experiments. WP2 (Apopto-sis) uses phylogenetic comparison to elucidate apoptotic functions of proteins involved in human diseases. WP3 (Autophagic PCD) aims to identify and analyse phylogenetically conserved pathways, subcellular events, and molecular mechanisms involved in autophagic/vacuolar cell death by using the most amenable models.

WP4 (Necrosis & other PCD) analyses necrotic/non-apoptotic cell death using methodolo-gies in diverse model systems. This strategy permits the analysis of aspects of non-apoptotic cell death from different angles and in organisms of increasing complexity. This vertical approach has the potential to reveal points of convergence for the underlying mechanisms that would otherwise go unnoticed.

Expected Results:

The Transdeath project will potentially provide cutting-edge tools and resources for the European and international scientific community, and additionally nucleate a larger pan-European network of laboratories aimed at exploiting these tools and resources to model human diseases and to address gene function. Both of these objectives are immediately relevant to the improvement of human health and quality of life.

Death in the mold – Top - during fruiting body development in the

social amoeba Dictyostelium, cells of the stalk under programmed

cell death. Bottom - cultured cells can be induced to die and are

used to study this process.


TransDeath

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-511983Starting date:1st December 2004Duration:36 monthsEC Funding:

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The partners are expected to identify all well-conserved and poorly-conserved eukaryotic homologs of cell death genes, and construct phylogenetic trees for all families. Further-more, the team will identify potentially missing family members, and establish a function-ing, basic web platform for data exchange between partners.

Potential Impact:

The results of Transdeath will be useful to the scientific community at large by making diverse PCD genes and models attractive and accessible platforms to study genes and biological phenomena of particular importance to biomedicine. These developments will bridge the gap between development and progress in the United States with European research on PCD in model organisms and biomedicine.

The project will signify a major achievement in terms of consolidating the fragmented European PCD research base, strengthening the European model organism research com-munity and laboratories, and providing new opportunities for European biomedical and biotechnology interests to acquire intellectual property.

Keywords: apoptosis, bioinformatics, cancer

Death Suppressor Screen – A mutant, transgenic plant in which death can be chemically-induced was used to screen~3 million progeny for secondary mutations that suppress death. The corresponding genes encoding death activators are now being identified.

Project Coordinator: Prof. John MundyUniversity of CopenhagenInstitute of Molecular BiologyNorregade 101017 Copenhagen, [email protected]@my.molbio.ku.dk

Prof. Kai-Uwe FröhlichUniversity of GrazInstitute of Molecular BiosciencesGraz, Austria

Dr. Corinne ClavéCentre National de la RechercheScientifique (CNRS) IBGC-UMR 5095Unit with U. Bordeaux 2Bordeaux, France

Dr. Pierre GolsteinCentre National de la RechercheScientifique (CNRS) CIML-UMR 6102Unit with INSERM & U. Aix-Marseille IIMarseille, France

Dr. Guido KroemerCentre National de la RechercheScientifique (CNRS) IGR-UMR 8125Unit with INSERM & U. Paris XIParis, France

Dr. Nektarios TavernarakisFoundation for Researchand Technology HellasInstitute of MolecularBiology and BiotechnologyHeraklion, Greece

Prof. Adi KimchiWeizmann Instituteof ScienceRehovot, Israel

Prof. Roberto TestiUniversity of Rome‘Tor Vergata’Department ofExperimental MedicineRome, Italy

Prof. Jonathan JonesThe Sainsbury LaboratoryNorwich, UK

Partners


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State-of-the-Art:Peroxisomes are single, membrane-bound organelles that are present in virtually all eu-karyotic cells. In mammals, the size, number and protein content of peroxisomes vary significantly, depending on the cell and tissue type as well as on the developmental and physiological stage in question. Consequently, peroxisomes are considered to be multi-purpose organelles.

In humans, impairments of these multiple functions lead to different peroxisomal disorders which can be divided into two groups. The first of these are peroxisome biogenesis disor-ders (PBDs), which are caused by a generalised or multiple loss of peroxisomal function due to a defect in the formation of the organelle. Many PBDs were named before their associa-tion with the organelle was recognised. These include Zellweger syndrome (ZS), neonatal adrenoleukodystrophy, infantile Refsum disease, and rhizomelic chondrodysplasia punc-tata. The second group of disorders is caused by a single peroxisomal enzyme deficiency.

Although they are essential for life, the various functions and dynamics of peroxisomes in health and disease are poorly understood. Most inherited peroxisomal disorders in humans have a low incidence, but collectively they represent an enormous burden on affected individuals, their families and society. At present, the number and nature of peroxisomal matrix proteins are unknown. Each year, several novel peroxisomal matrix proteins are dis-covered, and the number of metabolic pathways known to exist within peroxisomes, grows. Evidence is now emerging that peroxisomes play a role in modulating diseases of complex inheritance, such as arteriosclerosis, cancer and Alzheimer’s disease (AD).

Scientific/Technological Objectives:Using cutting edge proteomics tools, the Peroxisomes consortium will identify and charac-terise the functions of novel peroxisomal proteins, and establish a catalogue of peroxiso-mal matrix proteins in human liver, kidney and brain. In parallel, it will characterise and catalogue the mouse peroxisomal proteome in liver, kidney and brain, in order to gain a deeper understanding of species differences - the basis for a more accurate interpretation of existing mouse models of peroxisomal diseases.

The consortium will also evaluate the role of peroxisomes as modulators or modifiers of diseases of complex inheritance, such as AD and cancer. Tissue microarray analysis, cDNA chip and quantitative RT-PCR analysis will be used to verify the results, with the final goal of developing improved diagnostic and prognostic tools for these disorders.

Many of the functions affected by peroxisomal disorders are related to processes which take place at the peroxisomal membrane. A complete catalogue of peroxisomal membrane proteins in mouse and man will contribute to our understanding of what kind of metabolites are transported across this membrane, how peroxisomes import proteins and lipids, and how the organelles divide and are transmitted to a new cell. The distinction between matrix and membrane-localised proteins is based mainly on technical considerations. As mem-brane proteins are notoriously under-represented in conventional proteomic approaches, the consortium will apply state-of-the-art techniques for membrane isolation.


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Expected Results:Almost all peroxisomal diseases are as-sociated with childhood pathology. Most of them are incurable, and lead to death before the first decade. The Peroxisomes consortium’s fundamental studies on the role of peroxisomes, should shed light on the pathogenesis of these devastating dis-eases, and may lead to novel treatment regimens for them. It is clear that the ex-pertise brought together by this proposal will drive significant advances in this area. The consortium will also create and apply novel tools, including peroxisomal membrane anchor proteins for affinity purification of peroxisomes from different sources and tissues, transgenic animals permitting the regulated inactivation of peroxisomal function in distinct tissues only, and an automated tissue microar-rayer. Finally, by means of this joint ef-fort, it should be possible to decipher the molecular mechanisms of so far unchar-acterised peroxisomal disorders, thereby creating novel diagnostic and therapeutic opportunities.

Potential Impact:The motivation for this project was the realisation that peroxisomes have remained an ill-defined subcellular organelle for years, even though they are known to be essential for life, as is clearly demonstrated by the devastating consequences of the absence of peroxisomes in patients affected by ZS. Lack of knowledge about peroxisomes is a serious obstacle to determining their true significance in health and disease, and to designing effective diagnostic and therapeutic strategies for such diseases.

Some peroxisomal disorders, such as ZS, have a rapid, lethal course, causing death in the first year. Patients with other types of peroxisomal disorders, however, may survive for long periods with severe

Plasmalogen-deficient knockout mouse showing eye defectsand cataract

Peroxisomes visualised as dark granules by catalase immunostaining in human fetal renal cortex

Peroxisomes visualised as dark granules by catalase immunostaining in human fetal liver

Cytochemical incubation for catalase activity in mouse renal cortex (proximal tubule) revealing peroxisomes as electron-dense organelles


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handicaps which require chronic treatment and care, often in special institutions for mentally retarded people. This is obviously costly to society, but it also imposes an enormous emotional and psychological burden on the families affected. Clearly, increasing knowledge about the biological role of peroxisomes could reduce that burden, if it leads to therapeutic advances. Moreover, many patients with a likely defect of peroxisomal function currently remain undiagnosed. If this project leads to improvement in the diagnosis of peroxisomal disorders, such patients will benefit from a more rapid and more accurate diagnosis, which will in turn mean they can then be treated appropriately.

Keywords:peroxisome, genomics, proteomics, human diseases, diagnosis, therapy, mouse models

A molecular model of part of the structure of the (3R)-

hydroxyacyl-CoA dehydrogenase of human peroxisomal MFE-2

showing two residues, Val218 and Trp273, whose mutation to

other residues causes dysfunction of the enzyme in humans

Fluorescent image of peroxisomes

Morphometry of peroxisomes in normal mouse liver


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PartnersProject Coordinator:Prof. Johannes BergerCentre for Brain ResearchMedical University of ViennaSpitalgasse 231090 Vienna, [email protected]

Prof. Ron Wanders, Dr. Antoine van Kampen Academic Medical CentreAmsterdam, The Netherlands

Prof. Myriam BaesCatholic University of LeuvenLaboratory of Clinical ChemistryLeuven, Belgium

Prof. Ralf Erdmann, Prof. Helmut MeyerRuhr-Universität BochumBochum, Germany

Prof. Wilhelm JustUniversität HeidelbergBiochemie-Zentrum der Universität HeidelbergHeidelberg, Germany

Prof. Andreas HartigUniversity of ViennaDepartment of BiochemistryVienna, Austria

Prof. Norbert LatruffeUniversité de BourgogneLaboratoire de Biologie Moléculaire et CellulaireDijon, France

Prof. Klaus-Armin NaveMax-Planck Institute for Experimental MedicineDepartment of NeurogeneticsGöttingen, Germany

Dr. Annamaria CiminiUniversity of L’AquilaDepartment of Basic and Applied BiologyCoppito, Italy

Prof. Jorge E. AzevedoIBMC-University of PortoInstituto de Biologia Molecular e CelularPorto, Portugal

Prof. Kalervo HiltunenUniversity of OuluBiocenter Oulu and Department of BiochemistryOulu, Finland

Prof. Stefan AlexsonKarolinska InstitutetDepartment of Medical Laboratory Sciences and TechnologyStockholm, Sweden

Prof. Gerald HoeflerMedical University GrazInstitute for Pathological AnatomyGraz, Austria

Prof. Marc EspeelUniversity of GentDepartment of Anatomy, EmbryologyHistology and Medical PhysicsGhent, Belgium


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State-of-the-Art:Understanding the pleiotropic effects of the time-dependent erosion of the genome, and the complexity of cellular responses to DNA damage, requires a comprehensive, multi-disciplinary approach ranging from molecule to patient. At the level of structural biology and biochemistry, the DNA Repair consortium will analyse individual components and path-ways, to identify new components and clarify reaction mechanisms. The interplay between pathways and crosstalk with other cellular processes will be explored using biochemical and cellular assays.

To better understand the function and impact of DNA damage response and repair systems in living organisms, the DNA Repair consortium will take full advantage of its unique and extensive collection of models (mutant yeast cells and mice), to engineer and analyse new mutants whose genome stability is impaired. The latest genomic and proteomic technolo-gies will be exploited to identify novel genes involved in genome surveillance. Bioinformat-ics, high throughput gene expression analysis and proteomics will be used to identify the putative functions of these genes and their proteins.

Similar global genome analytical tools will be used to identify interactions with, and effects on, other cellular processes. The ‘druggability’ of potential targets, in the context of anti-cancer therapies, will be tested in collaboration with SMEs. Through its existing contacts with clini-cians, the consortium will continue to ana-lyse patients with previously identified de-fects in DNA damage response and repair mechanisms, and will also screen patients for new disorders.

Scientific/TechnologicalObjectives:The study of the vast problem of DNA damage requires an integrated, multidis-ciplinary approach. European research

teams have played a prominent role in increasing understanding of individual pathways involved in this phenomenon, but many challenges remain, including the following: (1) Un-derstanding the complex interplay between the various genome stability systems, and plac-ing the pathways which have already been described into an integrated cellular context; (2) Gaining insight into the clinical impact of the systems, both individually and collectively, from the cellular level to that of intact organisms and the human population; (3) Translat-ing this knowledge into practical applications in the form of improved diagnosis, effective therapy and prevention or postponement of diseases associated with the functional decline of the genome.

Figure 1. DNA repair proteins at work. Treatment of cells with

ionising radiation can result in cell death because the irradiation

introduces breaks in the DNA. DNA repair proteins counteract the lethal effect of irradiation

by restoring the integrity of the DNA. After irradiation the DNA

repair proteins are organised into clusters, called foci, at sites of

repair. This dynamic relocalisation can be visualised in living cells

by fusing DNA repair proteins to a naturally fluorescent protein.

The cells in the image have been irradiated and foci containing the

repair protein become visible.



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ExpectedResults:DNA Repair expects to produce the following results:

1) A detailed understand-ing of the biochemical mechanism of DNA repair and checkpoint pathways;

2) Insight into the cellular functioning and consequences of defects in one of the ge-nome surveillance pathways;

3) Identification of new components of DNA damage response pathways; 4) Extrapolation of findings from model organisms to humans. The expected results

will be accomplished firstly by the investigation of patients and cells from patients suffering from genome instability, cancer predisposition and premature ageing syn-dromes, and secondly by an extensive comparison of mouse mutants with these human conditions.

Potential Impact:Our DNA is constantly under attack from physical and chemical agents that compromise its integrity and represent a threat to genomic stability, potentially resulting in cancer and other health problems. A large number of chemical compounds in food have a potentially harmful influence on human genetic make-up, especially under conditions in which the DNA repair capacity is sub-optimal.

The proposed research will be im-portant for assessing potential risks posed by environmental hazards (such as food components and envi-ronmental pollutants). A better under-standing of genome-wide responses to genotoxins, in relation to the DNA repair status of an organism, will en-able the evaluation of possible risks to consumer health and contribute to the eventual elimination of identified toxins.

The consortium’s genomics and proteomics approaches could also be applied to the assessment of the health risks of such compounds for specific sub-groups who carry subtle mutations in DNA repair genes, and for the ageing population.

Figure 2. Accumulation of the Mre11 DNA repair complex at sites of DNA double-strand breaks (DSBs). The left panel shows a cell immunostained for the Mre11 complex (in green) at DSBs. The linear arrangement of the DSBs is caused by the passage of an α-particle through the cell (DNA shown in blue). The length of the linear track is about 10 μm. The panel on the right shows the archtitecture of the Mre11 DNA complex as determined by Atomic Force Microscopy. The arms protruding from the globular domain are 50 nm in length.

Figure 3. Chromosomal aberrations, associated with carcinogenesis, induced by interstrand crosslink (ICL)-inducing agents. In the absence of the Ercc1/Xpf DNA repair protein ICLs cause numerous chromosomal aberrations, most notably fusion of chromatids. Shown is a metaphase spread of an Ercc1/Xpf deficient Chinese ovary hamster cell line.


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PartnersProject Coordinator:Prof. Jan HoeijmakersErasmus Universitair Medisch Centrum RotterdamDept. of Cell Biology and Genetics‘s Gravendijkwal 2303015 CE Rotterdam, The [email protected]

Project Manager:Dr. Rini de CromErasmus Universitair Medisch Centrum RotterdamDept. of Cell Biology and Genetics‘s Gravendijkwal 2303015 CE Rotterdam, The [email protected]@erasmusmc.nl

Prof. Roland Kanaar, Dr. Wim VermeulenDr. G.T.J. van der HorstErasmus Universitair Medisch Centrum RotterdamDepartment of Cell Biology and GeneticsRotterdam, The Netherlands

Dr. Stephen West, Dr. Jesper Q. SvejstrupCancer Research UK Genetic Recombination LaboratoryLondon, UK

Prof. Jiri Bartek, Dr. Jiri LukasDanish Cancer SocietyInstitute of Cancer Biology and Centre for Genotoxic Stress ResearchCopenhagen, Denmark

Prof. Karl-Peter HopfnerUniversity of MunichGene CentreMunich, Germany

Prof. Stephen P. JacksonWellcome Trust/Cancer Research UK Gurdon InstituteUniversity of CambridgeCambridge, UK

Keywords:genome (in)stability, cancer, ageing, molecular biology, genomics, proteomics, human dis-ease, DNA damage, DNA repair mechanisms


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Prof. Josef JiricnyUniversity of ZürichInstitute of Molecular Cancer ResearchZurich, Switzerland

Prof. Alan R. Lehmann, Prof. Anthony M. Carr, Dr. Penelope A. JeggoUniversity of SussexGenome Damage and Stability CentreBrighton, UK

Prof. Hans E. KrokanNorwegian University of Scienceand TechnologyDept. of Cancer Research and Molecular MedicineTrondheim, Norway

Prof. Leon H. F. MullendersLeiden University Medical CenterDepartment of ToxicogeneticsLeiden, The Netherlands

Prof. Marco FoianiIstituto FIRC di Oncologia Molecolare (FIRC: Fondazione Italiana per la Ricerca sul Cancro)Milan, Italy

Prof. Paolo PlevaniUniversity of MilanoDipartimento di Scienze Biomolecolari e BiotecnologieMilan, Italy

Prof. Magnar BjøråsRikshospitalet OsloInstitute of Medical MicrobiologyOslo, Norway

Prof. Noel LowndesUniversity of IrelandGenome Stability LaboratoryDepartment of BiochemistryGalway, Ireland

Prof. Jean-Marc EglyCentre National de la RechercheScientifique (CNRS)Institut National de la Santé et de la RechercheMédicale (INSERM)Université Louise PasteurIllkirch, France

Dr. Graeme C. M. Smith, Dr. Mark O’ConnorKuDOS Pharmaceuticals LtdCambridge, UK


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State-of-the-Art:Cardiovascular diseases remain one of the major causes of mortality in the developed world. Dependence between cholesterol levels and mortality and the positive influence of cholesterol lowering effects are clearly established. Even if statins are still considered as relatively safe drugs, considerable attention is payed to the statin-based risk of muscular adverse drug reactions (ADR). Considering that 5-10% of population in developed societies is treated with statins, this represents an important health risk problem. Drugs are gener-ally metabolized by the cytochrome P450 (CYP) system. Once bound to nuclear receptors, drugs modulate the expression of the responsive CYPs, which represents the basis of ADR: a modulated metabolism of xenobiotics (and enobiotics) that are metabolized by the same CYP. Statins are often used in combination with other medications since patients with hyper-lipidemia frequently have other medical problems. 60% of statin-related rhabdomyolysis is attributed to ADR. Post-genomic approaches applied in Steroltalk offer venues to approach such complex physiological questions that have a great impact on human therapy.

Scientific/Technological Objectives:The vision of STEROLTALK is to develop a global approach by combining dedicated func-tional genomic tools, three model organisms and in silico modelling, for the discovery of new drug targets, new chemical entities and therapeutic strategies. Regulatory networks in human, mouse and S. cerevisiae will be assessed through integrative analysis of transcrip-

The STEROLTALK multidisciplinary functional genomics approaches

and models. Human primary hepatocytes and normal, hyperli-pidemic and nuclear receptor PXR

and CAR knockout mice were treated with known and novel

drugs. Transcriptome, limited proteome and sterol metabolome

have been measured and data incorporated into the in silico

model, together with the human-ized yeast data and literature

information. The model is able to simulate cholesterol homeostasis

and the cholesterol lowering effect of statins as well as novel

chemical entities. This gives an insight into the mechanism of

hypolipidemics action.


STEROLTALKwww.steroltalk.net

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2004-512096 Starting date:1st September 2005Duration:36 months EC Funding:

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tome, proteome, metabolome and by yeast engineering. For the first time this will allow the deciphering of multi-level response of cholesterol homeostasis to known and candidate drugs, and its modulation in pathologies. Typical investigation targets will be mouse livers and primary human hepatocytes. The first task of our project is to develop original tools for functional genomic analyses of drug-modulated responses of STEROLTALK genes, proteins and metabolites in biological models. Tools include a dedicated microarray, an antibody set, siRNA knockouts, humanised yeast and a database. Deposited analytical data will be evaluated by numerous bioinformatic approaches, to assist in building relevant in silico models with predictive values, ready for implementation in novel drug discovery strate-gies. These models will allow, for the first time, the identification of potential cholesterol homeostasis-related targets that will be validated in vivo in biological models by the original STEROLTALK tools.

Expected Results:The project STEROLTALK will for the first time undertake a systematic post-genomic evalu-ation of the cholesterol homeostasis and its cross-talk to drug metabolism and contribute to understanding the effects/side effects of the hypolipidemic therapy and the combined therapies. Original functional genomics tools will be developed with focus on the genes, enzymes and metabolites that are involved in cholesterol homeostasis and in drug me-tabolism. The Steroltalk tools include dedicated mouse and human Steroltalk microarrays containing genes of the cholesterol homeostasis and the entire CYP and nuclear receptor gene families, a structured Steroltalk database, a set of novel Steroltalk antibodies raised against membrane-bound choelsterogenic enzymes, humanized yeast strains synthetizing cholesterol, representing novel drug screening tools and predictive in silico models. The novel tools will be used in combination with commercial tools, to experimentally determine the cross-talk between cholesterol homeostasis and drug metabolism in drug-treated human primary hepatocytes and in livers of normal, hyperlipidemic and nuclear receptor-knockout mice, at the level of transcriptome, proteome and metabolome.

The original tools developed within the STEROLTALK project. The Steroltalk microarray exists in the human and mouse version, containing 300 gene of each species. The Steroltalk database contains protocols used within the consortium as well as data. It is restricted to access by Steroltalk partners through a safe web portal. The Steroltalk antibody set consists of over 20 antibodies. Some are commercial, some original and raised against the membrane proteins of the cholesterol homeostasis and drug metabolism network. The prototype Steroltalk protein chips and protein maps are under development. Several humanized yeast strains have been developed by yeast engineering, synthetizing cholesterol and being evaluated as novel hypolipidemic drug screening tools.The first set of data regarding the Steroltalk transcriptome, limited proteome and sterol metabolome is available for drug treated mice and human primary hepatocytes. Novel findings regarding statin and original hypolipidemics action have been acquired and drug discovery strategies discussed


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These data will be interpreted, and when appropriate, also included into in silico models. The Steroltalk tools and experimental data will together with mathematical models aid in determining novel correlations and in resolving unknown molecular mechanisms of the cho-lesterol homeostasis/drug metabolism network.

Potential Impact:STEROLTALK will compare the effects of clinically approved ‘safe’ statins with novel, non-sta-tin hypolipidemics, at the levels of transcriptome, proteome and metabolome. This will have a high impact on understanding the multi-level effects and potential side effects of drugs. This innovative functional genomic approach, which involves development of original and dedicated tools, will reinforce the competitiveness in developing new and, for humans, safe hypolipidemics.

Keywords: functional genomics, medical pathway modelling, yeast engineering, improved human health


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PartnersProject Coordinator:Prof. Rita BernhardtSaarland UniversityDepartment of BiochemistryCampus, Building B2.266123 Saarbrücken, [email protected]

Prof. Damjana RozmanUniversity of LjubljanaInstitute of BiochemistryDepartment of Electrical EngineeringLjubljana, Slovenia

Dr. Denis PomponCentre National de la Recherche Scientifique CNRS-CGMGif-sur-Yvette, France

Prof. Steven KellyUniversity of Wales, SwanseaSchool of MedicineSwansea, Wales

Prof. Ingemar BjörkhemKarolinska InstitutetDivision of Clinical ChemistryStockholm, Sweden

Prof. Urs MeyerUniversity of BaselBiozentrumBasel, Switzerland

Dr. Patrick MaurelInstitut National de la Santé et de la Recherche Médicale (INSERM)U632Montpellier, France

Dr. Katalin MonostoryHungarian Academy of SciencesChemical Research CenterBudapest, Hungary

Dr. Drago KuzmanLek Pharmaceuticals d.d.Ljubljana, Slovenia

Dr. Andrej GustinCREA storitve in svetovanje, d.o.o.Ljubljana, Slovenia


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State-of-the-Art:Numerous cellular proteins are post-translationally modified by a conjugation of ubiquitin and ubiquitin-like (UbL) proteins. Among them are cell cycle regulators, tumour suppressors, growth regulators, transcriptional activators and inhibitors, signalling proteins and regula-tory enzymes in key metabolic, replicative and quality control/stress pathways. Membrane proteins, which include cell surface receptors, ion channels and ER proteins, are also tar-geted by the system. Finally, mutated and denatured/misfolded proteins are specifically recognized and efficiently removed.

With this diverse repertoire of substrates it is not surprising that the system regulates a broad array of cellular processes inclusive of the following: cell cycle and division, differ-entiation and development, signal transduction, regulation of transcription, modulation of the immune and inflammatory responses, intracellular trafficking of proteins, biogenesis of organelles, morphogenesis of neuronal networks and axon guidance, modulation of cell surface receptors, ion channels and the secretory pathway, DNA repair, long-term memory, circadian rhythms, and the cellular stress response and quality control machineries.

Aberrations of the system are implicated in the pathogenesis of human diseases, seen in many malignancies, neurodegenerative disorders and pathologies of the inflammatory and immune response. Consequently, a great deal of effort has been channelled into the de-velopment of drugs, which target the different components of the system, namely enzymes, substrates and modifiers. One of these drugs is already on the market, while others are in the pipeline. Within this context, a better understanding of the underlying mechanisms in-volved in this complex post-translational modifying system has important biological, clinical and therapeutic implications.


RUBICON


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Overview of the RUBICON project

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Scientific/Technological Objectives: Malfunctions of the ubiquitin and ubiquitin-related systems are strictly connected to the pathogenesis of numerous diseases, including cancer and inflammation. Insights into the role of ubiquitin-dependent pathways in disease development, may ultimately lead to the identification of novel therapeutic targets. A striking instance of this is the recent finding, on behalf of network members, of the central role of ubiquitin in DNA repair in yeast, a finding that impacts crucially on cancer research. This discovery highlights the potential importance of basic research in the understanding of disease-related processes.

Moreover, the understanding of functional genomics and protein-protein interactions is an essential prerequisite for rational structure-driven drug design. This is expected to have an impact on future drug discovery processes, on the competitiveness of pharmaceutical industries and, ultimately, on the health of the world population. Improved information on altered signalling pathways and on modifications in the target structure is essential for the acceleration of the development of a drug. In this sense, it is expected that network research will lead to patent applications relevant to medical research and, ultimately, to the develop-ment of new drugs and therapeutic procedures in clinics.

The RUBICON project aims to foster translational research, by bringing together basic sci-entists, clinicians and biotech SMEs. They will form a communication network that will pro-vide the industry with new therapeutic avenues, which can be investigated and exploited in a mutually beneficial manner.

Expected Results: The RUBICON consortium will substantially enhance the competitiveness of basic European research on ubiquitin and ubiquitin-like molecules, and explore their role in the regulation of basic cellular processes. Moreover, the project will promote translational research on the system’s involvement in human diseases; by acting as a catalyst, it will also encourage progress, and facilitate further coordination of biotech research enterprises, within this key area of biomedicine.

The European contribution to the ubiquitin field has been both pioneering and substantial, and Europe is currently home to some of this field’s world-leading scientific groups. For many years, research funding for this field has been provided at a national level, and de-spite the high degree of specialisation, it has resulted in poor dissemination of the acquired knowledge to new and relevant research areas. RUBICON will overcome this apparent fragmentation and further the combined efforts of European laboratories, by establishing collaborative multi-centre research projects.

The “virtual core facilities” of RUBICON will allow all laboratories to access and employ highly specialised, cutting-edge technology on demand, thus accelerating scientific progress. The rapid dissemination of such sophisticated methodology is greatly hampered by the high start-up and maintenance costs, and the lack of specifically trained technical personnel. In addition, RUBICON will support pre-existing technical platforms created through national funding, making them available for use on behalf all the partners. RUBICON, through the development, collection and dissemination of commonly required research tools, will coor-dinate research activities, eliminate a duplication of effort, and allow for the faster and more


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economic use of resources in ubiquitin research. RUBICON will generate new knowledge, which will be published in specialist journals and presented at international meetings, thus ensuring the dissemination of the project’s findings to the scientific community. The website, press releases, media events and seminars in schools will be instrumental in transmitting discoveries to the general public.

Potential Impact: RUBICON is expected to have a lasting impact on European research. The training of research workers in networked laboratories will foster a rich source of young and talented people, who will enter the academic and industrial spheres where they will continue con-ducting research and teaching in this area. Collectively, these multi-disciplinary researchers will contribute to the ongoing effort to make Europe the global leader in this field.

Moreover, interaction with researchers from countries in Eastern Europe, coupled with the training of young scientists from these countries, will have a long-standing impact on the European scientific community. As a result, not only will these countries be able to rapidly attain the highest international standards, but the position of Europe as a competitive par-ticipant in global science will also be strengthened.

Finally, RUBICON will form research collaborations with SMEs and large pharmaceutical companies in Europe. An improved understanding of the complementary needs of basic sci-ence and biomedical companies, will facilitate affiliations and encourage the development of new drugs for the treatment of human diseases.

Keyword: ubiquitin


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Project Coordinator: Prof. Maria MasucciKarolinska InstitutetDepartment of Cell and Molecular Biology Nobels vag 1617177 Stockholm, [email protected]

Prof. Rene BernardsNetherlands Cancer InstituteAntoni van Leeuwenhoek HospitalDivision of Molecular CarcinogenesisAmsterdam, The Netherlands

Prof. Ger StrousUtrecht University Medical Center Department of Cell BiologyDivision of Biomedical GeneticsUtrecht, The Netherlands

Dr Colin Gordon Medical Research CouncilHuman Genetics UnitEdinburgh, UK

Prof. Ronald T. HayUniversity of Dundee Dundee, UK

Prof. Ronald ThomasUniversity of DundeeDundee, UK

Dr. Anne De JeanInstitut Pasteur Unité de Recherche Organisation Nucléaire et OncogenèseParis, France

Dr. Pascal GenschikCentre National de la Recherche Scientifique (CNRS)Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS UPR 2357Strasbourg, France

Prof. Stefan JentschMax-Planck Institute for BiochemistryMartinsried, Germany

Prof. Frauke MelchiorBereich Humanmedizin der Georg-August-Universitaet Göttingen Stiftung Oeffentlichen Rechts Göttingen, Germany

Prof. Martin ScheffnerUniversitat KonstanzKonstanz, Germany

Dr. Thomas SommerMax-Delbrueck-Centrum fuer Molekulare MedizinBerlin, Germany

Prof. Dieter H. WolfUniversität Stuttgart Institute of BiochemistryStuttgart, Germany

Prof. Pier Paolo Di FioreIFOM Fondazione Istituto Fircdi Oncologia MolecolareMilan, Italy

Prof. Aaron CiechanoverTECHNION - Israel Instituteof TechnologyHaifa, Israel

PartnersProf. Yinon Ben-NeriahHebrew University of JerusalemJerusalem, Israel

Dr Hans LangedijkPepscan SystemsLelystad, The Netherlands

Dr Henk ViëtorDrug Discovery Factory BVAbcoude, The Netherlands

Dr Dominique ThomasCytomics Systems SAGif-Sur-Yvette, France

Dr Paul SheppardAffiniti Research Products Ltd(trading as BIOMOLInternational LP)Exeter-Devon, UK

Dr Yuval ReissProteologics LtdRehovot, Istrael


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State-of-the-Art:Endocytic trafficking plays a more active role in the regulation of polypeptide growth factor (GF) signalling than was previously recognised. Despite great progress in the description of the endocytic routes and their molecular regulation, the scientific community is far from pos-sessing a complete understanding of the endocytic trafficking of GF receptor (GFR) complexes and to what extent their signalling activity requires, and is modulated by, these routes. The EndoTrack project aims to fill this gap by gaining a basic understanding of the relationship between the endocytic transport and signalling activity of GFRs.

EndoTrack combines leading European interdisciplinary research teams to pursue the follow-ing aims:

1) Define the trafficking routes of various GFR complexes in cultured cells with an unprec-edented degree of precision, combining high-throughput microscopy with automated image analysis and electrochemiluminescence technology.

2) Define the molecular machinery responsible for this transport using proteomics and functional genomics approaches, and generate proof of concept that trafficking con-tributes to GF signalling activity in cultured cells;

3) Integrate the information from cultured cells with in vivo studies in animal model sys-tems, in particular Drosophila, zebrafish, Xenopus and mouse;

4) Test the relevance of the modulation of endocytic trafficking on signal transduction in disease model systems;

5) Within four years, the use of knockdown approaches, reporter cell lines and animals, combined with target validation proprietary technology from biotech SMEs, will pro-vide a new generation of assays to measure GFR trafficking and signalling. These assays will lead to the identification of novel key regulatory components and hence, to a new generation of diagnostic markers and potential targets for modulation of GF signalling in the treatment of human diseases. EndoTrack’s translational research will thus strengthen the innovation potential of the European biotech and pharmaceutical industries.

Scientific/Technological Objectives:EndoTrack has twin objectives. The first is to fill a gap in basic knowledge by providing new insights into how cells transduce extracellular stimuli in the form of polypeptide GFs to changes in gene expression, exploiting the enormous potential of the spatio-temporal regulation provided by the endocytic pathway. The second is to develop new concepts that will lead in future to novel opportunities for therapeutic intervention in human disease. The results of EndoTrack will be relevant to the treatment of many diseases that are currently ei-ther incurable or can only be treated inadequately, such as cancer and neurodegenerative and cardiovascular disorders.

The EndoTrack project is aimed at gaining conceptual advance into the signalling function of GFs from an unconventional perspective, namely by exploring the role of endocytic traf-ficking in the modulation of GF signalling. It further aims to translate such basic knowledge into novel opportunities for the development of a new generation of tools to combat dis-eases like cancer, cardiovascular, metabolic, infectious and neurodegenerative diseases. To achieve this ambitious goal, a multidisciplinary action plan carried out by a consortium of academic groups and SMEs will define the intracellular routes of GFR complexes, identify



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selective regulators of trafficking, and provide mechanistic insights into the contribution of endocytic trafficking to the signalling outcome. The plan will use in vitro, ex-vivo and in vivo systems. These efforts should result in the proof of principle that it is possible to qualitatively and quantitatively modify the signal transduction output of a variety of GFs via the modula-tion of endocytic routes, with predictable consequences at the patho-physiological level.

Expected Results: After 48 months, EndoTrack will provide:

1) A new generation of cell-based assays tracking the endocytic routes of GFR com-plexes and the position of signalling components downstream of the GFRs along these routes;

2) A comprehensive description of the machinery that regulates GFR trafficking along these endocytic routes;

3) Proof of principle that modulation of trafficking can modulate the signalling output of GFs;

4) Proof of principle that trafficking modulators are novel potential therapeutic targets for the treatment of various human diseases.

Schematic diagram of the endocytic pathway. Various internalization routes and internal endocytic compartments are depicted. The continuous lines represent experimentally characterized trafficking routes; the dashed lines illustrate the postulated or cell-type specific transport steps. GEEC, GPI-anchored protein enriched early endosomal compartment.


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Potential Impact:The societal impact of EndoTrack lies in the opportunity it provides to alter the textbook model of how cytoplasmic cascades transduce proliferation and differentiation signals from the plasma membrane to the cell nucleus. The current models barely acknowledge the im-portance of endocytic trafficking routes, and when they do address them, they ignore their complexity at the subcellular level. Taking advantage of this opportunity implies gaining novel mechanistic insights into the regulation of signalling pathways, and how these are integrated in a multi-GF environment with the fundamental principles of cellular organisa-tion and its overall significance in embryogenesis. Besides enhancing basic knowledge, advances in this area will also have implications for the treatment of severe diseases result-ing from dysfunction of signal transduction and gene expression.

The economic impact of the project will be most evident in the middle and long term. EndoTrack itself will not carry out screening of small molecule libraries to identify novel potential drug candidates in disease model systems. Nevertheless, by defining new mecha-nistic principles, it will conduct the groundwork necessary for the development of novel opportunities for intervention. Specifically, these opportunities are based on the following deliverables:

1) Development of new cell-based, multi-parameter assays that can be scaled up for high-throughput screening and will consequently be amenable to the screening of chemical libraries;

2) Identification of a large number of novel key signalling regulators that can serve as potential drug targets.

3) The generation of new cellular and animal models systems that recapitulate different aspects of human disease.

4) Proof of principle for the value of intervention via trafficking regulators to modulate signalling functions required for normal development and which are altered in hu-man diseases. Altogether, at the end of the funding period, EndoTrack will deliver not only new knowledge but also an entirely novel technology platform with the potential to provide higher efficiency of drug development, hence improved cost effectiveness of health care and increased competitiveness of European biotech companies.

Keywords:high-throughput screen, high-throughput techniques, cancer metastasis, receptor trafficking, signalling, endocytosis

Knocking down gene expression of the kinase EEF2K in HeLa

cells via siRNA oligonucleotides deregulated clathrin-mediated

endocytosis and led to a different phenotype.


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PartnersProf. Michael BrandTechnische Universität Dresden Biotechnology CenterDresden, Germany

Prof. John HeathUniversity of Birmingham School of BiosciencesBirmingham, UK

Prof. Jim SmithUniversity of CambridgeWellcome Trust/Cancer Research UK Gurdon InstituteCambridge, UK

Dr. Carol Murphy Foundation for Research &Technology-Hellas Biomedical Research InstituteUniversity of Ioannina,Ioannina, Greece Dr. Jérôme Pansanel Imaxio SALyon, France

Project Coordinator: Prof. Marino ZerialMax-Planck Institute of MolecularCell Biology and GeneticsPfotenhauerstr. 10801307 Dresden, [email protected]

Project ManagerDr. Jutta TatzelMax-Planck Institute of Molecular Cell Biology and GeneticsPfotenhauerstr. 10801307 Dresden, [email protected]

Prof. Carl-Phillipp HeisenbergMax-Planck Institute of Molecular Cell Biology and GeneticsDresden, Germany Prof. Danny HuylebroeckFlanders Interuniversity Institute for Biotechnology (VIB)Department of Molecular and Developmental GeneticsKatholieke Universiteit LeuvenLeuven, Belgium

Prof. Carl-Henrik HeldinUppsala University Ludwig Institute for Cancer ResearchUppsala, Sweden

Prof. Christof NiehrsDeutsches KrebsforschungszentrumDepartment of Molecular EmbryologyHeidelberg, Germany

Dr. Marta MiaczynskaInternational Institute of Molecular and Cell BiologyWarsaw, Poland

Dr. Ruediger KleinMax-Planck Institute of NeurobiologyMartinsried, Germany

Dr. Jean-Paul VincentNational Institute for Medical ResearchLondon, UK


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State-of-the-Art: AnEUploidy is the term used to describe the abnormal copy number of genomic elements (i.e. when one chromosome set is incomplete). This predisposition is one of the most com-mon causes of morbidity and mortality in human populations. The importance of AnEU-ploidy is often neglected, because its effects only materialise in the embryonic and fetal periods. The prototype of extra genomic material is trisomy 21 (Down syndrome), and some common microdeletion syndromes are the models of monosomies.

It is likely that numerous other unknown pathologic conditions (including common pheno-types) are attributable to segmental aneuploidies. In addition, an extensive variability of the copy number of numerous genomic regions has been found to be polymorphic in human populations. Aneuploidy is related to gene expression perturbation and abnormalities, but the molecular pathogenesis of the numerous aneuploid disorders is largely unknown.

Scientific/Technological Objectives:The project has the ambitious goal of contributing to the understanding of the molecular basis and pathogenetic mechanisms of aneuploidies. The project proposes to use experi-mental strategies that will incorporate and take advantage of recent achievements within this field of research. The project incorporates the following areas of existing research:

1) human genome sequencing, 2) comparative genome analysis, 3) genome variation, 4) mouse transgenesis, 5) technological platforms for transcriptome and genotypic analysis, 6) bioinformatics tools, and 7) systems biology.

The overall goal of this integrated project is to understand the molecular mechanisms of gene dosage imbalance (aneuploidy) in human health using genetics, functional genomics and systems biology. The project will focus on the following 2 models of aneuploidy: 1) trisomy 21 as the prototype for supernu-merary copies of a genomic segment, and 2) monosomy for 7q11.23 (Williams-Beuren syndrome) as one prototype of haploinsuf-ficiency for a genomic segment.

In terms of looking at specific objectives, the phenotype of heart defect in the monosomy 22q11 (VCFS) will be used. Furthermore, certain novel emerging syndromes of aneu-ploidy and Copy Number Variation (CNV) will be also used as experimental and dis-covery models.

Karyotype


AnEUploidy

Project Type:Integrated ProjectContract number:LSHG-CT-2006-037627Starting date:1st December 2006 Duration:48 monthsEC Funding:

12 000 000

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The specific aims are as follows: 1. To study the phenotypic consequences of gene dosage imbalance in humans at the

cellular and organism level, by focusing on two prototype human model phenotypes: trisomy 21 (T21, Down syndrome; DS) and the monosomy model Williams Beuren syndrome (WBS at 7q11.23). We hypothesise that it is feasible to identify a small number of genes, or even single genes, that are responsible for a given phenotype.

2. To identify and characterise novel microaneuploidy syndromes. Clinically well-de-fined entities will be used as a starting point for high-resolution analysis of copy number. In addition, patients with specific syndromes will be selected and screened for gene dosage alterations, using ultra high-resolution microarrays. The project will allow the identification of genes and biological pathways potentially involved in new aneuploidy syndromes. Furthermore, a catalogue of copy number variants (CNVs) and segmental duplications (SDs) of the human genome will be established in Euro-peans.

3. To exploit the unique advantages of the mouse embryonic stem (ES) cell as an ex-perimental paradigm, so as to identify the effects of gene dosage imbalance on the global transcriptome and proteome. The effects of dosage imbalance on the ability of pluripotent ES cells to differentiate into lineages that are relevant to human aneu-ploidy phenotypes, will also be investigated.

The project will focus on two regions of the human genome, which are subject to gene dosage imbalance: HSA21 and 7q11.23, respectively involved in DS and WBS. Global transcriptome and proteomics analysis of the cell lines will be per-formed through specific platforms, and systematic analysis and integration of tran-scriptome and proteomics data will be carried out.

4. To use a large number of mouse models of aneuploidy

Expected Results: The AnEUploidy project will result in the identification of genes involved in Down Syn-drome, Congenital Heart Defect, and of ma-jor dysregulated pathways in human cells of Down Syndrome and Williams Beuren Syndrome patients; functional genomics and systems biology analysis in Lymphoblastoid cell lines and isogenic lines will be applied to this end.

AnEUploidy will also identify new aneuploi-dy syndromes, assess their clinical signifi-cance, and develop appropriate diagnostic methods. In addition, emerging aneuploidy syndromes will be characterised at a mo-lecular level, so as to identify key dosage imbalanced genes. This project will gener-ate a comprehensive ES-cell line resource of single-gene and segmental overexpres-

Down Syndrome Karyotype


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sion, comprising the large majority of genes within HSA21 and WBS regions. Microarray analysis, fol-lowed by systems biology analysis, will allow the con-sequences of dosage im-balance leading to the pa-thology of these disorders to be revealed. The new mouse models for T21, HSA22q11.2 deletion syn-drome and WBS, generat-ed during this project, will elucidate the contribution of different genomic segments to the complex phenotypes present in these aneuploi-dies syndromes.

The AnEUploidy project represents a complementary approach to the identification of genes involved in Down Syndrome Congenital Heart Defect, and to the identification of new aneuploidy syndromes. AnEUploidy will result in the characterisation of the functional role of conserved non-genic sequences, micro-RNAs and HSA21 transcription factors, and an exposition of their contribution to disease, in the context of dosage imbalance.

Potential Impact:AnEUploidy has major clinical implications, and countless patients with their support networks of families and carers, are suffering from its consequences; the results of the project’s outcome will go some way towards supporting the work undertaken in this field. The impact of the AnEUploidy project can be summarised as follows:

1. The results of this research could lead to the identification of novel targets for therapeu-tic interventions.

2. This proposal could ultimately result in diagnostic tests of novel disorders, the identifica-tion of diagnostic markers, or the improvement of exciting methodologies.

3. All of the above will contribute to the overall improvement of health in Europe. It should not escape our attention that disorders of aneuploidy in Europe are relatively more common than in many other countries, owing to the reduction of morbidity and mortality stemming from infectious diseases, and also because of the increased mean maternal age (which is a result of better educational and professional opportunities for women).

Furthermore, the individual component symptoms of trisomy 21, for example, are indistin-guishable from those of other serious diseases; therefore, research on the mechanisms of those components will benefit not only aneuploidies, but also memory decline, mental retardation, autism, epilepsy, diabetes, muscle hypotonia, infertility, immune system deficiencies, leuke-mias, neoplasias and a very important aspect of the understanding of Alzheimer’s disease.

Keywords: Aneuploidy, gene dosage imbalance, trisomy, monosomy, gene expression, transcriptome, copy number polymorphisms, mouse transgenesis


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Project Coordinator:Prof. Stylianos AntonarakisUniversity of GenevaFaculty of MedicineDepartment of Genetic Medicineand Development1, Rue Michel Servet1211 Geneva, [email protected]

Project Manager:Dr. Jérôme WuarinUniversity of Geneva Medical SchoolDepartment of Genetic Medicineand [email protected]

Dr. Yann HeraultCentre National de la RechercheScientifique (CNRS)Immunologie et embryologie moleculaireInstitut de TransgenoseOrleans, France

Prof. Yoram GronerWeizman InstituteBiomedical ResearchDepartment of Molecular GeneticsRehovot, Israel

Dr. Maria del Mar DierssenCentre de Regulacio Genomica (CRG) Barcelona, Spain

Dr. Jean Maurice DelabarUniversité Paris 7Paris, France

Dr Dean Nizetic Barts & the London School of Medicine and Dentistry Institute of Cell and Molecular Science London, UK

Dr. Victor TibulewiczNational Institute for MedicalResearch (NIMR)Immune cell biologyInfection and immunityLondon, UK

Dr. Marie-Laure YaspoMax-Planck Instituteof Molecular GeneticsChromosome 21Gene expression and regulationBerlin, Germany

Prof. Jiri ForejtAcademy of Sciencesof the Czech Republic Institute of Molecular GeneticsMouse Molecular GeneticsPrague, Czech Republic

Dr Luis Perez Jurado Universitat Pompeu Fabra Unitat de Genètica Departament de Ciències Experimentals Barcelona, Spain

Prof. Han G. BrunnerRadboud Universiteit Nijmegen Medical CentreHuman GeneticsNijmegen, The Netherlands

PartnersProf. Joachim KloseCharite-Universitatsmedizin BerlinInstitute for Human GeneticsBerlin, Germany

Prof. Andrea BallabioTelethon Institute of Geneticsand MedicineNaples, Italy

Prof. Alexandre ReymondUniversity of LausanneCenter for Integrative GenomicsLausanne, Switzerland

Dr. Henri BléhautInstitut Jérôme LejeuneParis, France

Dr. Fabrice TroveroKey-Obs SAParis, France


AnEUploidy: understanding gene dosage imbalance in human health using genetics, functional genomics and systems biology





TISSUE ANDORGAN DEVELOPMENT,

HOMEOSTASIS AND DISEASE

7.2NFG

LYMPHANGIOGENOMICS

EuroHear

MYORES

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State-of-the-Art:Neurons are not all the same — many thousands of different classes of neurons, defined by a variety of criteria such as morphology, patterns of connectivity, and expression of particular neurotransmitters and receptors, serve as the cellular building blocks of the brain. Each of these neuronal types has a specific physiological role in brain function. Neurological and psychiatric diseases target particular neurons or neural circuits. The brain is a natural mosaic of a large variety of different cell types and a combined approach is necessary in order to describe them fully. Northern blot analysis, RT_PCR amplifications and cDNA microarraya-nalysis allow rapid testing of many genes, but lack spatial resolution. One promising alterna-tive is to tag individual genes in transgenic animals using a marker such a green fluorescent protein (GFP), thereby revealing their pattern of expression in vivo. Not only does this tech-nique reveal cell morphologies with high resolution, it also allows particular cell types to be harvested for molecular analysis. The complexity of brain cell types and circuits is reflected in the complexity of gene expression patterns in the brain. It is not yet known how many cell types are in the brain, but it seems likely that a classification of neuronal types based on gene expression, will reveal many more neuronal subtypes than can be recognized with traditional electrophysiological and morphological methods. Therefore, a proper classification cannot be obtained through the exclusive use of anatomy and electrophysiology.

The most efficient approach is to start mapping transcription factors for individual neurons: they may provide powerful markers for adult cell types and neural development. It is likely that a specific combination of transcription factors will determine many cellular properties, both morphological and electrophysiological, i.e. excitability, connectivity and synaptic properties. A cellular list for the nervous system is a powerful resource, not only for understanding the development of the nervous system, but also for understanding brain functions.

Scientific/Technological Objectives: There will be three milestones involved in this process:

1) Objective one focuses on delivering the first cDNA chips; developing the technique of single cell gene profiling; in part WKP 1 and 2 of the project are transferred to the electrophysiological laboratories.

2) This objective will ascertain whether preliminary experiments of gene expression profiling have been performed in specific parts of the project; whether specific tasks have been carried out; and lastly, whether the technique for the selective ablation of specific neuronal populations is working.

3) At this point, NFG will further assess whether the characterisation of sensory, cortical and hippocampal neurons combining gene profiling, electrophysiology and mor-phology has been effectively obtained, and if real advancements towards the main objectives of the project have occurred.

Expected Results: Functional genomics tools will be developed. This technological development consists of the construction of cDNA arrays, and of the optimisation of the procedure to harvest mRNA from single neurons, and for global amplification of single cell cDNA. Using the tools developed within the project it will be possible to examine the gene expres-sion profile from single neurons identified either by their morphological or their electrophysi-ological characteristics. Such data enable the identification of gene abundantly expressed in particular classes of neurons, which can be used as markers. Having identified these markers, transgenic mice will be constructed using BAC technology, in order to specifi-cally label particular cell types with a fluorescent label, whose expression will be identical


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to the cell-specific marker. When specific neuronal populations have been marked with a fluorescent label, they are selected by FACS, and can also be tagged with a toxin whose expression is driven by a promoter specific to the identified neuron of interest, allowing selective ablation of that neuronal population. This technological development is carried out in a coordinated way in Cambridge, Trieste and Tokyo, and additional groups are per-forming the electrophysiological experiments of the present project. Part of the NFG project is dedicated to understanding the relation of sensory transduction and gene expression in olfactory sensory neurons and photoreceptors.

Potential Impact: NFG plans to answer questions relating to basic functional properties of the genome in olfactory sensory neurons and photoreceptors. The project’s findings will impact our knowl-edge of the links between gene expression and sensory adaptation. Furthermore, it will improve our understanding of existing and potentially new cell types in the cortex, based on expression patterns using cortical neurons. Finally, NFG’s research into the hippocam-pus will be aimed at elucidating the links between gene expression in identified neurons, and changes in their electrical and functional properties during the major changes associ-ated with mammalian development. These developments are expected to further enhance research efforts in the area of brain function, and potentially establish a clear European advantage in this field.

Keywords: functional genomics, genetics, DNA chips, development, brain

Project Coordinator: Prof. Anna MeniniSISSA (Scuola InternazionaleSuperiore di Studi Avanzati /International School for Advanced Studies)Neurobiology Sectorvia Beirut 2-434014 Trieste, [email protected]

Prof. Hugh Robinson, Dr. Frederick LiveseyUniversity of CambridgeCambridge, UK

Dr. Richard MilesInstitut National de la Santéet de la Recherche Médicale (INSERM)0224 Cortex et EpilepsieParis, France

Dr. Piero CarninciRIKEN (The Institute for the Physicaland Chemical Research)Wako, Saitama, Japan

Dr. Simona CapsoniLLG (Lay Line Genomics)Rome, Italy

Partners


Functional Genomics of the Adult and Developing Brain



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State-of-the-Art:The lymphatic vasculature is essential for the maintenance of fluid balance in the body, for immune defence and for the uptake of dietary fat. Absent or damaged lymphatic vessels may lead to lymphoedema, a chronic and disfiguring swelling of the extremities which sometimes necessitates the amputation of affected limbs. In addition, lymphatic vessels promote metastatic spread of cancer cells to distant organs, a leading cause of death in patients with cancer and a major obstacle to the design of effective cancer therapies. The lymphatic vessels were identified hundreds of years ago, yet their development and func-tion, and the molecular mechanisms underlying their role in disease processes is in effect, poorly understood.

Scientific/Technological Objectives:The aim of this project is to discover novel genes that are important for lymphatic vascular versus blood vascular development and function, and to study the functional role and thera-peutic potential of their gene products in lymphangiogenesis, using state-of-the-art technolo-gies. The methods planned by the consortium include large-scale knockout and knockdown of the mouse genome, embryonic stem (ES) cell technology, knockdown of zebrafish genes by morpholino-antisense technology and positional cloning of disease susceptibility genes involved in lymphangiogenesis.

Although historically it has been somewhat neglected, the field of lymphatic biology has ex-perienced a dramatic growth in the last year, this, due for the large part, to the availability of enhanced techniques and tools and a greatly improved understanding of basic aspects of lymphatic physiology. The LYMPHANGIOGENOMICS project has been an essential driver of this development. Lymphatic biologists, physiologists, biomedical engineers and physi-cians have a great need for a forum in which to collaborate and discuss developments, so as to determine the future direction of research within this field. The project brings together the leading laboratories working in lymphangiogenesis. The project has been brought into action, in an effort to understand, at the molecular level, the mechanism of growth of lym-phatic vessels and the key molecules in the lymphatic differentiation programme.

Expected Results:The project’s research outcomes may hold significant therapeutic potential for the two foremost causes of morbidity and mortality in Europe: cancer and vascular diseases. The project will provide fundamental insights into the molecular and cellular basis of lymphang-iogenesis and thereby enabling scientists to develop therapies that suppress (e.g. for the treatment of cancer and inflammatory diseases), or stimulate the growth of lymphatic vessels (e.g. for the treatment of tissue ischaemia and lymphoedema).

The consortium’s many and greatly significant achievements to date include the following: (1) Several new target candidate genes have been identified, some of which have been validated in Xenopus and Zebrafish models; (2) The new amphibian genetic system, as developed and validated for the analysis of lymphatic vascular development, has been made available to the consortium for semi-high throughput functional lymphangiogenomics; (3) Immortalised cell lines have been developed from primary lymphatic endothelial cells;


LYMPHANGIOGENOMICSwww.lymphomic.org


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(4) Several neural molecules that provide guidance cues in the lymphatic vessel development have been discovered. A great advance was the identification of a role for vascular endothelial growth fac-tor C (VEGFC) in the regulation of neural progenitor cells; (5) Protocols have been optimised for the isolation of multipotent adult progenitor cells from mouse and rat bone marrow, for the study of lymphatic endothelial cell (LEC) differentiation ; (6) Striking new results on the trans-differen-tiation of macrophage-like cells into lym-phatic endothelium; (7) New vascular malformation mutants have been identi-fied, including a novel VEGFR-3 receptor mutation in a sporadic lymphoedema; (8) Different monoclonal antibodies directed to human LECs have been obtained, in some cases from a human antibody phage display library; (9) A web-accessible da-tabase, QRISP, that provides a platform for integrated bioinformatics analysis of consortium and public expression data, has been implemented and is now fully operational; (10) An extensive database of blood vascular and lymphatic endothe-lial transcriptomes has been compiled; (11) A company, Lymphatix Ltd, has been established and has started to develop VEGFC and VEGFD for the therapy of lymphoedema and tissue ischaemia.

Potential Impact:While the focus of this project is on pro-viding new insights into the pathophysiol-ogy and biology of lymphangiogenesis, its broad scope and multidisciplinary na-ture mean that it will also have a positive impact on the wider scientific community and on society in general. This statement is supported by evidence of the central role that lymphangiogenesis plays in hu-man disease. It is estimated that in Europe alone, three to five million people are af-fected by secondary lymphoedema (due to radiation therapy, cancer, surgery or infections). This number increases when one considers the role of the lymphatic


Genome-Wide Discoveryand Functional Analysis of Novel Genes

in Lymphangiogenesis

Fig.1. Lymphatic vessels in red are shown encircling a very small tumor (0.1 mm in diameter) that is grown in the mouse ear. The tumor secretes growth factors that promote the growth of lymphatic vessels into the tumor. Individual tumor cells gain entry into the lymphatic vessels, and use them as routes for spreading to nearby lymph nodes.

Fig. 1

Fig. 2

Fig. 3

Fig.2. Lymphatic vessels (green) and blood vessels (red) intermingle in the mouse ear skin. The lympahtic vessels are blind-ended vessels that take up fluid, large molecules and cells, which leak out of the blood vessels and return them back to the blood circulation via larger lymphatic vessels.

Fig.3. A high magnification microscopic image of a small lymphatic vessel (green) that has been stimulated with a growth factor protein called VEGF-C. Note the very thin projections of lymphatic endothelial cells sprouting from the vessel. VEGF-C does not affect the nearby blood vessels (red), which indicates that it can be used to specifically grow new lymphatic vessels for example in patients suffering from lack or impairment of lymphatic vessel function.

Images by: Tuomas Tammela,Molecular/Cancer Biology Laboratory, University of Helsinki, Finland.


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system and blood vessels in the spread of inflammatory and infectious diseases (e.g. tuber-culosis and filariasis). If one also takes into account the millions of people who suffer from metastatic spread of cancer via the lymphatic vasculature, it becomes clear that the inte-grated project described here stands to have a profound impact on the burden of human disease in Europe. Novel therapies for cancer, inflammatory diseases, lymphoedema and tissue ischaemia will also be developed.

Keywords:vascular diseases, cancer, inflammatory diseases, vascular biology, molecularbiology, stem cells, lymphoedema, genomics, lymphangiogenesis


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PartnersProject Coordinator:Prof. Kari AlitaloUniversity of Helsinki Faculty of MedicineBiomedicum HelsinkiMolecular Cancer Biology Program Haartmaninkatu 8 P.O. Box 6300014 Helsinki, [email protected]

Project Manager :Dr. Pirjo LaakkonenUniversity of HelsinkiMolecular Cancer Biology [email protected]

Dr. Anne EichmannInstitut National de la Santé et de la Recherche Médicale (INSERM) U36Paris, France

Prof. Christer BetsholtzKarolinska InstitutetDepartment of Medical Biochemistry and BiophysicsStockholm, Sweden

Prof. Dontscho KerjaschkiMedical University ViennaClinical Institute of PathologyVienna, Austria

Prof. Elisabetta Dejana FIRC Institute of Molecular OncologyMilan, Italy

Prof. Gerhard ChristoforiUniversity of Basel Institute of Biochemistry and Genetics Basel, Switzerland

Prof. Lena Claesson-WelshUppsala University Department of Genetics and PathologyRudbeck LaboratoryUppsala, Sweden

Prof. Miikka VikkulaChristian de Duve Institute of Cellular PathologyLaboratory of Human Molecular Genetics Brussels, Belgium

Prof. Peter CarmelietFlanders Interuniversity Institute for Biotechnology (VIB) Centre for Transgene Technology and Gene TherapyLeuven, Belgium

Prof. Hellmut AgustinDeutsches KrebsforschungszentrumVascular MedicineHeidelberg, Germany Prof. Seppo Yla-Herttuala University of KuopioA.I. Virtanen InstituteKuopio, Finland

Dr. Per LindahlGothenburg University Institute of Medical BiochemistryGöteburg, Sweden

Dr. Jyrki IngmanLymphatix OyHelsinki, Finland

Dr. Bernhard BarleonRELIATech GmbH Braunschweig, Germany


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State-of-the-Art:Hearing impairment is the most common human sensory deficit, affecting more than 10 per-cent of the European population (40 million people). This causes a considerable social and economic burden to those afflicted and to society, but early identification and intervention has proved to be cost-effective. Seventy percent of human hearing impairment is genetic in origin and classified as non-syndromic hereditary hearing impairment, meaning it has only one symptom. The remaining 30 percent of human hearing impairments have other symptoms and are therefore described as syndromic.

Hearing impairment is the most common birth defect in humans. Of the non-syndromic, prelingual cases, about 80 percent are due to recessive inheritance, with the majority of parents hearing normally. About 20 percent are due to dominant inheritance, with at least one of the parents found to be hearing-impaired. Whereas single gene defects probably account for over half of cases of childhood deafness, no such quantitative data exists for the proportion of hearing impairment in adults that may be due to hereditary causes.

Over 45 genes responsible for isolated (nosyndromic) hearing impairment in humans are known, but at least as many as this still need to be identified. The involvement of hearing-im-paired individuals and their families in research made these breakthroughs possible, and their ongoing support will be the key to future success in understanding the molecular basis of audi-tory function. Moreover, as a result of their participation, molecular diagnostics have been de-veloped and the quality of genetic counselling has been dramatically improved. The ultimate goal of this research is the development of new ways of treating hearing impairment.

Scientific/Technological Objectives:The Eurohear project, comprised of 25 research teams, is building on their work on genetic and molecular mechanisms underlying hearing impairment. EuroHear aims to identify the molecules that play a critical role in the inner ear, and more specifically in the cochlea or the auditory sensory organ. The project has three closely re-lated objectives:

1) To identify the genes underlying sensorineural hearing impairment, in turn enabling research on these molecular mechanisms involved in the development and function-ing of the inner ear. The consortium proposes to identify the human and mouse genes that underlie early and late onset forms of hearing impairment - both those that are monogenic and those that are multifactorial in origin. Special emphasis will be placed on late-onset forms of hearing impairment (age-related hearing loss) and more specifically on the sensorineural form, presbycusis, since these are better tar-gets than congenital hearing impairment for preventive and curative therapies.

2) To understand the mechanisms underlying normal and impaired hearing. EuroHear will not only address the hair bundle, the ribbon synapse of the hair cells and outer hair cell electromotility mechanisms, it will also investigate the cochlear ion channels, transporters and gap junctions that contribute to potassium homeostasis.

3) To develop tools for preventing and treating hearing impairment. This includes test-ing candidate drugs in vivo, developing high throughput screening of organotypic cochlear cultures for testing of drugs, and in-depth exploration of three possible therapeutic approaches (gene therapy, cell transplantation, and therapy based on the use of inner ear progenitor/stem cells, especially hair cell progenitors). Experi-mental evidence show that pharmacological compounds can significantly reduce the progression of hearing impairment and this approach could lead to more efficient

Hair bundles


EuroHear

Project Type:Integrated ProjectContract number:LSHG-CT-2004-512063Starting date:1st December 2004Duration:60 monthsEC Funding:

12 500 000

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treatment strategies. Recent observations on cell and gene therapy, as well as the discovery of inner ear progenitor cells, suggest entirely new methods for treating the inner ear deficits. Within the next five years, EuroHear expects to realise some of these methods.

EuroHear has a strong, cross-disciplinary training programme whose objective is to create a network of scientific expertise on the development and function of the inner ear and hear-ing impairment. The training programme aims to provide high-standard, multi-curricular in-ner ear training courses in Europe to favour the growth of a generation of young European scientists with multi-disciplinary research training.

Expected Results:So far, Eurohear has made a significant advance with the identification of several novel genes and their mutations respon-sible for different forms of deafness. This was made possible by the active involve-ment of hearing-impaired patients and their families. Some of these results are:

1) Mouse mutants are an invaluable resource for studying the mecha-nisms of hearing and deafness. The consortium has been work-ing on 21 mutant mice. Loci for 14 mutants have been mapped and genes for 13 mutants have been cloned;

2) Human deafness: 13 novel genes causative for isolated or syndro-mic forms have been discovered by EuroHear;

3) Dysfunction of the hair cell’s ribbon synapse has been shown by the project to be the cause of human hereditary deafness. This finding is a major breakthrough in the understanding of how auditory information is relayed to the central nervous system, and reveals that cochlear implants are likely to be successful in the “treatment” of children diagnosed with mutations in the Otoferlin gene;

4) The amplification of low level sound signals by a motile protein localised in the membranes of hair cells is crucial for proper hearing. Eurohear’s research has re-cently identified unique regions within the sequence of this protein that are essential for its function as a cellular motor;

5) Mutations in the gene encoding connexin 26, a gap junction required for intercel-lular communication within the ear, are the major cause of deafness in human beings. Work carried out in the consortium has now identified two genes that are downregulated as a consequence of the loss of connexin 26, and are likely thera-peutic targets for intervention;

6) Eurohear is also seeking tools for prevention and cure. Promising observations in cell and gene therapy, as well as the recent discovery of progenitor cells (stem cells) in the inner ear, suggest new ways to treat the inner ear in the future. Tests have been initiated using several new in vitro models for drug screening, and novel methods for stimulating the regeneration of the replacement of inner ear cells are being actively explored.

The ear consists of external, middle, and inner structures.The eardrum and the three tiny bones conduct sound from the eardrum to the cochlea.


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Other expected results of EuroHear include a standardisation of investigative protocols, the provision of access to large-scale platforms for genetics and genomic analysis, and the development and diffusion of physiological and biophysical techniques of relevance for functional investigations of the inner ear.

Potential Impact:This research has direct implications for pa-tients. For example, it will lead to improve-ments in presymptomatic diagnosis, which in the case of Usher syndrome type 1 (deaf-ness associated with blindness) will allow cli-nicians to provide hearing-impaired children with cochlear implants at the best possible stage, i.e. when they are young and before they lose their sight. It will allow the diagno-sis of a predisposition to a form of hearing impairment that is induced by aminoglyco-sides, so that the treatment of affected in-dividuals with this class of antibiotics can be avoided. It will also enable clinicians to predict, on the basis of information about a patient’s underlying genetic defect, whether or not a cochlear implant will be successful.

In the case of late onset hearing impairment, molecular diagnosis will allow susceptible individuals to make informed career choices in order to avoid excessive noise exposure. Obviously, the effective treatment of hearing impairment will significantly improve quality of life for deaf or hard-of-hearing individu-als. Among the molecular mechanisms that contribute to hearing impairment, those that involve potassium homeostasis could be-come a therapeutic target within a reason-able timeframe.

Keywords:hearing impairment, inner ear, synapse, K+ homeostasis, hair bundle, therapy, cell physiology, functional genomics

Partners

Sensory cells of the cochlea

Project Coordinator:Prof. Christine PetitInstitut National de la Santé et de la Recherche Médicale (INSERM)UMRS 587- Institut Pasteur Unité de Génétique et Physiologie de l’Audition25 rue du Dr Roux75724 Paris, [email protected]

Project co-Coordinator:Prof. Karen Avraham University of Tel AvivDepartment of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Ramat Aviv39040 Tel Aviv, [email protected]

Project Manager:Laurent CharvinINSERM Transfert7 rue Watt75013 Paris, [email protected]

Prof. Jonathan AshmoreUniversity College LondonDepartment of PhysiologyLondon, UK

Prof. Stephen BrownMedical Research CouncilMammalian Genetics UnitOxfordshire, UK

Prof. Cor W. R. J. CremersUniversity Medical Centre Nijmegen (UMCN)OtorhinolaryngologyNijmegen, The Netherlands

Prof. Dominik OliverPhilipps-Universität MarburgInstitut für Physiologie und PathophysiologieMarburg, Germany

Prof. Jonathon HowardMax Planck Society for the Advancement of ScienceMax-Planck Institute of Molecular Cell Biology and GeneticsDresden, Germany

Prof. Thomas Jentsch Max-Delbrück-Centrum für Molekulare MedizinMetabolic Diseases, GeneticsGenomics and BioinformaticsBerlin, Germany


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Prof. Guy P. Richardson, Prof. Corné KrosUniversity of SussexSchool of Life SciencesBrighton, UK

Prof. Christian KubischUniversity Hospital of the University of CologneInstitut of Human GeneticsCologne, Germany

Prof. Mark Lathrop Consortium National De Recherche En Genomique (CNRG)Centre National de GénotypageEvry, France

Prof. Fabio MammanoIstituto Veneto Di Medicina Molecolare (VIMM)Centro Di Ricerca Della Fondazione PerLa Ricerca BiomedicalPadova, Italy

Prof. Felipe MorenoFundación para la Investigación Biomédica del Hospital Universitario Ramón y CajalUnidad De Genetica MolecularMadrid, Spain

Prof. Tobias MoserBereich Humanmedizin Georg August Universität GöttingenDepartment of OtorhinolaryngologyGöttingen, Germany

Dr. Ulla Pirvola University Of Helsinki lnstitute of BiotechnologyHelsinki, Finland

Dr. Pascal Martin lnstitut Curie, Division de RechercheLaboratoire Physico-Chimie ‘Curie’ (UMR 168)Paris, France

Prof. Karen P. SteelGenome Research LtdWellcome Trust Sanger InstituteCambridge, UK

Prof. Mats UlfendahlKarolinska InstituteDepartment of Clinical Neuroscience Center for Hearing and Communication ResearchStockholm, Sweden

Prof.Guy Van CampUniversity of AntwerpDepartment of Medical GeneticsAntwerp, Belgium

Prof. E. Sylvester Vizi Institute of Experimental MedicineHungarian Academy of SciencesDepartment of PharmacologyBudapest, Hungary

Dr. Christian Vieider ACREO ABMicroTechnology DepartmentStockholm, Sweden

Dr. Jörg HagerIntegraGen SAResearch & DevelopmentEvry, France

Stéphane Silvente AffichemResearch and DevelopmentToulouse, France

Prof. Hammadi AyadiUniversity of SfaxFaculty of Medicine of SfaxHuman Molecular Genetics LaboratorySfax, Tunisia

Prof. Klaus Willecke University of BonnInstitute of GeneticsBonn, Germany


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State-of-the-Art:In Europe, over 300,000 people are affected by muscular dystrophies leading to decreased mobility and loss of independence. This has severe consequences at both a personal and economic level. The aim of this proposal is to understand how these muscular defects can be repaired.

To date, the genetic mechanisms responsible for the emergence of these diseases have only been identified for some of the most common muscular dystrophies, such as Duchenne or Limb Girdle dystrophies, and it is still necessary to identify the genetic determinants for a number of other myopathies. In addition to identifying the genetic determinants of muscle diseases, it is crucial to acquire a profound understanding of the molecular and physi-opathological mechanisms associated with aberrant gene function in order to be able to design efficient therapies.

Inherited diseases are not the sole pathologies associated with muscle dysfunction: the bed-ridden and the elderly suffer from muscle degeneration too, which has huge implications for the economy, particularly with the latter group as life expectancy continues to rise in Europe. For these reasons as well as the large economical burden that these diseases place on our societies it is an urgent matter to find cures for muscle pathologies. Since a number of avenues are explored by various laboratories in isolation around Europe it is becoming clear that the integration of European potential in this domain is an important step in de-signing successful therapies. To address efficiently the problem posed by muscular diseases, three fundamental rules must be followed: i) breadth of investigations in order not to miss important routes of research; ii) clear and focused research to provide patients with fast relief; iii) rapid transfer of new information to health providers.

All aspects of muscle differentiation will be investigated in this project and this will be translated into the mechanisms of repair in the adult. Fundamental to the advancement of our knowledge is the recent demonstration that throughout evolution many of the molecular mechanisms regulating muscle differentiation have been highly conserved. As molecular pathways can be easily assessed in invertebrates, the European Muscle Development Net-work (MYORES) will exploit this advantage and rapidly extend the knowledge gained in these systems to determine gene function in higher vertebrates. This is a unique aspect of the proposal and places the consortium at the international forefront of understanding gene function during normal muscle development and disease.

Scientific/Technological Objectives: MYORES aims to target various aspects of muscle disease by bringing together European specialists in muscle development and function. This integrated approach is aimed at pro-viding a critical mass of researchers with complementary expertise who will be able to tackle more difficult problems and make more key advancements than when working alone. The MYORES participants will utilize different animal models to investigate various aspects of muscle development, from myogenic induction morphogenesis to terminal differentiation. This is complemented by teams with expertise in muscle protein structure, muscle disease and degeneration and tissue engineering as well as human therapy or bio-computing. In addition, the MYORES project will maximise the scientific and commercial potential of Eu-ropean research in muscle biology by: i) promoting the sharing of data and research tools; ii) enhancing exchanges of personnel between laboratories and through the organisation of training programmes; iii) developing and implementing an integrated multiorganismic approach to accelerate investigations and improve understanding of normal muscle devel-opment, function and pathological dysfunction.

Satellite cell (in blue) and muscle cell nuclei


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The overall objectives of the project are: 1) To integrate internationally recognised European specialists working on various as-

pects of muscle biology and pathology in a number of model organisms.2) To coordinate research on well-defined aims and obtain a critical mass of researchers

who will be able to make significant scientific advancements.3) To create state-of-the-art technical platforms and resources. 4) To organise the rapid transfer and application of knowledge acquired in genetically

amenable organisms into specific applications for human muscle diseases.5) To publicise scientific actions broadly and, through education, attract a younger gen-

eration of scientists into this essential field of research.6) To contribute to reducing the incidence and impact of muscle diseases on the European

population and help the European healthcare sector to compete internationally. Further-more, MYORES is working to restructure the field of muscle biology, providing added value by strengthening the impact of European research.

In achieving its objectives, MYORES further aims to coordinate the efficient transfer of knowl-edge and information from research projects to regulatory bodies and industrial sectors.

Expected Results: A fundamental aspect of the MYORES network is the extensive use of recently developed technologies of high-throughput screening to isolate novel molecules and to rapidly test their relevance in the various aspects of muscle function and repair in a number of animal models. Special emphasis will be put on the interaction, coordination and efficient transfer of knowledge between experimental models and clinical demands to ensure that the infor-mation obtained is fully exploited. As a result of this collaborative effort, we expect to gain broad insight into the regulatory interactions and cellular pathways that underlie normal and aberrant muscle formation and function. Hopefully, this will lead to designing new therapeutic approaches for muscular diseases and muscle weakening in humans. We expect isolation of about 100 novel genes expressed during the various steps of myo-genesis in invertebrates and/or vertebrates. The function of about 30 novel genes will be determined. The network expects to publish at least one collaborative publication per RP in the second year of funding and at least two co-signed publications per RP in the next years of funding. Thus, by the end of the funding period MYORES plans to publish about 40 pub-lications, co-signed by at least two of the network’s participants. An Internet resource will be developed that will be used by MYORES participants and by the scientific community. The first release of MyoBase is expected during the second year of funding to augment exchanges between scientists working in the muscle biology field in Europe. This will result in an increase in competitiveness of European research in this field. MYORES members will also contribute to the designing of novel therapeutic strategies and to the generation of diagnostic tools. An important aspect of the project is to transfer efficiently the knowledge present within the MYORES network to young researchers and doctors, and to this effect MYORES is organ-izing summer schools and workshops to provide technical training and up-to-date knowl-edge in the field of mycology. In 2006, one summer school dedicated to various aspects of muscle biology took place in Spain with 20 students from MYORES laboratories attending. Moreover, in house training and mobility programmes have been initiated allowing techni-cal training for young researchers in collaborating laboratories within the network.

Potential Impact: The MYORES network will create the necessary framework to accelerate the pace of muscle research, and generate, much more efficiently, the important advances in our understand-

Drosophila transgenesis platform created in Clermont-Ferrand and supervised by INSERM for gain and loss of function of autologous and heterologous genes in vivo


Multiorganismic Approachto Study Normal and Aberrant Muscle

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ing of muscle patholo-gies and in defining cures or treatments for human muscle diseases. EC funding will promote the development of par-ticipating groups and im-prove their contribution to the EC as a whole, by allowing cross-discipline and cross-border links to be established and fostered. Shared use of research infrastructures and development of mutual specialisation is expected to result from jointly undertaken par-ticipant activities. These will further strengthen

both the participants’ expertise and the European knowledge base, and will have an important impact on the job market by attracting young researchers to the field of muscle biology. The MYORES network has been structured to extend previously exist-ing smaller scale collaborations. Both short-term and long-term projects are designed to provide important information and research tools for the academic and industrial sec-tors, and patient associations. An impor-tant MYORES deliverable for the scientific community will be the MyoBase database. The intention is that this regularly updated database will become the main source of information in muscle biology and represent a durable contribution to the network, which will have far-reaching impacts on the entire scientific community.

Keywords:

degenerative diseases, developmental biol-ogy, molecular biology, myogenic specifica-tion, muscle differentiation, diversification of muscle fibres, muscle patterning, myoblasts fusion, functions of muscle-specific proteins, muscle stem cells, muscle regeneration

Project Sub-Coordinator: Prof. Christophe MarcelleCentre National de la Recherche Scientifique (CNRS)LGPD UMR6545 Université de la MéditerranéeDevelopmental Biology Institute of MarseilleLGPD, Campus de Lumigny13288 Marseille, [email protected]

Project Manager:Anton OttaviINSERM Transfert SAHôpital du VinatierBat. 452b 95 Bd Pinel69500 Paris, [email protected]

Dr. Dominique Daegelen, Dr. Pascale Maire,Dr. Bénédicte Chazaud, Dr. Frédéric RelaixInstitut National de la Santé et dela Recherche Médicale (INSERM)Paris, France

Dr. Patrick Lemaire, Dr. Laurent Ségalat, Dr. Josiane Fontaine-Perus, Dr. Delphine DuprezCentre National de la Recherche Scientifique (CNRS)Paris, France

Dr. Anne-Gaëlle Boricky, Prof. Phil InghamUniversity of SheffieldCentre for Developmental GeneticsDepartment of Biomedical ScienceSheffield, UK Prof. Beate Brand Saberi, Prof. Bodo ChristUniversitatklinikum FreiburgInstitut fur Anatomie und Zellbiologie IIFreiburg, Germany

Dr. Baljinder Mankoo, Dr. Mathias Gautel, Dr. Simon Hughes, Dr. Susanne Dietrich, Dr. Philippa Francis-West, Dr. Peter Zammit King’s College LondonRandall Centre for Molecular Cell BiologyGKT School of Biomedical SciencesLondon, UK

Dr. Andrea Munsterberg University of East AngliaSchool of Biological SciencesCell and Developmental BiologyNorfolk, UK

Dr. Michael Victor TaylorUniversity of Wales, CardiffCardiff School of BiosciencesCardiff, UK

PartnersProject Coordinator: Dr. Krzysztof Jagla Institut National de la Santé et dela Recherche Médicale (INSERM) U384 28 place Henri Dunant 63000 Clermont-Ferrand, France [email protected]

Example of identified ortholog muscle-specific genes from

Drosophila, Ciona and Zebrafish.

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Dr. Chava Kalcheim, Dr. Orna HalevyHebrew University of JerusalemDepartment of Anatomy and Cell BiologyJerusalem, Israel

Prof. John Sparrow, Dr. Belinda BullardUniversity of YorkDepartment of Biology York, UK

Dr. Vincent MoulyUniversité Pierre et Marie CurieUMR 7000, Cytosquelette et DéveloppementParis, France

Prof. Thomas BraunMax-Planck Institute for Physiological and Clinical ResearchW.G. Kerckhoff-Institut Bad Nauheim, Germany

Prof. Peter Rigby Institute of Cancer ResearchRoyal Cancer HospitalSection of Gene Function and Regulation, Chester Beatty LaboratoriesLondon, UK

Prof. Margaret Buckingham, Dr. Shahragim Tajbakhsh Institut PasteurDépartement de Biologie du DéveloppementParis, France

Dr. Eileen FurlongEuropean Molecular Biology Laboratory (EMBL)Developmental Biology and Gene Expression ProgrammesHeidelberg, Germany

Prof. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)Mouse Biology unitMonterotondo,Italy

Prof. Bernard ThisseCentre Européen de Recherche en Biologie et en Médecine (CERBM)Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirch, France

Prof. Hans Henning ArnoldTechnical University BraunschweigCell and Molecular Biology/BiosciencesBiochemistry and BiotechnologyBraunschweig, Germany

Prof. Stefano SchiaffinoUniversita degli Studi di PadovaDipartimento di Scienze Biomediche SperimentaliPadova, Italy

Dr. Tomas SoukupInstitute of Physiology, Academy of Sciences of the Czech RepublicDepartment of Functional MorphologyPrague, Czech Republic

Prof. Renate Renkawitz-Pohl Philipps-Universitat MarburgDevelopmental of Developmental BiologyMarburg, Germany

Prof. Carmen Birchmeier Max-Delbruck-Centrum fur Molekulare MedizinSignaltransduction and Developmental Biology GroupBerlin, Germany

Prof. Alberto Ferrus, Dr. Mar Ruiz-GomezConsejo Superior de Investigaciones CientificasInstituto CajalMadrid, Spain

Yann DantalSoluscience SA Biopôle Clermont-LimagneSt. Beauzire, France

Dr. Peter CurrieVictor Chang Cardiac Research InstituteDarlinghurst, Australia

Dr. Thierry TourselAssociation Française contre les Myopathies (AFM)Direction Recherche et Développement des TherapeutiquesEvry, France

Dr. Jonathan BeauchampRoyal Holloway and Bedford New CollegeSchool of Biological SciencesEgham, UK

Prof. John SquireUniversity of BristolDepartment of PhysiologyBristol, UK


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State-of-the-Art:Diseases of the kidney represent a major cause of morbidity and mortality in Europe. The elderly are disproportionately affected, but renal disease is also a condition that severely affects children. An estimated 4.5 million Europeans suffer from renal disorders. The annual death rate in patients with renal failure is 20%.

The focus of the European Renal Genome Project (EuReGene) is to challenge kidney dis-eases. Elucidation of human and other genomes heralds a new era in biomedical research, offering unprecedented opportunities to understand disease processes and to identify strate-gies, so as to improve health. The project embraces these opportunities and plans to imple-ment an interdisciplinary research programme. EuReGene integrates European excellence in research relevant to renal development, pathophysiology and genetics. The goal is to discover the genes responsible for renal development and disease, and to examine their proteins and their actions. To this end, a consortium has been established, comprising leading scientists, clinicians and SME partners that will focus on the development of novel technologies and discovery tools in functional genomics, and their application to kidney research. Moreover, we will look to comparative genomic studies in many systems that pro-vide utilitarian models, ranging from zebrafish to Xenopus, and from mice and rats to man. The studies will be performed at different levels, including the gene, the cell, the organ and the organism. Ultimately, identification of disease genes will lead to a better understanding of renal disease processes, to improved diagnosis and to new concepts in therapy. The programme will establish a paradigm for an integrated post-genomic approach to analyse renal disease-related developments that may be transferred to other organ systems or dis-ease entities, in the future.

Scientific/Technological Objectives: EuReGene will pursue objectives in four areas:

1. Functional genomics technologies: EuReGene will develop new high throughput gene expression analysis methods; renal organ cultures to study gene function; databases for tools, methodologies and results; and kidney atlas for spatio-temporal description of renal mechanisms.

2. Renal development: EuReGene will develop new cell lines for the study of develop-mental programmes, as well as detailed gene expression maps of developing an adult kidney; and identify genes involved in nephrogenesis/differentiation.

3. Pathophysiology: EuReGene will develop new mouse and rat models; study regula-tory networks in cell differentiation, injury and repair and cellular transport; and identify new targets for therapeutic intervention in renal diseases.

4. Complex genetics: EuReGene will establish new ENU models in zebrafish and mice; map modifier QTLs for proteinuria and progressive renal injury in rats, and for glomerulosclerosis and renal stone disease in mice; and identify modifiers in diabetic nephropathy in mice.

Expected Results: The project’s integrated research approach will have a fundamental impact on the current understanding of renal development and disease in humans. At the end of the project (which has a 4-year duration) the following measurable results will be delivered:


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1. Methods for high throughput in situ expression analysis at organ level 2. Methods for 3D reconstruction of expression maps at organ level 3. Bioinformatic tools to integrate data from various genomic approaches into an kid-

ney atlas of spatio-temporal relationships of developmental/pathophysiological proc-esses at organ level

4. A comprehensive kidney atlas of renal developmental and pathophysiological proc-esses (as data and as 3D image reconstructions)

5. Novel discovery tools including zebrafish, Xenopus, mouse and rat models (knock-outs, knockdowns, transgenics, GFP reporter lines, Cre lines), as well as new cell and organ cultures

6. Repositories (models, cell lines, biopsies, DNA) and databases (expression maps) that are accessible throughout the scientific community

7. A list of candidate genes responsible for (i) developmental, (ii) complex genetic and (iii) acquired renal diseases (diabetic nephropathy, glomerulosclerosis, nephrotoxic-ity, proteinuria, end-organ damage) representing major new targets for diagnosis, drug development, and therapeutic intervention

8. A patent portfolio that protects the intellectual property rights of the EuReGene con-sortium, and forms the basis for commercial exploitation and funding beyond the FP6 period

9. Websites that inform stakeholders (patient advocacy groups, health care providers, scientists) of latest developments in renal disease research.

Potential Impact: EuReGene’s integrated approach will have a profound impact on the current understanding of renal development and disease, and will contribute to fundamental knowledge produc-tion, and novel concepts for improving health. It will focus on innovative aspects of tech-nology development such as animal models, organ cultures and imaging techniques. The burden of renal disease is vast in terms of financial cost, as well as in increased mortality


European Renal Genome Project

Steering Committee

Advisory Board EU Commission

MDC Berlin

MRC Edinburgh

University Nice Necker Hospital, Paris UCL Brussels ETH Zürich MRC Harwell Mario Negri Inst. Bergamo University Paris University Zurich MPI Hannover University Oulu University Hamburg Aarhus University

LMU Münich ReceptIcon

Project coordinator

Thomas Willnow

Topic 1 Genome

Technologies

Topic 2 Renal

Development

Topic 3 Patho-

physiology

Topic 4 Complex Genetics

General Assembly

Panel “Ethics, Gender”

University Oxford

Nick Hastie Corinne Antignac Erik Christensen Andreas Schedl

Elizabeth Robertson, Enyu Imai, Mathias Brandis, Nine Knoers Alastair Kent, Steve Hebert, Luigi Baroni, Karl-Heinz Wilbers

Iwan Meij,Dorothee Saar

Dominik Müller, Carsten Wagner, Andreas Schedl,Raj Thakker, Seppo Vainio, Friedrich Luft

ReceptIcon, Ascenion, Thomas Willnow

Ariela Benigni,Mathias Kretzler,Raj Thakker,Friedrich Luft,Rikke Nielsen

Topic coordinators Jamie Davies Gregor Eichele

Andreas Schedl André Brändli

Pierre Verroust Olivier Devuyst

Roger Cox Corinne Antignac

Thomas Willnow Dominik Müller Friedrich Luft

Duncan Davidson Jamie Davies Nick Hastie

Andreas Schedl Corinne Antignac

Olivier Devuyst Pierre Courtoy

André Brändli

Roger Cox

Giuseppe Remuzzi

Pierre Verroust

Heini Murer

Gregor Eichele

Steffen Ohlmeier Seppo Vainio

Thomas Jentsch

Erik Christensen

Raj Thakker

Mathias Kretzler

Anders Nykjaer

Panel “Exploitation, IPR”

Panel “Training”

Project Management Office

EuReGene management structure


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and medical and psychological morbidity of patients and their families. Through the iden-tification of the mechanisms underlying disease processes, EuReGene will have a major impact on lifting the societal and economic burdens caused by renal disease. It will also address the ongoing problem of fragmented research activities that hampers efficient medi-cal research in Europe.

Keywords:animal models, transgenic animals, mouse, zebrafish, Xenopus, organogenesis, kidney diseases, transcriptome analysis, cardiovascular diseases, renal pathogenesis, complex genetics, QTL mapping, solute carrier

Expression of Slc12a1 in adult kidney visu-

alised by ISH on a 10 micron paraffin section using optimised meth-ods for automated ISH


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Graphic representation of the four interrelated topics

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PartnersProject Coordinator: Thomas WillnowMax-Delbrück-Center for Molecular MedicineCardiovascular Research Centre Department of Cardiovascular ResearchLipids and Experimental Gene Therapy Robert Roesslestrasse 1013125 Berlin, [email protected]

Project Manager:Dr. Iwan C. MeijMax-Delbrück-Center for Molecular MedicineCardiovascular Research Centre Robert Roesslestrasse 1013125 Berlin, [email protected]

Prof. Friedrich Luft, Dr. Dominik MüllerProf. Thomas Jentsch Max-Delbrück-Center for Molecular Medicine Berlin, Germany

Prof. Nick Hastie, Dr. Duncan Davidson MRC Human Genetics Unit Western General Hospital Edinburgh, UK Dr. Jamie Davies University of Edinburgh Centre for Integrative Physiology Edinburgh, UK

Dr. Roger Cox Medical Research Council Harwell MRC Mammalian Genetics Unit Diabetes, QTL and Modifier Loci Group Oxfordshire, UK

Prof. Andreas Schedl Institut National de la Santé et de la Recherche Médicale (INSERM) U 470 Université Nice - Sophia Antipolis - Centre de Biochimie Nice, France

Prof. Corinne Antignac, Prof. Pierre Verroust Institut National de la Santé et de la Recherche Médicale (INSERM) U 574 & 538Necker Hospital, & Faculté de Médecine Saint-Antoine Paris, France

Prof. Pierre Courtoy, Dr. Olivier Devuyst Université Catholique de Louvain (UCL)Faculté de médecine Brussels, Belgium

Prof. André Brändli Swiss Federal Institut of Technology ETHZ Institute of Pharmaceutical Sciences Department of Chemistry and Applied Biosciences Zürich, Switzerland

Dr. Giuseppe Remuzzi, Dr. Ariela Benigni Mario Negri Institute for Pharmacological Research Negri Bergamo Laboratories Bergamo, Italy Prof. Jürg Biber, Prof. Carsten Wagner University of Zürich Institute for Physiology Zürich, Switzerland Prof. Gregor Eichele Max-Planck Institute of Biophysical Chemistry Genes and Behaviour Organisation Göttingen, Germany

Prof. Seppo Vainio University of Oulu Biocenter Oulu Department of Biochemistry Oulu, Finland

Prof. Erik Ilsø Christensen, Dr. Anders Nykjaer Aarhus University Aarhus C, Denmark

Prof. Raj Thakker University of Oxford Nuffield Department of Clinical Medicine Oxford Centre for DiabetesEndocrinology and Metabolism Churchill Hospital Oxford, UK


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State-of-the-Art: About 90 percent of all the information humans use in order to interact in society, is received through their eyes. But despite major clinical and therapeutic achievements in ophthalmol-ogy, the number of people suffering from serious eye problems is growing. This paradox reflects the fact that we have yet to find ways of stemming and repairing the damage caused by diseases that affect the retina, such as Inherited Retinal Degenerations (IRD) and Age-Related-Macular Degeneration (ARMD). Furthermore, visual handicaps are a particular problem in a society in which visual communication is ever increasing.

The retina — the part of the eye that converts light into sight — is a highly complex system that accommodates both numerous tissue-specific and ubiquitously expressed developmen-tal and pathologic pathways. The number of genes identified in IRDs has steadily increased. Over the past 20 years, a massive accumulation of knowledge has led to the recognition of more than 180 mapped loci and the identification of about 120 genes. The most com-mon form of visual impairment of people above 60, with 12.5 million people affected in Europe, is ARMD, caused by mostly unknown genetic factors. Preventing blindness from IRD and ARMD requires understanding of the genetic and cellular interactions controlling retinal development, maintenance and function. Understanding complex diseases of the retina is not only challenging, but it also offers a major incentive to use the knowledge that can be gathered by using state-of-the-art functional genomics technologies in order to generate a more comprehensive analysis of retinal degenerations.

Scientific/Technological Objectives: In the EVI-GENORET project, 25 academic and industrial partners have formed five interact-ing components — phenotyping, development, genetics, functional genomics and therapy — to establish working platforms and share tools and knowledge in the field of the retina within and outside the academic community.

Development of standards and information

networking system



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The aim of EVI-GENORET is to build on the current understanding of the fundamental mo-lecular and cellular biology of the retina. The project will help to prevent blindness caused by IRD and ARMD by aiming its work at pursuing a greater understanding of the genetic and cellular interactions that control retinal development, maintenance and function. The consortium plans to overcome the lack of critical knowledge in single EU countries by struc-turing retinal research from leading scientists throughout Europe in order to offer a source of expertise for those involved in that research field.

Further focus is on: (1) Obtaining and integrating the information on gene function through numerous human, animal and in vitro models of retinal degeneration available as well as data from studies during development; (2) Standardising and analysing this information (databases, bioinformatics, transcriptome, proteome and expression studies); (3) Valida-tion of the information (bioinformatics and functional assays); (4) Generating conceptual and biological models of genes, gene networks and pathways relevant to major functions involved and/or impaired in retinal health and disease; (5) Designing novel cell-based and genomic-based therapies that will potentially benefit patients but also validate the pathways and targets identified, using the above-described approaches.

Expected Results: The project has already provided some significant results towards the above objectives, and these are listed as follows: (1) Harmonisation of Standard Operating Procedure and devel-opment of the relational EVI-GENORET database. The EVI-GENORET database is a Euro-pean database devoted to fundamental and clinical scientists, as well as patients and aims at the centralization, sharing, exploitation and dissemination of the data and knowledge related to retinal health and disease. The database integrates heterogeneous data encom-passing population genetics, experimental phenotyping of human and animals, molecular genetics, high throughput functional genomics. Its design is specifically oriented towards the harmonization, standardization and interoperability of retinal data, protocols and clini-cal practices allowing the establishment of an effective networking systems at the European level; (2) Identification of several novel candidate genes involved in retinal degeneration by DNA chips and proteomic analysis in dominant retinitis pigmentosa (RP) and in a severe inherited retinal disease in children(3) Retinoid dehydrogenases/reductases (RDH) catalyse key oxidation reduction reactions in the visual cycle that converts vitamin A , the chromo-phore of the rod and cone photoreceptors; that the consortium has shown that mutations in RDH12, encoding a retinal dehydrogenase, result in severe and early-onset autosomal re-cessive retinal dystrophy (arRD) (4) development of vectors as potential gene therapy tools. The project has already initiated a gene therapy clinical trial in a specific form of IRD.

Potential Impact: EVI-GENORET will increase the scientific community’s understanding of the function of the retina, its cellular components, and molecular princi-ples as well as the mechanisms of retinal degeneration. The project aims is to develop and validate innovative therapeutic approaches.

This is a unique opportunity to implement a structured project, gathering the most active and experienced professional research teams on retin-opathies and basic retinal biology. The team expects will to deciphering

Fundus photograph of the human eye Acknowledgement: Dr. S. Mohand-Saïd, INSERM, PARIS

Cross-secion of the retina (microphotograph) Acknowledgement: Dr. O. Goureau, INSERM PARIS


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Project Coordinator: Prof. Jose-Alain SahelInstitut National de la Santé et de la Recherche Médicale (INSERM) U592Laboratoire de Physiopathologie Cellulaire et Moleculaire de la Retine Institut de la VisionCHNO des Quinze-vingts, 17 rue Moreau,75012 Paris, [email protected]

Project Scientific Manager:Dr. Olivier LorentzINSERM Transfert SA7, rue Watt75013 Paris, [email protected]

Project Administrative Manager:Dr. Thomas Wheeler-SchillingEuropean Vision Institute EEIGBrussels, Belgium

Prof. Jose-Alain Sahel, Dr. Thierry Leveillard,Dr. Serge Picaud, Dr. Olivier Goureau,Dr. Josseline Kaplan, Dr. Christian Hamel,Dr. Francine Behar-Cohen, Dr.Frédéric Mascarelli,Dr. Ségolène AyméInstitut National de la Santé et de la RechercheMédicale (INSERM)Laboratoire de Physiopathologie Cellulaire etMoléculaire de la RétineParis, France

Prof. Shomi Bhattacharya, Prof. Alan Bird, Dr. Robin Ali,Dr. John Greenwood, Dr. Stephen MossUniversity College LondonInstitute of OphthalmologyLondon, UK

Prof. Eberhart Zrenner, Dr. Mathias Seeliger,Dr. Frank Schuettauf, Dr. Bernd Wissinger, Dr. Ulrich SchrayermeyerEberhard-Karls-Universitaet TuebingenUniversity Eye HospitalTuebingen, Germany

Prof. José Cunha-VazAibili - Associação Para Investigação Biomédica EInovação Em Luz E ImagemCNTM - Centro De Novas Tecnologias Para A MedicinaAzinhaga De Santa Comba - CelasCoimbra, Portugal

Dr. Sandro BanfiTelethon Institute of Genetics and MedicineNaples, Italy

Dr. Ronald Roepman, Dr. Frans CremersThe University Medical Centre NijmegenDepartment of Human GeneticsNijmegen, The Netherlands

Dr. Theodorus Van Veen, Dr. Per Ekstroem,Dr. Maria-Theréza PerezLund UniversityDepartment of OphthalmologyWallenberg Retina CenterLund, Sweden

Partners

the mechanisms underlying retinal diseases, and setting up functional assays which will con-tribute to advance practical development of therapeutics. EVI-GENORET has great potential for breakthroughs at each of the many incremental steps towards integrated system biology as well as in the outcome measures. Thus, with the potential impact on public health, it will convince basic and applied scientists of the importance of such concerted effort.

The goal, at the completion of the project, is to help integrate a broad and in depth under-standing of the function and interactions of major cells and gene networks, thereby propos-ing functional models. The unique knowledge base on molecular networks thus generated will facilitate identification and validation of novel therapeutic targets of broad interest. Developing stem cell culture methods and new approaches to gene and drug delivery mechanisms is expected to provide novel tools for future therapeutic interventions after test-ing in this privileged organ.

Keywords:vision, gene expression, retinal developement, photoreceptors, age-related macular degen-eration (AMD), retinal dystrophies, animal dystrophies, animal mutants, genotype-pheno-type-correlation


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Prof. Angelo Luigi VescoviUniversity of Milano BicoccaDipartimento Di Biotecnologie E Bioscienze BtbsMilan, Italy

Prof. Veronica Van Heyningen, Prof. Alan WrightMedical Research CouncilMRC Human Genetics UnitEdinburgh, UK

Dr. Marius UeffingGSF-Forschungszentrum Fuer Umwelt UndGesundheit GmbhInstitute of Human GeneticsNeuherberg, Germany

Prof. Andreas GalUniversity Hospital Hamburg-EppendorfInstitute of Human GeneticsHamburg, Germany

Dr. Christian GrimmUniversity of ZurichDepartment of OphthalmologyUniversity HospitalLab For Retinal Cell BiologyZurich, Switzerland

Prof. Frank G Holz, Hendrik SchollUniversity of BonnDepartment of OphthalmologyFaculty of MedicineBonn, Germany

Prof. Peter HumphriesThe Provost, Fellows and Scholars of The College of The Holy and Undivided Trinity of Queen ElizabethOcular Genetics UnitDublin, Ireland

Dr. Christina FasserRetina InternationalZurich, Switzerland

Dr. Frank MuellerResearch Centre Juelich GmbhInstitute for Biological Information ProcessingJuelich, Germany

Dr. Geraoid TuohyGenable Tehnologies LtdSmurfit Institute of GeneticsTrinity College DublinDublin, Ireland

Prof. Usha ChakravarthyQueens University BelfastOphthalmology and Vision ScienceBelfast, UK

Dr. Pascal Dolle, Dr. Olivier PochCentre Européen pour la Recherche en Biologie etMédecine-Groupement D’Intérêt Economique(CERBM-GIE)Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Illkirch, France

Dr. Kader ThiamGenowayLyon, France

Dr. Carmen AyusoFundacion Jimenez Diaz UTEDepartment of Medical GeneticsMadrid, Spain

Dr. Smaragda KamakariNational and Kapodistrian University of AthensSchool of Medicine, Laboratory of BiologyAthens, Greece

Dr. Valeria MarigoUniversità di Modena e Reggio EmiliaDipartimento di Scienze BiomedicheModena, Italy


Functional genomics of the retina in health and disease



STEM CELLS

7.3FunGenES

PLURIGENES

ESTOOLS

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State-of-the-Art:Current knowledge of the genetic mechanisms regulating pluripotency and differentiation is limited. While many of the conditions that facilitate lineage commitment and differentiation are known, an in-depth understanding of the underlying genetic programmes is lacking. FunGenES aims to systematically identify genes that are involved in different aspects of development, such as maintenance of pluripotency, formation of the three germ layers and further differentiation into somatic lineages. An approach of this scale has not previously been attempted, and therefore there is considerable potential for advancing the field.

The FunGenES consortium addresses fundamental issues of stem cell biology and functional genomics, pursuing an integrated strategy based on cultured mouse embryonic stem (ES) cells. Traditionally, studies in developmental genetics have used a variety of animal models. These studies are time-consuming and their results cannot be directly compared, due to the heterogeneity of methods and species used. In contrast, the FunGenES approach using cultured murine ES cells, offers a standardised, well-characterised, in vitro model of pluripo-tency and differentiation.

Scientific/Technological Objectives:FunGenES will identify the gene subsets that are active at different stages of ES cell differen-tiation. Its major objective is to produce a gene expression atlas covering the development of ES cells into all three germ layers (ectoderm, mesoderm and endoderm) and the various somatic cell types.

More specifically, the consortium has several objectives, inclusive of the following: (1) De-veloping a detailed understanding of ES cell self-renewal, differentiation and lineage com-mitment, and identifying potential novel target genes for therapeutic intervention; (2) Deriv-ing new molecular and cellular tools for characterising gene function in tissue-specific cell populations; (3) Developing new ES cell-based methods for high throughput screening of small candidate molecules for therapeutic applications in human diseases.

Expected Results:FunGenES expects to deliver the following results:

1) A phenotypic and expression profile atlas of cell lineage commitment from the pluripo-tent state (ES cells) to the three major germ lineages. Based on the information in this atlas, the intention is to develop a detailed understanding of the following items: (i) The genetic mechanisms and extrinsic and intrinsic signalling cascades responsible for ES cell proliferation and self-renewal; (ii) The molecular basis of pluripotency; (iii) The processes determining fate from precursors to differentiated cells; (iv) The mecha-nism of mesodermal commitment, and identification of master genes, extrinsic and intrinsic signalling cascades and transcription factors involved in the determination of cardiac cells, endothelial cells, adipocytes, osteoblasts and haematopoietic cells; (v) The mechanism of ectodermal commitment and identification of master genes, extrinsic and intrinsic signalling cascades and transcription factors involved in the determination of neurons and glial cells; (vi) The mechanism of endodermal commit-ment and identification of master genes, extrinsic and intrinsic signalling cascades


Project Type:Integrated ProjectContract number:LSHG-CT-2003-503494Starting date:1st March 2004Duration:46 monthsEC Funding:

8 500 000

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and transcription factors involved in determination of hepatocytes and insulin produc-ing β-cells.

2) Determination of gene expression patterns at landmark differentiation points in ES-derived somatic cell lineages.

3) Engineered ES cell lines, including physiological information on the behaviour of these cells.

4) A set of standard operating procedures, to be used for the following purposes: (i) Use of ES cell models and differentiation protocols; (ii) Technical tools (RNA prepa-ration, standard formatted chips for gene expression analysis, bacterial artificial chromosome methods, endoribonuclease-prepared small interfering RNA methods); (iii) Data analysis using bioinformatics and cluster gene analysis.

Potential Impact:New knowledge about the genetic pathways that underlie the differentiation of ES cells to somatic cells will contribute to novel therapeutic strategies for human diseases that are char-acterised by the irreversible loss of functional cells. Potential clinical applications include tissue and cell transplantation, and new therapies for diseases such as cancer, liver disease, diabetes and cardiovascular and neurodegenerative diseases.

Murine ES cells represent a valuable tool for understanding developmental processes and for screening for embryo-toxicology without the use of animals. They are therefore expected to have a major impact on drug development, considering that the high failure rate in this process is the result of toxicity in both the early and late phases of development, including clinical trials. These failures increase the costs of drug development dramatically, and raise ethical concerns.


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Basic research on murine ES cells is a highly competitive field which offers the prospect of economic growth in Europe, as long as technological tools, diagnostic targets and long-term drug development are successfully translated into advances in clinical science. Growth is expected to occur in the following areas in the near future: ES cell developmental biology and genomics tools, drug development and gene and cell therapy.

Keywords: functional genomics, murine embryonic stem cells, differentiation, gene atlas, cellular, stem cells

Project Coordinator:Prof. Jürgen HeschelerUniversity of CologneInstitute of NeurophysiologyFaculty of MedicineRobert-Koch-Str. 3950931 Cologne, [email protected]

Project Manager:Annette RingwaldARTTI58A, rue du Dessous des Berges75013 ParisFrance

Dr. Laurent PradierAventis Pharma Recherche-Développement,(now Sanofi-Aventis)Neurodegenerative Disease GroupGenomics DepartmentVitry sur Seine, France

Dr. Pierre SavatierInstitut National de la Santé et de la Recherche Médicale (INSERM)Unité 371 “Cerveau et vision”Bron, France

Dr. Antonis HatzopoulosGSF-Research Center for Environment and HealthGSF-Institute of Clinical Molecular Biology and TumorGenetics - Laboratory of Vascular GeneticsMunich, Germany

Dr. Lesley Margaret ForresterUniversity of EdinburghJohn Hughes Bennet Laboratory / Division of OncologySchool of Molecular and Clinical MedicineWestern General HospitalEdinburgh, UK

Partners


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Dr. Timothy E. AllsoppStem Cell Sciences LtdRoger Land BuildingEdinburgh, UK

Dr. Matthias AustenDeveloGen AktiengesellschaftStem Cell ResearchGoettingen, Germany

Dr. Norbert Hübner, Michael BaderMax-Delbrück-Center for Molecular MedicineMolecular Biology and GeneticsBerlin, Germany

Prof. Angelo Luigi Vescovi (until 31 October 2006)Fondazione Centro San Raffaele del Monte TaborDIBIT-Stem Cell Research InstituteMilan, Italy

Dr. Frank BuchholzMax-Planck Institute of Molecular CellBiology and GeneticsDresden, Germany

Dr. Heinz HimmelbauerMax-Planck-Institute for Molecular GeneticsDepartment of Vertebrate GenomicsAG HimmelbauerBerlin, Germany

Dr. Christian Dani, Dr. Hélène BoeufCentre National de la Recherche Scientifique (CNRS)Institute of Signalling, Developmental Biologyand Cancer Research-UMR6543 (Nice)/Laboratoire Composantes innées de la réponseimmunitaire et différenciationUMR 5164 (Bordeaux)Paris, France

Prof. Domingos HenriqueInstituto e Medicina MolecularFaculdade Medicina LisboaInstituto Histologia e EmbriologiaLisbon, Portugal

Prof. Francis StewartTechnical University DresdenBiotec, GenomicsDresden, Germany

Dr. Androniki KretsovaliFORTH, Foundation for Research & Technology HellasInstitute of Molecular Biology and BiotechnologyHeraklion, Greece

Dr. Melanie J. WelhamUniversity of BathDepartment of Pharmacy and PharmacologyFaculty of Science, Laboratory of Molecular SignallingBath, UK

Prof. Anna M. WobusInstitute of Plant Genetics and Crop Plant ResearchCytogenetic, In vitro Differentiation GroupGatersleben, Germany


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State-of-the-Art:A first step towards regenerative medicine consists in finding a mean to cause controlled ded-ifferentiation of adult tissue. The project Plurigenes aims at achieving major breakthroughs in the discovery and understanding of the function of genes controlling pluripotency in the central nervous system. Plurigenes will start by identifying candidate genes in model organ-isms, following original approaches involving screens performed by in situ hybridisations on well-characterised neural structures or by gain-of-function analysis. Innovative technolo-gies of transgenesis and imaging in several model organisms will be settled to reach this goal. The project will first characterise the functions of candidate genes in vitro and in vivo. Then, for selected genes, it will validate the possibility to restore the pluripotency of terminally differentiated cells through transgenesis of the candidate genes. Thus, Plurigenes should identify molecular actors and related pathways associated with pluripotency.

Scientific/Technological Objectives: The overall objective of Plurigenes is to allow the dedifferentiation of differentiated neural cells into pluripotent cells and, consequently, to improve the ability to manipulate those cells and combat diseases, such as brain injury and/or aging. By using different animal models belonging to the Chordate phylum and a large panel of in vitro and in vivo meth-ods, the project partners plan to take advantage of a multi-organism approach. In parallel, Plurigenes will improve transgenesis methods and develop novel imaging techniques in several model organisms.

PLURIGENES aims to identify novel (that is, so far uncharacterised) pluripotency associated genes in model organisms. This will be achieved through in situ hybridisation screens on fish and gain-of-function screens in ascidians on several thousands genes. It will result in 30-40 genes considered as candidate regulators. The sequence identity of basal chordates’ proteins with their human counterpart will allow a straightforward exploitation of the newly isolated genes in the frame of human researches.

Secondly, the consortium aims to assess the role of the latter genes in the maintenance of pluripotency and the dedifferentiation process, using fish, mice, and human cultured cells. From the pool of 30-40 candidate genes identified, it will lead to the selection of about one dozen selected genes. A third objective consists of validating the physiological role of the selected genes in vivo. To achieve this, the expression of these genes will be perturbed (abolished, over-expressed, and mis-expressed) primarily in the nervous system of the ani-mal models. The effects on the neural stem cells (NSC) and neural progenitors will also be examined. Finally, the Plurigenes team aims to create improved methods for transgenesis and imaging in model organisms via an improvement of transgenesis. This will be achieved by using meganucleases, a very promising class of endonucleases for many applications, via the development of a novel technology for microscopy (SPIM) and the development of highly innovative analyses of 4D images of embryos.

Expected Results: PLURIGENES aims at finding and characterising new determinants that regulate the mainte-nance of the neural stem cell undifferentiated state and the reversal of differentiated neural cells (neurons and glia) towards a neural stem cell pluripotent state. The partners predict that several important regulators remain to be discovered, notably in the still large fraction of vertebrate predicted genes (the function of which is not presently documented), and that these novel actors could have many therapeutic uses. Once assayed for their dedifferentia-tion activities, these newly identified genes may allow improved protocols for dedifferentia-

Medaka embryo hybridised with a probe for a gene signalling for

cell cycle arrest (‘stop signal’)

Histological section through the optic tectum showing expression

of one gene in the arrrest zone


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tion of neural cells to be established, sole or in combination with already known factors. Other important enhancements expected from this project concern the development of new methodologies, in particular the manipulation of gene expression (transgenesis) in model organisms, and innovative microscopy methods for in vivo imaging of the fate of dediffer-entiated cells.

Potential Impact: PLURIGENES constitutes a unique opportunity to bring together specialists in developmental genetics of model organisms, cellular biology of human NSC, and oncology. Compared to programmes underway in non-European countries, the project focuses on a competitive area. The ability to isolate and transplant NSC in vivo from differentiated cells should sim-plify the development of stem cell-based therapies for a range of neurological disorders. Pathways that regulate self-renewal of normal stem cells are deregulated in cancer stem cells, resulting in the continuous expansion of cancer cells. Therefore, finding of new gene families involved in pluripotency should have a significant impact on pharmaceutical com-panies by allowing novel strategies of anti-tumour drug design.

Keywords: de-differentiation, pluripotency, transgenesis, central nervous system, regenerative medecine, model organisms, embryos

Project Coordinator: Dr. Jean-Stéphane JolyInstitut National de la Recherche Agronomique (INRA)Physiologie animale et systèmes d’élevage (PHASE)UNIT 1126. DEPSN-bt 32-33 Avenue de la Terrasse91198 Gif-sur-Yvette, [email protected]

Dr. Jochen WittbrodtEuropean Molecular Biology Laboratory (EMBL)Developmental Biology UnitHeidelberg, Germany

Dr. Patrick LemaireCentre National de laRecherche Scientifique (CNRS)Genetics and Physiology Development LaboratoryMarseille, France

Dr. Filomena RistoratoreStazione Zoologica Anton DorhnNaples, Italy

Partners

Prof. Manfred SchartlUniversity of WurzburgDepartment of Physiological Chemistry Wurzburg, Germany

Dr. Philippe GennesONCODESIGNDijon, France

Dr. François GuillemotMedical Research CouncilMolecular NeurobiologyLondon, UK

Prof. Angelo VescoviUniversity of Milano BicoccaIstituto di Ricerca per le Cellule StaminaliMilan, Italy


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State-of-the-Art:ESTOOLS will significantly advance the fundamental understanding that will underpin bio-medical application of human embryonic stem (hES) cells. Pluripotent hES cells present a unique opportunity to study human cellular differentiation and pathogenesis. hES cells also offer a new resource for cellular transplantation in human degenerative disease and a powerful platform for pharmaceutical and toxicology screening. The promise of hES cells rests largely on unlimited expansion in stem cell numbers without genetic or epigenetic com-promise, and on directing differentiation with absolute phenotypic fidelity. Success entails understanding the mechanisms controlling the choice between (a) proliferation and self renewal, and (b) apoptosis or commitment to differentiation.

Genetic intervention is a key tool for delineating the molecular circuitry of hES cells. ES-TOOLS will develop the tools needed to elucidate the genetic and molecular networks that control the self renewal, commitment and terminal differentiation of hES cells. Neural commitment provides a paradigm for understanding the mechanisms by which embryonic stem cells choose between self renewal and lineage commitment. Neuronal and glial dif-ferentiation of hES cells offer major new experimental avenues for cellular neurobiology and pathogenesis, with potential eventual application in bio-industry and medicine via pharmaceutical and toxicological screening and cell replacement therapies. By character-ising progression from embryonic stem cell through naive neuroectodermal precursors to functionally differentiated neuronal and glial sub-types and establishing conditions for the quantitative production of neurons and glia, ESTOOLS will provide vital new experimental avenues for study of cellular neurobiology and neuropathogenesis. In parallel, an ethics team will research ethical issues pertinent to the derivation and use (including commercial) of hES cells and will engage with scientists in ESTOOLS and with stakeholders.

Scientific/Technological Objectives:The overall goal of ESTOOLS is to standardise and optimise protocols for the culture of hu-man embryonic stem cells, to ensure their genotypic and phenotypic stability and to estab-lish techniques and understanding to allow their robust differentiation into functional cells of the neural lineage. Other objectives include:

1) developing optimised culture conditions to enable standardised propagation of hu-man embryonic stem cells;

2) permitting the use of reliable, defined serum-free culture protocols and automated cell culture systems;

3) providing a toolkit of protocols and reagents for routine genetic manipulation of hu-man embryonic stem cells, to establish them as a genetically tractable system compa-rable with mouse embryonic stem cells;

4) determining mechanisms that control self renewal and commitment to differentiation of human embryonic stem cells, allowing: (a) improved techniques to monitor the ge-netic and epigenetic integrity of human embryonic stem cell cultures (b) development of culture methods that minimise the genetic instability of human embryonic stem cells (c) definition of the key parameters of epigenetic stability and variability in human embryonic stem cells (d) development of methods to maintain human embryonic stem cells in an undifferentiated state and prevent unwanted spontaneous differentiation;

5) establishing models of fate, choice and pathogenesis for the human central nervous system and elucidation of the molecular mechanisms, regulatory networks and key


ESTOOLSwww.estools.eu

Project Type:Integrated ProjectContract number:LSHG-CT-2006-018739Starting date:1st August 2006Duration:48 monthsEC Funding:

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signalling pathways that govern choice between self-renewal and lineage commit-ment, allowing: (a) development of protocols to promote the differentiation of human embryonic stem cells to the neuroectodermal lineage; (b) delineation of the epige-netic contribution to lineage commitment; (c) development of new tools for genetically monitoring specific states of the cells from ‘undifferentiated’ to ‘lineage committed and ‘terminally differentiated’; (d) identification of conditions for the robust produc-tion of functionally validated, mature neuronal phenotypes;

6) promoting bio-industry exploitation of human embryonic stem cell biology through small to medium sized enterprise (SME) partners and the biopharmaceutical sector by developing: (a) procedures to automate biomanufacturing of human embryonic stem cells and their differentiated progeny; (b) novel monoclonal antibodies to cell surface markers for the identification of undifferentiated human embryonic stem cells and for monitoring their differentiation; (c) tools for neurodegeneration.

Expected Results:By the end of its fourth year ESTOOLS will have established that human embryonic stem cells provide a genetically tractable system, comparable with mouse embryonic stem cells, facilitating realisation of the potential benefits that these cells offer to human health care. The following expected achievements will provide evidence for these conclusions:

1) a refinement, standardisation and optimisation of the culture conditions needed to propagate human embryonic stem cells with phenotypic and genotypic fidelity and to create associated user-friendly and reliable protocols;

2) the ability to monitor multiparametrically the genotypic and epigenotypic integrity of human embryonic stem cell cultures;

3) a toolkit of protocols and reagents for the routine genetic manipulation of human embryonic stem cells;

4) an understanding of the molecular mechanisms and regulatory networks that govern a stem cell’s choice of self-renewal or lineage commitment;

Neuronal cells differentiated from hES derived neural stem cells stained with beta-III tubulin positive (green) and Hoechst 33342 (blue) University of Sheffield (UK) Centre for Stem Cell Biology, 2006


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5) a definition of the key parameters of epigenetic stability and variability in the human embryonic stem cells;

6) an understanding of the molecular process and mechanism of lineage commitment;7) a delineation of the epigenetic contribution to lineage commitment; 8) an ability to direct neuroectodermal lineage choice to 90% efficiency; 9) a description of the necessary conditions for robust production of functionally vali-

dated mature neuronal phenotypes and the generation of specific classes of neuronal and glial progenitors;

10) the initiation of neuro-degeneration modelling and of neuro-modulatory drug screens;

11) the introduction of quality-controlled ‘good manufacturing processes’ for human em-bryonic stem cells;

12) procedures to automate the bio-manufacturing of human embryonic stem cells and their differentiated progeny.

Potential Impact:Human embryonic stem cell biology provides new tools for applications in a wide range of fields from understanding hu-man development and disease processes to drug discovery and toxicology and, eventu-ally, to regenerative medicine. ESTOOLS will help realise this potential by widening and deepening the range of skills and experience in human em-bryonic stem cell research across Europe. The project will play a significant role in the development of standardised techniques, protocols and rea-gents, permitting standardisa-tion of research with human embryonic stem cells in Eu-

rope, and throughout the world, through the close relationship between ESTOOLS and the International Stem Cell Initiative. The SME partners in ESTOOLS will be the springboard for bio-industrial exploitation of the project’s results. Future research into the mechanisms of human embryonic stem cell lineage commitment and differentiation, and development of biopharmaceutical industry applications - eventually for regenerative medicine - requires these cells to be genetically manipulated robustly in well-defined ways. Thus ESTOOLS will develop a genetic ‘toolkit’ to help realise the potential of human embryonic stem cell re-search in Europe. ESTOOLS will contribute to the social sustainability of continuing research and application of knowledge outputs by analysis of the ethical issues surrounding use of human embryos and their stem cells in the different social contexts of European countries.

Keywords:differentiation, self-renewal, neural, stem cells, human embryonic stem cells


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PartnersProject Coordinator:Prof. Peter W AndrewsUniversity of Sheffield Centre for Stem Cell BiologyDepartment of Biomedical SciencesWestern BankSheffield, S10 2TN, [email protected]

Project Manager:Andrew SmithESTOOLS Project Officec/o University of Sheffield - BMSWestern BankSheffield, S10 2TN, [email protected]

Dr. Tim AllsoppStem Cell Sciences UK LtdCambridge, UK

Prof. Yves-Alain BardeUniversity of BaselBiozentrumBasel, Switzerland

Prof. Nissim BenvenistyHebrew University of JerusalemDepartment of GeneticsInstitute of Life SciencesJerusalem, Israel

Prof. Riitta LahesmaaUniversity of TurkuTurku Centre for BiotechnologyTurku, Finland

Prof. Oliver Brustle Rheinische Friedrich-Wilhelms-Universität BonnInstitute of Reconstructive NeurobiologyBonn, Germany

Prof. Elena CattaneoUniversita Degli Studi di MilanoDepartment of Pharmacological SciencesMilan, Italy

Prof. Tariq EnverMedical Research Council Weatherall Institute of Molecular MedicineOxford, UK

Dr. Manuel EstellerCentro Nacional de Investigaciones OncológicasGrupo de Epigenética del CáncerMadrid, Spain

Dr. Jim WalshAxordia LtdSheffield, UK

Dr. Petr DvorakInstitute of Experimental MedicineAcademy of Sciences of the Czech RepublicPrague, Czech Republic

Prof. Goran HermerenLund UniversityFaculty of MedicineLund, Sweden

Prof. Outi HovattaKarolinska InstitutetDepartment of Clinical ScienceIntervention and TechnologyStockholm, Sweden

Dr. Maarten van LohuizenNetherlands Cancer InstituteDivision of Molecular Genetics Amsterdam, The Netherlands

Prof. Timo OtonkoskiUniversity of Helsinki Biomedicum Stem Cell CenterHelsinki, Finland

Dr. Danny KitsbergSCT Stem Cell Technologies LtdJerusalem, Israel

Dr. Andrew SmithUniversity of EdinburghInstitute for Stem Cell ResearchEdinburgh, UK

Dr. Konstantinos AnastassiadisTechnische Universität DresdenBIOTECDresden, Germany

Prof. Austin SmithUniversity of CambridgeSchool of the Biological Sciences Wellcome Trust Centre for Stem Cell Research Cambridge, UK

Dr. Meng LiImperial College of Science Technology and Medicine LondonMRC Clinical Sciences CentreLondon, UK


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State-of-the-Art: The EuTRACC consortium proposes to determine the regulation of the genome by mapping the regulatory pathways and networks of transcription factors (TFs) that control cellular functions. EuTRACC will be part of and work in close collaboration with the International Regulome Consortium (IRC), a worldwide network that will address the regulation of ge-nome function at a higher level by mapping the genetic regulatory nodes and networks that control the activity of embryonic stem cells and the process of differentiation to specific cell types. It will focus on mapping the genetic circuitry that controls the formation of neural tissues and the blood system. The project will utilise genetics, proteomics and genomics tools in the mouse, zebrafish and Xenopus model organisms. These approaches will allow the characterisation of transcription factor complexes and the genome-wide identification of binding sites for these TFs in undifferentiated and differentiated ES cells or differentiated tissues (blood and neuronal system). It will systematically identify TF complexes and TF binding sites in vertebrate genomes required for the differentiation into haematopoietic and neural cells. The bio-informaticians will develop novel algorithms to extract and interpret the data and viewers to integrate the information in the ENSEMBL database. Data will be made available publicly through web based platforms and tools. Databases will be constructed that will include annotated TFs, TF-DNA interactions, protein- and RNA TF interactions and cellular regulation (gene, effect, cell type, cell state). The project databases will be inter-faced with existing micro-array databases as well as other public databases. The project will provide new insights into the regulation of cell function that stimulate translational re-search, which is critical for developing novel therapies, particularly in the areas of stem cell transplantation and tissue engineering.

Scientific/Technological Objectives: 1) to ensure a substantial contribution of EU based science to the field of transcriptional

regulation of differentiation and development; 2) to provide strong input from the EU to the International Regulome Consortium (IRC),

a worldwide consortium that represents a third generation genomics project ad-dressing the regulation of genome function at a higher level by mapping the genetic regulatory nodes and networks;

3) to identify protein complexes of basic, general and tissue-specific TFs and interacting partners expressed in neuronal and haematopoietic cell types;

4) to use bioinformatic methods to correctly annotate mouse genes that encode bona fide TFs and interacting proteins. Microarray data will be analysed to identify TF complexes expressed in the selected cell types;

5) to validate interactions by IPs and/or BiFC;6) to determine intracellular localisation of TFs and/or associated proteins; 7) to identify target genes of the different TF complexes;8) to functionally analyse TFs and selected interacting proteins by morpholino injections

in zebrafish and Xenopus embryos; 9) to create computational procedures and models that describe the mechanism of

regulation of gene transcription in order to differentiate embryonic stem cells from neuronal or haematopoietic cells. Specific databases and tools will be developed to facilitate the collection, curation and analysis of the data, as well as for the public dissemination of findings.


EuTRACCwww.eutracc.eu


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Technical objectives for this application are: 1) to generate 100 knock-ins of protein tags for affinity purification of TF complexes and

concurrently generate conditional TF KOs in ES cells;2) to generate homozygous null mutations in key TFs in ES cells and mice;3) to culture and differentiate TF tagged ES cells in vitro and isolate the relevant tissues

from ES generated mice for genomic and proteomic analyses;4) to characterise the protein components of transcriptional complexes containing the

tagged TFs in selected cell and tissue types; 5) to purify and identify TF binding sites in selected cell types by two approaches -

chromatin affinity purification, followed by DNA amplification, and hybridisation to genome wide microarrays (Affymetrix, Agilent or Nimblegen). Fine mapping, when required, will be done by in vivo footprinting.

6) to repeat cycles of tagging knock-ins for affinity purification etc. by tagging selected interaction partners from the previous screen.

Expected Results: The development of methodology to set up a ‘pipeline’ that allows:

1) the tagging of the N- or C-terminus of protein via homologous recombination in ES cells (and/or other cell lines) of the gene coding for the protein of interest;

2) rapid affinity-based purification of proteins of interest; 3) concomitant generation of conditional KO alleles of the gene coding for the protein of

interest by inclusion of loxP sites for Cre mediated recombination in vivo or in vitro; 4) two rounds of affinity purification and protease mediated release to rapidly obtain

highly purified protein complexes that can be used for a variety of functional and structural studies;


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5) rapid identification of transcription factor binding sites in vivo, using the protein tags;

6) rapid functional analysis using morpholinos to functionally identify the key proteins in a TF complex;

7) the generation of databases of transcription factors and interacting partners for stem cells, haematopoietic cells and neuronal cells. This will also help to improve the predictive power of in silico prediction methods;

8) the generation of algorithms to model transcription factor networks in collaboration with IRC.

Potential Impact: EuTRACC will focus on mapping the transcriptional circuitry on the molecular level and how it controls the formation of neural tissue and the blood system. Understanding the regulatory network is one of the big challenges for biology in the next decade. It will provide much bet-ter insight into the normal and abnormal formation of stem cells and tissues and into disease processes and be an essential part of future developments in medicine and biotechnology, in particular those areas that are concerned with stem cell biology. EuTRACC will provide a substantial impetus to fundamental and translational research by making its data publicly available and seeking new collaborations and alliances where appropriate. The expecta-tion is therefore that it will substantially contribute to the development of novel therapies and improved health benefits for society. EuTRACC provides an excellent opportunity for the EU to strengthen its competitive position in this area by bringing together a group of excellent researchers with a high level of expertise in the different areas required for a successful, comprehensive and integrated approach. Genomic research is an essential component of an innovation-based economy, generating Intellectual Property, leading to the development of new technologies, providing the basis for new companies and stimulating employment in new industries.

Keywords:transcriptome, regulome, cellular commitment, transcription factors, neurobiology, hemat-opoiesis, embryonal development

PartnersProf A. Francis Stewart Biotec, Genomics Dresden, Germany

Dr. Irwin Davidson, Dr. Laszlo Tora CERBM-GIE (IGBMC)Illkirch, France Prof. Dr. Meinrad Busslinger Research Institute of Molecular Pathology GmbHVienna, Austria

Prof. Dr. Yves-Alain Barde University of BaselDepartment of NeurobiologyBasel, Switzerland

Project Coordinator:Prof. Dr. Frank Grosveld Erasmus MC University Medical CenterDepartment of Cell Biology and GeneticsP.O. Box 20403000 CA Rotterdam, The Netherlands [email protected]

Project Manager:Dr. Rini de Crom Erasmus MC University Medical CenterDepartment of Cell Biology and GeneticsP.O. Box 20403000 CA Rotterdam, The Netherlands [email protected]


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Prof. Dr. Uwe Straehle Institute of Toxicology and Genetics Forschungszentrum KarlsruheKarlsruhe, Germany

Prof. Dr. Magdalena Goetz, Prof. Dr. Wolfgang WurstHelmhotz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt GmbHNeuherberg, Germany

Dr. W. SkarnesGenome Research LtdWellcome Trust Sanger InstituteHinxton, UK

Prof. Dr. H. Th. M. TimmersUniversity Medical Centre UtrechtDepartment of Physiological ChemistryUtrecht, The Netherlands

Prof. R. PatientUniversity of OxfordWeatherall Institute of Molecular MedicineJohn Radcliffe HospitalOxford, UK

Prof. J. SmithWellcome Trust/Cancer Research UK Gurdon InstituteCambridge, UK

Prof. C. BoniferUniversity of LeedsDivision of Experimental HaematologyLeeds Institute for Molecular MedicineWellcome Trust Brenner BuildingSt. James’ University HospitalLeeds, UK

Prof. Dr. M. VingronMax-Planck Institute for Molecular GeneticsDepartment of Computational Molecular BiologyBerlin, Germany

Prof. Dr. R. Aasland, Dr. Boris LenhardUniversity of BergenBergen, Norway

Prof. A. SimeoneCEINGE Biotecnologie Avanzate s.c.a.r.l.Naples, Italy

Prof. R. Di LauroInstituto Ricerche Genetiche Gaetano SalvatoreAriano Irpino (Av), Italy

Dr. Michael RudnickiOttawa Health Research InstituteOttawa, Canada

Dr. Ferenc MüllerUniversity of Birmingham Institute of Biomedical Research, Medical SchoolBirmingham, UK

Prof. Dr. Michael MeisterernstUniversity of Münster Department of Medicine, Tumor Biology Münster, Germany


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RNA BIOLOGY

7.4RIBOREG

FOSRAK

Callimir

EURASNET

BACRNAs

RNABIO

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State-of-the-Art:The post-genomic era is yielding tremendous amounts of data about plant and animal genomes and their expression. In order to exploit and understand this data it will be neces-sary to determine the mechanisms leading to patterns of gene expression in differentiation processes. The ability to understand how gene expression varies and how cytoplasmic processes communicate with the nucleus to establish an overall RNA-mediated regulation is of key importance in the post-genomics phase. Riboregulators can be separated into three major classes, namely, the small (21-25nt) si/miRNAs, the long non-protein coding RNAs produced by RNA polymerase II (npc-mRNAs) and the ncRNAs produced by RNA polymerase III or pol III riboregulators (e.g. snoRNAs, SINE elements). The RIBOREG project concentrates on the identification of novel riboregula-tors involving all three types of riboregulators, in plants and animals.

Scientific/Technological Objectives: RIBOREG aims to identify novel non-coding RNA (ncR-NA) genes linked to cell differentiation and disease and analyse their mechanisms of action by developing a multidisciplinary approach integrating bioinformat-ics, cell biology, genetics and genomic strategies.RIBOREG’s key objectives were to develop bioinfor-matics tools for gene mining; isolate novel regulatory ncRNAs; utilise genomics approaches to characterise expression patterns for these genes; identify cellular targets of ncRNAs by screening and/or preparing mutants affected in their function in model organisms; dissect cellular mechanisms involving selected RNAs in differentiation and disease; establish cell biologi-cal approaches for monitoring in vivo RNA-protein interactions; and to validate innovative technology for functional and structural analysis of ncRNAs. RI-BOREG also aimed to integrate the results obtained

in different systems on the function of riboregulators. The project was therefore of extreme importance for SMEs concerned with developing and validating tools for the analysis of this novel area of gene regulation. The project gave European biotechnology a lead in explor-ing the potential of genome information in relation to human health.

Expected Results: The main expected results were:

C. elegans and A. Thaliana;

Throughout the project RIBOREG published its results in scientific journals (approximately 30 scientific publications with several in high-impact journals such as Molecular Cell, Na-ture Genetics and Science). Technological developments in the project also resulted in two patents that were applied for in Spain by an SME partner (Biomedal); one was undertaken in collaboration with a University partner (ABC, Hungary) and the other with the Spanish National Research Council partner (CSIC). Finally, collaboration within the RIBOREG project has led to the acceleration of the devel-opment of Locked Nucleic Acid (LNA) probe technology, which has allowed RIBOREG’s partner, Exiqon, to commercialise a number of products based on this technology.

In situ hybridization of miRNAs in flower tissues of

arabidopsis thaliana using different LNA probes.


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Potential Impact:RIBOREG’s work proves tremendously beneficial to researchers interested in genome min-ing and novel regulatory mechanisms, biotechnologists dealing with RNA-based product development in plants and animals, and clinicians interested in new RNA-based therapies. The project also aims to integrate the results obtained in different systems on the function of riboregulators. In this sense, RIBOREG helps SMEs concerned with developing and validat-ing tools for the analysis of this novel area of gene regulation.

In general, the dissemination of project achievements, combined with a possible pooling of resources and an active networking approach contributes to the development of skills and know-how throughout the European industrial and scientific community. The technological progress stimulated by RIBOREG’s innovative solutions also provides the foundation for en-hanced cooperation between SMEs and public institutions. In particular, SMEs are able to compare their genomic approaches for the study of non-coding RNAs, and develop market-able products specifically suited for this purpose (as was notably the case for Exiqon and the LNA technology and for BIOMEDAL and the c-LYTAG system). The validation of these technologies is an area of considerable interest for SMEs.

Keywords: non-coding RNAs, riboregulator, differentiation, disease

Project Coordinator: Dr. Martin Crespi Centre National de la RechercheScientifique (CNRS) Institut des Sciences du Végétal (UPR no 2355)Avenue de la Terrasse 191198 Gif-sur-Yvette, [email protected]

Dr. Jean-Marc Deragon, Dr. Claude ThermesCentre National de la Recherche Scientifique (CNRS) Gif–sur-Yvette, France

Dr. Jozsef Burgyan Agricultural Biotechnology Centre (ABC)Plant Biology InstituteGodollo, Hungary

Dr. Hervé VaucheretInstitut National de la Recherche Agronomique (INRA)Unité de Biologie Cellulaire Versailles, France

Prof. Javier Paz-Ares Rodriguez Consejo Superior de Investigaciones Cientificas (CSIC)Centro Nacional de BiotecnologiaMadrid, Spain

PartnersDr. Erik Antonie Cornelis Weimer Erasmus Medical Center RotterdamDepartment of Medical OncologyJosephine Nefkens Institute RMB420Rotterdam, The Netherlands

Prof. Jürgen BrosiusWestfaelische Wilhelms – UniversitaetInstitute of Experimental Pathology ZMBEMünster, Germany

Dr. Peter Mouritzen Exiqon A/SDepartment of Functional GenomicsVedbaek, Denmark

Dr. Palmiro PoltronieriBIOTECGEN SrlNovoli, Italy

Dr. Angel Cebolla RamirezBIOMEDAL S.L.Sevilla, Spain


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State-of-the-Art:Traditionally, the focus of molecular biology and biochemistry has been on DNA and pro-teins. However, important findings over the last 15 years or so, suggest that the role of small RNAs (sRNAs) in the life sciences has been significantly underestimated. In eukaryotes, sRNAs of approximately 20-25 nucleotides in length — so-called small interfering RNAs (siRNAs), and micro RNAs (miRNAs) — either induce degradation of homologous target messenger RNAs (mRNAs) by RNA interference, or inhibit their translation.A second, important class of non-coding RNAs, involved primarily in the modification of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs), is the small nucleolar RNAs (snoRNAs) of eukaryotes and archaea. There are indications that some snoRNAs act on hitherto unidentified cellular mRNAs. Equally of interest, is the high prevalence of regula-tory RNAs in bacteria. Bacterial sRNAs regulate specific functions in plasmids, phages and transposons. Bacterial chromosomes encode many non-coding RNAs, most of which ap-pear to regulate target genes by antisense mechanisms. In Escherichia coli, sRNAs control stress responses, while in Staphylococcus aureus they control virulence.

RNAs act as regulators of gene expression and also perform other activities, often aided by proteins. Creating a division between bacterial and eukaryotic systems can be detrimental for the development of a profound understanding of RNA biology. By contrast, it proves extreme-ly fruitful to bridge the gap between different experimental systems, organismic backgrounds and scientific cultures. FOSRAK aims to develop an understanding of the peculiarities of each system. Furthermore, the team plans to ascertain what the fundamental similarities are be-tween the functions of regulatory RNAs across kingdoms. Europe is currently lagging behind in the field of RNA biology, and FOSRAK intends to make headway in closing that gap.

Scientific/Technological Objectives:FOSRAK addresses the recently recognised importance of sRNAs in organisms across kingdoms, and the mechanisms of gene regulation by which they control physiological responses, developmental checkpoints and virulence in several human pathogens. The gen-eral objective is to advance knowledge of sRNAs beyond the state-of-the-art, but also, more specifically, to explore their potential for application in the prevention or treatment of human diseases.The project has several specific aims, summarised below: (1) Identification of molecular targets for various RNAs acting in gene regulation (regulatory RNAs); (2) Characterisa-tion of protein components that are part of the cellular machinery, and are involved in the functionality of small regulatory RNAs; (3) Understanding the mechanisms by which small regulatory RNAs recognise and interact with their cognate molecular targets; and (4) Deci-phering the biological role of different classes of small regulatory RNAs and their general functional significance in regulating gene expression.

Expected Results:Elucidation of the major aspects of RNA biology across kingdoms, and understanding the similarities and differences in RNA-mediated molecular mechanisms between organisms, are among the expected results of FOSRAK. During the first stage of the project, tremendous progress was made relating to the identification of experimentally validated or strongly pre-dicted targets for miRNAs, imprinted miRNAs and regulatory RNAs in protists and bacteria (non-pathogenic and pathogenic). The enzymology of proteins associated with, or required for, the functioning of regulatory RNAs, has been another focus of the project so far. For instance, the role of the Hfq protein in bacteria, the roles of Dcr, helicases, RDRs and Ago proteins in RNAi/miRNA-dependent regulation, and the role of ribonucleases in RNA me-tabolism and regulation, have proved fruitful areas of investigation.

Spontaneous systemic spreading of silencing

of a GFP (green fluorescent protein)

transgene in a Nicotiana benthamiana

leaf. Red areas indicate loss of GFP

expression.



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Potential Impact:The identification of the targets of regulatory RNAs and mechanistic studies, will have critical implications for our understanding of cellular gene expres-sion. The project also deals with the potential role of small regulatory RNAs in human diseases, research that may influence the development of RNA-based therapeutics.FOSRAK will contribute to conceptual and technological advances, such as the development of a bioinformatics platform for the prediction of sRNA targets, and the use of sophisticated instruments (e.g. scanning force microscopy and biosensors), which are not yet being used as standard methods for the analysis of RNA-RNA and RNA-protein interactions.

Keywords: regulatory RNA, non-transcriptional gene regulation, Dicer, non-coding RNA, bioinformatics, fundamental genomics, functional genomics, gene expression, structure analysis, miRNA, snoRNA

Upper left: Electron microscopy picture of Escherichia coli cells (artificially colored)Upper right: 3D model of the catalytically active hammerhead ribozymes in Arabidopsis thaliana (acc. to Przybilski et al., 2005, Plant Cell). The catalytic centre is shown in green and orange, and the tertiary interacting apical loops are in magenta.Lower left: Schematic model of antisense RNA inhibition of ri-bosome “standby” in control of a bacterial toxin (acc. to Darfeuille et al., 2007, Mol. Cell).Lower right: Example of a lead(II) probing experiment; binding of a complementary RNA to its target site results in a “footprint” on the 5’-end-labeled mRNA (two right-hand lanes).

PartnersProject Coordinator:Prof. E.Gerhart WagnerUppsala UniversityDepartment of Cell and Molecular BiologyBiomedical CenterHusargatan 575124 Uppsala, [email protected]

Prof. Wolfgang Nellen,Christian HammannUniversität KasselFaculty of Natural SciencesInstitute of BiologyLaboratory of GeneticsKassel, Germany

Dr. Martina PaulsenUniversität des SaarlandesFR 8.3 BiowissenschaftenGenetik / EpigenetikSaarbrücken, Germany

Dr. Pascale RombyCentre National de la Recherche Scientifique (CNRS)UPR 9002 CNRS-SMBMR “Structure des Macromolecules et Mecanismes de Reconnaissance Moleculaire”Institut de Biologie Moleculaire et CellulaireStrasbourg, France

Dr. Fredrik SöderbomSwedish University of Agricultural SciencesDepartment of Molecular BiologyUppsala, Sweden

Prof. Martin Tabler †, Dr. Kriton KalantidisFoundation for Research and Technology - HellasRNA laboratoryHeraklion, Greece

Dr. Michael WasseneggerRLP AgroScience GmbH,AIPlanta-Institute for Plant Research Gene Silencing and EpigeneticsNeustadt/Weinstrasse, Germany

Prof. Witold FilipowiczFriedrich Miescher Institute for Biomedical ResearchBasel, Switzerland

Dr. Bastian ZimmermannBiaffin GmbH & Co KGFaculty of Natural SciencesInstitute of BiologyKassel, Germany


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State-of-the-Art:In addition to the protein-encoding messenger RNA (mRNA), genome transcription gener-ates a flurry of so-called non-coding RNA genes, including ribosomal RNAs, transfer RNAs, small nuclear and small nucleolar RNAs (snRNAs and snoRNAs respectively). This family has recently witnessed a spectacular expansion, with the discovery of a multitude of small RNA species that are involved in RNA interference-related biology (including micro RNAs, or miRNAs), and long, non-coding RNA species of unknown function.The aim of Callimir is to decipher the biological role of non-coding RNA genes by studying the imprinted Dlk1-Gtl2 domain, due to this domain possessing one of the highest densities of miRNAs in the mammalian genome. The region contains several long, non-coding RNA genes exclusively expressed by the maternal allele, which are the hosts of a very large number of snoRNAs and miRNAs. A series of unique genetic mutants will permit the study of these non-coding RNAs.

Scientific/Technological Objectives:The Dlk1-Gtl2 domain is an evolutionarily con-served, 1 megabase cluster of imprinted genes that contains at least three protein-encoding genes ex-pressed by the paternal allele (Dlk1, Rtl1, Dio3), a series of non-coding RNA genes expressed by the maternal allele (Gtl2, Meg8, Mirg), and multiple, small, non-coding RNA genes. The latter include a pair of miRNA genes (mir127 and mir136) that are antisense to Rtl1, a cluster of snoRNA genes processed from the introns of Meg8, and a cluster of miRNA genes processed from a large precursor transcript (Mirg). Callimir intends to analyse the biological function of miRNA in Mirg, and the role of Mirg miRNAs in mediating the CLPG trans effect. Callimir aims to elucidate the function and mode of action of these miRNA genes, by studying the nature of their interaction and the consequences of

their elimination. Due to an existing battery of unique reagents already available or generated as part of the project, the con-sortium is well-equipped to determine the role of mir127 and mir136 in regulating the expression of Rtl1, and to analyse the developmental roles of Rtl1 and mir127/136.

Expected Results: There have been several major achievements within the project’s first year:1) For the first time, there has been demonstration of the role of miRNA-mediated RNA interference in regulating imprinted genes.2) Using multicolour RNA FISH at the single nucleus level, there has been demonstration that non-coding RNAs transcribed from the Dlk1-Gtl2 domain form large elongated ‘nuclear track’ structures, and accumulate as single-molecule nuclear RNA foci within the interchromatin space.

Schematic representation of the Dlk1-Gtl2 imprinted domain:Key elements are depicted: paternally expressed genes in

blue, maternally expressed non coding RNA, including clusters of snoRNA and miRNA in red, localization of two regulatory

elements, the callipyge mutation (yellow dot) and the intergenic differentially methylated region (IG-DMR, black dot when

methylated, white dot when unmethylated).Brackets and numbers represent animal models currently

analysed: [1] the callipyge sheep (left picture) and two transgenic mice lines for this mutation; [2] a

mouse model with a deletion of the IG-DMR; [3] several mouse models targeting each miRNA of

the antiPeg11 gene as well as introducing a stop codon in the Rtl1/Peg11 gene; [4] a mouse model carrying a conditional deletion of the entire miRNA

cluster in Mirg.


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3) A comparative evolutionary analysis identified the origin and identity of members of the Rtl1/Peg11 gene family in the mammalian genome. The hypothesis that this retrotransposon-like gene plays a role in conferring imprinting was tested and dis-proved.

4) By studying a muscular hypertrophy in sheep, the Callimir consortium has identified an important novel class of mutations that affect the interaction between miRNAs and their targets. Bioinformatics analyses of SNPs databases for human and mice has demonstrat-ed that mutations creating or destroying putative miRNA target sites are abundant, and might be important effectors of phenotypic variation. A publicly accessible database with this information compiled on it, has been created - http://www.patrocles.org/

Potential Impact:Callimir is studying fundamental biological mechanisms related to the role and mode of action of miRNAs. It has been demonstrated recently that miRNAs regulate as much as a third of our genes, if not more. Hence miRNAs play a key role in orchestrating and fine-tuning mammalian gene expression, and perturbation of miRNA-mediated gene regulation contributes to disease.

The Callimir consortium has unique genetic models, either created by genetic engineering or discovered as naturally-occurring oddities, which express mutations that perturb miRNA-mediated gene regulation, causing complex phenotypes. These models will allow the study of the mechanisms of miRNA-mediated gene regulation in vivo. In addition, the Patrocles database, which compiles mutations that have the potential to perturb miRNA-target interac-tions and hence gene regulation, in a variety of species including man and mouse, will be of benefit to the genetics community at large.

Keywords: micro RNA, sno RNA, imprinting, callipyge

Project Co-Coordinators:Dr. Michel Georges,Dr. Carole CharlierUniversity of LiègeUnit of Animal GenomicsFaculty of Veterinary Medicine1 Avenue de l’Hôpital4000 Liège, [email protected]@ulg.ac.be

Dr. Jérôme CavailléCentre National de la RechercheScientifique (CNRS)Laboratoire de Biologie Moléculairedes EucaryotesUMR 5099Toulouse, France

PartnersProf. Anne Ferguson-SmithUniversity of CambridgeDepartment of PhysiologyDevelopment & NeuroscienceCambridge, UK


Studying the biological role of microRNAs in the Dlk1-Gtl2 imprinted domain


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State-of-the-Art: The rationale behind the sequencing of the human genome and that of other model organ-isms stemmed from the assumption that, by knowing the content of the genetic material, it would be possible to understand the processes that control development and reproduction in living organisms. This would consequently lead to better insights into how these processes are altered in disease.

The concept of the gene is central for the understanding of these issues. The “dogma” of molecular biology has classically treated a gene, as a genetic unit directing the synthesis of a single protein product. From this perspective, the genetic program of an organism is dic-tated by the subset of genes transcribed into RNA and translated into protein in a particular cell or at a particular time during development.

One of the most surprising results of the human genome project and of similar projects on other metazoan genomes was the surprisingly low number of protein-coding genes found. A dramatic gap was noted between the possibly only 25 000 protein-coding genes and the observed huge diversity of the human proteome, that is, the complete spectrum of all expressed protein forms in the cell. This figure has to be placed at least in the order of 100 000 proteins. The “missing diversity” on the DNA level is compensated for by the alternative mRNA-splicing mechanism. This posttranscriptional event affects most human genes and is responsible for the creation of potentially thousands of distinct proteins from a single gene.

A eukaryotic gene encoding the message used for the production of a protein during trans-lation is composed of various DNA segments: protein coding exons alternate with DNA sequences that do not carry a protein coding function (introns). During the first step of gene expression, DNA is transcribed into messenger RNA (mRNA). While the primary RNA tran-

Schematic overview of the gene-expression pathway in eukaryo-

tic organisms. The genome is located in the cellular nucleus

where it is transcribed and the pre-mRNA is formed. After

several RNA processing steps (including splicing) the mature

mRNA is transported to the cytoplasm where protein produc-

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script still contains both the exonic and the intronic sequences, only a mature mRNA without intronic sequences can serve as a template for ribosomal protein synthesis. The process which removes the introns from the primary mRNA transcript is called pre-mRNA splicing. Introns are excised and the remaining exons are joined to form a continuous stretch of protein-coding sequence.

Pre-mRNA splicing not merely removes introns, it also serves as a unique mechanism to create pro-tein diversity. During the splicing process not all of the exons are retained in the mature mRNA, some exons are either included or excluded, the inclu-sion of exons can be mutually exclusive, and for other exons there exists a large set of variants of which only one is selected for inclusion. By employing such a combinatorial approach, alternative splicing creates a variety of distinct proteins from one single gene. Protein variants (isoforms) thus created often have distinct and often antagonistic functions.

Consequently, alternative splicing can greatly expand the information content of genom-es, and understanding the mechanisms that lead to alternatively spliced transcripts will be essential for a functional interpretation of genomic sequences. We will not be able to decipher the genetic program of a higher eukaryotic genome unless we understand the rules leading to the generation of alternatively spliced transcripts and the functional diversity they provide.

The splicing reaction is catalyzed in the cell nucleus by a highly complex molecular ma-chine, the spliceosome. The spliceosome is an RNP (for ribonucleoprotein) machine com-posed of several RNAs and numerous proteins organized in several distinct subcomplexes which are themselves RNP particles. A plethora of highly dynamic RNA-RNA, RNA-protein and protein-protein interactions holds together this intricate mechanism. The recognition and selection of the intron-exon borders (that is the substrates of the splicing reaction), the assembly of the spliceosome and the structural and functional remodelling the spliceosome undergoes during the course of the splicing reaction, are all part of an extraordinarily com-plicated process.

It is therefore not surprising that alternative splicing during recent years has been in-creasingly recognized as the causative agent or as a severity modifier behind an ever increasing number of human pathologies, including cancer, neurodegenerative diseases, viral infection and inflammatory responses. Current conservative estimates assume that more than 15% of genetic diseases are caused by aberrant splice events. Our current understanding of alternative splice events still lacks sufficient insight into the molecular mechanisms of the combinatorial action of multiple regulators that govern splice site selec-tion. Also the interplay between alternative splicing and other cellular processes requires enhanced research efforts.

Thirty leading laboratories in the field of pre-mRNA splicing and splicing regulation have joined efforts to create a Network of Excellence. These groups cover a wide range of complementary expertise including computational, biochemical, proteomic, genomic, cell-biological and organism-biological approaches to the study of post-transcriptional gene regulation and its alterations in disease.

Alternative splicing dramatically increases the complexity of the proteome.


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The primary purpose of this network will be to develop an integrated approach to the study of alternative splicing that will (1) provide durable structures that will change the way re-search in this research topic is carried out in Europe, (2) establish an ambitious, innovative and multidisciplinary program of joint research activities with high impact, and (3) spread excellence within Europe, disseminate knowledge about alternative splicing in the molecu-lar biology and medical communities, and foster public awareness of genomics and RNA research and their applications.

Scientific/Technological Objectives: EURASNET aims not only to improve our knowledge of alternative splicing but also to raise awareness on alternative splicing related issues, particularly in the health science community.

Mis-splicing and disease: The Joint Program of Research has a strong focus on alternative splicing events and regulatory mechanisms related to genetic disease or influencing disease progression. Our understand-ing of signals involved in the mis-regulation of splice events is incomplete. Moreover, their often elusive nature as mutations not resulting in obvious amino acid changes complicates diagnostics and therapeutic strategies of aberrant splicing. Regulatory splicing factors and their disease-dependent changes in abundance and tissue-specific concentration will be scru-tinized.

Data on particular diseases is still too sparse and, in order to establish the concept of “RNA and Disease”, a wide range of diseases needs to be surveyed. Deciphering the regulatory networks of cell-type specific alternative splicing, governed by expression and regulation of splicing factors and their isoforms associated with a particular pathology, poses a problem addressable through the concepts and tools of systems biology. In parallel therapeutic strate-gies to correct splicing defects will be developed.

Development of High-Throughput-Enabling Technologies: Another important Network activity comprises development and application of High-Through-put-Enabling Technologies for the study of alternative splicing, in particular of microarrays for the detection of alternative splice forms and the screening of small chemical compound libraries. Most of the currently available microarray designs ignore the fact that the majority of genes in higher eukaryotes generates multiple mRNAs that encode proteins with distinct, sometimes opposite functions. Therefore results from such designs are at best incomplete, if not misleading. Analyzing the full complement of cellular transcripts under different biological or pathological conditions requires microarray platforms able to distinguish between alterna-tively spliced mRNAs. EURASNET envisions the task of establishing these microarrays as one of the key contributions of EURASNET to European scientists, regardless of whether they are in the splicing field or not, and to the clinicians.

A second Network effort is directed towards high-throughput identification of compounds that inhibit or modulate specifically the splicing reaction. An initial explorative phase will comprise the development of an assay with suitable fluorescence readout for screening purposes and the screening of small to medium-sized chemical libraries. Selecting appropriate target reac-tions and the right class of chemical compound are then preconditions for large-scale screen-ing. While exhaustive screens for compounds useful as therapeutic agent for specific splicing defects associated with a human disease are clearly beyond the scope of this Network, the validation of the general screening strategy will help to raise interest among potential com-mercial partners to engage in further collaborative studies.

The alternative splicing databaseEURASNET research requires close communication and joint activities between computer biologists and experimentalists. The mere task of accurate intron identification in eukaryotic

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genomes still poses a considerable challenge. Even more so the prediction, which potentially alternatively spliced mRNA will appear in which tissue and under what conditions. The ex-ploding number of mRNA and EST sequences and high-throughput enabling technologies producing large data sets of transcripts, their structure, abundance, tissue distribution and developmental specificity, require a strong bioinformatics infrastructure to secure the acquisi-tion of quality data in user-friendly databases and to ensure efficient data analysis which in the long run wants to become a highly predictive analysis of splice signals and regulatory elements.

The Young Investigator ProgramAs part of the Network’s integration activities, young investigators and their research will be integrated.

Expected Results: As the outcome of EURASNET research activities the team expects: i) a significant number of important publications (estimated 150 publications in the five years period) ii) a several-fold increase in high impact joint publications by members of the network iii) the develop-ment and optimization of experimental designs and technological platforms applicable to studies of alternative splicing in a variety experimental systems. In particular, standards for High-Throughput technologies like microarrays and small-compound screening will be de-veloped. iv) the development of user-friendly software of high predictive power to support the experimental design of experimentalists.

Potential Impact: The ambitious, innovative and multidisciplinary Joint Programme of activities of EURASNET will give a massive impetus to progress in elucidating the mechanisms of alternative splic-ing and will thus greatly enhance the scientific community’s understanding of one of the most important steps in the expression of genetic information. Insights into this process are a prerequisite for allowing us to decipher, and ultimately to predict, the genetic program of eukaryotic genomes. EURASNET and its Young Investigator Program (YIP) will also play an important role in making Europe attractive for young and talented scientists in the field. Moreover, it will ensure their integration into the “alternative splicing” community and, on account of the importance of this field today, it will in turn make a significant contribution to the spread of sustained excellence within European life sciences.

The information generated from the activities of this NoE can realistically be expected to have a significant impact, not only on the academic research community, but also on the industri-al research and medical communities. Further, developments resulting from the information generated by EURASNET will form an important knowledge base that ultimately will aid public policy makers in making decisions that will shape the socio-economic future of our society. Efforts by EURASNET will also contribute to the enhancement of public awareness of genomics and RNA research, with corresponding indirect benefits to society as a whole. EURASNET represents a con-sortium of many of the world’s best laboratories investigating the process of alternative splicing and its implications for hu-man health.

Keywords: alternative RNA splicing, RNA splicing

Transcribed genes localize in close proximity two nuclear speckles

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Project Coordinator:Prof. Reinhard LührmannMax-Planck Institute for Biophysical Chemistry Department of Cellular BiochemistryAm Fassberg 1137077 Göttingen, [email protected]

Project Manager:Dr. Reinhard RauhutMax-Planck Institute for Biophysical ChemistryDepartment of Cellular BiochemistryAm Fassberg 1137077 Göttingen, [email protected]

Dr. Karla NeugebauerMax-Planck Institute of Molecular Cell Biology and GeneticsDresden, Germany

Dr. Henning UrlaubMax-Planck Institute for Biophysical ChemistryGöttingen, Germany

Dr. Juan ValcárcelCentre de Regulació GenòmicaRegulation of Alternative Pre-mRNA SplicingBarcelona, Spain

Prof. Stefan StammFriedrich-Alexander-Universität Erlangen-NürnbergInstitute for BiochemistryErlangen, Germany

Prof. Göran AkusjärviUppsala UniversityDepartment of Medical Biochemistry and Microbiology (IMBIM)Faculties of Medicine and PharmacologyUppsala, Sweden

Dr. Peer BorkEuropean Molecular Biology Laboratory (EMBL)Structural and Computational Biology ProgrammeHeidelberg, Germany

Dr. Rolf Apweiler,European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Sequence Database Group Hinxton, UK

Dr. Gil AstTel Aviv UniversityDepartment of Human GeneticsTel Aviv, Israel

Prof. Francisco E. BaralleInternational Centre for Genetic Engineeringand BiotechnologyMolecular Pathology GroupTrieste, Italy

Prof. Andrea BartaMedical University ViennaDepartment of Medical BiochemistryVienna, Austria

Prof. Jean BeggsUniversity of EdinburghInstitute of Cell BiologyEdinburgh, UK

Dr. Giuseppe BiamontiConsiglio Nazionale delle Ricerche (CNR)Istituto di Genetica MolecolarePavia, Italy

Prof. Glauco Tocchini-ValentiniConsiglio Nazionale delle Ricerche (CNR)Istituto di Biologia CellulareMonterotondo Scalo, Italy

Prof. Albrecht BindereifJustus Liebig Universität GiessenInstitut für BiochemieGiessen, Germany

Prof. Jamal Tazi, Dr. Edouard BertrandCentre National de la Recherche Scientifique (CNRS)Institut de Genetique Moleculaire(JRU 5535 CNRS-UMII)Montpellier, France

Dr. Bertrand Séraphin Centre National de la Recherche Scientifique (CNRS)Centre de Genetique Moleculaire (CGM), UPR2167 Gif-sur-Yvette, France

Dr. Christiane BranlantCentre National de la Recherche Scientifique (CNRS)UMR 7567 CNRS-UHPMaturation des ARN et Enzymologie Moléculaire MAEM Vandoeuvre les Nancy, France

Prof. Daniel SchümperliUniversität BernInstitut für ZellbiologieBern, Switzerland

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Dr. John W.S. BrownScottish Crop Research InstituteGene Expression Programme - RNA Processing LabDundee, UK

Dr. Javier Fernando CáceresMedical Research CouncilMRC Human Genetics UnitEdinburgh, UK

Prof. Maria Carmo-FonsecaInstituto de Medicina MolecularCell Biology UnitLisbon, Portugal

Prof. Ian EperonUniversity of LeicesterDepartment of BiochemistryLeicester, UK

Prof. Artur JarmolowskiAdam Mickiewicz University in PoznanDepartment of Gene Expression / Institute ofMolecular Biology and Biotechnology (IMBB)Poznan, Poland

Prof. Jørgen KjemsUniversity of AarhusDepartment of Molecular BiologyAarhus, Denmark

Prof. Alberto R. KornblihttUniversidad de Buenos AiresDepartamento de FisiolgíaBiología Molecular y CelularBuenos Aires, Argentina

Prof. Angela KrämerUniversité de GenèveDépartement de Biologie CellulaireGeneva 4, Switzerland

Prof. Angus LamondUniversity of DundeeDivision of Gene Regulation & ExpressionSchool of Life SciencesDundee, UK

Dr. Christopher SmithUniversity of CambridgeDepartment of BiochemistryCambridge, UK

Prof. Hermona SoreqHebrew University of JerusalemDepartment of Biological Chemistry Institute of Life SciencesJerusalem, Israel Dr. James StéveninCentre Européen de Recherche en Biologie et Médecine – GIEInstitut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)Illkirch, France

Dr. Didier AuboeufInstitut National de la Santé et de la Recherche (INSERM)AVENIR/Inserm U685 Centre Hayem-Hôpital Saint LouisParis, France

Dr. Davide GabelliniFondazione Centro San Raffaele del Monte TaborMilan, Italy

Dr. Mihaela ZavolanBiozentrum, University of BaselISB-SIB RNA Regulatory Networks GroupBasel, Switzerland


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State-of-the-Art:From being regarded as a minor class of RNAs, non-coding RNAs (ncRNAs - mostly an-tisense RNAs) have recently emerged as ubiquitous players in important life processes in animals, plants, fungi and metazoans. Similarly, over 85 small ncRNAs, encoded by the Escherichia coli genome, have recently been identified, while others are being discovered in many bacterial species. Many of these RNAs play key roles in global regulatory net-works. The BACRNAs consortium investigates novel ncRNAs and their targets (messenger RNA (mRNA) and proteins) in several representative pathogens and analyses their roles in the establishment of bacterial pathogenicity. Infection studies using cell cultures will allow the validation of ncRNAs and their targets in virulence. Exploration of structural and mecha-nistic aspects of ncRNAs will elucidate how they interact with those targets. This research will lead to an understanding of how regulatory ncRNAs are integrated into the general network that controls stress responses, host adaptation and bacterial virulence.

Scientific/Technological Objectives:1) Many non-coding RNAs act as antisense RNAs, via a base-pairing mechanism, where-

as sensor elements, mostly located in the 5’ untranslated region (UTR) of mRNA, can act as ‘riboswitches’. The consortium focuses mainly on ncRNAs that belong to these two classes, and that are implicated in the regulatory networks controlling bacterial pathogenicity. It develops tools for the identification, characterisation and structural analysis of ncRNAs in pathogenic bacteria, as well as for the identification and vali-dation of targets (virulence factors) controlled by ncRNAs involved in virulence.

2) Current studies have reported a growing number of small RNAs, including ncRNAs that play key roles in the regulation of fundamental adaptive processes such as cell-to-cell communication (quorum sensing), transition to the stationary phase, iron homeostasis and bacterial virulence. The BACRNAs project aims to elucidate how regulatory RNAs are integrated into the general network of pathogenesis control whilst also taking into account other mechanisms such as response and adaptation to bacterial stress or changing environment.

3) The determination of the most relevant virulence factors amenable to drug develop-ment is the concluding step within the present BACRNAs project. The relevance to drug development is determined by the ability of small molecules to bind virulence factors. These small molecules (compounds) on one hand are needed to verify the functionality and on the other the modification ability of identified virulence factors. The outcome describes the prove-of-concept and builds the basis for further drug development by the pharmaceutical industry. Therefore the analysis of the virulence mechanism that is triggered by ncRNAs, as well as the expression/regulation of virulence factor and its influence to pathogenicity needs to be investigated by the consortium. Further information on drug design will be guided by structural informa-tion provided by nuclear magnetic resonance techniques.

Expected Results:The consortium expects to see the following results: (1) Development of tools for the identifi-cation/analysis of ncRNAs involved in bacterial pathogenicity; (2) Identification of ncRNAs


BACRNAs

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018618Starting date:1st February 2006Duration:36 monthsEC Funding:

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involved in bacterial pathogenicity; (3) Identification of targets (virulence factors) controlled by ncRNAs involved in virulence; (4) Identification of the structure of the ncRNAs as well as the regulatory mechanisms of ncRNAs involved in bacterial pathogenicity and (5) Valida-tion of novel targets for therapy and initial identification of compounds that interfere with the function of those targets.

Potential Impact:The project has set its sights on facilitating the establishment of European leadership in the innovative field of regulatory RNAs. It aims to generate fundamental knowledge that can be translated directly into new therapeutic strategies. The identification of novel drug targets builds the basis to develop new drugs and thus to combat widespread bacterial infections.

Keywords: antisense RNA, non-coding RNA, biochemistry, antimicrobial agents, regulatory networks, bacterial virulence

Partners


Non-coding RNAsin Bacterial Pathogenicity

Project Coordinator:Prof. Renée SchroederUniversity of ViennaDepartment of Biochemistry“Max F. Perutz Laboratories”Dr Bohr Gasse 9/51010 Vienna, [email protected]

Dr. Pascale RombyCentre National de la Recherche Scientifique (CNRS)UPR 9002 CNRS-ARN “Architecture et réactivité des ARN”Strasbourg, France

Prof. Pascale CossartInstitut Pasteur Unité des Interactions Bactéries-CellulesParis, France

Prof. Gerhart WagnerUppsala UniversityDepartment of Cell and MolecularBiology (ICM), Biomedical Center Uppsala, Sweden

Dr. Jörgen JohanssonUmeå UniversityDepartment of Molecular Biology Umeå, Sweden

Dr. Shoshy AltuviaHebrew University of JerusalemInstitute for MicrobiologyJerusalem, Israel

Ms Brigitte RohnerBrigitte Rohner punktVienna, Austria



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State-of-the-Art: RNA molecules such as microRNAs, riboswitches, or regulatory RNAs in bacteria (broadly called noncoding RNAs or ncRNAs) have become extremely active areas of research in basic science such as cell development, cancer and therapeutic research. The prediction of the secondary structure of an RNA molecule is the most extensively studied aspect in com-putational methods for ncRNAs. Despite this, the accuracy in predicting secondary structure is limited (56 to 76 percent). Alternatives to standard models are probabilistic models, the systematic use of comparative analysis, and the incorporation of known 3D structures. RNA bioinformatics is now following two paths.

The first is structure-based analyses in which three-dimensional structures are central. The second is sequence-based analyses in which sequence and sequence recognition dominate the analysis. These two paths are running parallel courses at the moment, but they will soon converge. This must occur if scientists are to fully understand RNA evolution and the relationships between sequence, structural folding and reactivity. Science is now facing new challenges in trying to identify the function of these ncRNAs. For this to happen, it is necessary to refine the algorithms involved so that structures can be systematically searched in genomes and reliably predicted. The result will be that homology searches for ncRNAs can take into account the overall structure, alignment algorithms for RNA structure and will be fast enough to search whole databases.

Scientific/Technological Objectives: A workshop entitled ``Computational approaches to noncoding RNAs’’ and organized by Elena Rivas (Washington University, USA) and Eric Westhof (University Louis Pasteur, France) was held in Benasque (Spain) from the 16th of July to the 28th of July 2006. It gath-ered a group of 55 researchers mostly theoreticians and computational scientists working on problems related to the computational analysis of functional and regulatory RNAs.

The main objectives of the RNABIO workshop were:

1) To present and discuss the state of RNA computational biology, to identify the needs and to propose new developments for the identification, annotation and the computa-tional analysis of functional and regulatory RNAs present in genomes.

2) To try to identify the function of ncRNAs. In order to do this it is necessary to refine al-gorithms in order to perform structure predictions reliably and do research on ncRNAs that take into account the structure and alignment algorithms for RNA structures and are fast enough to search whole databases. This permits, for instance, the alignment of thousands of ribosomal RNA molecules.

3) To identify new ncRNAs, which may lead to novel regulator mechanisms.4) For biologists working on RNA to make reliable annotations of eukaryotic genomes. 5) To make grammatical models to describe RNAs, to provide more information on the

parameters of the models, along with more complex objective functions to describe the nature of a functional RNA.

6) The development of improved methods for the efficient classification of short RNAs (using techniques such as support vector machines).

7) To create statistical modelling of new high throughput data in the RNA context.8) To relate genome location of small RNAs to RNA type (eg through characterising

clustering behaviour).


RNABIO

Project Type:Specific Support ActionContract number:LSSG-CT-2006-037604Starting date:1st July 2006Duration:4 monthsEC Funding:

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Project Coordinator:Prof Eric Westhof Centre National De La Recherche Scientifique (CNRS)Université Louis PasteurInstitut de biologie moléculaire et cellulaireARN ‘Architecture et Réactivité de l’ARN’15 Rue Rene DescartesF-67084 Strasbourg, [email protected]

Partners

Expected Results: One major problem with ncRNA prediction has been that they require substantially more com-puter time than the methods employed for more traditional protein coding gene finding, which can exploit much more regular search patterns. However, the recent progress in ncRNA gene discovery promises to reduce search time significantly.

Secondary structures predicted by various methods are at variance with the fact that RNAs are three-dimensional molecules. Thus, basepairing can be impossible due to steric clashes. An at-tempt to approach this problem is currently being planned. The result will be the incorporation of a model for the RNA backbone, using directional statistics, into the secondary structure predic-tion. This should weed out impossible structures and could, in time, be extended to do ab initio 3D prediction of RNA structures. The data produced on RNA is made freely available without restrictions through web pages and database downloads. The computational RNA community already makes heavy use of Rfam data as training and testing sets for developing algorithms. Both RNA databases, Rfam and miRBase are heavily used by genome annotation projects, and miRBase is central to the rapid growth and progress of microRNA research. One of the expected results of the project is to make such resources far more community oriented by hosting diverse data types on the database. The RNA bioinformatics community are immensely supportive and the RNABIO workshop proved to be very efficient at generating and maintaining ideas and collaborations to this end.

Potential Impact:Now, several groups, especially in Europe, have been involved in developing computational methods which seek simultaneously to align and fold two or more RNA sequences while screening - eg two genomes or matching up regions with low sequence similarity. The major outcome was to valuate the state of RNA computational biology, to identify the needs, and to propose new developments for the identifi-cation, annotation, and the computational analysis of functional and regulatory RNAs present in genomes. The long- term goal of applying such methods is to help identify ncRNA genes or structural elements, which will have an important impact on phenotypes, diseases and production traits in domestic animals.

Keywords: microRNAs, riboswitches, noncoding RNAs


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State-of-the-Art:RNA silencing is the natural ability of a cell to turn off genes. Only a few years ago it was unknown, but now RNA silencing is one of the most powerful tools available to researchers. Recent discoveries have revealed a previously unknown role for RNA (ribonucleic acid). They have shown how, in addition to the previously understood role as a cellular messenger that directs protein synthesis, RNA can also silence expression of genes. By introducing specific silencing RNAs into an organism, the expression of genes can be turned down in a controlled way. The phenomenon of RNA silencing is thought to have evolved as a defence mechanism against viruses. In primitive cells it was a type of immune system that could recognize and then silence viral genes. Later in evolution the silencing mechanism was recruited for switching off genes involved in normal growth of cells and responses to stress. Small regulatory RNAs (sR-

NAs) are the mediators of RNA silencing and are important integrators of genetic, epigenetic and other regulatory systems. They are the focus of the SIROCCO programme. sRNAs have been referred to as the dark matter of ge-netics: a recently discov-ered mass of molecules that crucially affect the behaviour of the genetic universe through interac-tions at the RNA level. The exploitation of sRNAs offers many opportunities for improving the diagno-sis and therapy of human disease and for advances in biotechnology.

sRNAs fall into two major classes: i) short interfering RNAs (siRNAs) which are 21-24 nucle-otide RNAs derived from long double-stranded RNA and ii)microRNAs (miRNAs) which are derived from transcripts containing partially double-stranded stem-loop “hairpin” structures about 70 nucleotides long. Both are cleaved from their precursor RNA by double stranded RNA-specific endonucleases. One strand of the resulting small RNA is loaded into RNA-induced silencing complex (RISC) that also contains Argonaute (AGO) proteins. Binding to the correct Argonaute protein is necessary for cleavage of the target messenger RNA. siRNAs and miRNAs have been found in a variety of organisms including plants, fruit flies, zebrafish, mice, and humans. sRNAs are also a useful tool in the laboratory, where they can be used to silence gene expression (RNA interference).

Scientific/Technological Objectives:The overall objectives of the SIROCCO project are:

1) Create catalogues of sRNAs from healthy and diseased cells. Novel sRNAs will

Secondary siRNA production in plants and animals. Baulcombe DC Amplified silencing Science

2007 Jan 12;315(5809): 199-200.


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be identified through using a combination of bioinformatics and high throughput se-quencing.

2) Determine the tissue- and cell-type pattern of miRNA expression using microarray, RNA blot and in situ hybridisation methods

3) Fully refine methods for sRNA detection. These detection methods will be enhanced using locked nucleic acid-containing and other oligonucleotide probes, and by modi-fied PCR methods.

4) Characterise proteins and subcellular com-partments required for sRNA processing and activity. At present, there is a foundation of knowledge about miRNAs, but very little is known about siRNAs. Genetic, biochemi-cal and imaging approaches will be used to fully characterise the molecular machines responsible for both miRNA and siRNA bio-genesis

5) Dissect sRNA regulatory networks. It is known that miRNAs may affect particular target mRNAs but how their activity fits into more complex regulatory networks is poorly understood. Developing this understanding is one of the major objectives of the SIROC-CO programme.

6) Identify rules for sRNA efficiency and spe-cificity. The RNA-silencing efficiency of sR-NAs will be determined by assay of sRNAs, their precursors or their DNA in transgenic organisms, in cell cultures or in vitro

7) Explore delivery methods for sRNAs or sRNA precursors.

Efficient use of sRNAs as pharmaceuticals will depend on the development of methods for their efficient delivery into cells and animals. Current technology uses modified viruses to introduce siRNAs into cells to reduce expression of a target gene. In the later stages of the project, the SIROCCO consortium will initiate research into the suppression of genes impli-cated in various diseases.The mechanism of RNA silencing must be thoroughly understood in order to use RNA as a drug without side effects. It is also necessary to understand more about the role of silencing RNAs in normal growth and development. That information will then allow us to use the presence of silencing RNAs to diagnose disease states in a cell.

Expected Results:The SIROCCO consortium will investigate the stages in growth, development and disease that are influenced by sRNAs. The project can be considered to have three overlapping phases. The first is descriptive and will continue throughout the programme. This phase aims to describe the full complement of sRNAs in a range of organisms and cell types and

FIGURE 1: Somite-specific expression of miR-206. Mouse embryo (E10.5) was hybridised to an LNA oligonucleotides complementary to miR-206. The blue staining indicates the very specific accumulation of miR-206 in the somites.Wheeler G, Valoczi A, Havelda Z, Dalmay T. In situ detection of animal and plant microRNAs.DNA Cell Biol. 2007 Apr;26(4):251-5.

FIGURE 2: RNA silencing of a green fluorescent protein. The red areas illustrate how a signal of silencing is spreading out of the veins in a leaf of Nicotiana benthamiana. Eventually the signal spreads throughout the plant.

Fig.1

Fig.2


Silencing RNAs:organisers and coordinators

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correspondingly to develop a complete understanding of the proteins that act as enzymes, co-factors and structural components of the sRNA machinery.

The second phase involves testing the function of sRNAs and sRNA-related proteins in the basic sRNA mechanisms, and eventually establishing their role in regulatory networks through experimental intervention. Genetic and molecular methods will be used to manipu-late the expression of these components, while biological assays and molecular profiling of RNA will be used to assess the role of the targeting components.

In the third, predictive phase of the programme, the aim will be to develop rules to describe the behaviour of sRNA systems as isolated regulatory modules and as part of complex regulatory networks. Component activities in this phase will involve the computation of rules and their validation by experimentation. It will be possible from this phase to design sRNA mimics of natural sRNAs, and to predict their effects in cells and organisms. It will also be possible to predict the behaviour of cells or organisms in which the sRNA machinery is regulated by developmental or external stimuli.

Potential Impact:RNA silencing technology has enormous potential for use as a therapeutic agent in the treatment of infectious diseases and for any condition involving the mis-regulation of gene expression. It is known that different microRNAs can function as tumour suppressors or on-cogenes and that their expression levels have diagnostic and prognostic significance. The role of small RNAs in complex neuropathological disorders such as schizophrenia and in neurodegenerative conditions such as Alzheimer’s Disease is being investigated by mem-bers of the SIROCCO consortium. Diagnostic or therapeutic advances in these areas would have powerful public health implications.

The SIROCCO consortium aims to understand and exploit the diversity of sRNA mecha-nisms. The elucidation of the genomics of sRNA and of sRNA-based regulation will lead to novel and fundamental insights into the composite genetic networks that underlie nor-mal and diseased growth and development. Achieving these aims will reinforce European competitiveness in fundamental research and innovation and will solve important societal problems relating to public health by improving diagnosis and treatment of diseases.

Keywords:

RNA silencing, microRNA, RNA interference, short interfering RNA, developmental biol-ogy, molecular biology, gene expression

Project Coordinator:Prof. David BaulcombeThe Sainsbury LaboratoryJohn Innes CentreNorwich, NR4 7UH, [email protected]

Project Manager:Dr. Aileen HoganThe Sainsbury LaboratoryJohn Innes CentreNorwich, NR4 7UH, [email protected]

Dr. József BurgyánAgricultural Biotechnology Centre Institute of Plant Biology, Molecular Virology GroupGodollo, Hungary

Partners


SIROCCO




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Dr. Annick Harel-BellanCentre National de la Recherche Scientifique (CNRS)FRE 2944 - Epigenetique et cancerInstitut André LwoffVillejuif, France

Dr. Olivier VoinnetCentre National de la Recherche Scientifique (CNRS)UPR 2357Institut de Biologie Moléculaire des PlantesStrasbourg, France

Prof. Witold FilipowiczFriedrich Miescher Institute for Biomedical ResearchBasel, Switzerland

Dr. René KettingNetherlands Institute for Developmental BiologyHubrecht LaboratoryUtrecht, The Netherlands

Dr. Detlef Weigel, Dr. Elisa IzaurraldeMax-Planck Institute for Developmental BiologyTübingen, Germany

Dr. Gunter MeisterMax-Planck Institute for BiochemistryLaboratory for RNA BiologyMartinsried, Germany

Prof. Thomas MeyerMax-Planck Institute for Infection BiologyBerlin, Germany

Dr. Gyorgy Hutvagner, Dr. Simon Arthur University of DundeeDundee, UK

Dr. Tamas DalmayUniversity of East AngliaSchool of Biological Sciences Norwich, UK

Prof. Irene Bozzoni. Prof Giuseppe MacinoUniversity of Rome ‘La Sapienza’Rome, Italy

Dr. Eric MiskaUniversity of CambridgeWellcome Trust/Cancer Research UK Gurdon Institute Cambridge, UK

Prof. Roberto Di LauroBIOGEM Biotecnologie Avanzate s.c.a r.l.Laboratory of Animal GeneticsNaples, Italy

Prof. Jørgen KjemsUniversity of AarhusDepartment of Molecular BiologyAarhus, Denmark

Prof. Xavier EstivillCenter for Genomic Regulation (CRG) Genes and Disease Program Barcelona, Spain

Prof. Caroline DeanJohn Innes Centre, Norwich Research ParkDepartment of Cell & Developmental BiologyNorwich, UK

Dr. Michael WasseneggerAlPlanta-Institute for Plant ResearchNeustadt, Germany

Dr. Peter MouritzenExiqon A/SResearch and DevelopmentVedbaek, Denmark

Dr. Stephen CohenTemasek Life Sciences Laboratory LtdNational University of Singapore Singapore, Republic of Singapore


Silencing RNAs: organisers and coordinators of complexity in eukaryotic organisms



CHRONOBIOLOGY7.5

EUCLOCK

TEMPO


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State-of-the-Art: Behaviour, physiology and biochemistry are temporally structured, and therefore gener-ate daily oscillations. These cycles are not driven simply by external changes (such as the changes of light/dark or warm/cold), but are controlled by an endogenous clock that exists in the most diverse organisms, from cyanobacteria to humans. In real life, this circadian clock is synchronised with the outside world by rhythmic environmental signals, called ‘zeit-gebers’, through a process called entrainment. Circadian rhythms exist at all levels of biol-ogy. They are present, for example, in rest, arousal or vigilance activities; in temperature, urinary output, blood pressure or heart rate; in enzyme activity, hormone concentrations or gene expression. Previous experiments have shown that circadian rhythms continue even in the absence of environmental time cues. This internal ‘day’ is self-sufficient but not entirely independent from the external day. A critical feature of the clock is its synchronisation with the external day. This so-called entrainment is the key to understanding the circadian clock and its control mechanisms. Human beings rarely experience constant conditions and, as a consequence, any research on humans entails concentrating on the entrained state.

EUCLOCK, a large research network, was launched in January 2006. Its main aim is to investigate the circadian clock in different organisms, from cells to humans. More specifi-cally, the project seeks to understand how circadian clocks synchronise with their cyclic environment.

Scientific/Technological Objectives: Within this field of research, EUCLOCK investigates the circadian clock in the context of entrainment. The project aims to understand, for example, the misalignment between inter-nal and external time, as a consequence of shift-work, as well as insufficient entrainment owing to age-related changes, both elements which can have a strong impact on health and well-being. A major objective of EUCLOCK is to enable large-scale, non-invasive studies (the CLOCK-watcher device) that can prove or disprove the efficacy of medical treatment of pathologies, ranging from heart diseases to cancer, using 24-hour monitoring of impact of these treatments.

Expected Results: In EUCLOCK, European researchers join forces to investigate the circadian clock under en-trainment. Utilising the most advanced methods of functional genomics and phenomics, the team will compare genetic model organisms and humans. Important findings, such as the prerequisites for large-scale, non-invasive research on human entrainment as well as the first animal models for shift-work, will be developed. As with 20% of the human working popula-tion, flies and mice will likewise be exposed to ‘shift work’ schedules, i.e. will be active and feed out of phase, with respect to their natural rhythms. The ensuing ‘dys-entrainment’ will be investigated at different levels, from genes to behaviour, so as to provide insights into the prevention of negative consequences of human shift-work.

New genetic components that control the circadian clock and its entrainment will be identi-fied (both in animals and humans). Moreover, new tools will be developed and new circadi-an model organisms will be explored. These findings will enable the field of chronobiology to exploit the advantages of systems’ biology research on circadian timing, and to perform and integrate the findings at the level of the genome, the proteome, and the metabolome. The innovations of EUCLOCK are predestined to shape the future of circadian research.


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Potential Impact: Contributions to standards This IP uses an entirely novel approach to

understanding entrainment of the circadi-an clock. It will, therefore, establish stand-ards on several levels.

A tissue bank from EUCLOCK lab subjects will be established. The EUCLOCK web-site will compile the accumulating data on tissue-specific clock gene expression under different entrainment of dys-entrainment protocols. The integrated use of many dif-ferent entrainment protocols will produce standard operating procedures, for means of investigating the effects of clock gene polymorphisms on the endogenous daily programme, from behaviour, to physiology, and to molecules. The first-time use of dawn and dusk simulation in entrainment will have wide-ranging consequences on how entrainment will be investigated in all circadian model systems.

The first-time use of forced dys-entrainment protocols will set new standards for animal models for shift work research. The development of a “Real Life Routine” (CLOCK-watch-er), will provide researchers of the human clock with a standard set of parameters that are useful and meaningful, when the daily programme of humans is investigated in field experiments (e.g. in shift workers).

Our results concerning circadianly effective light environments will be shared (via an advisory committee) with the European lighting industry.

Impact on European science The circadian clock was discovered in Europe. With the advent of molecular genetics,

the centre of gravity in circadian biology shifted from Europe to the USA. This IP now supports a developing area of European scientific expertise (the accumulative impact factor of EUCLOCK’s scientists is well over 11,000, with an average of 420), and importantly lends financial support in an area where dedicated financial funding in all European countries cannot match corresponding funding in the USA.

Impact on European healthcare EUCLOCK will contribute significantly to the understanding of how the different parts

of the circadian clock come together to form an entrained system, from molecules to behaviour. These insights will form an essential basis for understanding all temporal aspects of normal physiology and of pathology. They will also contribute to developing chrono-pharmacological interventions.

Impact on Europe’s societal problems and economy Modern society creates conditions which frequently challenge the optimal function of the

circadian clock. For example, approximately 20% of employees have shift- or night-work schedules; this creates enormous societal problems. Any measure intended to counteract the detrimental effects of shift-work, must encompass both health and sociological issues (e.g. who undertakes the responsibility of childcare while one of the parents is working night shifts?). In order to solve these problems (e.g. through the development of better shift schedules) the bio-medical sciences need to strongly communicate with the social sciences. The management of EUCLOCK will facilitate bridges between its own basic science approaches, and the approaches of other networks which deal with the cogni-tive and social aspects of daily work (e.g. the Daimler-Benz-network, “Optimising the daily structure of work”).

Due to their ‘mal-entrained’ circadian clocks, shift-workers show reduced vigilance (both in night and other shifts), and suffer from health problems. The consequences are far-reaching, in terms of both societal and economic costs, due to reduced productivity, faulty


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workmanship, absenteeism and increased health problems upon retirement, not to mention mistakes and accident rates. The results of EUCLOCK could therefore vitally impact on work productivity.

EUCLOCK will also increase the poten-tial for development and optimisation of industrial products. For example, lighting conditions have profound effects on cir-cadian entrainment in particular, and on human health in general. By developing the potential for measuring the human clock in real life, we enable scientific ap-proaches to test new products, which aim to improve entrainment.

Added value in carrying out the work at aEuropean level At the end of the last century, attention

in the field was focused on the search for the molecules and intracellular regu-latory mechanisms of the circadian clock — with great success. As a consequence, a consortium of US universities (the NSF Center for Biological Timing) was estab-lished, which has now completed opera-tions, concluding 10 years of success. The next critical step will be EU-based. EUCLOCK is poised to become the pre-eminent chronobiological ‘power’ of the new century.

The objectives and aims of EUCLOCK can only be implemented if many laboratories, specialising in different circadian aspects and methods, cooperate with clearly defined SOPs. This can work only if resources are drawn Europe-wide.

Keywords: circadian clock, shift work models, light, en-trainment, chronobiology, animal models

PartnersProject Coordinator: Prof. Till RoennebergLudwig Maximilians UniversityInstitute for Medical PsychologyGoethstr. 31Munich, [email protected]

Prof. Urs Albrecht University of FribourgDepartment of Medicine Fribourg, Switzerland

Dr. Howard CooperInstitut National de la Santé et de laRecherche Médicale (INSERM)Unite 371, Cerveau et VisionBron, France

Prof. Rodolfo CostaUniversity of Padua Dipartimento di BiologiaPadova, Italy

Prof. Dominicus G.M. BeersmaUniversity of Groningen Department of ChronobiologyGroningen, The Netherlands

Prof. Charlotte FörsterUniversity of RegensburgInstitut für Zoologie/Entwicklungsbiologieund ChronobiologieRegensburg, Germany

Prof. Russel FosterUniversity of OxfordNuffield Laboratory of OphthalmologyCircadian and Visual Neuroscience GroupOxford, UK

Prof. Achim KramerCharité Universitatsmedizin BerlinInstitute of Medical ImmunologyBerlin, Germany

Prof. Charalambos KyriacouUniversity of Leicester,Department of GeneticsLeicester, UK

Dr. Johanna MeijerLeiden University Medical CenterDepartment of NeurophysiologyLeiden, The Netherlands

Triangle plot of the NPAS2 gene variants.


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Prof. Thomas MeitingerGSF Institute of Human GeneticsGSF Nat. Res. CentreNeuherberg, Germany

Prof. Andres MetspaluEstonian BiocentreGene Technology LaboratoryTartu, Estonia

Prof. Dr. Andrew MillarUniversity of EdinburghInstitute of Molecular Plant ScienceEdinburgh, UK

Prof. Ferenc NagyPlant Biology InstituteBiological Research CenterSzeged, Hungary

Dr. Pat NolanMedical Research CouncilMammalian Genetics UnitNeurobehavioural GeneticsOxfordshire, UK

Dr. François RouyerCentre National de la Recherche Scientifique (CNRS)Institute de Neurobiologie Alfred FessardGif-sur-Yvette Cedex, France

Prof. Ueli SchiblerUniversity of GenevaDepartment of Molecular BiologyGeneva, Switzerland

Prof. Debra SkeneUniversity of SurreyNeuroendocrinology GroupGuildford, UK

Dr. Alena SumovaThe Academy of Sciences of the Czech RepublicInstitute of PhysiologyDepartment of Neurohumoral RegulationsPrague, Czech Republic

Dr. G.T.J. van der HorstErasmus MC-RotterdamDepartment of Cell Biology and GeneticsRotterdam, The Netherlands

Prof. Dr. Anna Wirz-JusticeUniversity of BaselUniversity Psychiatric Clinics / Centre for ChronobiologyBasel, Switzerland

Dr. Konstantin DanilenkoChronobiology CentreInstitute of Internal Medicine SB RAMSNovosibirsk, Russia

Dr. Emma PerfectLUX BiotechResearch and Development DepartmentEdinburgh, UK

Uwe StrobelTechnical Light Control DevelopmentLichtblickBonstetten, Germany

Prof. Hans-Peter LippNewBehavior AGZurich, Switzerland

Anand KumarPersonal Health InstInt. VOFAmsterdam, The Netherlands,

Dr. Juha HintsaSowoon TechnologiesLausanne, Switzerland

Dr, Jakob WeberBuehlmann Laboratories AGSchonenbuch, Switzerland

Prof. Ralf StanewskyQueen Mary, University of LondonSchool of Biological and Chemical SciencesLondon, UK


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State-of-the-Art:Non-communicable, chronic diseases represent the bulk of morbidity, disability and prema-ture deaths in Europe, and account for 75 per cent of disability-adjusted life years. Among those diseases, cancer is the second most important cause of morbidity and mortality. Dif-ferences in the molecular characteristics of tumour cells, as well as differences in patients’ genetic make-up, gender, age, lifestyle and circadian rhythms, account for large variability in the time-course of cancer and in patients’ responses to treatment.

Scientific/Technological Objectives:The general objective of TEMPO is to design mouse and in silico models that reflect this variability and allow the prediction of optimal chronotherapeutic delivery patterns for anti-cancer drugs.

Expected Results:TEMPO combines functional genomics, proteom-ics, cell signalling, systems biology and pharma-cokinetics to optimise the therapeutic index in pa-

tients. This index in turn determines the chronotherapeutics schedules, according to which temporal delivery patterns of the same anticancer drug vary. Each schedule is adjusted to a different dynamic class of temporal genomics and phenomics parameters, relating to interwoven circadian and cell division cycles as well as drug metabolism. The multidiscipli-nary nature of the consortium means that in vivo, in vitro and in silico approaches will be integrated to achieve this end.

Potential Impact:TEMPO epitomises the transla-tion of basic research findings into useful clinical applications. Through the identification of nodes in the interplay between the circadian timing system, the cell division cycle and drug pharmacology parameters, it will provide critically important information for the targeted de-velopment of new anti-cancer drugs.

Keywords: cell cycle, circadian clock

Schematic representation of cellular circadian rhythms.

Programmable in time drug delivery pump.


Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2006-037543Starting date:1st October 2006Duration:36 monthsEC Funding:

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Project Coordinator:Dr. Francis LéviInstitut National de la Santé et de laRecherche Médicale (INSERM)U776 - Rythmes biologiques et cancersHôpital Paul BrousseAvenue Paul-Vaillant Couturier 1494807 Villejuif, [email protected]

Project Manager:Dr. Isabelle GeahelINSERM - Transfert SAEuropean Project Management DepartmentRue de Tolbiac 10175654 Paris, France

Prof. Franck DelaunayCentre National de la Recherche Scientifique (CNRS)Université de Nice - CNRS UMR 6348Bâtiment de Sciences NaturellesPhysiologie cellulaire et moléculaire dessystèmes intègresNice, France

Prof. Laurent MeijerCentre National de la Recherche Scientifique (CNRS)Laboratoire Mer et Sante UMR7150Station Biologique - Amyloïds and Cell Division CycleRoscoff, France

Dr. Jean ClairambaultInstitut National de Recherché en Informatiqueet Automatique (INRIA) Rocquencourt Research Unit -Teams Bang and ContraintesLe Chesnay, France

Partners

Circadian rhythms in cellular proliferation in humans.

Prof. Stefano IacobelliConsorzio Interuniversitario Nazionaleper la Bio-oncologiaLaboratory of molecular oncology center ofexcellence on aging Ce. S.I.Chieti, Italy

Dr. Marco PirovanoH.S. Hospital Services S.p.A.Therapeutic deliveryAprilia (Latina), Italy

Dr. Todor VujasinovicHelios Biosciences SarlCréteil, France

Dr. Christophe ChassagnolePhysiomics PlcThe Magdalen CentreOxford, UK


Temporal Genomics for Tailored Chronotherapeutics




BIOLOGY OF PROKARYOTES AND OTHER ORGANISMS

7.6BACELL HEALTH

DIATOMICS


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State-of-the-art: Pre-genomic research in cell biology has yielded a wealth of knowledge about individual regulatory pathways and metabolic processes that are obligatory for the survival of patho-gens in their host, and for the productivity of microbes in industrial bioprocesses. The major challenge for the BACELL HEALTH consortium, using state-of-the-art post-genomic technolo-gies, is to understand how individual regulatory pathways are networked to maintain cel-lular homeostasis. The networking of individual regulatory pathways ensures that the cell provides a balanced response to stress, sensing both the magnitude of the stress, and the effectiveness of the response. In the case of pathogens, the identification of key nodes in these regulatory networks will provide new targets for the development of antimicrobial compounds that perturb or disrupt the cell stress management system. For industrial produc-tion strains, the inactivation of stress-induced processes that limit the production of heterolo-gous proteins will lead to the development of a new generation of host/vector systems for the production of pharmaceutically-active proteins.

Scientific/Technological objectives: The BACELL HEALTH consortium aims to unravel the integrative cell stress-management sys-tems and stress-resistance processes required to sustain a bacterial cell when exposed to the types of environmental insults that are encountered in two very specific environments — macrophages and industrial fermentors. Although both of these environments induce generic stress responses, they also induce non-overlapping specific stress responses (eg. pH, iron and oxidative stress in the case of macrophages, protein synthesis, secretion and nutrient stress in the case of industrial fermentations). A specific scientific objective is to determine how the induced responses function to relieve the applied stress. In the case of pathogens, the consortium has identified key elements in stress-resistance mechanisms, and their signalling

pathways, for development as potential drug targets. With respect to bio-production strains, the consortium has identified stress path-ways that specifically limit product formation and have constructed prototype production strains. Previous EU-funded studies (BACELL NETWORK) have demonstrated regulatory crosstalk between gen-eral and specific stress responses. A further specific scientific objec-tive is to develop a model for the regulatory interactions that occur within the cell’s stress management system. The scientific objectives were therefore aimed at improving European competitiveness and helping to meet the health needs of society.

Expected results: BACELL HEALTH has built on the technological knowledge and in-

dustrial base developed in Europe by focusing on aspects that directly influence human health, namely the establishment of novel targets for anti-infective agents and the improved production of pharmaceutically-active proteins. The added-value nature of this project was confirmed by the participation of three European companies and the support of the Bacillus Industrial Platform (BACIP). The realised deliverables included knowledge of fundamental biological systems, the identification of novel targets for the development of broad-spectrum and/or Gram-selective drugs, an improved understanding of microbial virulence and the regulatory response of bacteria to host-mediated stress responses, prototypes of production strains and new protein functions. In addition, the consortium trained a group of young Eu-ropean scientists, and disseminated its knowledge via European and international meetings and publications.

Detail of a non ribosomal peptide synthetase as

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Potential impact: European research groups and industries are global leaders in the development of Bacillus technology and the commercial exploitation of bacilli. A direct industrial benefit of BACELL HEALTH will therefore be to help maintain Europe’s competitive market position in the face of competition from the US and the Far East. The project will impact on human health by providing knowledge of the mechanisms bacteria use to avoid the immune response.

Keywords: bacterial pathogens, drug targets, comparative genomics, proteome, transcriptome, iron homeostasis, infectious diseases, biopharmaceuticals

Project Coordinator:Prof. Colin R HarwoodNewcastle UniversityMolecular Microbiology GroupInstitute for Cell and Molecular Biosciences6 Kensington TerraceNewcastle upon Tyne, NE1 7RU, [email protected]

Project Manager:Dr. Sierd BronUniversity of Groningen Department of Genetics Haren, The [email protected]

Prof. Kevin DevineTrinity College DublinDepartment of GeneticsDublin, Ireland

Prof. Mohamed MarahielMarburg UniversityFach Bereich ChemieMarburg, Germany

Prof. Wolfgang SchumannBayreuth University Institute of GeneticsBayreuth, Germany

Dr. Tarek. MsadekInstitute PasteurUnit de Biochimie MicrobienneParis, France

Prof. Michael HeckerGreifswald UniversityInstitut for MikrobiologieGreifswald, Germany

Dr. Rocky CranenburghCobra BiomanufacturingStephenson BuildingThe Science ParkKeele, UK

Prof. Jan Maarten van DijlGroningen University Department of Medical MicrobiologyLaboratory of Molecular BacteriologyGroningen, The Netherlands

Prof. Oscar KuipersGroningen UniversityDepartment of GeneticsGroningen, The Netherlands

Dr. Marc KolkmanR&D Genencor International BVLeiden, The Netherlands

Dr. Michael Dolberg RasmussenBacterial Gene TechnologyBagsvaerd, Denmark

Partners


Bacterial stress management relevant to infectious disease and biopharmaceuticals




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State-of-the-Art:The world’s oceans cover 70 percent of the Earth’s surface and are the largest ecosystem on our planet. This ecosystem is formed by more than 5,000 species of marine phyto-plankton, but only a few taxonomic groups of phytoplankton are responsible for most of the system’s primary production and subsequent energy transfer to higher trophic levels as well as vertical export to the deep ocean. The most significant phytoplankton are diatoms, which contribute around 40 percent of marine primary production, thereby providing close to one fifth of the oxygen we breathe. Diatoms are therefore central to all life on Earth, although to date, remarkably little is known about their basic biology and how it is affected by environmental change.

The challenge for marine biologists in the genomics era is to exploit genomics technologies for all the potential they have, whilst maintaining the holistic view necessary for understanding marine ecosystem function. For diatom researchers, this is especially difficult because there are more than 100,000 extant species occupying widely varying habitats, from temperate to polar waters, and so it has been extremely difficult to derive a consensus ‘model’ species.

Scientific/Technological Objectives:DIATOMICS will make use of whole genome sequences from diatoms to provide information about gene function and its relationship to ecology and evolution. Four scientific work packages will deal with aspects of diatom biology that are ecologically relevant and critical for diatom success and survival. Important topics that will be addressed include carbon-concentrating mechanisms, nutrient acquisition, the rise and fall of blooms and adhesion. Investigations into these areas will be carried out through the following steps: (1) The study

of gene expression profiles in response to a range of ecologically relevant stimuli, such as nutrients and stress; (2) The manipulation of the expression of key candidate genes in Phaeodactylum tricornutum, by reverse genetics; (3) The study of the phylogenetic histories and ecological significance of these genes in a range of diatoms. A fifth work package is designed to utilise the knowledge generated from the other four work packages for the development of non-neutral probes for assessing diatom physiology in the natural environment.

Expected Results:The DIATOMICS project is divided into five scientific work packages, plus one work package dealing with project management. Four of the scientific work packages will deal with an aspect of diatom biology that is ecologically relevant and critical for diatom success and survival. Important topics that will be ad-

dressed include carbon-concentrating mechanisms, nutrient acquisition, the rise and fall of blooms, and biofouling. A fifth work package is designed to utilise the knowledge generated from these other four work packages for the development of non-neutral probes for assessing diatom physiology in the natural environment.

Potential Impact:Climate change is occurring on a global scale and it is of major concern. It is therefore es-sential that the secrets of diatom biology be discovered so as to increase our knowledge of the role they play in global biogeochemical cycles, and to understand how they are influenced by environmental change. These issues are being addressed in DIATOMICS using post-genomics tools. Furthermore, the SME partner in DIATOMICS is interested in transferring diatom genes into rice, in order to reduce fertiliser inputs, to increase stress tolerance and to improve their carbon sequestering capabilities.

Pictures of fusiform, oval, triradiate cells respectively.

There is a big difference in shape between the morphotypes.


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An improved understanding of diatom biology can lead to advances in human health care and well being, due to the phylogenetic relatedness of diatoms to important human patho-gens, eg ciliates and apicomplexans, and to the potential biomedical applications of diatom silica nanofabrication. In summary, DIATOMICS is stimulating multidisciplinary basic research in Europe to exploit the full potential of diatom genome sequences to underpin applications of relevance for human health, and for predicting and monitoring global climate change.

Keywords: cell biology, diatoms, genomics, reverse genetics

Project Coordinator:Dr. Chris Bowler Stazione Zoologica Anton DohrnCell Signalling LaboratoryVilla Comunale 80121 Naples, [email protected]

Prof. Colin BrownleeMarine Biological Association of the UKThe Laboratory, Citadel HillPlymouth, UK

Prof. Veronique Martin-JezequelUniversity of NantesFaculty of Sciences ISOMer EA 2663Nantes, France

Prof. James A CallowUniversity of BirminghamSchool of BiosciencesBirmingham, UK

Prof. Julie La RocheLeibniz Institut fuer MeereswissenschaffenDepartment of Marine BiogeochemistryKiel, Germany

Prof. Aaron KaplanHebrew University of JerusalemDepartment of Plant SciencesInstitute of Life SciencesJerusalem, Israel

PartnersDr. Chris BowlerCentre National de la Recherche Scientifique (CNRS) UMR 8186 Biologie Moléculaire des Organismes Photosynthétiques Ecole Normale SupérieureParis, France

Prof. Linda Karen MedlinStiftung Alfred Wegener Institut fur Polar und MeereschforschungDepartment of Biological OceanographyBremerhaven, Germany

Dr. Leszek RychlewskiBioInfoBank Institute Bioinformatics LaboratoryPoznan, Poland

Prof. Valerie FrankardCropdesign NVTechnology Management GroupZwijnaarde, Belgium

Prof. Wim VyvermanUniversity of GhentLaboratory of Protistology and Aquatic EcologyGhent, Belgium

Dr. Richard WetherbeeUniversity of MelbourneSchool of BotanyParkville, Australia


Understanding Diatom Biology by Functional Genomics Approaches




SYSTEMS BIOLOGY8.



SYSTEMS BIOLOGY

8.EUSYSBIO

SYMBIONIC

EMI-CD

QUASI

COMBIO

COSBICS

DIAMONDS

EU-US Workshop

ELIfe

ESBIC-D

YSBN

AMPKIN

RIBOSYS

EUROBIOFUND

VALAPODYN

AGRON-OMICS

BaSysBio

BioBridge

SYSBIOMED

SysProt

Streptomics

SYSCO

Proust


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State-of-the-Art:Systems biology (SB) covers research into in silico simulation of complex life processes, combining concepts from molecular biology, engineering sciences, mathematics and IT in a holistic approach to complex biological systems such as living cells. SB is currently receiv-ing widespread attention in Japan and the USA and is being intensively researched and promoted. Europe is lagging behind in systems biology research and EUSYSBIO was set up with the aim of bringing together research groups to create a future research network.

Scientific/Technical Objectives:A survey carried out by the EUSYSBIO team indicated that the training of young scientists is essential to the creation of a European systems biology network and also university training programmes in interdisciplinary subjects. The consortium therefore set up training activities, including a series of lectures in Austria. They also began a search for research networks outside Europe to make links with groups for future cooperative research projects. The team carried out the task of identifying the strengths and weaknesses in the European systems biology field and consequently began the task of forming a research network that can compete worldwide.

Expected Results:The project laid the foundations of the successful start of European systems biology research and will form the foundation of further SB research activities. Researchers met in Germany in 2004 to discuss how to establish standards for cooperation and data exchange across Europe and beyond. EUSYSBIO also set up a website and database to contact potential research collaborators and advertise vacancies in the field of SB.

Potential Impact:European SMEs have the necessary knowledge to use opportunities given by the commer-cialisation of SB results. If Europe exploits this competitive advantage it can move into a leading position in the field of international SB research.

Keywords:systems biology, research policies


Project Type:Specific Support ActionContract number:LSSG-CT-2003-503218 Starting date:1st November 2003Duration:24 monthsEC Funding:

500 000

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Project Coordinator:Dr. Petra Wolff Forschungszentrum Juelich GmbH Project Management Juelich (Ptj)Leo-Brandt-Strasse52425 Juelich, [email protected]

Dr. Thomas Reiss Fraunhofer Institute for Systems andInnovation Research (Isi)Munich, Germany

Prof. Hans Victor Westerhoff Vrije Universiteit AmsterdamFaculty of Earth and Life SciencesDepartment of Molecular Cell PhysiologyAmsterdam, The Netherlands

Prof. Karl Kuchler University of ViennaDivision of Molecular GeneticsVienna, Austria

Dr. Roland Eils Deutsches KrebsforschungszentrumTheoretical BioinformaticsHeidelberg, Germany

Dr. Barbara StreicherDialog GentechnikVienna, Austria

Dr. Rudiger MarquardtDechema Gesellschaft Fuer Chemische Technik Und Biotechnologie E.V.Vbu Vereinigung Deutscher Biotechnologie-Unternehmen (Vbu)Frankfurt, Germany

Dr. Sirpa NuotioAcademy of FinlandHealth Research UnitHelsinki, Finland

Partners


The Take-off of European Systems Biology



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State-of-the-Art:In the next few years, systematic data from proteomics and genomics will allow the design of an in silico virtual cell, a model that will have an enormous impact on biomedical and pharmaceutical areas, as it will contribute to a rational design of treatments for human neu-rodegenerative diseases. Hence, there is a pressing need to start a European-wide initiative on the systems biology (SB) of neuronal cells and synapses. The SYMBIONIC project aims at putting the issue of a systems biology approach in the field of neuronal cell study at the centre of interest for a wide scientific community, from cell and molecular neurobiology and neurophysiology to functional genomics, proteomics, bioinformatics, biophysics and computational biology.

Scientific/Technological Objectives:The SYMBIONIC project was designed to capitalise on the enormous scientific potential in Europe and fill a significant void in the international scientific arena. Its long-term aim is to be the driving force for a future set-up of a European-based exhaustive and reliable compu-tational model of the neuron. The activity of the SYMBIONIC project was mainly focused on training and dissemination and on the coordination of the project with other European initiatives in the SB field. Further objectives were:

-tional and experimental fields

-ences

about the great potential of neuronal cells

and technological projects

Expected Results:The SYMBIONIC project helped to integrate knowledge and expertise, provided a general assessment of the existing data and know-how in several different scientific domains (from neurophysiology to computer science), triggered the growth of a consensus on the initiative from pharmaceutical, biotechnological and computing industries and found new strategies for fundraising. Furthermore, it helped to integrate and coordinate the ongoing European-wide initiatives on different aspects of systems biology. The project organized workshops, conferences and training courses on the scientific and technological themes involved for the growth of a future generation of scientists.

Potential Impact:SYMBIONIC is creating a broad European network of research institutions and industries with interdisciplinary expertise in the SB field, which will be a driving force for future am-bitious initiatives in neuronal cell modelling. Through its workshops and conferences the project is contributing to the training of young scientists and to making the pharmaceutical


SYMBIONIC

Project Type:Specific Support ActionContract number:LSHG-CT-2003-503477Starting date:1st November 2003Duration:24 monthsEC Funding:

200 000

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and biotechnology industries more aware of the opportunities offered by SB and its huge potential impact on the economy, The European network of scientists and research groups created through SYMBIONIC activities are now likely to generate new and more ambitious research projects in the area of SB.

Keywords:protein-protein interaction, simulation, neuron, protein network, signaling pathway, syn-apse, computational systems biology, in silico models, research policies

Project Coordinator:Dr. Ivan ArisiLay Line Genomics SpA.c/o San Raffaele Scientific ParkBuilding B, Floor 4Via di Castel Romano 10000128 Rome, [email protected]

Prof. Antonio CattaneoScuola Internazionale Superiore Di Studi AvanzatiDepartment of BiophysicsTrieste, Italy

Dr. Christopher SandersonMedical Research CouncilMRC Human Genome Mapping Project London, UK

Prof. Marta CascanteUniversitat de BarcelonaDepartament de Bioquimica i Biologia MolecularBarcelona, Spain

Partners


Towards European Neuronal Cell Simulation: a European consortium to integrate

the scientific activities for the creation of a European Alliance devoted to

the complete in-silico model of Neuronal Cell



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State-of-the-Art:The main sociological and economical impact of genome research lies in the molecular un-derstanding of major human diseases, and the development of new therapies. However, de-spite significant increases in pharmaceutical R&D spending, the number of new approved medicines has remained fairly constant. One possible reason for this development might be the fact that analytical methods and tools are not yet significantly installed in the drug develop-ment process. While bioinformatics are used in drug target discovery, this is not the case for the later stages. In particular, the simulation and modelling of biological processes, such as disease-relevant signalling pathways and metabolic processes, are underdeveloped in drug target validation. experiments could be the basis for successful screening, and the en-tire drug development process should be accompanied by bioinformatics and systems biology approaches, especially through the introduction of simulation techniques and experimental design at all phases of the process. Furthermore, the need for integration of rules and methods is fundamental in current functional genomics research. Multiple databases exist already, a va-riety of experimental techniques have produced gene and proteome expression data from vari-ous tissues and samples, and important disease-relevant pathways have been investigated.

Scientific/Technological Objectives: The analysis of the processes involved in the course of multigenic diseases, necessitates coping with data from diverse experimental platforms. Consequently, important elements of the EMI-CD software platform target data integration, as well as data standardisation. In particular, the EMI-CD platform is designed in a modular way. The main modules are set out below: Database integration: The role of several partners (BioWisdomSRS, EBI and MicroDiscovery) in the EMI-CD project is to provide an information layer on the biological objects needed by the modelling software (Max Planck Institute for Molecular Genetics), and is therefore of key importance to the project, due to it providing a central repository for the data sources used by the project. Experimental data integration: Due to limitations of the current state-of-the-art in data integra-tion, there is an essential need for a computer application. Even more crucial for the EMI-CD project is access to data of high quality, indispensable for modelling and simulation tasks. Modelling of high-throughput data: Computational methodologies are expected to direct biological discovery, by enabling formalisation of the current biological knowledge into a formal model, and improving our knowledge, by refining the model systematically, according to the high-throughput data. Tel-Aviv University has introduced an extended computational framework for studying biological systems. The approach combines formalisation of existing qualitative models that are in wide but informal use today, with probabilistic modelling and integration of high throughput screening.

Expected Results: The main purpose of EMI-CD is to provide a software platform complex enough to cope with various experimental techniques, aimed at discovering the gene function, and at understand-ing disease processes. Another important issue is the tight cooperation with experimental projects, on the design of experiments for combined strategies to combat human diseases (such as cancer and diabetes). Compatibility with other systems is also an issue, but by using SBML, models can be interchanged between different systems. A further issue stems from scal-ing of the platform to large systems (i.e. whole cell models). At the current stage, systems with a few thousand reactions are computationally feasible. EMI-CD will be an open system for the integration of advanced analysis tools and other database systems.


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Project Coordinator: Dr. Ralf HerwigMax Planck Institute for Molecular GeneticsVertebrate GenomicsIhnestr. 7314195 Berlin, [email protected]

Prof. Dr. Ron ShamirTel Aviv UniversitySchool of Computer ScienceTel Aviv, Israel

Dr. Ewan BirneyEuropean Moleculer Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Dr. Chris HodkinsonBioWisdom LtdCambridge, UK

Potential Impact: In silico modelling ap-proaches will have an in-creasing impact on Life Sci-ence and Health programs. More specifically, they will create immense potential for improving the quality of life, through their crea-tion of highly skilled jobs in the health sector, improved competitiveness and eco-nomic growth in Europe, and better healthcare and new tools to address the diverse and important chal-lenges of the European Community. In terms of health care, the post-genomics era will enable the invention and production of new diagnostic and analysis tools. A revolution in health care is anticipated with the move towards personalised medical treatments, by means of genetic medicine and the modelling of patient-specific therapy. This is bound to have an important impact on the future health status and quality of life of European citizens, and also to affect the cost implications for the population.

Keywords: bioinformatics, modelling complex diseases, network analysis, complex diseases

PyBioS database interface. The PyBioS system is linked to the other platforms of the EMI-CD project that are providing topological data on cellular reaction systems and experimental data via specific interfaces.

Partners

Dr. Arif MalikMicroDiscovery GmbHBerlin, Germany


European Modelling Initiative combating complex diseases



440

State-of-the-art:Present understanding of cellular signal transduction is restricted, at best, to the wiring schemes of signalling pathways. Little is known about the details of their dynamic operation and the importance of quantitative, spatial and time-dependent parameters for signalling output. These are, however, crucially important for drug discovery and application. QUASI is a multidisciplinary project which aims at obtaining a coherent and detailed pic-ture of the dynamic operation of a model signalling transduction network. The signalling pathways contain the evolutionarily conserved MAP kinase cascade module, which is of central importance for signalling in human cells and is implicated in human diseases such as cancer and inflammatory disorders. MAP kinase pathways are currently being explored as drug targets. A better understanding of the dynamic operation of these pathways offers new opportunities for drug discovery and for efficient individualised treatment based on the genetic makeup of the patient (pharmacogenomics).

Scientific/Technological objectives: The overall objective of QUASI is to assess the dynamic and quantitative operation of sig-nal transduction pathways and to elucidate relevant paradigms. The individual scientific, technical and innovation objectives of the project are:

1. To monitor activated protein kinases in the cell. A range of immunoreagents is being used to quantify key phosphorylation events.

2. To determine dynamic signalling events in single living cells using advanced micro-scopic and optic tools. These methods aim at the determination of protein movements within the living cell.

3. To specifically, rapidly and temporarily inhibit signalling components in the living cell. For this purpose, the team will design functional protein kinase variants that are sensitive to highly specific inhibitory compounds. In addition, QUASI is initiating development of inhibitors based on protein kinase target structure.

4. To identify direct protein kinase targets and quantify kinase-substrate reactions. In or-der for QUASI to reach its objective the team will develop and verify ATP analogues recognised by specific, modified protein kinases.

5. To follow protein complex formation dynamics in the living cell. More specifically, the team is employing protein tags that allow the use of specific cross-linking reagents for protein complexes in solutions as well as on DNA templates in the cell. In addition, activatable Green Fluorescent Protein (GFP) variants and advanced microscopy/op-tics are also being used to determine cellular movement and assembly of individual subunits and protein complexes.

Expected results: 1. A better understanding of the importance and role of quantitative aspects of signal

transduction. Particular attention will be given to the signal amplitude and period for the quality and intensity of different responses. This is vital for improved concepts in drug development and in drug applications such as personalised medication.

2. A better understanding of the signalling of protein complex formation and protein movement as possible targets for pharmacological intervention.

3. Identification of overriding rules of signalling pathway control including feed-forward and feed-back control principles and robustness.

4. A better understanding of how pathway specificity is achieved and maintained dur-ing signal transduction and how cross-talk between pathways is regulated.

5. A set of optimised tools and approaches of general applicability.6. Mathematical models, which could be applied with adjusted parameters to MAP

Yeast cells stained for cell wall usinf calcofluor white (top) and

plasma membrane Using an Aqy2-GFP fusion (bottom). The diameter of the cell is about 5

micrometer. Yeast cells actively control their volume via con-

served signalling systems that are Studied in QUASI using a

systems biology approach.


Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503 230Starting date:1st January 2004Duration:42 monthsEC Funding:

1 920 410

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kinase pathways from any system. 7. Information design and visualisation tools of wide applicability for the communica-

tion of signalling and other dynamic events.

Potential impact: QUASI is a project at the frontline of fundamental biomedical research. The results obtained will have a direct impact on drug development and drug application in diseases associ-ated with altered MAP kinase signalling, and therefore can potentially contribute to giving Europe a competitive advantage in signal transduction research. Diseases such as cancer, and chronic inflammatory diseases such as rheumatoid arthritis, asthma and autoimmunity affect many millions of Europeans; they are either life-threatening or affect a person’s quality of life for many years. Because of this they require treatment over long periods of time and are a huge financial burden on society. Hence, QUASI has the potential to open new avenues leading to better treatment of these diseases, thereby contributing to disease prevention in Europe and cost reductions for health services.

Keywords: signal transduction, MAP kinases, cellular dynamics, mathematical models

Project Coordinator:Prof. Stefan HohmannGothenburg UniversityDepartment of Cell and Molecular BiologyBox 462 (Medicinaregatan 9E)405 30 Gothenburg, [email protected]

Dr. Per Sunnerhagen,Dr. Markus TamasDr. Morten GrötliGothenburg UniversityDepartment of Cell and Molecular Biologyand Department of ChemistryGothenburg, Sweden

Prof. Francesc PosasUniversitat Pompeu Fabra (UPF)Cell Signalling UnitDepartment de Ciències Experimentals i de la SalutBarcelona, Spain

Dr. Gustav AmmererUniversity of ViennaInstitute of Biochemistry and Molecular Cell Biology Vienna BiocenterVienna, Austria

Prof. Matthias PeterSwiss Federal Institute of Technology Zurich (ETH Zurich)Institute of BiochemistryZurich, Switzerland

Dr. Edda KlippMax-Planck Institute for Molecular GeneticsDepartment of Vertebrate GenomicsBerlin Centre for Genome Based Bioinformatics (BCB)Berlin, Germany

Dr. Rune PetterssonMälardalens Högskola Institutionen för Innovation Design och ProduktutvecklingEskilstuna, Sweden

Partners


Quantifying signal transduction



442

State-of-the-Art:It is increasingly becoming recognised that progress in biology depends on an understand-ing of the interactions between genes and proteins, and the functional systems they gener-ate. Given the complexity of even the most primitive living organism, and the fact that our knowledge of these interacting networks is still very limited, it is unreasonable to expect that we might achieve such understanding at the level of the cell in the near future. However, sig-nificant progress towards a system-level understanding should be achievable by applying an integrated approach to the analysis of a set of well-defined and biologically important cellular processes.By combining experimental, simulation and bioinformatics approaches, COMBIO aims to increase understanding of two biologically important systems: the first is the p53-Mdm2 regulatory network, in which the oncoprotein Mdm2 controls the activity of the tumour sup-pressor ‘gatekeeper’ protein p53, via a negative feedback loop, and the second is the self-organisation process whereby chromatin controls microtubule nucleation and organisation during spindle formation. These two systems have been selected because they represent two important and different kinds of biological system — one which can be described approximately as a network of free components, and the other in which localisation, self-organisation and gradients play an important role.

Scientific/Technological Objectives:The general objective of COMBIO is to benchmark the ability of current modelling and simulation methods to generate useful hypotheses for experimentalists, and to provide new insights into complex biological processes.In both systems COMBIO has selected to study — the p53-Mdm2 regulatory network, and the dynamics of spindle assembly — the consortium will use different approaches to obtain quan-titative data, as well as data regarding localisation and the dynamics of the system. Three of the consortium’s partners are leaders in the field of database construction and display. Work-ing in close collaboration with experimentalists, they will develop databases that are adapted to experimental work and computer modelling. Data will be stored in such a way that they will be accessible to various simulation packages, and will be displayed in such a way that non-experts will be able to make sense of them. This aspect of the project will require signifi-cant technological innovation. Two of the groups in COMBIO develop modelling approxima-tions while simultaneously conducting experiments to validate the models’ predictions. These groups will act as a kind of bridge between the dry and wet labs in the consortium. The dif-ferent modelling tools will be assessed and a handbook drawn up, which will allow the rapid dissemination of these tools to the broader experimental community.

Expected Results:It is the ambition of the COMBIO consortium to create a truly interdisciplinary environment, in which a range of theoretical and experimental approaches that were hitherto considered separate areas of research, will be integrated and applied to the understanding of complex biological systems. In so doing, it hopes to make an important contribution to functional genomics, and to provide means for elucidating the mechanisms of action of pharmacologi-cal compounds.

Potential Impact:Systems biology recognises the importance of wholeness, acknowledging that systems can-not be understood by investigation of their parts in isolation. Today, systems biology brings mathematics, engineering, physics and computer science expertise to the exploration of complex biological systems and their regulation.The current emphasis on systems in biology is the result of recent developments in molecular

Prolonged oscillations in the nuclear levels of fluorescently-

tagged p53 and Mdm2 in individual MCF7 cells following

gamma irradiation.


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biology and biochemistry, which have enabled researchers to collect comprehensive data sets on the performance of systems, and to acquire information about their molecular sub-strates. These developments have implications for medicine and drug development.Human disease phenotypes are controlled not only by individual genes and their products, but also by networks of interactions that exist between those genes and their products, and the system-wide dynamic behaviour that they display. The networks range from metabolic pathways to signalling pathways that regulate hormone action. Study of the dynamics of these networks, using approaches such as metabolic control analysis (for metabolic networks), or stochastic or logical approaches (for gene regulation networks), may provide new insights into the patho-genesis and treatment of complex diseases such as cancer.

Keywords: systems biology, computer modelling, gene & protein networks, gra-dients, software evaluation, network design, computational biology, signalling

Project Coordinator:Prof.. Luis SerranoCRG - Centre de Regulació GenòmicaSystems Biology Research UnitDr. Aiguader 8808003 Barcelona, [email protected]

Dr. Francois NedelecEuropean Molecular Biology Laboratory (EMBL)Cell Biology and Biophysics UnitHeidelberg, Germany

Dr. Olga Kel-MargoulisProf. Edgar WingenderBIOBASE Pathway DatabasesWolfenbüttel, Germany

Dr. Uri AlonWeizmann Institute of Science Department of Molecular Cell BiologyRehovot, Israel

Dr. Marcelle Kaufman Université Libre de Bruxelles Centre for Nonlinear Phenomena and Complex Systems Brussels, Belgium

Dr. Amancio CarneroCentro Nacional de Investigaciones OncológicasMadrid, Spain

Prof. Edgar WingenderUniversity of Göttingen Department of BioinformaticsGöttingen, Germany

Prof. Béla NovákTechnical University of Budapest Molecular Network Dynamics Research GroupBudapest, Hungary

Prof. Alfonso ValenciaNational Centre for Biotechnology Protein Design GroupMadrid, Spain

Dr. Cayetano GonzalesInstitute of Biomedical ResearchCell Division LaboratoryBarcelona, Spain

Dr. Isabelle VernosCentre for Genomic Regulation (CRG)Barcelona, Spain

Partners


An integrative approach to cellular signalling and control processes: Bringing computational biology to the bench



444

State-of-the-Art:Cancer can be considered a disease of communication at molecular level. The area of cell signalling investigates the transmission of information from receptors to gene activation by means of biochemical reaction pathways, which form complex signalling networks and impinge on the development and health of organisms. COSBICS will establish and apply a novel computational framework in which it will investigate dynamic interactions of mole-cules within cells. Instead of simply mapping proteins in a pathway, COSBICS is concerned with ‘dynamic pathway modelling’. Dynamic pathway modelling establishes mathematical models to predict quantitatively the spatial-temporal response of signalling pathways and subsequent target gene expression. This project considers two important systems: the Ras/Raf/MEK/ERK and the JAK-STAT pathways. With these pathways, COSBICS will investigate the heart of the intracellular communication network that governs cell growth, differentiation and survival.

Scientific/Technological Objectives:COSBICS’ main goals are to identify and quantify dynamic interactions of signalling path-ways using system- and signal-orientated approaches, and to develop methodologies that are applicable to the dynamic and predictive analysis of signalling networks in general. As paradigms, we consider two important systems at the heart of the intracellular communica-tion network that govern cell growth and survival: the Ras/Raf/MEK/ERK pathway and the JAK-STAT pathway. COSBICS combines mathematical modelling with biological knowledge to improve our understanding of how these two central communication networks are sub-verted in tumour cells.

Expected Results:The COSBICS project will develop two complete mathematical models of the JAK2-STAT5 and Ras/Raf1/MEK/ERK pathways. The structure and parameter values of these models are based on quantitative time series data generated by the consortium. The consortium

JAK2-STAT5 pathway map


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will develop mathematical and computational methods that are generic and should be applicable to a wide range of cell signalling systems. The ultimate biological goal is an understanding of the two signalling pathways that play an important role in cell differentia-tion and proliferation. We are hoping that our models and experiments will reveal general principles by which cells decide upon cell growth and development.

Potential Impact:The tools we are developing for the mathematical analysis of nonlinear signal transduction pathway models are generic and can be applied to other systems biology projects as well. We aim to develop models that can predict the biochemical behaviour of pathways in re-sponse to perturbations, which will be experimentally tested. We also will use this informa-tion to help in the design of biological experiments, for example, by determining how many measurements need to be taken at what time intervals for a robust result to be obtained. Both applications will be useful for academic as well as industrial research mainly through minimising the ‘wet’ experimental load, which is very expensive and time-consuming.

Keywords: dynamic modelling of signal transduction pathways

Project Coordinator:Prof. Olaf WolkenhauerUniversität RostockDepartment of Computer ScienceUniversitätsplatz 118051 Rostock, [email protected]

Dr. Ursula Klingmuller Deutsches KrebsforschungszentrumTheodor Boveri Nachwuchsgruppe: Systembiologie der SignaltransduktionHeidelberg, Germany

Prof. Walter KolchBeatson Institute for Cancer ResearchGlasgow, UK

Dr. Julio Rodriguez BangaInstituto de Investigaciones Marinas del Consejo Superior de Investigaciones CientificasProcess Engineering Group Madrid, Spain

Prof. Valko PetrovBulgarian Academy of SciencesInstitute of Mechanics and BiomechanicsLaboratory of Biodynamics and BiorheologySofia, Bulgaria

PartnersDr. Jens TimmerAlbert-Ludwigs-Universität FreiburgFreiburger Zentrum für Datenanalyse und Modellbildung Freiburg, Germany


Computational Systems Biology of Cell Signalling



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State-of-the-Art:The field of systems biology aims to build on the success of novel functional genomics tech-nologies, by improving data extraction and data modelling in order to get an understand-ing of biological processes as ‘control systems’. Essential to systems biology is the math-ematical modelling of biological processes, and its use to build hypotheses and to carry out subsequent experimental validation. The complexity of biological processes is such that without modelling and simulation its dynamics cannot be fully understood. Systems biology requires strong skills in biology and in computational analysis. Within DIAMONDS we wish to set in motion a multinational systems biology effort to study and model cell cycle control in baker’s and fission yeast, and in and human cells.

Scientific/Technological Objectives:The overarching objective is to demonstrate the power of a systems biology approach to study fundamental biological processes. We focus on eukaryotic cell cycle regulation, and will develop and implement a computational model that will function as a hypothesis-generating engine in a systems biology ‘wet lab’ environment. To reach this we set out to develop two parts: a cell cycle knowledge base and an integrated platform of data mining, modelling and simulation tools. This will allow the integrated analysis of that data in a sys-tems biology approach: the development of a basic model, the use of this model to design new experiments, the production and analysis of novel data and the integration of these into a refined model. The major means of reaching this target is to harvest and/or produce a large body of cell cycle-related biological knowledge. This will function as the central resource for the model-ling and simulation environment that will be developed. The project will showcase the fact that a systems biology approach toward analysis of a fundamental biological process can in fact become mature today, and hinges on an integrated data analysis pipeline, extended with modelling and simulation tools.

Expected Results:At the end of the project we will have an integrated toolbox for the analysis of functional genomics data, and the modelling of cell cycle information for simulation purposes. We will also de-liver a knowledge base (GIN-db) containing detailed information about core cell cycle genes. The project is in its final year. We have begun concrete experiments to synchronise cells in culture in order to study the dynamics of expression with microarrays and proteomics approaches. We have also finished the design of the data analysis platform and will deliver the first working version by early 2008.

Potential Impact:The project will allow extensive data integration and modelling, and will deliver new insights in cell cycle regulation and the mechanisms that prevent the uncontrolled proliferation of cells,

opening the way to novel anti-tumour drugs and strategies. The potential for applications of life sciences and biotechnology promises to be a growing source of wealth creation in the future, leading to the creation of jobs, particularly in the areas of highly skilled labour, and new opportunities for investment in further research.


DIAMONDSwww.SBcellcycle.org


2 500 000


http://www.SBcellcycle.org

447

Keywords: functional genomics, systems biology, cancer, regulatory networks, dynamical modelling

Project Coordinator:Prof. Martin KuiperFlanders Interuniversity Institute for BiotechnologyDepartment of Plant Systems BiologyComputational Biology GroupTechnologiepark 9279052 Ghent, [email protected]

Dr. Kristian HelinUniversity of CopenhagenBiotech Research and Innovation CentreCopenhagen K, Denmark

Prof. Denis ThieffryUniversité de la MéditerranéeTechnologies Avancées pour le Génome et la Clinique (TAGC)Faculté des Sciences de LuminyMarseille, France

Prof. Søren BrunakTechnical University of DenmarkCenter for Biological Sequence Analysis (CBS), BioCentrum, DTUKgs. Lyngby, Denmark

Dr. Alvis BrazmaEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK

Prof. Michal LinialHebrew University of JerusalemDepartment of Biological ChemistryInstitute of Life Sciences, Faculty of ScienceJerusalem, Israel

Dr. Tor-Kristian JenssenPubGene ASOslo, Norway

Marta AciluNoray Bioinformatics, S.L.Derio, Spain

Dr. Jürg BählerGenome Research Ltd Wellcome Trust Sanger InstituteCambridge, UK

Prof. Alfonso Valencia Fundación Centro Nacional De Investigaciones Oncológicas Carlos IiiStructural Biology And Biocomputing ProgrammeMadrid, Spain

Partners


Dedicated Integration and Modellingof Novel Data and Prior Knowledge

to Enable Systems Biology



448

State-of-the-Art:DNA is under constant attack from physical and chemical agents that weaken and com-promise it. This means there is a potential risk for cancer and other health problems. Large numbers of chemicals in our food and in the environment have a potentially harmful affect on our DNA under conditions in which its repair capacity is lowered. More research is needed to increase our knowledge of DNA repair pathways and interacting processes and to obtain a better understanding of DNA responses at cellular level. As a response to this the Systems Biology of DNA-Damage-Induced Stress Responses workshop was organised as a follow up to the Molecular Signature of DNA Damage Induced Stress Responses work-shop that was held in 2003.

Scientific/Technological Objectives: The main objective was to provide unique opportunities for interactions between American and European researchers in DNA repair and systems biology and to discuss a future vision for this series of workshops.

Expected Results:

researchers that will be of great benefit to both.

DNA repair (possibly NIH-EU co-funded).

-shops.

combines approaches represented by CEBS, the Reactome Database and Fabio Pi-ano’s C. elegans developmental phenotype database.

Potential Impact: It is hoped that the workshop will lead to an invigorating effect on the international scientific community, particularly scientists researching DNA repair pathways, and it was agreed that participants of the workshop would make a point of researching into specific collaborations that have been organised as a direct result of the previous workshop.


EU-US Workshop

Project Type:Specific Support ActionContract number:LSSG-CT-2004-013079Starting date:1st September 2004Duration:18 monthsEC Funding:

60 000

The Workshop was held in Vermont and had about 70

participants both from the EU and the USA. The relatively small size of the group and

open mindedness allowed for very fruitful discussions on the state of the art in the field of

“Systems level understanding of DNA damage responses” and an assessment of future possibilties

and collaborations.


449

Project Coordinator:Dr. Harry VrielingLeiden University Medical CenterAlbinusdreef 22300 Leiden, The [email protected]

Partners

Keywords:systems biology, DNA damage, stress response, EU-US collaboration, genome wide tran-scriptional profiling

Y2H and literature–curated interactions. This figure shows the human protein interactome deduced from yeast-two-hybrid (Y2H) data (red edges) or from literature–curated (LC) data (blue edges). The overlap is relatively low (2.3% of all LC interactions and 8.4% of the most highly conserved LC hypercore interactions), suggesting relatively strong sociological or technical bias for literature-based or Y2H-based interactome mapping, respectively.


Workshop on “Systems biology of DNA-damage-induced stress responses”



450

State-of-the-Art:Research dealing with the molecular constituents of cells is referred to as genomics for genes and nucleic acids, proteomics for proteins and glycomics for carbohydrates. What has been missing in the ‘-omics’ realm to date has been lipidomics. Since both carbohy-drates and lipids are cellular metabolites, glycomics and lipidomics represent sub-divisions of metabolomics. Lipids are essential constituents of cell membranes, where multiple cellular machines and signalling systems carry out their functions. An imbalance in lipid metabolism results in vari-ous diseases, such as obesity, cardiovascular disease, stroke and Type 2 diabetes, which pose a serious human and economic burden on the developed world. Lack of technology has hampered the analysis of lipids. However, new, fast and sensitive mass spectrometry methods are now revolutionising the field, and are on the verge of being applied to dis-eases related to the lipidome.

Scientific/Technological Objectives:The aim of ELIfe was to mobilise and organise key stakeholders in the field of metabolomics, especially in lipidomics research. Its objectives were as follows:

1) Encourage the formation of alliances between stakeholders in the metabolomics field, including academic research groups and representatives of the healthcare profession and industry;

2) Link metabolomics initiatives with genomics and proteomics initiatives, and to adapt bioinformatics tools used in the latter for metabolomics;

3) Define a strategy for metabolomics research, using lipidomics as an example; 4) Establish a Lipidomics Expertise Platform as a first step towards mobilising the field.

This virtual platform should be linked to the European Federation for the Science and Technology of Lipids (Euro Fed Lipids) and was to act as a test centre for benchmark-ing new lipidomics technology;

5) Hold both science-related and policy meetings.

Expected Results:The ELIfe consortium was to make significant contributions towards the development of a comprehensive classification system for lipids. In addition to this, it expected to produce the following two results: 1) The Lipidomics Expertise Platform (http://www.lipidomics-ex-pertise.de), based on a survey of lipidomics expertise and infrastructure in Europe and 2) The organisation of, and contribution to, multiple workshops and conferences (http://www.lipidomics.net).

Potential Impact:ELIfe brought together and co-ordinated European expertise in metabolomics and lipid-omics, drawing attention to these fields and establishing strategic alliances that should result in the translation of basic research findings into medical and commercial applications.The project will help shape European and national policies and activities in relation to ap-plied and fundamental research. The improvements in analysis of lipid patterns in diseased and healthy people that it aims to generate, will yield insights into the potential effects of different types of (lipid) nutrition on human health.

Cholesterol monohydrate crystals in murine gallbladder bile at the

polarizing light microscopy.


ELIfe www.lipidomics.net


487 200


http://www.lipidomics-ex-pertise.de



http://www.lipidomics.net



451

Keywords: lipidomics, metabolomics, clinical application of lipids

De P4-ATPase structure is from: Lenoir, G. & Holthuis, J. C. The elusive flippases Curr Biol 14, R912-913 (2004).

Project Coordinator:Prof. Gerrit van MeerUtrecht UniversityBijvoet Center and Institute of BiomembranesUtrecht, The [email protected]

Prof. Gerd SchmitzUniversity Hospital RegensburgInstitute for Clinical Chemistry and Laboratory MedicineRegensburg, Germany

Prof. Kai SimonsMax-Planck Institute of Molecular Cell Biology and Genetics: MPI-CBG Dresden, Germany

Prof. Jürgen BorlakFraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V. Fraunhofer Institut für Toxikologie und Experimentelle Medizin Hannover, Germany

Prof. Raymond DwekUniversity of OxfordGlycobiology InstituteOxford, UK

Prof. Pam FredmanGothenburg UniversityInstitute of Neuroscience and Physiology Mölndal, Sweden

Prof. Félix M. GoñiUniversidad del País Vasco/Euskal Herriko Unibertsitatea Department of Biochemistry and Molecular Biology Leioa (Bizkaia), Spain

Prof. Elina IkonenUniversity of HelsinkiInstitute of Biomedicine Helsinki, Finland

Prof. Michel LagardeInstitut National des Sciences Appliquées de LyonPathophysiology of Lipids and Membranes (PLM)Villeurbanne, France Prof. Konrad SandhoffRheinische Friedrich-Wilhelms Universität BonnKekulé-Institut für Organische Chemie und BiochemieBonn, Germany

Prof. Balázs SarkadiNational Medical CenterInstitute of Haematology and ImmunologyDepartment of Molecular Cell BiologyBudapest, Hungary

Prof. Friedrich SpenerUniversität GrazDepartment of Molecular BiosciencesGraz, Austria

Prof. Sandro SonninoUniversity of MilanDepartment Medical ChemistryBiochemistry and BiotechnologySegrate, Italy

Prof. Gerd UtermannMedical University InnsbruckInstitute for Medical Biology and Human GeneticsInnsbruck, Austria

Partners


The European Lipidomics Initiative: Shaping the life sciences



452

DNA microarrays. Andre Nantel ©Shutterstock,2007

State-of-the-Art:Activities to combat multigenic complex diseases such as cancer, diabetes, obesity, heart diseases and diseases of the nervous system are primary targets of the Sixth Framework Programme. After decades of research, cancer remains a devastating disease, responsible for roughly one quarter of the deaths in Europe.

Essentially, there are three main causes of cancer: infection, environmental influence and genetic predisposition. However, on a more analytical and molecular level, the ontogeny of cancer is less evident and both clinical as well as basic research suggests that cancer is the result of an accumulation of many factors that promote growth and metastasis (Hanahan and Weinberg, 2000). Consequently, it is not clear whether much of the current cancer research, especially the research focussed on analysing subprocesses which involve at most a few genes or gene products at a time, will ever be able to “understand” such a complex phenomenon and form the basis for dramatic improvements in cancer treatment. It is also clear that, in spite of all the successes in some specific areas, the current research approaches have not resulted in any dramatic increase of the rates of cure for the most common cancers. Within this context, it is the goal of the project’s Coordination Action (CA) to establish a European framework for a systems’ biology approach to combat complex diseases using cancer as a prototypical problem. The project’s Coordination Action will be fundamentally based on existing resources of leading research groups in Europe. It unites groups with a strong clinical focus, with experience in high throughput functional genomics, as well as with computational and systems biology resources. Moreover, it brings together groups from some of the largest European cancer research organisations and centres.

Scientific/Technological Objectives: ESBIC-D will set up a cancer-relevant model repository consisting of known pathways and gene regulatory networks associated with cancer, the role of specific mutations or other changes in key genes/gene products in these pathways, and, as far as available, detailed clinical data with special emphasis on the influence of different anti-cancer drugs on these pathways. In this CA, important test cases that combine experimental and clinical data with theoretical models and which will guide further analyses and approaches of the participat-ing groups, will be identified. Attention will be given to in silico models of cancer-related (e.g. signalling) pathways, which analyse the feedback of theoretical models and experi-mental data as well as the construction of a complete human metabolic network in order to test responses to drugs and chemical treatments. Moreover, the ESBIC-D project aims to create a network of leading groups in the fields of cancer research, genomics, proteomics and computational biology and to strengthen the expertise and research infrastructure in Europe.

Expected Results: 1) Change and dissemination of information by combining leading EU wide resources;2) Performance of joint studies and analyses by bridging experiment and model; 3) Performance of benchmarking exercises by defining test cases for systems biology ap-

proaches in Cancer; 4) Organisation and management by setting up an expert group for a European wide

systems approach towards the combat of complex diseases (cancer).

The major added-value of ESBIC-D to the European scientific community is the provision of the necessary groundwork for the integration and dissemination of essential parts of systems biology initiatives to tackle cancer.


ESBIC-D


350 000


453

Potential Impact: Systems biology approaches will have an increasing impact on Life Science and Health programmes in general and on anticancer drug development in particular. They provide a huge potential for improving the quality of life through the creation of highly skilled jobs, improved competitiveness and economic growth in Europe, better healthcare and new tools to address different important challenges of the European Community.

In health care, the post genomics era will enable the invention and production of new diag-nostic tools and analysis tools. A revolution in health care is anticipated through a move to-wards personalised medical treatments by means of genetic medicine and the modelling of patient-specific therapy. This will represent an impact on the future health status and quality of life of European citizens as well as on the cost implications. The technical progress within the health care sector will make many new or improved, but costly, medical treatments pos-sible. However, in the long run this is expected to change as there will be a direct positive effect on the exploding health budgets throughout Europe.

Keywords: systems biology, complex diseases, mathematical modelling, bioinformatics

Project Coordinator: Prof. Dr. Hans LehrachMax-Planck Institute for Molecular GeneticsVertebrate GenomicsIhnestr. 7314195 Berlin, GermanyE-mail: [email protected]

Prof. Dr. Annemarie PoustkaGerman Cancer Research Center (DKFZ) Molecular Genome AnalysisHeidelberg, Germany

Dr. Jean-Philippe VertEcole des Mines de Paris Computational Biology GroupParis, France

Prof. Dr. Ron ShamirTel Aviv University School of Computer ScienceTel Aviv, Israel

Dr. Crispin MillerUniversity of ManchesterPaterson Institute for Cancer ResearchManchester, UK

Dr. Emmanuel BarillotInstitut Curie Bioinformatics GroupParis, France

Prof. Dr. Kurt ZatloukalMedical University GrazInstitute for PathologyGraz, Austria

Partners


European Systems Biology Initiative for Combating Complex Diseases



454

State-of-the-Art:The field of systems biology is expected to significantly affect biological and medical re-search. It aims to develop a systems-level understanding of biological processes, by em-ploying mathematical analyses and computational tools, so as to integrate the information content obtained in experimental biology. Gaining insight into the complete behaviour of the cell will assist in the understanding of specific cellular processes and human diseases. Systems biology will also be used for biotechnological production of pharmaceuticals, food ingredients, fuels and chemicals. The Yeast Systems Biology Network (YSBN) project uses the yeast Saccharomyces cerevi-siae as a model system, in order to advance the understanding of cellular systems. The central focus of YSBN is on facilitating cooperation between experimental and theoretical yeast researchers, thus exploiting the interdisciplinary characteristics of a systems biology approach.

Scientific/Technological Objectives: The YSBN project aims to provide a platform that will integrate data acquisition, data generation, modelling and recursive model optimisation. The achievement of the overall objectives of YSBN involves meeting the following targets:

metabolome, interactome, locasome and fluxome data;Saccharomyces cerevisiae, allow-

ing for queries about experimental conditions and data from miscellaneous sources;-

able model development;

-tion as a port, allowing the entire international community to access the tools pro-duced by YSBN;

biology in Europe;

for the production of fuels and chemicals.

Expected Results: The YSBN collaboration action is expected to:

generating new ideas for future projects and collaborations;-

mentation and mathematical model development;

biology;

take place in Helsinki, in June 2006 (http://issy25.vtt.fi);

be collected, maintained and queried, also allowing for links to information contained in other databases;

a dissemination site for the tools generated by the project, and as an interface for the communication between experimental and theoretical scientists

www.ysbn.eu



1 300 000

YSBN


http://www.ysbn.eu

http://issy25.vtt.fi

455

Potential Impact: YSBN is expected to have a powerful impact upon the scientific community; by setting standards and providing a template for a focussed systems biology initiative, the project will decrease fragmentation in European research, consequently benefiting systems biology of other organisms. More specifically, the positive effects of YSBN will be noted in drug dis-covery (directly connected to human health), in the development of new biotech processes (which influence society), and also in education and training. Within YSBN, there are two SMEs that will further improve the competitiveness of the Euro-pean Biotechnology industry, by providing a new software platform for model simulations, and by developing biotechnological processes based on cell factories.

Keywords: systems biology, Saccharomyces cerevisiae, bioinformatics, mathematical modelling

Project Coordinator: Prof. Jens NielsenTechnical University of Denmark Centre for Microbial BiotechnologyBiocentrumLyngby, [email protected]

Prof. Stefan HohmannUniversity of Gothenburg Department of Cell and Molecular Biology/MicrobiologyGothenburg, Sweden

Prof. Stephen OliverUniversity of Manchester School of Biological SciencesManchester, UK

Prof. Hans WesterhoffFree University of AmsterdamBiocentrumAmsterdam, The Netherlands

Prof. Karl KuchlerMedical University of Vienna Division of Molecular GeneticsMedical BiochemistryVienna, Austria

Prof. Peter PhilippsenUniversity of Basel0BiocentrumBasel Switzerland

Prof. Matthias ReussUniversity of StuttgartInstitute of Biochemical EngineeringStuttgart, Germany

Prof. Jack PronkTechnical University of DelftDelft, The Netherlands

Prof. Merja PenttiläVTT BiotechnologyEspoo, Finland

Dr. Edda KlippMax-Plank Institute forMolecular GeneticsDepartment of Vertebrate GenomicsBerlin, Germany

Prof. Bela NovakBudapest University of Technology and EconomicsBudapest, Hungary

Prof. Lilia AlberghinaUniversity of MilanBicocca, Italy

Dr. Uwe SauerSwiss Federal Institute of Technology Institute of Molecular Systems BiologyZurich, Switzerland

Dr. Bärbel Hahn-HägerdalUniversity of LundLund, Sweden

Dr. Jochen FörsterFluxome Sciences A/SCopenhagen, Denmark

Dr Johan GunnarssonInNetics ABLinköping, Sweden

Dr. Macha NikolskiUniversity BordeauxBordeaux, France

Prof. Betul KirdarBogazici UniversityIstanbul, Turkey

Partners


Yeast Systems Biology Network



456

State-of-the-Art:Systems Biology aims at understanding design principles and dynamic operation of cellular modules, entire cells, and organisms. The quantitative approach to biological systems is driven by technological advances and close collaboration between different disciplines. A better understanding of the properties of biological systems is vital for drug development, treatment of diseases and for the improvement of bioprocesses.

In the AMPKIN project, experimental and theoretical studies will be integrated to achieve an advanced understanding of the dynamic operation of the AMP-activated protein kinase (AMPK) signalling pathway. This pathway plays a central role in monitoring the cellular en-ergy status and controlling energy production and consumption. The main objective of the project is to generate predictive kinetic mathematical descriptions of pathway activation/deactivation in yeast and mammalian cells and thereby to identify potential drug targets to treat human metabolic diseases.

Scientific/Technological Objectives: The main technological and scientific objectives of the AMPKIN project are the following:

1. Establish and critically compare the network structures of the AMPK pathway from acti-vation to response in yeast and mammalian cells by using existing data and knowledge from literature, databases and own research;

2. Generate, optimise and verify assay systems for as many different steps as possible in the AMPK pathway of yeast and mammalian cells in order to generate quantitative data and maximise the use of real data in modelling;

3. Generate reference quantitative dynamic datasets following activation and deactivation of the AMPK pathway in yeast and mammalian cells. This reference data set will be used for generating dynamic models of the pathways and to optimise parameters that can not be determined experimentally;

4. Generate and critically compare dynamic models for the yeast and mammalian AMPK pathway. In addition, the project aims to use information from the yeast model to com-plement gaps in the mathematical description of the mammalian model;

5. Produce tools for system perturbation, which will be used to generate data for model testing, iterative model improvement, and for the potential development of drug screen-ing approaches;

6. Provide ‘dynamic’ datasets from experiments, employing a range of defined system perturbations in both yeast and mammalian cells with the aim of testing and iteratively improving the models and of optimising the underlying parameters;

7. Generate iteratively improved mathematical models in order to determine system prop-erties and to provide an assessment of similarities and dissimilarities of the models in yeast and mammalian cells. As a consequence, to establish the significance and the limitations of the approach of comparative modelling from experimental and theoretical perspectives;

8. Predict the result of pharmacological system perturbations and, where possible, to assess these experimentally, thereby implementing the models in drug screening programmes.

Expected Results: The AMPK pathway plays a central role in yeasts, fungi, plants, animals and humans in the control of the energy balance, and therefore it is crucial for life. The overall objective of this project is to generate mathematical models, that is, computational replicas of the AMPK pathway that will be used in drug target identification and drug screening. The results have major potential for tackling some of the most rapidly advancing diseases in the modern



2 106 593

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http://www.sbi.uni-rostock.de/projects_ampkin.html

457

world, such as obesity and type-2 diabetes. The project will result in a case study for em-ploying systems biology in drug target identification and in drug development. Moreover, it will produce results exploitable for engineering of microbial metabolism and systems biol-ogy software development.

Potential Impact: Innovation: the project is at the frontline of post-genomic research. Competitiveness: the project strengthens the European research base in an emerging field and it helps European companies to develop and optimise products for worldwide markets. Exploitation: the results will be exploited by SMEs’ in different sectors of the European bio-industries. Dissemination: the results will be made widely visible to different audiences. Solving societal problems: AMPKIN supports the development of treatments for emerging diseases, such as obesity and type-2 diabetes. Integration of research activities: the project uses EC funding to mobilise national resources. It makes use of the results obtained in other EC-funded projects and is linked to other European initiatives. Training of the work force: the project will contribute to training and life-long learning of the people employed by the project. European added value: in order to tackle the project, AMPKIN brings together strong and unique European expertise that cannot be found in a single country.

Keywords:signal transduction, matabolism, mathematical models, drug development, diabetes,protein kinase, systems biology

Project Coordinator:Prof. Stefan HohmannGothenburg UniversityDepartment of Cell andMolecular BiologyBox 462 (Medicinaregatan 9E)40530 Gothenburg, [email protected]

Prof. Olaf WolkenhauerUniversity of RostockSystems Biology & BioinformaticsRostock, Germany

Prof. David CarlingImperial College LondonMRC Clinical Sciences CentreCellular Stress GroupHammersmith Hospital CampusLondon, UK

Partners

Prof. Jens NielsenTechnical University of DenmarkCenter for Microbial BiotechnologyBioCentrum-DTUKgs. Lyngby, Denmark

Dr. Thomas SvenssonArexis AB (Biovitrum AB) BioinformaticsStockholm, Sweden


Systems biology of the AMP-activated protein kinase pathway



458

This figure shows the use of fluorescence to detect the

localisation of molecules in yeast cells. Red represents protein; blue

represents nuclear DNA. Shown are RNA-associated proteins

that are present A) exclusively in the nucleus, B) throughout

the whole cells, C) exclusively in the cytoplasm. The cellular

localisations of these proteins reflect where they function in

RNA metabolism.

State-of-the-Art:The RIBOSYS project will use systems biology approaches to model RNA metabolism in yeast. In order to develop kinetic models, we will quantify RNA precursors and determine their rates of production, their processing and degradation through the various post-tran-scriptional pathways. Starting with ab-initio models describing the processing and deg-radation of yeast pre-messenger RNAs and pre-ribosomal RNAs, we will produce two comparable mathematical representations and populate the parameters using quantitative experimental data. Manipulation of the parameters will permit predictions to be made about the behaviour of the systems. These will be tested experimentally, using yeast mutants that block specific steps. Imaging techniques will be refined to visualise individual transcripts to determine whether the population data reflect the situation in individual cells. Comparison of the performance of the two models should provide further insights and enrich our under-standing of both pathways.

Scientific/Technological Objectives:

optimised experimental protocols (standard operating procedures) for quantitative analyses of in vivo RNA processing

models with each other and with data existing in the literature

a mathematical representation and populate it with parameters from the experimen-tal data; perturb model parameters and make qualitative predictions about system behaviour and verify against other experimental data

-scripts as normalisation standards for evaluation of processing defects observed in mutants affecting downstream processing/degradation events

wide mRNA polyadenylation status using microarrays

degradation factors on rates of pre-mRNA transcription, processing and degradation -

mates for levels of their degradation. Development of a quantitative model for the flux through the pathway. Testing and refinement of the model by analyses of the effects of different growth conditions and mutations in the ribosome synthesis machinery and in the rRNA precursors

of gene expression, using yeast tiling arrays and wild-type or mutant strains grown under different conditions

thereby test and refine the RNA processing models

Expected Results:A notation for RNAA notation system is needed that permits RNA molecules to be described in a universal format, comparable between species/organisms, which are also compatible with a math-ematical description.Enhanced mechanistic understanding Quantitative analyses will allow us to understand better the relationships between different


RIBOSYS

Project Type:Specific Targeted Research ProjectContract number:LSHG-CT-2005-518280Starting date:1st January 2006Duration:48 months EC Funding:

2 400 000


459

steps, activities and factors in the pathway than has been achieved by qualitative analyses and intuitive interpretations. This will lead to fresh insights into, for example, the key steps at which regulation would most likely be exerted, and should lead to testable hypotheses, which would be addressed experimentally.Enhanced insight across systemsComparison of the pre-mRNA and pre-rRNA models will enrich our understanding of each pathway, providing further insights. This should illuminate equivalent pathways in human cells which are less amenable to direct experimentation, enhancing understanding of hu-man genetic disorders.

Potential Impact:This project will provide valuable new biochemical and genetic tools for the community and will set experimental standards for a variety of other RNA studies.Modelling precursor RNA processing in yeast will be of great benefit for understanding these pathways in human cells, which are less amenable to direct experimentation, and their significance for human genetic disorders.This collaboration will bring together experimental biologists, mathematicians and compu-ter scientists and promote better understanding across these disciplines.

Keywords: modelling, yeast, RNA metabolism

Project Coordinator:Prof. Jean BeggsUniversity of Edinburgh,The Wellcome Trust Centre for Cell Biology The Kings Buildings, Mayfield Road EH9 3JREdinburgh, [email protected]

Dr. Edouard BertrandCentre National de la Recherche Scientifique (CNRS)Universite Montpellier IIInstitut de Génétique Moléculaire de MontpellierMontpellier, France

Zipi Fligelman-ShaqedCompugen LtdComputational Life-SciencesTel Aviv, Israel

Prof. Bernhard DichtlUniversität Zürich-IrchelInstitut fur MolekularbiologieZurich, Switzerland

Partners

Dr. Joanna KufelWarsaw UniversityDepartment of GeneticsBotany FacultyWarsaw, Poland

Dr. Oleg DeminInstitute for Systems BiologySPb Company LtdDepartment of BioenergeticsSaint Petersburg, Russia


Systems Biology of RNA Metabolism in Yeast



460

State-of-the-Art:Life sciences and biotechnology have become extremely important in our knowledge-based economy. However, they have also undergone a revolution in terms of research approaches, infrastructure, technology developments, and costs. The EuroBioFund project will address these challenges by combining expertise and resources in an organized and coordinated manner. Currently, the lack of coordination at the European level is a major obstacle to achieving EuroBioFund’s objectives and is jeopardizing Europe’s position on the global scene. Against this background new strategies are needed to help match research dynam-ics and funding opportunities.

Scientific/Technological Objectives: The EuroBioFund project has been created to foster dialogue and coordination between funding organizations and to promote and coordinate interaction among European life sci-ences researchers and funders. Other important objectives are: i) to provide a platform for funding organisations and life science researchers to foster joint research initiatives through networking; ii) to help organise research communities and facilitate Europe-wide research programmes; iii) to develop a new funding process in Europe by helping to develop joint investments and funding of life sciences research. The project also aims to identify future challenges in the life sciences which require a coordinated European approach for their financing and implementation. Identification of these topics will be based on ideas put forward by the scientific community in line with the strategic goals of public and private funding organisations across Europe.

Expected Results:EuroBioFund will formulate answers to some of the numerous challenges faced by the life sciences in Europe. It will provide a platform for funding organizations and life sciences researchers to create joint research initiatives through networking. It will also organise re-search communities and facilitate research programmes of European scale and scope and promote information exchanges and discussions of research policies. All of the above will be crystallized through an annual conference, consisting of national agencies, intergov-ernmental organisations, private foundations, charities and industry. The conference will provide a framework for dialogue between the various bodies funding the life sciences and help achieve better programme and policy coordination.

Potential Impact:EuroBioFund will help to establish an invigorating new approach to life sciences in Europe through new methods of funding and research, joint investments and information exchang-es, creating a single European market for research. The project will have an impact on European science by bringing together leading scientists and research funding agencies to debate, plan and implement initiatives, resulting in European life sciences becoming much more dynamic and competitive.



907 790

EuroBioFund


461

Keywords:life sciences, networking, research initiatives

Project Coordinator:Prof. Marja Makarow European Science Foundation (ESF)1 quai Lezay-Marnésia67080 Strasbourg, [email protected]

Project Manager:Dr. Wouter SpekEuropean Science Foundation (ESF)1 quai Lezay-Marnésia67080 Strasbourg, [email protected]

Partners


A Strategic Forum for the Dialogue and Coordination of European Life Sciences,

Funders and Performers




462

State-of-the-Art:Mathematical modelling is generally based on (1) the understanding or theory of the way the modelled system behaves, and (2) experimental data (e.g. measures) of elements of the system, and how it reacts under certain conditions. Genetic regulatory networks (or MINs) are very robust; it is therefore possible to model them, although this means that a vast amount of data (thousands of genes and proteins) needs to be considered, with highly redundant interactions. Moreover, the different networks behave with non-linear and non-additive responses. All these characteristics therefore necessitate the development of a large-scale MIN modelling method, allowing one to rationally address the physiopathology of many diseases.

Scientific/Technological Objectives: The overall aim is to develop an innovative systems biology approach, in order to model the dynamics of Molecular Interaction Networks (MINs) related to cell death and survival in the organism. The aim of the VALAPODYN project is to set up the scientific and technological basis, for tasks within the following areas:

functional annotation of genes and proteins, investigation of structure and dynamics of signal transduction and transcription regulatory networks.

use of innovative biomathematics / bioinformatics to integrate experimental MIN data with biological tissue and pathological states data obtained through the use of transcriptomic and proteomic approaches.

establishment of a highly specialised database on the genomics and proteomics of MIN modelling.

analysis of validated animal models of brain pathologies to evaluate gene/protein expression during initial cell death.

extensive multi-level global gene expression profiling using the Affimetrix platform.

application of advanced quantitative proteomics technologies (MALDI, ICAT, 2-DPAGE, Heavy Peptides isotopic dilution) for large-scale proteome screening.

characterization of molecules in the MIN of cell death, the modulation of which should improve or cure neurodegenerative brain disease.

Expected Results: The VALAPODYN network is composed of leading authori-ties in the fields of genomics, proteomics, bioinformatics and neuroscience in Europe. They have decided to join their ef-forts to develop a new innovative System Biology approach

to model the dynamics of Molecular Interaction Networks (MIN) related to cell death and survival in the brain.

This model will be dedicated to the selection of drug targets for human brain. The project will first validate dynamic models for cell death through the characterisation of new poten-tial drug targets in an animal model for epilepsy where neurodegeneration is the initial step of the development of epileptic seizures.

Cell loss and plasticity observed in the hippocampus in a mouse model

of mesiotemporal lobe epilepsy (A) compared to controls (B)

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Project Type:SME-Specific Targeted Research ProjectContract number:LSHG-CT-2006-037277Starting date:1st October 2006 Duration:36 months EC Funding:

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Potential Impact: The development of new and unique dynamic model-ling tools will allow the Consortium to participate in the process of applying integrative biology to pathology research. This should significantly improve the quality of life for EU citizens, by advancing the identifica-tion of new generations of more efficient drug targets; these drugs will be used to treat numerous diseases accounting for mortality and several serious illnesses in the EU, such as cancer, cardiovascular diseases, neurological diseases, etc. Dynamic models will form the basis for the next generation of biological vali-dations for novel therapeutic targets, instead of the methods currently in use. VALAPODYN will also have a significant impact on the ERA, by creating a new foundation for the exchange of fundamental research and knowledge. The development of the international R&D network of SMEs in the biotechnology sector (HELIOS, BIOBASE and SynapCell through INSERM during the project) will accelerate the emergence of the EU as a powerful contender in the global technological market. The VALAPODYN consortium will also allow for optimal use of the available EU resources and human potential.

Keywords: predictive dynamic models, systems biology, molecular interaction networks, cell death and survival, neurodegeneration

Project Coordinator: Dr. Antoine DepaulisGrenoble – Institut des NeurosciencesCentre de Recherche INSERM U 836Université Joseph FourierBP 17038042 Grenoble, France

Dr. Olga Kel-Margoulis,Prof. Edgar WingenderBIOBASE, GmbHWolfenbuettel, Germany

Dr. Todor VujasinovicHELIOS BiosciencesCreteil, France

Dr. Despina SanoudouFoundation of Biomedical Researchof the Academy of Athens (FBRAA)Molecular Biology DivisionCenter for Basic ResearchAthens, Greece

Prof. Edwin de PauwUniversity of LiegeDepartment of ChemistryMass Spectrometry LaboratoryLiege, Belgium

Prof. Hermona SoreqHebrew University ofJerusalemDepartment ofBiological ChemistryInstitute of Life SciencesJerusalem, Israel

Dr. Raffaella CatenaAlma Consulting Group ALMALevallois Perret Cédex, France

Partners


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State-of-the-Art:Agriculture is crucial to humankind. Crops supply food, animal feed, chemicals, pharma-ceuticals and renewable sources of materials and energy. Plant growth results in biomass accumulation, which, in turn, is the major determinant of crop yield. Despite its importance and complexity, plant growth is, however, a poorly understood trait. Plants evolved multicel-lular bodies independently from animals and fungi. This evolutionary step, coupled with the unique photosynthetic lifestyle, explains why plants rely on mechanisms for growth and development that are unique. It is therefore crucial to investigate how these mechanisms function in plants in order to forge novel technological tools for tomorrow’s agriculture.

At the present time, Arabidopsis thaliana is the only plant species for which the necessary resources are accessible for studying complex traits. The typical growth and development of Arabidopsis has been accurately described, providing a solid platform on which to base experimental studies of growth processes. Arabidopsis also has unparalleled genom-ics resources, including high quality genome sequence and annotation comprising over

30,000 genes of which 26,000 code for proteins; tagged mutant alleles for 73 percent of these genes; a choice of DNA arrays to investigate genome transcrip-tion; modification and polymor-phisms; comprehensive transcrip-tome, proteome and metabolome atlases; cloned repertoires for functional proteomics; and RNA interference. Furthermore, haplo-type maps of unprecedented den-sity for any eukaryote, including humans, will soon be released for 20 Arabidopsis ecotypes, helping association mapping. Finally, the genome sequencing of close rela-tives (Arabidopsis lyrata, Capsel-la rubella) has been launched and will help to improve the accuracy of comparative genome analyses.

Growth results from a complex network of processes occurring at different organisational levels (whole plant, organ, cell, molecu-lar module, molecule). Some of the key factors involved in these processes have been identified in the past decades via (eco)physiol-ogy, cell biology and molecular genetics but many more still have to be found. The major challenges are the elucidation of the interac-tion networks (eg macromolecular complexes, cell-to-cell signalling etc) that constitute each of the dif-ferent levels of organisation, and the understanding of how these



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different levels are linked. For example, plant growth regulators such as auxin and cytoki-nin, which coordinates the integration of growth at the cell-organ and organ-whole plant interfaces, have been extensively studied in plants for many years. However, although a few components of their biosynthetic and signalling networks have been uncovered, very little is known about how they impinge on the machinery underlying cell expansion and cell division.

Scientific/Technological Objectives: The main research goals of the project are: (i) to investigate systematically the components controlling growth processes in plant cells (genome sequences, proteins, metabolites); (ii) to understand how they coordinate their action; (iii) to explain quantitative growth phenotypes at the molecular level. The growth process will be studied within a common research frame-work of five work packages (WP). In particular, the project will generate high-throughput (HTP) quantitative data defining growth variables, genetic components of growth, the mo-lecular composition of leaves at successive stages of development, molecular interaction networks and small molecules affecting growth (WP1-5). Finally, mathematical and statisti-cal methods to model and predict leaf processes will be developed and tested in close collaboration with computer scientists, statisticians and experimentalists (WP7). The suite of analytical tools will be exhaustively tested and modified before being made available as a package of integrated systems biology applications and as web services.

The technology platforms at the core of the research programme have been selected to provide quantitative information at all relevant levels of organisation: growth variables re-corded at the level of whole plant, organ and cell; profiling of the genome, transcriptome, proteome and metabolome; protein-protein and protein-DNA interaction networks. They can be ranked in four classes:

1) Well-established methods, but only exceptionally applied at this scale to study a single biological system in an integrative framework, requiring standardisation of existing protocols and datasets; they include microarray transcript profiling, HTP real time RT-PCR, flow cytometry, large-scale recombinational cloning methods, GFP-fusion subcel-lular localisation, yeast two-hybrid, tandem affinity purification, mass spectrometry, chromatin immunoprecipitation.

2) More advanced profiling techniques; they include large-scale SNP genotyping, sys-tematic enzyme profiling (>40 activities) of identical samples, ITRAQ for relative pro-tein quantification, cell flow sorting, FT-IR microspectroscopy, bimolecular fluorescence complementation.

3) Novel HTP techniques requiring extensive development and aimed at taking full ad-vantage of Arabidopsis as a model species; they include automated leaf structure analysis at cell-level resolution, in planta two-hybrid based on antibiotic selection, Arabidopsis cell-based assays and high content screening to study systematically the results of genetic (genome scale) or chemical (library scale) perturbations.

4) Software tools enabling data integration and biological system modelling.

Expected Results: AGRON-OMICS will yield four types of results:1) Novel analytical pipelines will be developed to measure cellular processes across

multiple levels, including mass spectrometry, remote macroscopic and microscopic imaging and environmental control. These research efforts require the generation


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of specific informatics infrastructure, common data standards and analytical tools required to capture, store, distribute and analyse high-throughput data. The resulting knowledge and equipments will be accessible to the participant’s laboratories and the know-how will be propagated further through training programmes and scientific exchanges.

2) Novel well-documented integrated software applications will form the basis for a “plant systems biology toolbox”. These applications will be constructed to allow adaptability and integration with pre-existing software, and will be made freely available to other scientists working in systems biology.

3) Transgenic lines, genetic stocks and constructs created or characterised in the project’s framework will be disseminated via stock centres.

4) AGRON-OMICS will generate primary data and biological knowledge including the identification of genes/loci and molecules that control growth, and the construc-tion of models that explain how these components interact and function across path-ways and processes. The information relative to leaf growth control networks will be exploited to postulate how best to combine inputs to increase plant biomass produc-tion via improved germplasm and the use of growth regulators. AGRON-OMICS results will be published as soon as practicable both in peer-reviewed articles and via online databases. Unlike most data produced in biological investigations, data obtained in this project will be represented according to standard formats, in the context of networks, and supported by ontology.

Potential Impact: AGRON-OMICS will have a significant impact in several research ar-eas. Firstly, the consortium is pioneering systems biology approaches in order to understand biological complexity in the context of a mul-ticellular organism, and across multiple levels of organisation (cells, tissue, and whole organism). The tools, techniques and expertise built up in the course of the project may be used to inform research on the complex mechanisms involved in human disease, which result in alteration of cell growth and development. In particular, current knowledge shows that core molecular processes regulating cell pro-liferation and cytoplasmic growth are conserved between plants and animal cells. Secondly, progress in the mechanistic analysis of these molecular pathways in plants may contribute fundamental insight into the biology of human cancers. In addition, in-depth knowledge and modelling of specific molecular pathways may result in the potential to develop translational research projects for biomedical purposes (eg production of natural compounds for therapeutic use, and produc-tion of vaccines against human diseases in plants). Thirdly, growth processes are difficult to characterise in mammalian species at a scale comparable to the one which is the target of AGRON-OMICS, or without breaching ethical barriers. In this respect, the ability to systematically genotype, phenotype and profile at the molecular level thousands of individual plants in a unique asset of this project and will be of great value in developing similar system level research in mam-mals. Fourthly, AGRON-OMICS may help to reduce the environmen-

tal impact of agriculture. Agricultural practices withdraw about 70 percent of groundwater resources worldwide. In the long-term, irrigation increases soil salinity and leads to the permanent destruction of otherwise fertile soils. Using plants that have improved water use efficiency will help contain the amount of water consumed by agriculture and mitigate the impacts of irrigation. Finally, a major goal in plant science is the development of crops as a source of renewable resources and industrial feedstock. In the coming years, 20 percent of transport energy will hopefully come from renewable resources. As leaves are the primary harvesters of energy, the integrated knowledge of mechanisms controlling metabolism,


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Project Coordinator: Dr. Pierre HilsonGhent UniversityFlanders Institute for Biotechnolgy (VIB) VIB Department of Plant Systems BiologyTechnologiepark 9279052 Ghent, [email protected]

Project Manager:Dr. Fabio FioraniGhent UniversityVIB Department of Plant Systems BiologyTechnologiepark 927 9052 Ghent, [email protected]

Prof. Herman HöfteInstitut National de la Recherche Agronomique (INRA)Institut Jean-Pierre Bourgin (IJPB)Versailles, France

Dr. Christine Granier Institut National de la Recherche Agronomique (INRA)Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE)Montpellier, France

Dr. Claire Lurin Institut National de la Recherche Agronomique (INRA)Unité de Recherche en Génomique Végétale (URGV)Evry, France

Prof. Lothar WillmitzerMax-Planck Institute of Molecular Plant PhysiologyPotsdamGolm, Germany

Prof. Detlef WeigelMax-Planck Institute for Developmental BiologyDepartment of Molecular BiologyTübingen, Germany

Prof. George CouplandMax-Planck Institute for Plant Breeding ResearchCologne, Germany

Prof. Wilhelm GruissemETH ZurichSwiss Federal Institute of TechnologyInstitute of Plant SciencesZurich, Switzerland

Prof. John DoonanJohn Innes CenterNorwich Research Park Department of Cell and Developmental BiologyNorwich, UK

Dr. Vicky Buchanan WollastonUniversity of WarwickWarwick Systems Biology CenterWarwick, UK

Partners

growth and environmental responses developed in this project will provide a strong founda-tion for future work in this area.

Keywords: Arabidopsis, plant, leaf, functional genomics, growth, integrative biology, systems biology

Prof. Sean MayEuropean Arabidopsis Stock Centre (NASC)University of NottinghamLoughborough, UK

Prof. Gerco AngenentPlant Research International (PRI)BioscienceWageningen, The Netherlands

Prof. José Luis MicolUniversidad Miguel HernándezInsituto de BioingenieríaDivisión de GenéticaElche, Alicante, Spain

Dr. Johan GeysenMaia ScientificGeel, Belgium


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State-of-the-Art:BaSysBio aims to achieve major breakthroughs in the understanding of the regulation of gene transcription in bacteria, on a global scale. The highly dynamic gene regulation is me-diated by transcription factors (TFs), which trigger or repress the expression of their target genes. Transcription control is embedded into a hierarchical flow of information from genes to phenotype, in which many regulatory steps can occur.

BaSysBio adopts a systems biology approach, in which quantitative experimental data will be generated for each step of the information flow, and will fuel computational mod-elling. High-throughput technologies (such as living cell arrays, tiling DNA microarrays, multidimensional liquid chromatography proteomics and quantitative metabolomics) will be developed, in conjunction with new computational modelling concepts, so as to facilitate the understanding of biological complexity. In addition, models will simulate the cellular transcriptional responses to environmental changes, and their impact on metabolism and proteome dynamics. The iterative process of simulations and model-driven targeted experi-ments will generate novel hypotheses about the mechanistic nature of dynamic cellular re-sponses, unravel emerging systems properties and ultimately provide an efficient roadmap to assist in tackling novel, pathogenic organisms.

This system-based strategy will enable BaSysBio not only to understand how transcriptional regulation and metabolism are quantitatively integrated at a global level, but also to under-stand cellular transcriptional responses in conditions mimicking pathogenesis. Finally, the project will validate the general applicability of the findings, and integrate the modelling-experimental strategy developed in the highly tractable B. subtilis model, towards an un-derstanding of regulatory networks controlling pathogenesis in disease-causing bacteria. BaSysBio will make a significant contribution towards overcoming the structural obstacles that hinder the development of systems biology in Europe.

Scientific/Technological Objectives: The overall objective of BaSysBio is to generate quantitative data about the network compo-nents at all the levels of the information flow, in order to understand, at the system’s level, the global regulation of gene transcription in bacteria. To achieve this objective, BaSysBio will focus on developing and adapting high-throughput technologies to facilitate quantita-tive measurements, in conjunction with developing and validating computational systems biology methodologies; this will enable quantitative interpretation of the data and unravel the underlying principles of regulatory network interactions.

At a technological level, BaSysBio aims to develop and adapt high throughput technologies for the quantitative determination of the cellular transcriptional responses to standardised genetic and environmental perturbations, as a function of time. In addition, the project will develop new concepts in computational modelling and simulation of regulatory networks. More specifically, the project involves the following activities:

1) Using a novel multi-purpose DNA tiling microarray to identify, in a systematic and unbiased way, all the RNA transcripts (mRNAs and small RNAs) produced in the B. subtilis cells, and to facilitate a comprehensive inventory of the cis-acting regulatory sequences bound by transcription factors;

2) Bridging technological gaps by developing living cell arrays which allow the ge-


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nome-wide determination of promoter activities as a function of time during the cell responses;

3) Exploiting the latest developments in mass spectrometry and non-gel-based protein separation techniques, to quantify proteins and determine their modifications in re-sponse to perturbations;

4) Developing methods for quantitative high-throughput metabolomics, using comple-mentary mass spectrometry-based approaches (e.g. GC-TOF, LC (CE)-ESI-TOF and LC-MS/MS), to analyse the vast chemical diversity of intracellular metabolites in response to perturbations;

5) Extending the use of parallel 13C-flux analyses to novel substrates; 6) Developing chromosome engineering tools, based on the recombination systems of

prophages of Gram-positive bacteria, to facilitate high throughput tagging of genes in Bacillus subtilis and related pathogens;

7) Developing new concepts and methodologies to improve modelling and simulation of regulatory networks. This includes standardised and unequivocal representation of networks basic components and interactions to be modelled; hybrid mathematical models combining constraint-based approaches and detailed dynamic modelling.

Expected Results: In contrast to the present large-scale and mostly descriptive studies on genome-wide data sets, BaSysBio’s systems biology approach relies on iterative cycles of model prediction, system perturbations and system response monitoring, which will incrementally refine the models, thereby generating quantitative understanding of the in vivo operation of complex regulatory networks. This system-based approach will combine an unprecedented number of different experimental approaches, to generate data in a limited number of standard-ised conditions for two biological processes, thus considerably reducing the need to make hypotheses.

BaSysBio has made several technological contributions: 1) B. subtilis living cell arrays to study the temporal regulation and the design principles of the transcription networks that control the timing of gene expression; 2) efficient chromosomal engineering techniques for Gram-positive bacteria, including the pathogens B. anthracis and S. aureus; 3) parallel flux analysis based on 13C-labelling experiments in microtiter plates; and 4) adaptation and improvement of existing high throughput technologies for the specific project needs. Significantly, the developed methodologies will have additional benefits beyond the scope of this project. The novel conceptual aspect of BaSysBio is the development of a theo-retical framework for comprehensive, system-wide data interpretation. This differs from the current fo-cus of much of systems biology, which concentrates

Proteomic analysis of mutants of Bacillus anthracis to oxidative stress. The ability of Bacillus anthracis to resist oxidative stress is a key component of this bacterium’s ability to resist the innate immune response and to cause infection. To determine the relative contributions of two genes, hemH2 encoding a ferrochelatase and katB encoding a catalase to combating oxidative stress, mutant cells were grown in the presence or absence of the oxidising agent hydrogen peroxide and the resulting protein profiles determined by two-dimensional gel electrophoresis. The resulting images were false-coloured (untreated = green; treated = red), superimposed on each other and warped so that corresponding proteins were coincident on the resulting image. Proteins whose expression was up- regulated in the mutant in response to oxidative stress appear as red spots. (Dr. Susanne Pohl, University of Newcastle upon Tyne, UK)


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on signalling networks and metabolic networks recon-structed through compara-tive genomics. It extends conceptually beyond data acquisition and interpreta-tion approaches, through quantitative interpretation with the mathematical rigor of computational models. By integrating the multiple regulatory levels in a bio-logical system, models will have high potential to simu-

late them accurately, to predict novel systems properties and properties of uncharacterised systems components, and to drive mechanistic understanding of the global regulation of B. subtilis metabolism, and of the adaptive transcriptional responses to stresses encountered by cells during pathogenesis.

Potential Impact: BaSysBio embraces the broad issues of the integration of transcriptional regulation and me-tabolism at a global level in cells. It thereby has the ambition to understand the general prin-ciples, as well as the mechanistic details of regulatory networks, and to drive key discoveries and applications in systems biology. An important element that is critical for the success of BaSysBio, is the integration effect generated by concentrating resources in European re-search.

The common development and use of standardised methodologies, procedures and tools will generate a large and unique body of data that will potentially allow a genuinely global under-standing of genetic control in bacteria. The BaSysBio iterative theoretical-experimental strat-egy, which provides quantitative data about the regulatory steps in the information flow from DNA to phenotype, will become applicable to multiple cellular processes. This will open the way to the construction of mechanistic models integrating basic regulatory components and their combined interactions at a global scale, potentially leading to in silico models simulating the dynamic behaviour of the whole cell. By elaborating on new concepts in computational modelling, BaSysBio will provide new ways to grasp biological complexity, and will reveal as yet unknown properties of dynamic biological systems. This will open entirely new fields of investigation to experimental biology.

The new knowledge and the integrated modelling/experiments strategy developed by BaSys-Bio will be applicable to other micro-organisms, and will promote understanding of the global control of pathogenesis, thus leading to potential new strategies to combat disease-causing bacteria. The research in BaSysBio will yield a wealth of detailed knowledge about the key processes that lead to a bacterial cell ‘fit for pathogenesis’, and will also help translate gained knowledge into practical applications for the control of infectious diseases. Along the same lines, BaSysBio will facilitate the exploitation of the beneficial capabilities of microbes.

Keywords:

transcriptomics, metabolomics, fluxomics, proteomics, quantitative biology, modelling, bio-informatics, living cell array, DNA tiling microarrays, chromosome engineering, Bacillus, Staphylococcus

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PartnersProject Coordinator: Dr. Philippe NoirotInstitut National de la Recherche Agronomique (INRA)147 rue de l Université75338 Paris, [email protected]

Project Manager:Caroline Sautot INRA Transfert10 rue Vivienne75002 Paris, [email protected]

Dr. Alexander JungApplera Deutschland GmbHDarmstadt, Germany

Dr. Franck MolinaCentre National de la Recherche Scientifique (CNRS)Faculté de Pharmacie CPBS-CNRS UMR5160Montpellier, France

Dr. Julio R. BangaConsejo Superior de Inestigaciones CientificasMadrid, Spain

Prof. Michael HeckerErnst-Moritz-Arndt Universität GreifswaldInstitut fur MikrobiologieGreifswald, Germany

Prof. Uwe SauerSwiss Federal Institute of Technology (ETH Zurich)Department of BiologyInstitute of Molecular Systems BiologyZurich, Switzerland

Dr. Othmar Pfannes Genedata AGBasel, Switzerland

Dr. Benno SchwikowskiInstitut PasteurDepartment of MicrobiologyParis, France

Dr. Edda KlippMax-Planck Institute for Molecular GeneticsBerlin, Germany

Prof. Jan Maarten Van DijlUniversity Hospital GroningenDepartment of Medical MicrobiologyGroningen, The Netherlands

Prof. Kevin DevineTrinity College DublinSmurfit Institute of GeneticsDublin 2, Ireland

Dr. Hanne Ø. JarmerTechnical University of DenmarkCenter for Biological Sequence analysis Lyngby, Denmark

Prof. Colin HarwoodUniversity of Newcastle upon TyneDepartment of Cell and Molecular BiosciencesNewcastle upon Tyne, UK

Prof. Anthony WilkinsonUniversity of YorkDepartment of Chemistry York, UK

Dr. Peter J. LewisUniversity of Newcastle of AustraliaSchool of Environmental and Life Sciences Callaghan, Autsralia


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State-of-the-Art:Chronic diseases are usually the result of interactions between individual susceptibility and different environmental and/or lifestyle factors, and are often modulated by multiple genes. The interplay between these factors determines disease phenotype and hence, the prognos-tic and therapeutic implications of the disease. This interplay between genetically predeter-mined susceptibility and disease phenotype, can in turn be revealed by computer analysis integrating clinical and biomedical data. Some examples of the application of computer analysis to clinical practice are the classification and prognosis of ovarian cancer (Wu et al, 2003), the analysis of myocardial perfusion images and cardiograms (Fletcher et al, 1978) and the development of a screening device for the diagnosis of heart murmurs (Bhatikar et al, 2005). In addition, several projects in the European Union are implementing information technology-based services for diabetes management (Bellazzi et al, 2004). However, all the approaches currently implemented in clinical practice use very limited datasets, despite the availability of vast amounts of data from various life science disciplines since the “-omics” revolution. Only by integrating genomic, proteomic and metabolomic data can knowledge that is useful for the understanding and treatment of complex human pathologies, begin to be obtained. This is the goal of the BioBridge project.

Scientific/Technological Objectives:BioBridge will focus on the application of simulation techniques on top of multilevel data, in order to create models for understanding, how molecular mechanisms are dynamically related to complex diseases at the systemic level.The BioBridge objectives are twofold. Firstly, a bioinformatic aspect will involve the de-velopment of software for integrated genomic, proteomic, metabolomic and kinetic data analysis, in order to build a bridge between basic science and clinical practice. Secondly, a biomedical aspect will focus on understanding the distortion of cellular metabolism that is associated with certain target diseases. The diseases in question are congestive heart failure (CHF), chronic obstructive pulmonary disease (COPD) and type II diabetes. The available facts strongly indicate that these diseases comprise a cluster of chronic conditions, all of which are associated with nitroso-redox imbalance. The integration of data into a dynamic framework will enable the development of the first kinetic model of the metabolism shared by COPD, CHF and type II diabetes, thereby revealing the common and individual traits of these three complex diseases.

Expected Results:After 30 months, BioBridge will have achieved the following goals:

1) Creation of a structured database for the collection of clinical information relating to COPD, CHF and type II diabetes;

2) Identification of the metabolic pathways implicated in the target diseases; 3) Recording of genomic, proteomic, metabolomic and kinetic information into the rel-

evant structured databases; 4) Development of a software product designed for specific disease-related data search-

ing; 5) Development of standards for the different levels of data, which will be useful for their

integration from genomic and metabolomic databases, and from specific proteomics and metabolomics profiling experiments, including microarray analysis and stable isotope tracer data.;

6) Development of protocols for transferring data from the structured databases into dynamic models;

7) Using a differential equation approach, the design and development of an innova-


BioBridge

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2006-037939Starting date:1st December 2006Duration:30 monthsEC Funding:

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tive simulation environment that will accommodate the dynamic behaviour of com-plex networks, and in particular the metabolic pathways that are altered by the target diseases;

8) Development of generic tools that will be clinically useful beyond the target diseases addressed during the lifetime of the project.

Potential Impact:The main outcome of the project will be a protocol for organising multilevel data related to the target diseases into a convenient form for use in the construction and refinement of kinetic models of intracellular metabolic pathways. The software developed will be applica-ble to more general cases of multilevel data integration. In helping to provide insights into the key molecular mechanisms that determine poor prognosis in the CHF/COPD/type II dia-betes disease cluster, BioBridge will generate novel strategies for personalised prevention and enhanced delivery of patient care. Existing computational models have already proved powerful in this context. For example, one of the BioBridge partners has recently developed a statistical framework for analysis of multivariate models from large-scale datasets. This software environment (GALGO) uses a genetic algorithm search procedure, coupled with statistical modelling methods, for supervised classification and regression. BioBridge will build on and improve this and other computational models.

Keywords: diabetes, chronic obstructive pulmonary diseases, COPD, chronic heart failure, systemic effects, genomics, proteomics, metabolomics, modelling

PartnersProject Coordinator:Josep RocaInstitut d’InvestigacionsBiomèdiques August Pi i Sunyer (IDIBAPS)Villarroel 17008036 Barcelona, [email protected]

Dr. Marta CascanteUniversity of BarcelonaInstitut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Barcelona, Spain

Peter AronssonMathCore Engineering ABLinköping, Sweden

John BrozekGenfit LaboratoriesGenfit SALoos, France

Dieter MaierBiomax Informatics AGMartinsried, Germany

Dr. Jordi Villa i FreixaUniversitat Pompeu FabraComputational Biochemistry and Biophysics LaboratoryBarcelona, Spain

Dr. Pranav SinhaInstitut für Medizinische und Chemische LabordiagnostikLandeskrankenhaus KlagenfurtKlagenfurt, Austria

Dr. Francesco FalcianiUniversity of BirminghamSchool of BiosciencesBirmingham, UK


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State-of-the-Art:The goal of systems biology (SB), or ‘integrative biology’, is to progress from a qualitative, static description of the constituents of living cells, to a quantitative, dynamic understanding of their systemic and functional properties. It is an interdisciplinary endeavour that has emerged from the fields of genomics and bioinformatics. The obvious value of predictive SB models for the elucidation of pathological processes beyond the cellular level, calls for closer investiga-tion of the potential applications of such models to medical research. Medical SB (MSB) must demonstrate the ability to cross levels: from cells to organs and organisms, from cell function to physiological phenomena, and from model organisms to human diseases.Pioneering studies in the modelling of whole organ function have already demonstrated that models can correctly predict certain physiological and pathological functions of the heart, for example. However, SB as a field is in its infancy and this, combined with its emphasis on basic research, its focus on model organisms and individual intracellular pathway, are all obstacles to the application of SB to medical research. Although many SB groups are working on disease-related models and pathways, there is little crossover between this basic research and clinical research. Europe urgently needs to build capacity, both in terms of knowledge and in terms of personnel trained to bridge the gap between the two disciplines, so that the field of MSB can be launched in a correct and timely fashion.

Scientific/Technological Objectives:SYSBIOMED seeks to explore the potential application of SB to medical research, including the development of drugs and other therapies. It will do this through a series of workshops focusing on topics at the cutting edge of SB and physiology, which will be organised by a core group of young scientists working in relevant areas.The workshops will explore how SB can be applied to research in major disease areas identified by the World Health Organization (infectious, neurodegenerative, metabolic and cardiovascular diseases and cancer). They will promote the formation of collaborations, teams and research programmes, and they should also contribute to the breaking down of barriers — between theoreticians and clinicians, between basic researchers and those interested in medical applications/drug development, and between newcomers and estab-lished groups. These workshops will provide valuable opportunities for young academics to enter the SB field, for theoreticians to meet experimentalists, and for representatives of industry to meet academic researchers. Scientists from industrial enterprises are especially encouraged to participate, so that they may assess the potential outcomes of applying SB to medicine as early as possible.

Expected Results:SYSBIOMED intends to provide an appropriate and timely response to the imminent chal-lenge of applying SB to medical research. The field of MSB has potential for getting off to a promising start, provided that Europe’s strengths are exploited wisely. Translational by nature, it is expected to accelerate progress in medicine, in particular by opening up new avenues to personalised medicine and to the development of multi-drug therapies. The potential translation of MSB results into new markets will have a positive impact on both large and small enterprises.SYSBIOMED will supply decision-makers with useful information on the potential chal-lenges and opportunities for action in the MSB field. The multidisciplinary nature of the consortium means that it is well-placed to achieve its primary goal, which is to build a network of talented young researchers who will drive SB towards medical applications. SYSBIOMED will also benefit from an earlier, successful SSA, EUSYSBIO, when building its network of experts.


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The involvement of scientific journals in the SYSBIOMED consortium will be valuable for informing non-specialists about MSB, for attracting young scientists (including theoreticians and medical researchers) to the field, and for alerting ‘scouts’ from the biotechnology and pharmaceutical industries to new advances. To this end, SYSBIOMED is pleased to have the support of the journals The Scientist, Nature Biotechnology and IEE Proceedings Systems Biology. The participating media will also prove extremely useful for disseminating SYSBI-OMED’s results.

Potential Impact:SYSBIOMED complements both ongoing and planned European SB initiatives. A first step towards the establishment of MSB as a new discipline, has recently been taken by the Eu-ropean Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), which organised a workshop on the therapeutic applications of computational biology (TACB). Although this workshop emerged from a bioinformatics background, SYSBIOMED will con-sider its main findings and extend them, placing a stronger emphasis on the practical trans-lation of SB-related research into clinical applications, and identifying the disease areas which stand to benefit most from a coordinated SB approach. A representative of EMBL-EBI is a member of the SYSBIOMED core group, and TACB workshop organisers will be invited to join the consortium’s advisory board.Regarded as a branch of translational research, MSB is likely to benefit from the spirit of the younger generation of European SB experts. The success of SYSBIOMED will depend on the efficient cooperation of this still-small community, but the consortium is also commit-ted to joining forces with all relevant partners, including industry (both big pharma and SMEs). The project could lead to strategy adjustments in the healthcare sector, with respect to identifying the most promising therapies and technologies emerging from this branch of biomedical research. It is intended that the young scientists’ network should provide a consulting service beyond SYSBIOMED’s lifetime.

Keywords: systems biology, medicine, postgenomics

Project Coordinator:Dr. Karsten SchürrleDECHEMA e.V.Theodor-Heuss-Allee60486 Frankfurt am Main, [email protected]

Prof. Olaf WolkenhauerRostock University Systems Biology and BioinformaticsRostock, Germany

Carole Moquin-PatteyEuropean Science Foundation (ESF)European Medical Research CouncilsStrasbourg, France

Partners


Systems Biology for Medical Applications



476

State-of-the-Art:Bioinformatics methods for diagnostic screening are a bottleneck in current biomedical research. While exploratory methods – such as statistical hypotheses testing, clustering of gene expression profiles and classification methods – have been successful in the detection of molecular markers for interesting diseases, these techniques fail to validate these markers in their gene regulatory context and to integrate other data sources relevant for diagnostic purposes. For these tasks, novel modelling techniques, network analyses, and data integra-tion methods are indispensable. The analysis of processes involved in the course of complex polygenic diseases, such as obesity and type-2 diabetes, is in fact a multi-step procedure that has to cope with data from diverse experimental functional genomics platforms (gene and protein expression), physiological data, environmental factors, and others.

Scientific/Technological Objectives: The project SysProt aims to develop a new paradigm for the integration of proteomics data into systems biology. The goal is to gain relevant knowledge on the biological processes that are important for human health and to use this knowledge for the purpose of disease modelling. In order to achieve this objective, an innovative, explorative biological systems approach (on both the molecular and the physiological level) will be adopted, with a strong focus on protein function and modification. SysProt will produce proteomics data, indispensable for the identification of novel circulating protein factors, and post-translational protein modifica-tions that are important for the onset, dynamics, and progression of complex diseases. Data generation will be complemented by the development of computational analysis meth-ods for these novel data types and the creation of adequate modelling technology. The

project will benefit from the utilisation of established mouse disease models, existing benchmarking modules for compu-tational analysis, and the functional genomics platforms de-veloped by and accessible to the partners. In particular, the consortium aims to demonstrate newly developed technologies in a proof-of-principle study within an obesity-induced type-2 diabetes mouse model. The project consortium is headed by an SME and includes four academic partners from three European countries. This composition of commercial and academic interests guarantees high-level scientific research, as well as a strong focus on the commercial relevance and exploitation of the project’s results.

Expected Results: An important feature of the project’s approach will be the integration of phenotypic and physiological parameters with proteomics data and expression profiles from time course series representing the onset and progression of insulin resistance of type-2 diabetes. The expected results of this project are:

1) Model the knowledge about biological objects (genes, proteins and protein complex-es) in the context of nutrition and type-2 diabetes in equivalent computer objects;

2) Integrate heterogeneous data types from proteomics and functional genomics ap proaches;

3) Develop and use a prototype framework for the automatic detection and localisation of protein modifications on high-accuracy mass spectrometry data;

4) Generate specific proteomics and functional genomics data providing the necessary information for disease model generation with an appropriate animal model;

Mouse model (left NZO mouse in comparison to a C57BL/6

mouse) used in SysProt for the analysis of obesity induced type-2 diabetes. C57BL/6J mice serve

as control strain.



2 097 268

SysProtwww.sysprot.eu


http://www.sysprot.eu

477

5) Gain new knowledge on the pathways and marker genes relevant for obesity-in-duced type-2 diabetes disease progression that will lead to the discovery of novel diagnostic biomarkers for disease susceptibility;

6) Simulate perturbations of the disease-relevant pathways;7) Develop tools and methods for the correlation of phenotype and genotype;8) Accelerate the identification and positional cloning of disease candidate genes by

combining gene expression, proteomics, genotype, and clinical data;9) Set up a knowledge base that integrates all available data and methodology as an

exploitable product for disease modelling.

The main result of the project will be an exploitable prototype that allows medical research-ers to draw predictions on disease-relevant pathways.

Potential Impact: Systems biology approaches will increasingly have an impact on Life Science and Health pro-grammes in general and on drug development in particular. They provide a huge potential for improving the European competitiveness. Through the application and broadening of systems biology approaches, the SysProt project is likely to impact on the scientific understanding of biological processes, with particular relevance to improving human health and wellbeing.

Keywords: systems biology, fundamental biological processes, proteomics, bioinformatics

PartnersProject Coordinator: Dr. Arif MalikMicroDiscovery GmbHNutriSystemicsMarienburger Str.110405 Berlin, [email protected]

Dr. Hadi Al-HasaniDeutsches Institut fuer Ernaehrungsforschung Department of PharmacologyNuthetal (OT Bergholz-Rehbruecke), Germany

Dr. Ralph SchlapbachEidgenössische Technische Hochschule, ZürichFunctional Genomics Center ZurichZurich, Switzerland

Prof. Rainer CramerThe University of Reading The BiocentreReading, UK

Dr. Ralf HerwigMax-Planck Institute for Molecular GeneticsDepartment Vertebrate GenomicsBerlin, Germany


System-wide analysis and modelling of protein modification



478

State-of-the-Art:The biotechnology industry is constantly searching for better hosts for the production of bi-opharmaceuticals and enzymes of diverse origin. The Gram-positive soil bacterium STREP-tomyces has already proved an invaluable host for this purpose, since it can secrete several heterologous proteins in satisfactory amounts. However, in order to optimise strain selec-tion, knowledge is required, concerning the following points: (1) How protein secretion processes are integrated within the metabolome, and how they interact; (2) How heterolo-gous protein secretion stresses the metabolome and induces negative cellular cascades.

Systems biology, the science of analysing and modelling genetic, macromolecular and metabolic networks, provides the means to address these questions. By combining bio-chemical information with genetic and molecular data, the Streptomics consortium hopes to gain novel insights into the functions of genes related to protein secretion, as well as how that protein secretion mechanism responds to external and internal stimuli. With a better understanding of this mechanism at the cellular level, it should be possible to optimise pro-tein secretion.

*Automated protein engineering:* A precision

robot arm retrieves a custom manufactured 1536-well plate in one corner of a room full of robotics-compatible equipment

including nano-litervolume liquid handlers,single cell sorters,

humidified incubators, heating and cooling blocks, centrifuges,

confocal laser-based plate readers and other equipment

integrated for fully automated high throughput protein

engineering at Direvo Biotech AG in Cologne, Germany.


Streptomics


2 850 851

www.streptomics.org


http://www.streptomics.org

479

Scientific/Technological Objectives:Streptomics aims to enhance the production of heterologous proteins, using Streptomyces as a host. More specifically, it has the following goals:

1) To evaluate Streptomyces lividans as a cell factory for the production of heterologous proteins of interest;

2) To investigate the transcriptome and proteome of the host strain under different growth conditions, with different expression/secretion vectors, and using different fermenta-tion strategies, in order to identify the genes important for optimal cell performance, with respect to heterologous protein secretion;

3) To analyse metabolic flux control and flux balance with a view to engineering meta-bolic pathways found in a Streptomyces background, and hence to exploit cellular pathways which provide improved energy transduction, balanced growth and su-pramolecular assembly;

4) To engineer better production/secretion strains of Streptomyces based on the above, and based on information about secretion bottlenecks that will be identified through the production of muteins, either via direct mutation of specific amino acids, or by directed evolution;

5) To optimise the protein production process.

4. The secretome Platform

6. Production process optimization

5. Strain engineering Platform

3. MetabolomicsPlatform

2. Analytical Platform

SecA optimization

2.1 Transcriptomics

2.2. Proteomics

Flux analysis In silico In vitro In vivo

1. Heterologous genes cloned

Improved production process forprotein of interest

4. Bioinformatics Platform

PMF and PspA

SPase binding

• Rational mutagenesis

• Directed evolution

Fig. 1: The secretome Platform: Production process optimization

Fig. 2: Long oligo based/ S. coelicolor /microarray (courtesy of Eurogentec)

Fig. 1 Fig. 2


Systems biology strategiesand metabolome engineering for

the enhanced production ofrecombinant proteins in Streptomyces


480

Expected Results:Based on a better understanding of metabolome-secretome interplay, strategies for im-proved protein secretion will be designed. These will combine better energy generation and directed energy consumption for either cell mass production or heterologous protein secretion. Ultimately, a “toolbox” of Streptomyces strains will be engineered and refined, which optimally over-secrete proteins of interest during fermentation.

Consequently, Streptomics will generate knowledge which will assist SMEs in the biotech-nology and other industries to develop new and more efficient systems for the industrial production of heterologous proteins, using S. lividans as a cell factory. These systems will be useful in both red (medical) and white (industrial) areas of biotechnology.

Potential Impact:This project aims to increase the number of efficient cell factory platforms for the production of heterologous proteins important in health, biocatalysis and the environment, using Strep-tomyces as a host. It will therefore contribute to a competitive, knowledge-based economy and sustainable development in Europe, by serving the needs of a research-intensive indus-trial sector in which many SMEs have traditionally been involved.

Keywords: systems biology, Streptomyces, protein secretion, enzymes, biop-harmaceuticals, directed evolution, metabolomics, transcriptomics, proteomics

Fig. 3: *Modern fermentation capabilities:* Up to 100 liter fermentors and downstream

protein purification and characterization allow

preparation of engineered “optimized” protein variants

for injectable or ingestible animal trials, biorefining and

other industrial or pharmacetical biotechnology applications at

Direvo Biotech AG in Cologne, Germany.

Fig. 4: EM photograph of branching and sporulating /

Streptomyces coelicolor (courtesy of John Innes Institute,

Norwich, UK)

Fig. 3 Fig. 4


Streptomics


481

PartnersProject Coordinator:Prof. Jozef AnnéCatholic University of LeuvenLaboratory of BacteriologyRega InstituteMinderbroedersstraat 10B-3000 Leuven, [email protected]

Prof. Michael HeckerErnst-Moritz-Arndt-UniversityInstitute for MicrobiologyGreifswald, Germany

Dr. Wayne M. CocoDirevo Biotech AGCologne, Germany

Prof. Anastassios EconomouFoundation of Research and TechnologyInstitute of Molecular Biology and BiotechnologyHeraklion, Greece

Dr. Marc DaukandtEurogentecDNA MicroArray DepartmentSeraing, Belgium

Prof. Jakob KristjánssonProkaria LtdReykjavik, Iceland

Dr. Benjamin DamienBioXprNamur, Belgium

Prof. Roy GoodacreUniversity of ManchesterSchool of ChemistryManchester, UK

Prof. Anna Eliasson Lantz Technical University of Denmark Centre for Microbial BiotechnologyLyngby, Denmark


Systems biology strategies and metabolome engineering for the enhanced production of recombinant proteins in Streptomyces



482

State-of-the-Art:A study conducted by an international expert panel for the University of Toronto, ranked the computational examination of host-pathogen interactions among the top 10 biotechnolo-gies most likely to improve global health in the next 10 years (Daar et al, 2002). However, information about fundamental aspects of the cellular machinery involved in the interactions between macrophages and intracellular pathogens has not yet been sufficiently catego-rised, particularly with regard to macrophage function, and there is a need for a systematic and integrative approach to the identification of interconnected functional modules and salient modifications triggered by intracellular parasitism.

Scientific/Technological Objectives:The overall objective of the SYSCO project is to decipher the intracellular biological path-ways and basic cellular processes that act in physiological conditions as well as in the context of intracellular parasitism, in order to highlight the alteration in gene expression that stems from the conflict between the host and pathogen genomes. More specifically, the project will use human and mouse macrophages as cellular targets, and the Leishmania parasite as a prototype for intracellular pathogens. Leishmania is one of the most intensively studied biological models in terms of parasite, host immune response and genetics.

SYSCO will decipher and modularise the cascade of intracellular events generated by parasite-cell interactions, and also how they result in either parasite elimination or infection in humans. A comparative analysis with mouse strains expressing differing susceptibilities will help identify key determinants of natural resistance or susceptibility to parasites acting at the macrophage level.In a combined strategy of experimental and theoretical work, the SYSCO consortium will systematically capture data at different levels of cellular information, using state-of-the-art, multi-parametric molecular technologies (both in human and in mouse). These data will be used to identify regulatory motifs through systematic promoter analysis, and to populate computer models with the relevant motifs and associated signalling pathways. The com-puter models will be designed as independent modules covering gene regulation, gene expression, protein interactions and signalling. This modular approach will be used to mimic different types of innate macrophage responses, and to map theoretical predictions to experimental data.

Expected Results:After 36 months, SYSCO will have achieved the following aims:

1) Development of a hybrid, in silico model for the innate response of macrophages to an intracellular pathogen, based on the composition of interconnected modules that mimic different cellular events;

2) Development of a comprehensive systems ontology; 3) Experimental investigation and categorisation of four different modules, namely gene

regulation, gene and protein expression and signal transduction; 4) Complementary high throughput analysis of the macrophage transcriptome by Af-

fymetrix oligonucleotide arrays and serial analysis of gene expression, both in para-site-infected and in non-infected cells;

5) Prediction and validation of the regulatory networks in macrophages;


SYSCO

Project Type:SME- Specific Targeted Research ProjectContract number:LSHG-CT-2006-037231Starting date:1st September 2007 Duration:36 monthsEC Funding:

1 840 719


483

6) Experimental determination of cell regulation by quantitative transcription factor as-says and by RNA interference.

Potential Impact:Leishmaniasis is one of the world’s major parasitic diseases, but there is no vaccine for it as yet, and the drugs currently prescribed to treat it are fairly toxic. Millions of people living in developing countries, mainly in southern and eastern Mediterranean regions and in central and South America, are exposed to leishmaniasis. The Leishmania parasite is also a major co-pathogen in the context of HIV infection in southern Europe. The results of this project will be significant, not only in the context of leishmaniasis, but also for the understanding and treatment of infection by other intracellular pathogens, such as Mycobacterium tuberculosis, the bacterium which causes tuberculosis.

Prof. Winston HideUniversity of the Western CapeSouth African National Bioinformatics InstituteBellville, South Africa

Dr. Pierre-Andre CazenaveUniversité Pierre et Marie Curie-Paris VI,Laboratoire d’ImmunophysiopathologieInfectieuse – URA 1961Paris, France

Project Coordinator:Dr. Alexander KelBIOBASE GmbHDepartment of Research and DevelopmentHalchtersche strasse 3334090 Wolfenbüttel, [email protected]

Dr. David PiquemalSARL Skuld-TechMontpellier, France

Dr. Ralf HerwigMax-Planck Institute forMolecular GeneticsBerlin, Germany

Dr. Béatrice RegnaultInstitut PasteurPlate-forme Puce à ADN – Genopole PasteurParis, France

Prof. Patricia RenardFacultés Universitaires Notre-Dame de la PaixUnite de Recherche en Biologie CellulaireNamur, Belgium

Prof. Koussay DellagiInstitut Pasteur de TunisLaboratoire d’ImmunopathologieVaccinologie et Genetique Moleculaire (LIVGM)Tunis, Tunisia

Partners


Systematic Functional analysis of Intracellular Parasitism

as a model of genomes conflict



484

Picture taken at the Proust project first course, entitled

“The dimension of time and gene functioning: focus on the nervous

system” which was held at the Kristineberg Marine Station in

Sweden from June 7 to June 12.

State-of-the-Art:Knowledge about how regulatory genes and their mechanisms of expression change over time is expanding rapidly, and it is now clear that this temporal dimension is a common denominator of experimental systems studied in different life science disciplines. In the post-genomic era, the focus of research has shifted from the identification of genes to un-derstanding their function. Some fundamental aspects of gene function cannot be captured without taking into account the complex dynamics of interactions between genes, both in space and in time. A com-plete understanding of gene function therefore requires the development of novel tools for the analysis of those dynamics, particularly in the temporal domain. Given the complexity of known genetic networks, it seems inevitable that a purely deterministic approach will not generate realistic descriptions of cell function.

Scientific/Technological Objectives:The overall objectives of PROUST are as follows: to bring together scientists from different disciplines or fields of research, to establish genuinely leading-edge projects on gene and protein networks which focus on the temporal di-mension, and to standardise tools for the investigation of timescales in functional genomics. Furthermore, PROUST plans to coordinate knowledge on the temporal dimension of intracel-lular and intercellular signalling pathways, in order to define their role at the molecular, cellular, tis-sue and organism levels.

The above will be crucial for the identification of therapeutic targets with time-dependent sus-ceptibilities. The last general objective for PROUST is to foster and disseminate knowledge on the temporal dimension of biological processes not only among students and scientists work-ing in different disciplines, but also among other stakeholders in society. More specifically, the highly interdisciplinary PROUST consortium will address the following topics:

1) Oscillation in gene expression, and the development of tools for investigating dynamic parameters, including rhythmic expression of genes, rhythmic post-transcriptional regu-lation, regulation of the cell cycle, timing in microRNAs, timing by natural antisense transcripts, modelling of the timing factors in biological systems, and modelling of intracellular signalling pathways for therapeutic targeting;

2) The implications of the above on human disease, including cardiovascular, neurologi-cal and psychiatric diseases, abnormal cell proliferation and cancer, nutrition and me-tabolism, infections and immunity;

3) The implications of the above across the human lifespan, from childhood to old age, in males and females, as well as a focus on issues relating to reproduction and pregnancy;


Project Type:Specific Support ActionContract number:LSHG-CT-2006-037654Starting date:1st January 2007Duration:24 monthsEC Funding:

250 000

Proust


485

4) The implications of the above across populations and species. This aspect of the con-sortium’s research will draw on the disciplines of population genetics and comparative genomics, focusing on genes that are conserved throughout evolution, as well as on the issue of time and population history.

Expected Results:PROUST plans to organise workshops and two training courses, ultimately delivering a position paper on the temporal dimension in functional genomics. The expected output of PROUST will contribute firstly to the standardisation of approaches to gene expression anal-yses which take into account the temporal dimension as a stochastic variable. Secondly, it will assist in narrowing the gap between clinically correlative data and causative data for complex diseases such as cardiovascular and neurological diseases and cancer, as well as for the regulation of normal lifetime events (e.g. pregnancy).

The mathematical and modelling approaches, whose development PROUST will further, such as false discovery rate (FDR)-based methods for analysing time-course microarray data, are of particular interest: they can be applied to typical comparisons and sampling schemes or chaotic dynamics in neural networks.

Potential Impact:PROUST offers European scientists a unique opportunity to interact in an innovative and multidisciplinary field of research, providing them with a forum in which they can exchange scientific information relevant to developments in biomedical technology. In particular, PROUST will focus on common denominators (e.g. common genes, gene products and sig-nal transduction pathways) in functional genomics, in relation to time. Such a coordinated research effort will provide the European Research Area with an obvious strategic advan-tage in relation to drug discovery, drug delivery, disease prevention, disease therapy and the general wellbeing of the ageing European population.

Keywords: functional genomics, temporal dimension

Project Coordinator:Prof Marina BentivoglioUniversity of VeronaDepartment of Morphological Biomedical SciencesStrada Le Grazie 837134 Verona, [email protected]

Dr. Maris LaanEstonian BiocentreFunctional Genomics WorkgroupTartu, Estonia

Prof. Krister KristenssonKarolinska InstituetDepartment of NeuroscienceStockholm, Sweden

Partners

Prof. Francis LéviInstitut National de la Recherche Medicale (INSERM)U776 Chronotherapie des cancersHôpital Paul BrousseVillejuif, France


The temporal dimension in functional genomics




INDEXES



0 3D-EM New Electron Microscopy Approaches for Studying Protein Complexes

and Cellular Supramolecular Architecture //////////////////////////// 170 3DGENOME 3D Genome Structure and Function //////////////////////////////// 164 3D-Repertoire A Multidisciplinary Approach to Determine the Structures of Protein

Complexes in a Model Organism ////////////////////////////////// 190

A AGRON-OMICS Arabidopsis growth network integrating OMICS technologies ///////////// 464 AMPKIN Systems biology of the AMP-activated protein kinase pathway //////////// 456 AnEUploidy AnEUploidy: understanding gene dosage imbalance in human health

using genetics, functional genomics and systems biology //////////////// 350 ATD The Alternate Transcript Diversity Project ///////////////////////////// 300 Autoscreen AUTOSCREEN for Cell Based High-throughput and High-content Gene

Function Analysis and Drug Discovery Screens ///////////////////////// 98

B BACELL HEALTH Bacterial stress management relevant to infectious disease

and biopharmaceuticals ///////////////////////////////////////// 426 BACRNAs Non-coding RNAs in Bacterial Pathogenicity ////////////////////////// 408 BaSysBio Towards an understanding of dynamic transcriptional regulation

at global scale in bacteria: a systems biology approach ///////////////// 468 BioBridge Integrative Genomics and Chronic Disease Phenotypes: modelling

and simulation tools for clinicians ////////////////////////////////// 472 BIOSAPIENS A European Network for Integrated Genome Annotation //////////////// 296 BIOXHIT Bio-Crystallography on a Highly Integrated Technology Platform

for European Structural Genomics ////////////////////////////////// 166

C Callimir Studying the biological role of microRNAs in the Dlk1-Gtl2 imprinted

domain ///////////////////////////////////////////////////// 400 CAMP Chemical Genomics by Activity Monitoring of Proteases ///////////////// 114 CASIMIR Co-ordination And Sustainability of International Mouse Informatics

Resources //////////////////////////////////////////////////// 238 ChILL Chromatin Immuno-linked ligation: A novel generation of biotechnological

tools for research and diagnosis /////////////////////////////////// 156 COMBIO An integrative approach to cellular signalling and control processes:

Bringing computational biology to the bench ///////////////////////// 442 COMPUTIS Molecular Imaging in Tissue and Cells by Computer-Assisted Innovative

Multimode Mass Spectrometry //////////////////////////////////// 126 COSBICS Computational Systems Biology of Cell Signalling ////////////////////// 444

PROJECTS INDEX



D DanuBiobank The Danubian Biobank Initiative - Towards Information-based Medicine ///// 286 DIAMONDS Dedicated Integration and Modelling of Novel Data and Prior Knowledge

to Enable Systems Biology /////////////////////////////////////// 446 DIATOMICS Understanding Diatom Biology by Functional Genomics Approaches /////// 428 DNA REPAIR DNA Damage Response and Repair Mechanisms ////////////////////// 334

E ELIfe The European Lipidomics Initiative: Shaping the life sciences ////////////// 450 EMBRACE A European Model for Bioinformatics Research and Community Education /// 302 E-MeP The European Membrane Protein Consortium ///////////////////////// 176 E-MeP-Lab E-MeP-Lab Training events in membrane protein structural biology ////////// 196 EMERALD Empowering the Microarray-Based European Research Area to Take

a Lead in Development and Exploitation ////////////////////////////// 96 EMI-CD European Modelling Initiative combating complex diseases ////////////// 438 EndoTrack Tracking the Endocytic Routes of Growth Factor Receptor Complexes

and their Modulatory Role on Signalling ///////////////////////////// 346 ENFIN An Experimental Network for Functional Integration //////////////////// 306 EpiGenChlamydia Contribution of molecular epidemiology and host-pathogen genomics

to understand Chlamydia trachomatis disease //////////////////////// 290 ESBIC-D European Systems Biology Initiative for Combating Complex Diseases ////// 452 ESTOOLS Platforms for biomedical discovery with human ES cells ///////////////// 386 EUCLOCK Entrainment of the Circadian Clock ///////////////////////////////// 418 EUCOMM The European Conditional Mouse Mutagenesis Programme ////////////// 230 EUHEALTHGEN Harnessing the Potential of Human Population Genetics Research

to Improve the Quality of the EU Citizen ///////////////////////////// 280 EUMODIC The European Mouse Disease Clinic:

A distributed phenotyping resource for studying human disease /////////// 234 Eurasnet European Alternative Splicing Network of Excellence /////////////////// 402 EURATools European Rat Tools for Functional Genomics ////////////////////////// 244 EuReGene European Renal Genome Project ////////////////////////////////// 370 EURExpress A European Consortium to Generate a Web-Based Gene Expression Atlas

by RNA in situ Hybridisation ///////////////////////////////////// 218 EUROBIOFUND A Strategic Forum for the Dialogue and Coordination

of European Life Sciences, Funders and Performers ///////////////////// 460 EUROFUNGBASE Strategy to build up and maintain an integrated sustainable European fungal

genomic database required for innovative genomics research on filamentous fungi, important for biotechnology and human health /////////////////// 310

EuroHear Advances in hearing science: from functional genomics to therapies //////// 362 EUROSPAN EUROpean Special Populations Research Network: Quantifying

and Harnessing Genetic Variation for Gene Discovery ////////////////// 284 EUSYSBIO The Take-off of European Systems Biology //////////////////////////// 434 EuTRAC European Transcriptome, Regulome & Cellular Commitment Consortium ///// 390 EU-US Workshop Workshop on “Systems biology of DNA damage-induced stress responses /// 448 EVI-GENORET Functional genomics of the retina in health and disease ///////////////// 374 Extend-NMR Extending NMR for Functional and Structural Genomics ///////////////// 202

F FESP Forum for European Structural Proteomics //////////////////////////// 194 FGENTCARD Functional GENomic diagnostic Tools for Coronary Artery Disease ///////// 102 FLPFLEX A Flexible Toolkit for Controlling Gene Expression in the Mouse /////////// 228 FOSRAK Function of small RNAs across kingdoms //////////////////////////// 398 FSG-V-RNA Functional and Structural Genomics of Viral RNA ////////////////////// 180 FunGenEs Functional Genomics in Engineered ES cells ////////////////////////// 380



G GeneFun In-Silico Prediction of gene function///////////////////////////////// 174 GENINTEG Controlled gene integration:

a requisite for genome analysis and gene therapy ///////////////////// 130 GENOSEPT Genetics of Sepsis in Europe ///////////////////////////////////// 276

H HEROIC High-Throughput Epigenetic Regulatory Organisation in Chromatin ///////// 152 HT3DEM High throughput Three-dimensional Electron Microscopy ///////////////// 198 HUMGERI Human Genomic Research Integration ////////////////////////////// 270

I Impacts Archive Tissues: Improving Molecular Medicine Research

and Clinical Practice /////////////////////////////////////////// 288 IMPS Innovative tools for membrane structural Proteomics //////////////////// 204 INTERACTION PROTEOME Functional Proteomics: Towards defining the interaction proteome ////////// 108

LLYMPHANGIOGENOMICS Genome-Wide Discovery and Functional Analysis

of Novel Genes in Lymphangiogenesis ////////////////////////////// 358

M MAIN Targeting Cell Migration in Chronic Inflammation ////////////////////// 316 Med-Rat New Tools to Generate Transgenic and Knock-out Mouse and Rat Models /// 248 MEGATOOLS New tools for Functional Genomics based on homologous recombination

induced by double-strand break and specific meganucleases ///////////// 136 MICROSAT workshop Microsatellites and VNTRs: workshop on bioinformatics,

genomics and functionality /////////////////////////////////////// 278 MITOCHECK Regulation of Mitosis by Phosphorylation - A Combined Functional

Genomics, Proteomics and Chemical Biology Approach ///////////////// 322 MODEST Modular Devices for Ultrahigh-throughput and Small-volume Transfection //// 104 MOLECULAR IMAGING Integrated Technologies for In Vivo Molecular Imaging ////////////////// 120 MolPAGE Molecular Phenotyping to Accelerate Genomic Epidemiology ///////////// 272 MolTools Advanced Molecular Tools for Array-Based Analyses of Genomes,

Transcriptomes, Proteomes and Cells //////////////////////////////// 86 MUGEN Integrated Functional Genomics in Mutant Mouse Models as Tools

to Investigate the Complexity of Human Immunological Disease /////////// 222 MYORES Multiorganismic Approach to Study Normal and Aberrant Muscle

Development, Function and Repair ///////////////////////////////// 366

N NDDP NMR Tools for Drug Design Validated on Phosphatases ///////////////// 188 NemaGENETAG Nematode Gene-Tagging Tools and Resources //////////////////////// 260 NEUPROCF Development of New Methodologies for Low Abundance Proteomics:

Application to Cystic Fibrosis ///////////////////////////////////// 112 NFG Functional Genomics of the Adult and Developing Brain ///////////////// 356 NMR-Life Focusing NMR on the Machinery of Life ///////////////////////////// 200

PROJECTS INDEX



O OptiCryst Optimisation of Protein Crystallisation for European Structural Genomics //// 210

P PEROXISOMES Integrated Project to decipher the biological function of peroxisomes

in health and disease /////////////////////////////////////////// 330 PHOEBE Promoting harmonisation of epidemiological biobanks in Europe ////////// 282 PLASTOMICS Mechanisms of transgene integration and expression in crop plant plastids,

underpinning a technology for improving human health ///////////////// 132 PLURIGENES Pluripotency Associated Genes to Dedifferentiate Neural Cells

into Pluripotent Cells //////////////////////////////////////////// 384 PRIME Priorities for mouse functional genomics research across Europe:

integrating and strengthening research in Europe ////////////////////// 226 ProDac Proteomics Data Collection /////////////////////////////////////// 116 Proust The temporal dimension in functional genomics /////////////////////// 484

Q QUASI Quantifying signal transduction /////////////////////////////////// 440

R REGULATORY GENOMICS Advanced Genomics Instruments, Technology and Methods for

Determination of Transcription Factor Binding Specificities: Applications for Identification of Genes Predisposing to Colorectal Cancer //// 90

RIBOREG Novel non-coding RNAs in differentiation and disease ////////////////// 396 RIBOSYS Systems Biology of RNA Metabolism in Yeast ///////////////////////// 458 RNABIO Computational approaches to non-coding RNAs /////////////////////// 410 RUBICON Role of Ubiquitin and Ubiquitin-like Modifiers in Cellular Regulation //////// 342

S SIGNALLING & TRAFFIC Signalling and Membrane Trafficking in Transformation and Differentiation /// 326 Sirocco Silencing RNAs: organisers and coordinators

of complexity in eukaryotic organisms ////////////////////////////// 412 SMARTER Development of small modulators of gene activation

and repression by targeting epigenetic regulators ////////////////////// 158 SPINE2-COMPLEXES From Receptor to Gene: Structures of Complexes

from Signalling Pathways linking Immunology, Neurobiology and Cancer //// 206 STAR A SNP and Haplotype Map for the Rat ////////////////////////////// 242 STEROLTALK Functional Genomics of Complex Regulatory Networks from Yeast

to Human: Cross-Talk of Sterol Homeostasis and Drug Metabolism ///////// 338 Streptomics Systems biology strategies and metabolome engineering for the enhanced

production of recombinant proteins in Streptomyces //////////////////// 478 SYSBIOMED Systems Biology for Medical Applications //////////////////////////// 474 SYMBIONIC Towards European Neuromal Cell Simulation: a European consortium

to integrate the scientific activities for the creation of a European Alliance devoted to the complete in-silico model of Neuronal Cell //////////////// 436

SYSCO Systematic Functional analysis of Intracellular Parasitism as a model of genomes conflict ////////////////////////////////////// 482

SysProt System-wide analysis and modelling of protein modification ////////////// 476

PROJECTS INDEX



T TAGIP Targeted Gene Integration in Plants: Vectors, Mechanisms

and Applications for Protein Production ///////////////////////////// 134 TargetHerpes Molecular intervention strategies targeting latent

and lytic herpesvirus infections //////////////////////////////////// 100 Tat machine Functional genomic characterisation of the bacterial Tat complex

as a nanomachine for biopharmaceutical production and a target for novel anti-infectives //////////////////////////////////// 92

TEACH-SG Training and Education in High Volume and High Value Structural Genomics / 212 TEMPO Temporal Genomics for Tailored Chronotherapeutics //////////////////// 422 THE EPIGENOME Epigenetic plasticity of the genome ///////////////////////////////// 148 Tips4Cells Scanning Probe Microscopy techniques for real time, high resolution

imaging and molecular recognition in functional and structural genomics //// 124 TP Plants and Health The European Technology Platform on Plant Genomics and Biotechnology:

Plants for healthy lifestyles and for sustainable development ////////////// 262 TransCode Novel Tool for High-Throughput Characterisation

of Genomic Elements Regulating Gene Expression in Chordates //////////// 94 TransDeath Programmed cell death across the eukaryotic kingdom ////////////////// 328 TRANS-REG Transcription Complex Dynamics Controlling Specific

Gene Expression Programmes //////////////////////////////////// 142

U UPMAN Understanding Protein Misfolding and Aggregation by NMR ///////////// 186

V VALAPODYN Validated Predictive Dynamic Model of Complex Intracellular Pathways

related to cell death and survival ////////////////////////////////// 462 VIZIER Comparative structural genomics on viral enzymes involved in replication //// 182

W WOUND A multi-organism functional genomics approach

to study signalling pathways in epithelial fusion/wound healing /////////// 320

X X-OMICS Xenopus Comparative Genomics: Coordinating Integrated and Comparative

Functional Genomics for Understanding Normal and Pathologic Development 264 X-TRA-NET ChIP-Chip to Decipher Transcription Networks of RXR and Partners ///////// 144

Y YSBN Yeast Systems Biology Network /////////////////////////////////// 454

Z ZF-MODELS Zebrafish Models for Human Development and Disease ///////////////// 252 ZF-TOOLS High-throughput Tools for Biomedical Screens in Zebrafish /////////////// 256

PROJECTS INDEX



A ■ Amaxa AG, Dr. Birgit Nelsen-Salz, MODEST //////////////////////////////////////////// 105

■ Agricultural Biotechnology Center, Genetic Reprogramming Group, Dr. Andras Dinnyes, Med-Rat ///// 249

■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, E-MeP ////////////////// 178

■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, E-MeP-Lab /////////////// 197

■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, OptiCryst //////////////// 211

B ■ BIOBASE GmbH, Department of Research and Development, Dr. Alexander Kel, SYSCO /////////// 483

■ Biomedical Sciences Research Center, Dr. George Kollias, MUGEN /////////////////////////// 224

C ■ Catholic University of Leuven, Laboratory of Bacteriology, Rega Institute,

Prof. Jozef Anné, Streptomics /////////////////////////////////////////////////////////481

■ CELLECTIS SA, Dr. Frédéric Pâques, MEGATOOLS //////////////////////////////////////// 137

■ Centre de Regulació Genòmica (CRG), Systems Biology Laboratory,Prof. Luis Serrano, 3D repertoire ////////////////////////////////////////////////////// 192

■ Centre for Brain Research, Medical University of Vienna, Prof. Johannes Berger, Peroxisomes //////// 333

■ Centre National de la Recherche Scientifique (CNRS), Institut des Sciences du Végétal (UPR no 2355), RIBOREG /////////////////////////////////////////////////////////// 397

■ Centre National de la Recherche Scientifique (CNRS), UMR 8080 Développement et Evolution,Dr. Andre Mazabraud, X-OMICS ///////////////////////////////////////////////////// 265

■ Centre National De La Recherche Scientifique (CNRS), Université Louis Pasteur, Institut de biologie moléculaire et cellulaire, ARN ‘Architecture et Réactivité de l’ARN’, Prof. Eric Westhof, RNABIO ////// 411

■ Centre National de la Recherche Scientifique (CNRS)/Université Paris-7 UMR 7099,Institut de Biologie Physico-Chimique, IMPS ////////////////////////////////////////////// 205

■ Commissariat à l’Energie Atomique CEA), LIST/DETECS, Dr Haan Serge,Dr Robbe Marie-France, COMPUTIS /////////////////////////////////////////////////// 127

■ Consejo Superior de Investigaciones Cientificas (CSIC), Instituto de Biologia Molecular de Barcelona, Dr. Enrique Martin-Blanco, WOUND /////////////////////////////////////// 321

■ Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine Paramagnetiche, Magnetic Resonance Center (CERM), Prof. Ivano Bertini, NMR-Life //////////////////////////// 201

■ CRG - Centre de Regulació Genòmica, Systems Biology Research Unit, Prof. Luis Serrano, COMBIO // 443

D ■ DECHEMA e.V., Dr. Karsten Schürrle, SYSBIOMED //////////////////////////////////////// 475

■ Diagenode SA, Didier Allaer, ChILL //////////////////////////////////////////////////// 157

E ■ Erasmus MC University Medical Center, Department of Cell Biology and Genetics,

Prof. Dr. Frank Grosveld, EuTRACC //////////////////////////////////////////////////// 392

■ Erasmus Universitair Medisch, Centrum Rotterdam, Dept. of Cell Biology and Genetics, Prof. Jan Hoeijmakers, DNA Repair /////////////////////////////////////////////////// 336

INSTITUTION AND COORDINATOR INDEX



■ ERM-0206 TAGC, Institut National de la Santé et de la Recherche Médicale (INSERM), Prof. Daniel Gautheret, ATD ///////////////////////////////////////////////////////// 301

■ European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Dr. Graham Cameron, EMBRACE ////////////////////////// 304

■ European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Prof. Ewan Birney, ENFIN //////////////////////////////// 308

■ European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Prof. Janet Thornton, BioSapiens //////////////////////////// 298

■ European Molecular Biology Laboratory (EMBL), Mouse Biology Unit, Monterotondo Outstation, Prof. Nadia Rosenthal, FLPFLEX /////////////////////////////////////////////////////// 229

■ European Molecular Biology Laboratory (EMBL), Outstation Hamburg,Macromolecular Crystallography, Dr. Victor Lamzin, BIOXHIT //////////////////////////////// 168

■ European Plant Science Organisation, Dr. Karin Metzlaff, TP Plants and Health /////////////////// 263

■ European Science Foundation (ESF), Prof. Marja Makarow, EuroBioFund /////////////////////// 461

■ European Society of Intensive Care Medicine, Research Activities, Prof. Julian Bion, Dr. Nathalie Mathy, GenOSept /////////////////////////////////////////////////////// 277

F ■ Flanders Interuniversity Institute for Biotechnology, Department of Plant Systems Biology,

Computational Biology Group, Prof. Martin Kuiper, DIAMONDS ///////////////////////////// 447

■ Fondazione Centro San Raffaele Del Monte Tabor, Department of Molecular Biology and Functional Genomics, Prof. Ruggero Pardi, MAIN ///////////////////////////////////// 319

■ Fondazione Telethon, Telethon Institute of Genetics and Medicine, Molecular Biology Unit, Dr. Sandro Banfi, TransCode ////////////////////////////////////////////////////////// 95

■ Fondazione Telethon, TIGEM-Telethon Institute of Genetics and Medicine,Prof. Andrea Ballabio, EURExpress //////////////////////////////////////////////////// 221

■ Forschungsinstitut für Molekulare Pathologie GmbH, Dr. Jan-Michael Peters, MitoCheck ///////////// 325

■ Forschungszentrum Juelich GmbH, Project Management Juelich (Ptj), Dr. Petra Wolff, EUSYSBIO ////// 435

■ Foundation for Research and Technology – Hellas, Institute of Electronic Structureand Laser (IESL), Institute of molecular biology and biotechnology (IMBB),Prof. Eleftherios Economou, MOLECULAR IMAGING /////////////////////////////////////// 122

■ Foundation for Research and Technology – Hellas, Institute of Molecular Biology and Biotechnology, Dr. Nektarios Tavernarakis, NemaGENETAG //////////////////////////////////////////// 261

■ Foundation for Research and Technology – Hellas, Institute of Molecular Biology and Biotechnology, Prof. Iannis Talianidis, TRANS-REG //////////////////////////////////////////////////// 143

G ■ Ghent University/Flanders Interuniversity Institute for Biotechnology, Department of Plant Systems

Biology, Computational Biology group, Prof. Martin Kuiper, EMERALD ////////////////////////// 97

■ Ghent University, Flanders Institute for Biotechnolgy (VIB), Department of Plant Systems Biology, Dr. Pierre Hilson, AGRON-OMICS //////////////////////////////////////////////////// 467

■ Gothenburg University, Department of Cell and Molecular Biology, Prof. Stefan Hohmann, AMPKIN /// 457

■ Gothenburg University, Department of Cell and Molecular Biology, Prof. Stefan Hohmann, QUASI //// 441

■ Grenoble – Institut des Neurosciences Centre de Recherche INSERM U 836, Université Joseph Fourier, Dr. Antoine Depaulis, VALAPODYN //////////////////////////////// 463

■ GSF-Forschungszentrum fur Umwelt und Gesundheit GmbH, Institute of Molecular Radiation Biology, Prof. Dr. Jean-Marie Buerstedde, GENINTEG //////////////////////////////////////////// 131

H ■ Helmholtz Zentrum München, German Research Center for Environmental Health GmbH,

Institute of Developmental Genetics, Prof. Wolfgang Wurst, EUCOMM ///////////////////////// 233

I ■ Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Josep Roca, BioBridge /////////// 473




■ Institut Jacques Monod, Team ‘Avenir’ INSERM, Prof. Thierry Galli, SIGNALLING & TRAFFIC///////// 327

■ Institut National de la Recherche Agronomique (INRA), Dr. Philippe Noirot, BaSysBio ////////////// 471

■ Institut National de la Recherche Agronomique (INRA), Physiologie animale et systèmes d’élevage (PHASE), Dr. Jean-Stéphane Joly, Plurigenes //////////////////////////// 385

■ Institut National de la Santé et de la Recherche Médicale, Faculte de Medecine Necker Inserm U467, Dr. Aleksander Edelman, NEUPROCF //////////////////////////////////////////// 113

■ Institut National de la Santé et de la Recherche Médicale (INSERM), U384,Dr. Krzysztof Jagla, MYORES //////////////////////////////////////////////////////// 368

■ Institut National de la Santé et de la Recherche Médicale (INSERM) U592,Laboratoire de Physiopathologie Cellulaire et Moleculaire de la Retine, Institut de la Vision, Prof. Jose-Alain Sahel, EVI-GENORET ////////////////////////////////////////////////// 376

■ Institut National de la Santé et de la Recherche Médicale (INSERM), U776Rythmes biologiques et cancers ,Hôpital Paul Brousse, Dr. Francis Lévi, TEMPO /////////////////// 423

■ Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 587- Institut Pasteur, Unité de Génétique et Physiologie de l’Audition, Prof. Christine Petit, EuroHear /////////////////// 364

J ■ Johann Wolfgang Goethe-Universität, Center for Biomolecular Magnetic Resonance,

Institute for Organic Chemistry and Chemical Biology, Prof. Harald Schwalbe, UPMAN //////////// 187

K ■ Karolinska Institutet, Department of Cell and Molecular Biology, Prof. Maria Masucci, RUBICON ///// 345

■ King’s College, University of London, Department of Social Genetic and Developmental Psychiatry, Institute of Psychiatry, Prof. David Collier, MICROSAT workshop ////////////////////////////// 279

L ■ Lay Line Genomics SpA, c/o San Raffaele Scientific Park, Dr. Ivan Arisi, SYMBIONIC ////////////// 437

■ Leiden Institute of Physics, Leiden University, Dr. Tjerk Oosterkamp, Tips4Cells //////////////////// 125

■ Leiden University, Clusius Laboratory, Prof. Cees van den Hondel, EUROFUNGBASE ////////////// 311

■ Leiden University, Institute of Biology, Molecular Cell Biology, Dr. Annemarie H. Meijer, ZF-TOOLS //// 257

■ Leiden University Medical Center, Dr. Harry Vrieling, EU-US Workshop ///////////////////////// 448

■ Ludwig Maximilians University of Munich, Adolf-Butenandt Institute, Histone Modifications Group, Protein Analysis Core Facility, Prof. Axel Imhof, SMARTER /////////////////////////////////// 159

■ Ludwig Maximilians University, Institute for Medical Psychology, Prof. Till Roenneberg, EUCLOCK ///// 420

M ■ Max-Delbrück-Center for Molecular Medicine, Cardiovascular Research Centre, Department

of Cardiovascular Research, Lipids and Experimental Gene Therapy, Thomas Willnow, EuReGene //// 373

■ Max-Delbrück-Center for Molecular Medicine, Experimental Geneticsof Cardiovascular Diseases, Dr. Norbert Hübner,STAR ///////////////////////////////////// 243

■ Max-Planck-Institute of Biochemistry, Department of Cellular Biochemistry,Prof. F. Ulrich Hartl, INTERACTION PROTEOME ////////////////////////////////////////// 111

■ Max-Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry,Prof. Reinhard Lührmann, Eurasnet //////////////////////////////////////////////////// 406

■ Max Planck Institute for Developmental Biology, Department of Genetics,Dr. Robert Geisler, ZF-MODELS /////////////////////////////////////////////////////// 254

■ Max-Planck Institute of Molecular Cell Biology and Genetics, Prof. Marino Zerial, EndoTrack///////// 349

■ Max Planck Institute for Molecular Genetics, Vertebrate Genomics, Dr. Ralf Herwig, EMI-CD ///////// 439

■ Max-Planck Institute for Molecular Genetics, Vertebrate Genomics, Prof. Dr. Hans Lehrach, ESBIC-D /// 453

■ Medical Research Council, Mammalian Genetics Unit, MRC Harwell, Prof. Steve Brown, PRIME ////// 227

■ Medical Research Council, Mammalian Genetics Unit, MRC Harwell, Prof. Steve Brown, EUMODIC /// 236

■ Medical Research Council, Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Prof. Timothy J. Aitman, EURATools //////////////////////////////////////////////////// 246




■ MicroDiscovery GmbH, NutriSystemics, Dr. Arif Malik, SysProt /////////////////////////////// 477

N ■ Newcastle University, Molecular Microbiology Group, Institute for Cell and Molecular Biosciences,

Prof. Colin R Harwood, BACELL HEALTH //////////////////////////////////////////////// 427

■ Norwegian Institute of Public Health, Division of Epidemiology, Dr. Jennifer Harris, PHOEBE ///////// 283

R ■ Radboud University Nijmegen, IMM/Faculty of Science, Mathematics and Informatics,

Prof. Sybren Wijmenga,FSG-V-RNA /////////////////////////////////////////////////// 181

■ Research Institute for Molecular Pathology (IMP), Prof. Thomas Jenuwein, THE EPIGENOME ///////// 150

■ Ruhr-Universitaet Bochum, Medizinisches Proteom-Center, Prof. Helmut E. Meyer, ProDac /////////// 117

S ■ Saarland University, Department of Biochemistry, Prof. Rita Bernhardt, STEROLTALK //////////////// 341

■ SISSA (Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies), Neurobiology Sector, Prof. Anna Menini, NFG //////////////////////////////////// 357

■ Stazione Zoologica Anton Dohrn, Cell Signalling Laboratory, Dr. Chris Bowler, DIATOMICS ///////// 429

■ Stichting Katholieke Universiteit, Department of Molecular Biology, Prof. Henk Stunnenberg, HEROIC // 155

T ■ Technical University of Denmark, Centre for Microbial Biotechnology Biocentrum,

Prof. Jens Nielsen, YSBN /////////////////////////////////////////////////////////// 454

■ The Sainsbury Laboratory, John Innes Centre, Prof. David Baulcombe, Sirocco /////////////////// 414

■ The Wellcome Trust, Department of Biomedical Resources and Functional Genomics, Dr. Alan Doyle, EUHEALTHGEN ////////////////////////////////////////////////////// 281

U ■ Universitat Autonoma de Barcelona, Institut de Biotecnologia i de Biomedicina,

Protein Engineering and Enzymology Unit, Prof. Francesc Xavier Aviles, CAMP /////////////////// 115

■ Universität Rostock, Department of Computer Science, Prof. Olaf Wolkenhauer, COSBICS ////////// 445

■ Universiteit van Amsterdam, Science Faculty, Swammerdam Institute for Life Sciences, Prof. Roeland Van Driel, 3DGENOME ///////////////////////////////////////////////// 165

■ Université de la Méditerranée, Centre National de la Recherche Scientifique (CNRS), Laboratoire Architecture et Fonction des Macromolecules Biologiques UMR 6098, Dr. Bruno Canard, VIZIER////// 184

■ Université Libre de Bruxelles, Service de Conformation de Macromolecules Biolgiques et Bioinformatique, Biologie Moleculaire, Prof. Shoshana Wodak, GeneFun ///////////////////// 175

■ University Hospital Regensburg, Institute of Clinical Chemistry and Laboratory Medicine, Prof. Gerd Schmitz, DanuBiobank ///////////////////////////////////////////////////// 287

■ University Medical Center Groningen, Department of Medical Microbiology, Prof. Jan Maarten van Dijl, Tat machine ///////////////////////////////////////////////// 93

■ University of Basel, M.E. Miller Institute for Structural Biology, Biozentrum,Prof. Andreas Engel, 3D-EM ///////////////////////////////////////////////////////// 173

■ University of Basel, M E Mueller Institute for Structural Biology, Biozentrum,Prof. Andreas Engel, HT3DEM /////////////////////////////////////////////////////// 199

■ University of Bologna, Centro Interdipartimentale Galvani (CIG), Prof. Gabriella Campadelli-Fiume,TargetHerpes ////////////////////////////////////////// 101

■ University of Cambridge, Professor Ernest D. Laue, Extend-NMR ////////////////////////////// 203

■ University of Cambridge, Department of Plant Sciences, Prof. John Gray, PLASTOMICS ///////////// 133

■ University of Cambridge, Department of Physiology, Development and Neuroscience, Dr. Paul Schofield, CASIMIR ///////////////////////////////////////////////////////// 239

■ University of Cologne, Institute of Neurophysiology, Faculty of Medicine,Prof. Jürgen Hescheler, FunGenES ///////////////////////////////////////////////////// 382




■ University of Copenhagen, Institute of Molecular Biology, Prof. John Mundy, TransDeath //////////// 329

■ University of Debrecen, Medical and Health Science Center, Department of Biochemistry and Molecular Biology, Dr. László Fésüs, HUMGERI /////////////////////////////////////// 271

■ University of Edinburgh, Public Health Sciences, Prof. Harry Campbell, EUROSPAN /////////////// 285

■ University of Edinburgh, The Wellcome Trust Centre for Cell Biology, Prof. Jean Beggs, RIBOSYS ////// 459

■ University of Freiburg, Institute for Biology II, Faculty of Biology, Center for Applied Biosciences, Prof. Dr. Klaus Palme, Autoscreen ////////////////////////////////////////////////////// 99

■ University of Geneva, Faculty of Medicine, Department of Genetic Medicine and Development, Prof. Stylianos Antonarakis, AnEUploidy //////////////////////////////////////////////// 353

■ University of Helsinki, Faculty of Medicine, Biomedicum Helsinki, Molecular Cancer Biology Program, Prof. Kari Alitalo, LYMPHANGIOGENOMICS //////////////////////////////////// 361

■ University of Helsinki, Faculty of Medicine, Genome-Scale Biology Research Programme, Prof. Jussi Taipale, REGULATORY GENOMICS //////////////////////////////////////////// 91

■ University of Liège, Unit of Animal Genomics, Faculty of Veterinary Medicine,Dr. Michel Georges, Dr. Carole Charlier, Callimir ///////////////////////////////////////// 401

■ University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Prof. Mark McCarthy, MolPAGE ////////////////////////////////////////////////////// 275

■ University of Oxford, Prof. John Bell, MolPAGE /////////////////////////////////////////// 275

■ University of Oxford, Wellcome Trust Centre for Human Genetics,Dr. Dominique Gauguier, FGENTCARD ///////////////////////////////////////////////// 103

■ University of Oxford, Wellcome Trust Centre for Human Genetics, Division of Structural Biology, Prof. David Stuart, TEACH-SG //////////////////////////////////////////////////////// 213

■ University of Sheffield, Centre for Stem Cell Biology, Department of Biomedical Sciences, Prof. Peter W Andrews, ESTOOLS///////////////////////////////////////////////////// 389

■ University of Southern Denmark, Department of Biochemistry and Molecular Biology, Prof. Susanne Mandrup, X-TRA-NET /////////////////////////////////////////////////// 145

■ University of Trieste, Department of Clinical Morphological and Technological Sciences, International Centre for Genetic Engineering and Biotechnology, Molecular Histopathology Laboratory, Prof. Giorgio Stanta, Impacts /////////////////////////////////////////////// 289

■ University of Verona, Department of Morphological Biomedical Sciences, Prof. Marina Bentivoglio, Proust ////////////////////////////////////////////////////// 485

■ University of Vienna, Department of Biochemistry, “Max F. Perutz Laboratories”, Prof. Renée Schroeder, BACRNAs ///////////////////////////////////////////////////// 409

■ Uppsala University, Department of Cell and Molecular Biology, Biomedical Center, Prof. E. Gerhart Wagner, FOSRAK //////////////////////////////////////////////////// 399

■ Uppsala University, Department of Genetics and Pathology, Prof. Ulf Landegren, MolTools /////////// 89

■ Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Prof. Rolf Boelens, NDDP /////////////////////////////////////////////////////////// 189

■ Utrecht University, Bijvoet Center and Institute of Biomembranes, Prof. Gerrit van Meer, ELIfe ///////// 451

V ■ VU University Medical Center, Immunogenetics of Infectious Diseases, Department of Pathology,

Laboratory of Immunogenetics, Dr. Servaas A. Morré, EpiGenChlamydia /////////////////////// 291

W ■ Weizmann Institute of Science, Department of Structural Biology, Prof. Joel L. Sussman, FESP ///////// 195

■ Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, Prof. Avi Levy, TAGIP /////////////////////////////////////////////////////////////// 135

■ Wellcome Trust Centre for Human Genetics, Division of Structural Biology,Prof. David Stuart, SPINE2-COMPLEXES //////////////////////////////////////////////// 208



From Fundamental Genomics to Systems Biology: Understanding the Book of Life498

KEYWORDS INDEX

0

2D crystallisation: ................................................................................................1993D electron microscopy: .......................................................................................1723D structure: ..................................................................................................165, 1783D-electron microscopy: ........................................................................................192

A

adult stem cells: ...................................................................................................105ageing disorder: ..................................................................................................286ageing: ...............................................................................................................336age-related macular degeneration (AMD):...............................................................376alternative RNA splicing: ......................................................................................405amphipols: ..........................................................................................................205Aneuploidy: ........................................................................................................352animal dystrophies: ..............................................................................................376animal immunology: .............................................................................................224animal models: ................................................ 224, 227, 228, 236, 239, 249, 254, 257, 372, 420animal mutants: ...................................................................................................376anti-infectives: .......................................................................................................93antimicrobial agents: ............................................................................................409antisense RNA: ....................................................................................................409anti-tumor drug discovery: .....................................................................................257antiviral drugs: ....................................................................................................184apoptosis: .....................................................................................................105, 329applied optics: .....................................................................................................122Arabidopsis: ..................................................................................................135, 467association: .........................................................................................................279automated RNA ISH system: ..................................................................................220 automation techniques: .........................................................................................168

B

Bacillus, E. coli: .....................................................................................................93Bacillus: ..............................................................................................................470bacterial factors: ..................................................................................................290bacterial pathogens: .............................................................................................427bacterial virulence: ...............................................................................................409basic biological processes:....................................................................................301bioanalytical chemistry: ........................................................................................127biobank: .............................................................................................................286biobanks: ................................................................................................ 281, 283, 289biochemistry: .......................................................................................................409bioethics: ............................................................................................................283bioinformatics algorithms: ......................................................................................95bioinformatics: .............................. 93, 184, 192, 239, 254, 265, 303, 329, 399, 439, 453, 455, 470, 477



biomolecular complexes: .......................................................................................203biopharmaceuticals: ...................................................................................93, 427, 480biotechnology: .....................................................................................................131brain: .................................................................................................................357

C

Caenorhabditis elegans: .......................................................................................261callipyge: ............................................................................................................401cancer metastasis: ................................................................................................348 cancer: ................................................................................... 91, 325, 329, 336, 360, 447cardiovascular disease: ........................................................................................103cardiovascular diseases: .......................................................................................372cell adhesion: ......................................................................................................327cell biology: ........................................................................................................429cell cycle: ......................................................................................................325, 422cell death and survival: .........................................................................................463cell division: ........................................................................................................327cell fate determination: .........................................................................................150cell migration: ...............................................................................................318, 327cell physiology: ....................................................................................................364cellular commitment: .............................................................................................392cellular dynamics: ................................................................................................441cellular: ..............................................................................................................382central nervous system: .........................................................................................385chemical biology: ................................................................................................325chemical inhibitors: ..............................................................................................325chemiotherapeutics: ..............................................................................................101chemogenomics: ..................................................................................................115chemoproteomics: ................................................................................................115ChIP assay: .........................................................................................................157ChIP-chip: ...........................................................................................................145Chlamydia: .........................................................................................................290chromatin modification: ........................................................................................150chromatin remodelling: .........................................................................................157chromatin: ...........................................................................................................154chromatin-IP: ........................................................................................................145chromosome engineering: .....................................................................................470chronic heart failure: ............................................................................................473chronic obstructive pulmonary diseases: .................................................................473chronobiology: ....................................................................................................420circadian clock: .............................................................................................420, 422clinical application of lipids: ..................................................................................451co-factors: ...........................................................................................................145COGENE: ...........................................................................................................283comparative genomics: .................................................................................... 95, 427comparative: .................................................................................................249, 279complex disease: .................................................................................................283complex diseases: ..........................................................................................439, 453complex genetics: ................................................................................................372complex traits: .....................................................................................................246complex-complex interactions: ...............................................................................143computational biology: .........................................................................................443computational predictions: ....................................................................................308computational systems biology: ..............................................................................437computer modelling: .............................................................................................443conditionally mutated mouse ES cell library: ............................................................232



conserved genes: ...........................................................................................265, 321conserved non-genic sequences: .............................................................................95COPD: ................................................................................................................473copy number polymorphisms: ................................................................................352coronary artery:...................................................................................................103cryoelectron microscopy: ......................................................................................172crystal structure: ...................................................................................................184crystallization: .....................................................................................................205crystallography: .............................................................................................208, 213cystic fibrosis: ......................................................................................................113

D

data integration: ..................................................................................................298data management: ...............................................................................................283data modelling: ....................................................................................................97databases: .............................................................................................. 117, 239, 298datawarehouse development: ................................................................................290de-differentiation: .................................................................................................385degenerative diseases: .........................................................................................368development: .......................................................................................................357developmental biology: ..................................................................................368, 414developmental genetics: ........................................................................................265diabetes: .......................................................................................................457, 473diagnosis: .....................................................................................................301, 332diagnostics: .................................................................................................... 88, 103diatoms: ..............................................................................................................429Dicer: .................................................................................................................399differentiation: ......................................................................................... 382, 388, 397directed evolution: ................................................................................................480disease markers: ..................................................................................................301disease mechanisms: ......................................................................................246, 254disease: ..............................................................................................................397disorders: ............................................................................................................187diversification of muscle fibres: ..............................................................................368DNA chips: .........................................................................................................357DNA damage: ...............................................................................................336, 449DNA methylation: ................................................................................................157DNA repair mechanisms: ......................................................................................336DNA tiling microarrays: ........................................................................................470Drosophila: .........................................................................................................205drug design: ........................................................................................................189drug development: .........................................................................................246, 457drug screening: .....................................................................................................99drug targets: ..............................................................................................93, 254, 427dynamic modelling of signal transduction pathways: ................................................445dynamical modelling: ...........................................................................................447

E

electron microscopy techniques: .............................................................................172electron tomography:......................................................................................172, 192embryonal development: .......................................................................................392embryos:.............................................................................................................385endocytosis: ........................................................................................................348endophenotypes: .................................................................................................285entrainment: ........................................................................................................420

KEYWORDS INDEX



environmental factors: ...........................................................................................290enzymes: ............................................................................................................480epidemiology: ......................................................................................... 274, 277, 283epigenetic code: ..................................................................................................150epigenetics: ............................................................................................. 154, 157, 159ethics in health sciences: .......................................................................................289European technology platform: ..............................................................................263EU-US collaboration: ............................................................................................449exploratory drug discovery: ..................................................................................224expression profiling: .............................................................................................257

F

fluorescence: .......................................................................................................122fluorescent in situ hybridization: .............................................................................165fluxomics: ............................................................................................................470Function prediction: ..............................................................................................175function: ..............................................................................................................181functional analysis of the mouse genome: ................................................................232functional biology: ...............................................................................................224functional genomics: ......................................... 122, 135, 137, 203, 220, 224, 249, 254, 261, 289

308, 325, 340, 357, 364, 382, 399, 447, 467, 485functional in vivo studies: ......................................................................................265functional probing: ...............................................................................................115functions of muscle-specific proteins: .......................................................................368fundamental biological processes: ..........................................................................477fundamental genomics: .........................................................................................399fungal health applications: ....................................................................................311fungal pathogenicity: ............................................................................................311fusion; glycoproteins: ............................................................................................101

G

gene & protein networks: ......................................................................................443gene atlas: ..........................................................................................................382gene discovery: ...................................................................................................285gene dosage imbalance: ......................................................................................352gene expression analysis: .....................................................................................220gene expression regulation: .............................................................................. 95, 301gene expression: ............................................................... 133, 143, 165, 352, 376, 399, 414gene integration:..................................................................................................133gene knock-out: ...................................................................................................261gene regulation: ............................................................................................154, 159gene silencing/knockdown: ..................................................................................105 gene targeting: .................................................................................. 135, 137, 246, 249gene: ..................................................................................................................131general pathology: ...............................................................................................318genetic engineering: .......................................................................................122, 228genetic epidemiology and standardisation: .............................................................290genetic epidemiology: ..........................................................................................283genetic isolate: ....................................................................................................285genetic predisposition: ..........................................................................................277genetic testing: ....................................................................................................277genetic variation: ...........................................................................................243, 285genetics: .......................................................................................................279, 357genome (in)stability: .............................................................................................336genome annotation: .............................................................................................298

KEYWORDS INDEX



genome engineering: ...........................................................................................137genome structure and maintenance: .......................................................................135genome wide transcriptional profiling: ....................................................................449GenomEUtwin: ....................................................................................................283genomic databases: .............................................................................................311genomic function: .................................................................................................131genomics: .....................................88, 91, 99, 181, 184, 263, 265, 274, 285, 332, 336, 360, 429, 473genotype-phenotype-correlation: ............................................................................376genotyping: .........................................................................................................283global target site array: ........................................................................................145gradients: ...........................................................................................................443growth: ...............................................................................................................467

H

hair bundle: ........................................................................................................364haplotype map: ...................................................................................................243hard-to-transfect cell lines: .....................................................................................105hardware and software pipeline: ...........................................................................168HBV: ..................................................................................................................181HCV: ..................................................................................................................181health sciences: ...................................................................................................281hearing impairment: .............................................................................................364hematopoiesis: ....................................................................................................392herpes simplex virus: ............................................................................................101herpesvirus: .........................................................................................................101heterologous transposition: ....................................................................................261high resolution: ....................................................................................................125high throughput: ............................................................................................199, 211high-throughput imaging analysis: ..........................................................................165high-throughput screen: .........................................................................................348high-throughput screening: ....................................................................................184high-throughput techniques: ..................................................99, 145, 154, 203, 208, 257, 348Histones: ............................................................................................................157:HIV: ....................................................................................................................181homologous recombination: ...................................................................... 131, 135, 137host factors: .........................................................................................................290host response: .....................................................................................................101human cytomegalovirus: .......................................................................................101human development: ............................................................................................254human disease models: .........................................................................................236human disease:....................................................................................................336human diseases: ..................................................................................................332human embryonic stem cells: .................................................................................388human genetics: ...................................................................................................281human genomics: .................................................................................................271human health: .......................................................................................................93human herpesvirus 8: ...........................................................................................101

I

IFN: ...................................................................................................................101imaging techniques: .............................................................................................125imaging: ........................................................................................................ 99, 172immobilised proteins: ............................................................................................201immune response markers: ....................................................................................257immunology: .......................................................................................................318

KEYWORDS INDEX



imprinting: ..........................................................................................................401improved human health: .......................................................................................340in silico models: ...................................................................................................437infectious diseases: ...............................................................................................427inflammation: ......................................................................................................318inflammatory diseases: .........................................................................................360informatics: .........................................................................................................246infrastructures: .....................................................................................................227innate immunity: ..................................................................................................101 inner ear: ............................................................................................................364integrating research: ............................................................................................227integration: .........................................................................................................303integrative biology: ..............................................................................................467intensive care medicine: ........................................................................................277interaction networks: ............................................................................................175interactive databases: ...........................................................................................265inverse problem: ..................................................................................................122iron homeostasis: .................................................................................................427isolated populations: ............................................................................................283

K

K+ homeostasis: ...................................................................................................364kidney diseases: ..................................................................................................372

L

labelling, synthesis:...............................................................................................181lead: ..................................................................................................................105leaf: ...................................................................................................................467life sciences: ........................................................................................................461ligand interfaces: .................................................................................................208ligand specific effects: ..........................................................................................145light: ...................................................................................................................420linkage: ..............................................................................................................279lipid cubic phases: ...............................................................................................205lipidomics: ..........................................................................................................451living cell array: ...................................................................................................470low abundance proteins: .......................................................................................113lymphangiogenesis: ..............................................................................................360lymphoedema: .....................................................................................................360

M

MAP kinases: ......................................................................................................441mapping: ............................................................................................................279mass spectrometry: .........................................................................................127, 325massive data processing and information treatment: .................................................127mathematical modelling: .................................................................................453, 455mathematical models: .....................................................................................441, 457medical genetics: .................................................................................................228medical pathway modelling: .................................................................................340medicine: ......................................................................................................318, 475meganucleases: ...................................................................................................137membrane proteins:............................................................................ 178, 199, 201, 205membrane trafficking: ...........................................................................................327metabolic disorder: ..............................................................................................286

KEYWORDS INDEX



metabolism: .........................................................................................................457metabolomics: ..............................................................................103, 451, 470, 473, 480micro RNA: .........................................................................................................401microarray technology: ..........................................................................................97microarrays: ........................................................................................................301microcrystallography: ...........................................................................................205microRNA: ..........................................................................................................414microRNAs: .........................................................................................................411microsatellite: ......................................................................................................279microscopy: .........................................................................................................122miRNA: ..............................................................................................................399mitosis: ...............................................................................................................325model organisms: ..................................................................................... 135, 254, 385modelling complex diseases: .................................................................................439modelling: ............................................................................................... 459, 470, 473molecular biology: ........................................................................289, 336, 360, 368, 414molecular chemistry: .............................................................................................122molecular evolution: .............................................................................................187molecular genetics: ....................................................................................91, 224, 228molecular interaction networks: ..............................................................................463molecular medicine: .............................................................................................289molecular pathways: ............................................................................................224molecular phenotyping: ........................................................................................274molecular recognition: ..........................................................................................125monosomy: .........................................................................................................352morphogenesis: ...................................................................................................321mortality: ............................................................................................................277mouse disease models: ...................................................................................232, 236mouse functional genomics: ...................................................................................227mouse models: .....................................................................................................332mouse transgenesis: .............................................................................................352mouse: .........................................................................................220, 239, 249, 265, 372murine embryonic stem cells: .................................................................................382muscle differentiation: ...........................................................................................368muscle patterning: ................................................................................................368muscle regeneration: ............................................................................................368muscle stem cells: .................................................................................................368mutation genetics: ................................................................................................187Mycobacterium: ....................................................................................................93myoblasts fusion:..................................................................................................368myogenic specification: ........................................................................................368

N

nanodrop technology: ..........................................................................................208nanomachines: .....................................................................................................93nematode: ...........................................................................................................261network analysis: .................................................................................................439network design: ...................................................................................................443networking: ...................................................................................................213, 461neural: ................................................................................................................388neurobiology: ......................................................................................................392neurodegeneration: ..............................................................................................463neuro-degenerative disorder: .................................................................................286neuron: ...............................................................................................................437neuronal cells: .....................................................................................................105NMR spectroscopy: ..............................................................................................189

KEYWORDS INDEX



NMR: ..................................................................................................... 181, 201, 203non-coding RNA: ...........................................................................................399, 409non-coding RNAs: ..........................................................................................397, 411non-transcriptional gene regulation: ........................................................................399novel surfactants: .................................................................................................205nuclear magnetic resonance: .................................................................................203nuclear receptors: ................................................................................................145nuclear replacement: ............................................................................................249nucleation: ..........................................................................................................211nucleofection: ......................................................................................................105

O

oncogenic cell implants: ........................................................................................257Organogenesis: ...................................................................................................372overexpression:....................................................................................................205

P

P3G: ..................................................................................................................283pathological anatomy: ..........................................................................................289pathways: ...........................................................................................................308peroxisome: ........................................................................................................332personalised medicine: .........................................................................................289pharmacogenomics: .............................................................................................145phase diagrams: ..................................................................................................211phenotyping: ................................................................................122, 236, 243, 274, 283Phosphatises: .......................................................................................................189phosphorylation: ..................................................................................................325photoreceptors: ....................................................................................................376plant models: .................................................................................................133, 263plant technologies: ...............................................................................................135plant: ..................................................................................................................467plastid transformation: ..........................................................................................133pluripotency: .......................................................................................................385policy recommendations: ......................................................................................263population genetics: .............................................................................................281population:..........................................................................................................279population-based cohorts: .....................................................................................283positional cloning: ................................................................................................243postgenomics: .....................................................................................................475predictive dynamic models: ...................................................................................463primary cells:.......................................................................................................105protein complexes: ................................................................................... 172, 192, 208protein crystallisation: .....................................................................................168, 211protein degradation: ............................................................................................133protein deposition: ...............................................................................................187protein engineering: .............................................................................................137protein expression: ...............................................................................................208protein interactions: ..............................................................................................201protein kinase: .....................................................................................................457protein ligand interactions: ....................................................................................201protein network: ...................................................................................................437protein production: ................................................................................... 135, 178, 184protein secretion: .................................................................................................480protein structure: ............................................................................................175, 208protein-protein interaction:...............................................................................110, 437

KEYWORDS INDEX



protein-protein interactions: ...................................................................................175proteolytic enzymes: .............................................................................................115proteome: .....................................................................................................110, 427proteomics: .............................................88, 99, 113, 117, 133, 325, 332, 336, 470, 473, 477, 480

Q

QTL mapping: .....................................................................................................372quality assurance: .................................................................................................97quality control: ......................................................................................................97quantitative biology: .............................................................................................470quantitative genetics: ............................................................................................103quantitative traits: .................................................................................................285

R

rat model: ...........................................................................................................243rat: .....................................................................................................................249receptor trafficking: ..............................................................................................348regenerative medicine: .........................................................................................385regulation: ..........................................................................................................325regulatory networks: .......................................................................................409, 447regulatory RNA: ..................................................................................................399regulome: ...........................................................................................................392renal pathogenesis: ..............................................................................................372reporter cell lines: ................................................................................................257reprogramming: ...................................................................................................150research initiatives:...............................................................................................461research policies: .................................................................... 195, 197, 227, 271, 434, 437Research Projecttomyces: .......................................................................................93resources: ...........................................................................................................227retinal development: .............................................................................................376retinal dystrophies: ...............................................................................................376reverse genetics: ..................................................................................................429riboregulator: ......................................................................................................397riboswitches: .......................................................................................................411RNA in situ hybridisation: .....................................................................................220RNA interference: ................................................................................................414RNA metabolism: .................................................................................................459RNA polymerase-II: ..............................................................................................143RNA silencing:...............................................................................................150, 414RNA splicing: ......................................................................................................405RNA structure: .....................................................................................................181RNA viruses: .................................................................................................181, 184RNA: ..................................................................................................................181 RNAi: ..................................................................................................... 105, 181, 325robotics: .......................................................................................................168, 211

S

Saccharomyces cerevisiae: ....................................................................................455sample collections: ...............................................................................................290scanning force microscopy: ...................................................................................125screening: .................................................................................................99, 105, 181screening-cohorts: ................................................................................................290screens: ..............................................................................................................257self-renewal: ........................................................................................................388

KEYWORDS INDEX



sepsis: ................................................................................................................277shift work models: ................................................................................................420short interfering RNA: ...........................................................................................414signal transduction: ............................................................................ 143, 318, 441, 457signalling network: ...............................................................................................110signalling pathway: ..............................................................................................437signalling pathways:.......................................................................................208, 321signalling: ............................................................................................... 327, 348, 443simulation: ..........................................................................................................437single particle: .....................................................................................................172siRNA: ...........................................................................................................101,105site-specific, integration: ........................................................................................131skin: ...................................................................................................................321small molecules: ...................................................................................................159snoRNA: .......................................................................................................399, 401SNP: ..................................................................................................................243SNP-Chip: ...........................................................................................................290software evaluation: .............................................................................................443solute carrier: ......................................................................................................372somatic cell: ........................................................................................................249Specific Targeted: .................................................................................................93spectrum assignment:............................................................................................203splicing: ..............................................................................................................301stabilization: ........................................................................................................205stakeholder forum: ...............................................................................................263standardisation: .............................................................................................117, 168standards: ...........................................................................................................303Staphylococcus: .............................................................................................. 93, 470 stem cells: ............................................................................................... 360, 382, 388Streptomyces: ......................................................................................................480stress response: ....................................................................................................449structural biology: ................................................................................................172structural genomics: ................................. 93, 168, 175, 178, 184, 189, 192,195, 197, 203, 208, 211structural proteomics: ................................................................................ 195, 197, 213structure analysis: .................................................................................................399structure calculation: .............................................................................................203structure determination: ...................................................................................178, 213synapse: .......................................................................................................364, 437synchrotrons: .......................................................................................................168systematic high-throughput gene expression studies: .................................................265systemic effects: ...................................................................................................473systems biology: ......................... 97, 308, 434, 443, 447, 449, 453, 455, 457, 463, 467, 475, 477, 480

T

tandem repeat: ....................................................................................................279targeted mutagenesis: ...........................................................................................224technology development: .......................................................................................97technology platform: .............................................................................................168temporal dimension: .............................................................................................485therapy: ........................................................................................................332, 364three-dimensional electron microscopy: ...................................................................199tomography: ........................................................................................................122tools and technologies: .........................................................................................137Trachomatis: ........................................................................................................290training: ..............................................................................................................213transcript: ............................................................................................................301

KEYWORDS INDEX



transcription factors: .............................................................................91, 143, 145, 392transcription regulation: ..................................................................................143, 157transcription: .......................................................................................................143transcriptome analysis: .........................................................................................372transcriptome atlas: ..............................................................................................220transcriptome: .................................................................................... 301, 352, 392, 427transcriptomics: ..............................................................................................470, 480transformation: ....................................................................................................131transgenes:..........................................................................................................131transgenesis: .......................................................................................................385transgenic animals: ..............................................................................................372transposable elements: ..........................................................................................261transposon-mediated mutagenesis: .........................................................................261transposontagged mutants: ....................................................................................261trisomy: ...............................................................................................................352tumor markers: .....................................................................................................257twin-arginine translocation: ....................................................................................93

U

ultra high throughput transfection: ..........................................................................105

V

vascular biology: .................................................................................................360vascular disease: ...........................................................................................286, 360vertebrate models:................................................................................................265vision: ................................................................................................................376VNTR:.................................................................................................................279

W

web services: ......................................................................................................303web-based virtual microscope: ...............................................................................220web-linked gene expression database: ...................................................................220website: ..............................................................................................................213workshops: ..........................................................................................................213wound healing: ....................................................................................................321

X

Xenopus: .......................................................................................................265, 372X-ray crystallography: ............................................................................... 168, 178, 192

Y

yeast engineering:................................................................................................340yeast: ..................................................................................................... 192, 205, 459

Z

zebrafish embryo model: ......................................................................................257zebrafish: .......................................................................................... 254, 257, 265, 372

KEYWORDS INDEX


European Commission

EUR 23132 — From Fundamental Genomics to Systems Biology: UNDERSTANDING THE BOOK OF LIFE

Luxembourg: Office for Official Publications of the European Communities

2008 —512 pp. — 21.0 x 29.7 cm

ISBN 978-92-79-08004-3ISSN 1018-5593DOI 10.2777/49314

Price (excluding VAT) in Luxembourg: EUR 40



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PRO

JECT

SYN

OPS

ES

EUR 23132 EU-funded collaborative research projects

EUR

2313

2

FUNDAMENTAL GENOMICS RESEARCH

KI-N

A-23132-E

N-C

The sequencing of the human genome and many other genomes heralded a new age in human biology, offering unprecedented opportunities to improve human health and to stimulate industrial and economic activity. The global understanding of the complete function of approximately 22 000 human genes constitutes a major challenge for understanding normal and pathological situations. To tackle this challenge, the European Commission made fundamental genomics research a priority in the Sixth Framework Programme for RTD (FP6) (2002-2006).

The European Commission has allocated approximately 594 million in FP6 to fundamental genomics research activities with the overall aim of fostering the basic understanding of genomic information by developing the knowledge base, tools and resources needed to decipher the function of genes and gene products relevant to human health, and to explore their interactions with each other and with their environment.

The present publication provides a brief description of the goals, expected results, achievements and expected impact of all the projects supported during FP6 in the fundamental genomics priority area in the following scientific sub-areas: the development of tools and technologies for functional genomics; regulation of gene expression; structural genomics and proteomics; comparative genomics and model organisms; population genetics and biobanks; bioinformatics; multidisciplinary fundamental genomics research for understanding basic biological processes in health and disease; and the emerging area of systems biology.

During FP6, the European Commission has supported several systems biology initiatives which paved the way for further developing the genomics and systems biology programme in the Seventh Framework Programme for RTD (FP7) (2007-2013). The introduction provides an overview of the FP6 research policies and the steps taken to strengthen the European Research Area in each of the scientific sub-areas, as well as the FP7 vision in genomics and systems biology collaborative research.

Documents

NB000573