Functional - Be The Curebtcure.eu/wp-content/uploads/Functional-Genomics-Workshop... · Plenary 7 Holm Uhlig (University of Oxford, UK): The genetic landscape of monogenic forms of

Guy’s and St Thomas’ NHS Foundation Trustand King’s College London’s comprehensive

Biomedical Research Centre

FunctionalGenomics Workshop

10-12 February 2016

10-12th February 2016

St Thomas’ Hospital Governors’ Hall

King’s College London

London, UK

Aims of the workshop

• To highlight new advances in understanding the functional impact of geneticvariation in immune mediated inflammatory and related diseases.

• To provide delegates with an experimental framework for investigating thefunctional basis of genetic variation.

• To provide opportunities for investigators and their collaborators to networkin this field of research.

Organising Committee

Tim Vyse (KCL)

Lars Klareskog (Karolinska Institute)

Tom Huizinga (Leiden University Medical Centre)

Jane Worthington (Manchester University)

Frank Nestlé (KCL)

Richard Trembath (KCL)

Andrew Cope (KCL)

Workshop Sponsors

Functional Genomics Workshop

Introduction

BTCURE EU IMI ProgrammeNIHR/Biomedical Research Centre at Guy’s and St Thomas’

NHS Foundation Trust and King’s College London

1

12:30 Registration opens in Governor’s Hall, St Thomas’ Hospital

13:50 Welcome and Opening Remarks

14:00 - 15:30: Session 1 – Rheumatoid Arthritis (Chair: Jane Worthington)

Plenary 1 Soumya Raychaudhuri (Harvard Medical School, Boston, US): Using human genetics to define molecular mechanisms of rheumatoid arthritis

Plenary 2 Fina Kurreeman (Leiden University Medical Centre, The Netherlands): Novel ncRNA in the TRAF1-C5 region associated with Rheumatoid arthritis

Plenary 3 Andrew Cope (Kings College London, UK): PTPN22 links integrin-mediated adhesion with autoimmunity

15:30 - 16:00 Tea break with poster viewing

16:00 - 17:30: Session 2 – Genetics of the immune response (Chair: Kerrin Small)

Plenary 4 Frank Nestlé (Kings College London, UK): Genetic Architecture of the Human Immune System

Selected abstract presentations (10 min each, including discussion)

A1. Sylvie Grandemange (INSERM, Paris, France): NLRP1 mutations cause autoinflammatory diseases in human: implication of the NLRP1 inflammasome?

A2. Elena Lopez-Isac (CSIC, Madrid, Spain): Interrogating the common genetic background for systemic sclerosis and rheumatoid arthritis through a cross-disease meta-analysis of Genome-wide Association Studies.

Plenary 5 Julian Knight (University of Oxford, UK): eQTL mapping of induced innate immune response

17:30 - 18:15: Session 3 – Keynote Lecture (Chair: Tim Vyse)

Speaker: Manolis Dermitzakis (University of Geneva, Switzerland): Population and personal genomics to reveal disease biology

End of Day 1 Scientific sessions

18:30 – 21:00 Welcome Reception in Central Hall, St Thomas’ Hospital

Day 1: Wednesday 10th February

Keynote Lectures: 45minsPlenary Talks: 25mins

+ 5min discussionAbstract presentations: 10mins

(including discussion)

Workshop programme

2

MORNING SESSION

08:30 – 10:30: Session 4 – Functional genomics of mucosal and epithelial immunity (Chair: Graham Lord)

Plenary 6 Daniel Graham (Broad Institute, Boston, USA): Coping with stress in mucosal tissues

Plenary 7 Holm Uhlig (University of Oxford, UK): The genetic landscape of monogenic forms of inflammatory bowel disease

Plenary 8 Anne Bowcock (Imperial College, London, UK): Role of CARD14 in psoriasis pathogenesis

Plenary 9 Linde Meyaard (University Medical Centre, Utrecht, The Netherlands): A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the immune checkpoint gene SIRL-1

10:30 - 11:00 Coffee break with poster viewing

11:00 - 13:00: Session 5 – Novel approaches, technologies and tools – I(Chair: Richard Trembath)

Plenary 10 Richard Trembath (Kings College London, UK): Sequencing in a specific population for recessive variants

Plenary 11 Trevor Lawley (Sanger Institute, Cambridge, UK): Levels of genomic and functional diversity in the human intestinal microbiota

Plenary 12 Alka Saxena (NIHR-BRC at Guy’s and St Thomas’ NHS Foundation Trust, London, UK): Single cell technologies


A3. Eric Schordan (FIRALIS SAS, Huningue, France): miRNA profiling using HTG-Edgeseq platform predicts response to anti-TNFαtherapy in rheumatoid arthritis

A4. Chris Odhams (King’s College London, UK): Discovering SLE candidate genes and mechanisms by eQTL analysis using RNA-Seq.

A5. Angela Hodges (King’s College London, UK): AD-associated TREM2 variants lead to fewer microglia expressing HLA-DP, DQ, DR in the hippocampus of post-mortem human brains

13:00 - 14:00 Lunch with posters

Day 2: Thursday 11th February

Workshop programme

3

AFTERNOON SESSION

14:00 – 16:00: Session 6 – Whole organism models to dissect genefunction – I (Chair: Lars Klareskog)

Plenary 13 David Rawlings (Seattle Children’s Hospital, Washington, US): Altered B cell signaling orchestrates loss of tolerance and systemic autoimmunity

Plenary 14 Stephen McMahon (King’s College London, UK): Pain – why does it hurt so much?

Plenary 15 George Kollias (Alexander Fleming Institute, Athens, Greece): Mesenchymal causalities in chronic inflammation


A6. Miranda Houtman (Karolinska Institute, Solna, Sweden): Investigation of the associated PTPN2 locus in rheumatoid arthritis: importance of long non-coding RNA

A7. Olfa Khalifa (INSERM, Paris, France): New genes in the X chromosome associated with Rheumatoid Arthritis

A8. Klementy Shchetynsky (Karolinska Institute, Solna, Sweden): Discovery of new candidate genes for rheumatoid arthritis by integration of genetic association data with expression pathway analysis

16:00 - 16:30 Tea break

16:30 - 18:00: Session 7 – Novel approaches, technologies and tools – II(Chair: Frank Nestlé)

Plenary 16 Nicholas Luscombe (Francis Crick Institute, London, UK): Using hiCLIP to identify long-range loops in RNAs

Plenary 17 Aviv Madar (Cornell University, New York, USA): Computational biology as applied to hypersensitivity DNase analysis

Plenary 18 Phil de Jager (Harvard Medical School, Boston, USA): eQTL analyses and systems biology in MS and dementia

End of Day 2 Scientific sessions

Speakers Dinner (Meeting in the Park Plaza Westminster Bridge hotel lobby at 7:45pm)

Free evening for all other delegates


4

MORNING SESSION

09:00 – 11:00: Session 8 – Autoimmunity - I (Chair: Deborah Cunninghame-Graham)

Plenary 19 David Morris (Kings College London, UK): Genes, ancestry and prevalence in SLE

Plenary 20 Kim Simpfendorfer (Feinstein Institute, New York, USA): Investigating immune endophenotypes in healthy human carriers of autoimmune disease-associated risk haplotypes in BLK and TNIP1

Plenary 21 Ward Wakeland (University of Texas Southwestern, Dallas, US): A genomic analysis of susceptibility to systemic autoimmunity

Plenary 22 Gil McVean University of Oxford, UK): Dissecting the structure and phenotypic consequences of HLA genomic variation

11:00 - 11:30 Coffee break

11:30 - 13:00: Session 9 - Whole organism models to dissect gene function – II (Chair: Andrew Cope)

Plenary 23 Marc Dionne (Imperial College London, UK): Infections and immune responses in Drosophila

Plenary 24 Chrissy Hammond (Bristol University, UK): Using zebrafish to unpick the interactions between biomechanics and genes in making, shaping and maintaining a joint

Plenary 25 Rikard Holmdahl (Karolinksa Institute, Sweden): Positioning and analysis of the major genes controlling arthritis in rats

13:00 - 14:00 Lunch with posters

AFTERNOON SESSION

14:00 – 15:00: Session 10 – Autoimmunity – II(Chair: Tim Vyse)

Plenary 26 Stephen Sawcer (University of Cambridge, UK): Making progress in MS


A9. Michelle Krishnan (King’s College London, UK): Investigation of biological pathways involved in brain development in preterm neonates using a multivariate phenotype and sparse regression

A10. Gisela Orozco (University of Manchester, UK): Capture Hi-C reveals a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23

15:00 - 15:45: Session 11 - Keynote Lecture (Tim Vyse)

Speaker: John Todd (University of Cambridge, UK): Type I Diabetes

Closing remarks and Depart

Day 3: Friday 12th February

Workshop programme

5

Using human genetics to define molecular mechanisms of rheumatoid arthritis

Dr. Raychaudhuri is an Associate Professor at Harvard Medical School andat Brigham and Women’s Hospital. He is also appointed as an AssociateMember at the Broad Institute and a Professor in Genetics at the Universityof Manchester. He matriculated into the Stanford University NIH fundedMST program in 1997 after completing degrees in mathematics andbiophysics at the University at Buffalo. In 2004, he completed both hismedical training and his doctoral training in biomedical informatics underRuss Altman. After completing his clinical training in Internal Medicine, hejoined the rheumatology fellowship training program in 2006, andconcurrently completed his postdoctoral fellowship training under Mark Daly at the BroadInstitute. Since starting his own group in 2010 at Harvard Medical School and Brigham andWomen’s Hospital, his lab has focused on finding and fine-mapping disease alleles in rheumatoidarthritis (with a particular interest in the HLA region), age related macular degeneration and otherdiseases. He has also been devising integrative statistical genetics strategies to identify causalvariation by taking advantage of large-scale epigenetic data. He is the current Systems BiologyGroup Director for the NIH funded Accelerating Medical Progress (AMP) program in rheumatoidarthritis and systemic lupus erythematosus. He has published over 100 papers in peer-reviewedjournals including Nature Genetics, Nature, Science, and the PNAS.

Key references:

a. Hu X, Kim H, Stahl E, Plenge R, Daly M, Raychaudhuri S. Integrating Autoimmune Risk Loci with Gene Expression Data Identifies SpecificPathogenic Immune Cell Subsets. American Journal of Human Genetics. 89:496–50, 2011. PMC3188838.

b. Trynka, G, Sandor C, Han B, Xu H, Stranger B, Liu X, Raychaudhuri S. Identifying critical cell-types to fine-map complex trait variants withchromatin marks. Nature Genetics. 45:124-130, 2013 PMC3826950.

c. Stahl, EA, Wegmann D, Trynka G, Guitierrez J, Do R, Voight BF, et al… Raychaudhuri S#, and Plenge RM#. Bayesian inference reveals thehidden polygenic architecture of common disease. Nature Genetics. 44:483–489, 2012. PMC in Progress.

d. Raychaudhuri S*, Sandor C, Stahl EA, et al… de Bakker PIW*. Five amino acids in three HLA proteins explain most of the associationbetween MHC and seropositive rheumatoid arthritis. Nature Genetics. 44:291-6, 2012. PMC3288335.

e. Hu X, Deutsch AJ, Lenz TL, Onengut-Gumuscu S, Han B, Chen W-M, Howson JMM, Todd JA, de Bakker PIW, Rich SS, Raychaudhuri S.Additive and interaction effects at three key amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes genetic risk.Nature Genetics. 47(8):898-905. PMC in Progress.

f. Lenz TL*, Deutsch AJ*, Han B, Hu X, et al … de Bakker PIW*, Raychaudhuri S*. Widespread non-additive and interaction effects within theHLA modulate the risk of autoimmune diseases. Nature Genetics. 47(9):1085-90. PMC in Progress.

g. Seddon JM*, Yu Y, Miller EC, Reynolds R, Tan PL, Gowrisankar S, Goldstein JI, Triebwasser M, Anderson HE, Zerbib J, Kavanagh D, Souied E,Katsanis N, Daly MJ, Atkinson JP, and Raychaudhuri S*. Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Nature Genetics. 45:1366-70, 2013. PMC3902040.

Soumya RaychaudhuriDivisions of Genetics & RheumatologyBrigham & Women's HospitalHarvard Medical SchoolBoston USA

Session 1Day 1: Wednesday

10th February

6

7

Novel ncRNA in the TRAF1-C5 region associated with Rheumatoid arthritis

Dr Fina Kurreeman is assistant professor at Leiden University MedicalCenter. She graduated from her PhD in 2009 (Cum Laude) following thediscovery of the third genetic risk factor associated with rheumatoidarthritis. She spent three years doing her post-doctoral training in the labof Dr Robert Plenge at Harvard Medical School and at the broad instituteof MIT and Harvard. During this time, she implemented largescale NGStechniques to discover the role of genetic variation in human disease, inparticular rheumatoid arthritis. This work led to several importantpublications in American Journal of Human genetics (main author) andseveral papers in Nature genetics (co-author). She has contributed to the discovery of >100genetic regions linked with Rheumatoid Arthritis. Dr Kurreeman is the recipient of severalprestigious National and European Grants and is regularly invited by consortia and conferences togive lectures (BTCURE, EULAR).

Dr. Fina Kurreeman’s research currently focuses on (i) Understanding how genetic variation resultsin functional changes relevant in disease (ii) Understanding the role of specific cells in chronicactivation (iii) the possible role of microbes in disease. Her main interest is to leverage genomicstechniques to help unravel novel mechanisms underlying disease pathogenesis.

Fina Kurreeman Leiden University Medical CentreThe Netherlands


10th February

8

PTPN22 links integrin-mediated adhesion with autoimmunity

Andrew Cope graduated in Medicine from the University of London withfirst class honours. After training in general internal medicine at NorthwickPark Hospital, The National Hospital for Nervous Diseases and the RoyalBrompton Hospital, he trained in rheumatology with Professor Sir RavinderMaini and Dr. Barbara Ansell CBE. In 1990, he was awarded a WellcomeTrust Clinical Training Fellowship, studying for a PhD in Cytokine Biology withProfessor Sir Marc Feldmann at the Kennedy Institute of Rheumatology.Following a postdoctoral fellowship with Professor Hugh McDevitt atStanford University, California, studying transgenic models of autoimmunity,he returned to the Kennedy Institute to set up his own laboratory. In 2005 Andrew Cope wasappointed Reader in Molecular Medicine at the Kennedy Institute of Rheumatology, and in 2008 wasrecruited to the Arthritis Research UK Chair in Rheumatology at King’s College London. He iscurrently Head of the Academic Department of Rheumatology and Associate Director of the King’sClinical Trials Unit, and has been Lead for the NIHR Biomedical Research Centre’s School forTranslational and Experimental Medicine (STEM) at Guy’s and St Thomas NHS Foundation Trust since2012. His clinical research interests revolve around aspects of inflammatory arthritis, including veryearly inflammatory arthritis and disease remission states. Research in the Cope lab is focused aroundtwo key themes: the biology of T cell activation and differentiation in the context of chronicinflammatory diseases, such as rheumatoid arthritis, with an emphasis on antigen receptor signaltransduction and cell migration; understanding how allelic variants of immunologically importantgenes contribute to autoimmune disease pathogenesis. The Cope lab is housed in the Centre forMolecular and Cellular Biology of Inflammation (CMCBI) on the Guy’s Campus, Faculty of LifeSciences and Medicine, King’s College London.

Andrew Cope Academic RheumatologyKings College London, UK


10th February

9

Genetic Architecture of the Human Immune System

Professor Frank O Nestlé holds the post of Mary Dunhill Chair of CutaneousMedicine and Immunotherapy at St. John’s Institute of Dermatology, King’sCollege London. He is a Non Executive Director at Guy’s and St. Thomas’Hospital and a member of the Biomedical Research Centre (BRC) Executive.He is also Director of the Federation of Clinical Immunology Society (FOCIS)Centre of Excellence King’s College London. Professor Nestle is a NationalInstitute for Health Research (NIHR) Senior Investigator and a Fellow of theAcademy of Medical Sciences (FMedSci).

His main research interests include the pathogenesis and immunotherapy of inflammatory skindisease and skin cancer. He has given over 350 scientific lectures at national and internationalconferences. He was a Visiting Professor at the Mayo Clinic, Yale Medical School and RockefellerUniversity. He is a member of numerous national and international societies and is currentlyPresident of the Federation of Clinical Immunology Societies (FOCIS).

He has published over 200 scientific articles in publications such as Nature, Nature Medicine, Cell,New England Journal of Medicine, Journal of Experimental Medicine and Lancet. He has receivednumerous awards including the Alfred Marchionini Research Award at the 20th World Congress ofDermatology and the American Skin Association Achievement Award at the Tricontinental Meetingof the Societies of Investigative Dermatology.

Despite recent discoveries of genetic variants associated with autoimmunity and infection, geneticcontrol of the human immune system during homeostasis is poorly understood. We undertook acomprehensive immunophenotyping approach, analysing 78,000 immune traits in 669 femaletwins. From the top 151 heritable traits (up to 96% heritable), we used replicated GWAS to obtain297 SNP associations at 11 genetic loci, explaining up to 36% of the variation of 19 traits. Wefound multiple associations with canonical traits of all major immune cell subsets and uncoveredinsights into genetic control for regulatory T cells. This data set also revealed traits associated withloci known to confer autoimmune susceptibility, providing mechanistic hypotheses linking immunetraits with the etiology of disease. Our data establish a bioresource that links genetic controlelements associated with normal immune traits to common autoimmune and infectiousdiseases,providing a shortcut to identifying potential mechanisms of immune-related diseases.

Frank NestléDivision of Genetics and Molecular MedicineSt Johns Institute of DermatologyKings College London, UK


10th February

10

Abstracts

A1 Sylvie Grandemange : NLRP1 mutationscause autoinflammatory diseases in human:implication of the NLRP1 inflammasome?

Authors:Sylvie Grandemange1-2, Elodie Sanchez2-3, Pascale Louis-Plence2, Cécile Rittore1-2, John C Reed4 , FlorenceApparailly2, Isabelle Touitou1-2-5, David Geneviève2-3.

Affiliation:1. Laboratoire des maladies rares et auto-

inflammatoires, Hôpital Arnaud de Villeneuve, CHRU Montpellier, France

2. INSERM U1183, Institute of regenerative medicineand biotherapy, Montpellier, France

3. Département de Génétique médicale, HôpitalArnaud de Villeneuve, CHRU Montpellier, France

4. Sanford-Burnham Medical Research Institute, La Jolla, CA. United-States

5. University of Montpellier

Abstract text:

Inflammation is a vital and complex process in response todiverse tissue damaging stimuli such as trauma, injury andpathogen. NLRP1, NLRP3 and NLRC4 belonging to theintracellular proteins Nod like receptor family, are capableof sensing the inflammatory inducers and trigger theassembly of a large complex called the inflammasome. Byinducing the caspase-1 activation, inflammasome plays acrucial role in the release of IL-1β and IL-18, two criticalcytokines of the initial steps of inflammatory responses.

Whereas mutations in NLRP3 and NLRC4 have beenlinked to two rare monogenic systemic autoinflammatorydiseases (SAIDs), several polymorphisms in the NLRP1 genehave been associated extensively to an increased risk ofautoimmune disorders (e.g. vitiligo, psoriasis, type 1diabetes, and rheumatoid arthritis). We identified for thefirst time two distinct NLRP1mutations in patientsdisplaying a novel SAID combining autoinflammation andautoimmunity. The aim of our study was to unravel howmutation in NLRP1 impaired its function and triggeredautoinflammation.

Peripheral blood mononuclear cells from patients wereanalyzed to identify the immunologic components involvedin these novel diseases, using flow cytometry and ex vivoNLRP1 inflammasome stimulation. The pathogenic effect ofthe NLRP1 mutations in inflammation was investigatedusing in vitro functional assays in transfected HEK293T.

The level of caspase-1, IL-18 and IL-1β in serumsamples from patients was increased as compared tocontrols and unaffected parents. Moreover, patient’s cellsdisplayed constitutive production of IL-1β. Functionalstudies in HEK293T revealed that the NLRP1mutationsresulted in a constitutive activation of the NLRP1inflammasome.

We demonstrated for the first time that two mutationsin the NLRP1 gene are involved in autoinflammation inhuman. We named this disease NAIAD, for NLRP1-associated autoinflammation arthritis and dyskeratosis. Ourdata, combined to the literature, highlight the pleomorphicroles of NLRP1 in inflammation and immunity.

A2 Elena Lopez-Isac : Interrogating thecommon genetic background for systemicsclerosis and rheumatoid arthritis through across-disease meta-analysis of Genome-wideAssociation Studies.

Authors:Elena López-Isac1*, Shervin Assassi2, Carmen Pilar Simeón3,Patricia Carreira4, Norberto Ortego-Centeno5, the SpanishScleroderma Group, Benjamín Fernández-Gutiérrez7,Miguel A González-Gay8, Lorenzo Beretta9, ClaudioLunardi10, Gianluca Moroncini11, Armando Gabrielli11,Torsten Witte12, Nicolas Hunzelmann13, Jörg H.W. Distler14,Gabriella Riekemasten15, Annete H van der Helm-van Mil22,Jeska de Vries-Bouwstra16, Cesar Magro16, Alexandre E.Voskuyl17, Madelon C Vonk18, Øyvind Molberg19, TonyMerriman20, Roger Hesselstrand21,Annika Nordin22, LeonidPadyukov22, Ariane Herrick23, Steve Eyre23, Bobby PCKoeleman24, Christopher P. Denton25, Carmen Fonseca25,Timothy RDJ Radstake26, Jane Worthington23, Maureen D.Mayes2, Javier Martín1

Affiliation:

1. Institute of Parasitology and Biomedicine López-Neyra,IPBLN-CSIC, PTS Granada, Granada, Spain.

2. The University of Texas Health Science Center–Houston,Houston, USA.

3. Department of Internal Medicine, Valle de HebrónHospital, Barcelona, Spain.

4. Department of Rheumatology, 12 de Octubre UniversityHospital, Madrid, Spain.

5. Department of Internal Medicine, Clinic UniversityHospital, Granada, Spain.

7. Rheumatology Service, Hospital Clínico San Carlos,Madrid, Spain.

8. Health Research Institute of Santiago de Compostela(IDIS), Division of Rheumatology, Clinical UniversityHospital of Santiago de Compostela, Spain.

9. Referral Center for Systemic Autoimmune Diseases,Fondazione IRCCS Ca' Granda Ospedale MaggiorePoliclinico di Milano, Milan Italy.

10. Department of Medicine, Università degli Studi diVerona, Verona, Italy.

11. Clinica Medica, Department of Clinical and MolecularScience, Università Politecnica delle Marche andOspedali Riuniti, Ancona, Italy.

12. Department of Clinical Immunology, Hannover MedicalSchool, Hannover, Germany.

13. Department of Dermatology, University of Cologne,Cologne, Germany.

14. Department of Internal Medicine, Institute for ClinicalImmunology, University of Erlangen-Nuremberg,Erlangen, Germany.

15. Clinic of Rheumatology, University of Lübeck, Lübeck ,Germany

16. Department of Rheumatology, Leiden UniversityMedical Center, Leiden, The Netherlands.

17. Department of Rheumatology, VU University MedicalCenter, Amsterdam, The Netherlands.

11

continued overleaf

Abstracts

A2

Affiliation (continued)

12

18. Department of Rheumatology, Radboud UniversityNijmegen Medical Center, Nijmegen, The Netherlands.

19. Rheumatology Unit, Oslo University HospitalRikshospitalet and Institute of Clinical Medicine,University of Oslo, Oslo, Norway.

20. Department of Biochemistry, University of Otago, New Zealand.

21. Department of Rheumatology, Lund University, Lund,Sweden.

22. Rheumatology Unit, Department of Medicine,Karolinska University Hospital, Karolinska Institutet,Stockholm, Sweden.

23. Centre for Musculoskeletal Research and NIHRManchester Musculoskeletal Biomedical Research Unit,The University of Manchester, Manchester AcademicHealth Science Centre, Manchester, UK.

24. Section Complex Genetics, Department of MedicalGenetics, University Medical Center Utrecht, Utrecht,The Netherlands.

25. Centre for Rheumatology, Royal Free and UniversityCollege Medical School, London, United Kingdom.

26. Department of Rheumatology & Clinical Immunology,Laboratory of Translational Immunology, department ofImmunology, University Medical Center Utrecht,Utrecht, The Netherlands.

Abstract text:

Background: Systemic sclerosis (SSc) and rheumatoidarthritis (RA) are two autoimmune diseases that share clinicaland immunological features: Both are rheumatic connectivetissue disorders, characterized by an exacerbatedinflammatory response, deregulation of innate and adaptiveimmunity, including autoantibody production, and systemiccomplications. To date, several shared SSc-RA loci have beenidentified independently, pointing to a common geneticbackground underlying these two autoimmune processes.

Aim: To systematically identify new common SSc-RA locithrough a cross-disease meta-GWAS strategy.

Methods: We performed a meta-analysis combining GWASdatasets of SSc and RA using a strategy that allowedidentification of loci with both same-direction and opposing-direction allelic effects. The top single-nucleotidepolymorphisms (SNPs) showing a P-value < 5 x 10-6 in thecross-disease meta-analysis and nominal significance in theassociation study for each disease separately were followed-up in independent SSc and RA case-control cohorts. In total,this study comprises 8,830 SSc patients, 16,870 RA patientsand 43,393 controls.

Results: The cross-disease meta-analysis of the GWASdatasets identified several SNPs from different genomicregions showing a P-value < 5 x 10-6 and nominalassociation in the disease-specific GWAS scan. These lociincluded several genomic regions not previously reported asshared loci, besides risk factors associated with both diseasesin previous studies. The follow-up of the putatively new SSc-

RA loci identified IRF4 as a novel shared risk factor for thesetwo rheumatic conditions (Pcombined = 3.29 x 10-12). Inaddition, the analysis of the biological connection acrossknown SSc-RA shared loci pointed to the type I interferonand the interleukin 12 signaling pathways as the maincommon etiopathogenic factors.

Conclusions: The present study has identified a novel sharedlocus, IRF4, for SSc and RA and highlighted the usefulness ofinter-disease GWAS meta-analysis in the identification ofcommon risk loci. With this study, we provide additionalgenetic evidence for the IFN signature described for SSc andRA patients.

13

eQTL mapping of induced innate immune response

Julian Knight trained as a clinician scientist, studying Medicine at theUniversity of Cambridge and the University of Edinburgh before completinghis DPhil at the University of Oxford at the Weatherall Institute of MolecularMedicine in 1998. He developed his research interest in the functionalgenomics of immunity working in Oxford at the Wellcome Trust Centre forHuman Genetics (WTCHG) and at Harvard University in the Department ofMolecular and Cellular Biology. Since 2005 he has worked at the WTCHG asa Principal Investigator and as an Honorary Consultant Physician at theOxford University Hospitals NHS Trust. The core interest of the lab’s researchis how genetic variation between individuals modulates genes critical to mounting an appropriateimmune and inflammatory response and may contribute to susceptibility to autoimmune andinfectious disease (http://www.well.ox.ac.uk/knight-j).

Julian KnightNuffield Department of MedicineWellcome Trust Centre for Human GeneticsUniversity of OxfordUK


10th February

14

Population and personal genomics to reveal disease biology

Emmanouil (Manolis) Dermitzakis is currently a Professor of Genetics in theDepartment of Genetic Medicine and Development of the University ofGeneva Medical School. He is a member of the executive board of theInstitute of Genetics and Genomics in Geneva (iGE3), a member of theSwiss Institute of Bioinformatics and adjunct faculty member of theBiomedical Research Foundation of the Academy of Athens. He obtainedhis B.Sc. in 1995 and M.Sc. in 1997 in Biology from the University of Crete(Greece) and his PhD in 2001 from the Pennsylvania State University in theUSA, studying the evolutionary biology and population genetics ofregulatory DNA in mammals and Drosophila. His post-doctoral work wasat the University of Geneva Medical School, focusing on comparative genome analysis and thefunctional characterization of conserved non-genic elements. He, previously, was an Investigatorand Senior Investigator at the Wellcome Trust Sanger Institute in Cambridge from 2004 to 2009.He was elected an EMBO member in 2014 and has also been named Highly Cited Researcher by ISIin 2014 and 2015. He currently serves as the president of the Executive Board of the WorldHellenic Biomedical Association (2014-2015). His current research focuses on the genetic andmolecular basis of human disease. He has had leading roles in big international projects such asENCODE (ENCyclopedia Of Dna Elements), Mouse Genome Sequencing Consortium, InternationalHapMap project, 1000genome and GTEx. He has served as an editor for the journals Science, PLoSGenetics and eLife.

Manolis Dermitzakis Department of Genetic Medicine and Development University of Geneva Medical School Switzerland


10th February

15

Population and personal genomics to reveal disease biology

Daniel Graham is a principal investigator at the Broad Institute and facultymember at the Massachusetts General Hospital of Harvard Medical School.He received his PhD in immunology from the Mayo Clinic College ofMedicine and completed postdoctoral training at Washington UniversitySchool of Medicine in St. Louis. His work leverages insights gleaned fromhuman genetics to identify key pathways underlying inflammatory boweldisease (IBD). His research adopts multidisciplinary approaches comprised of(1) functional genetic screens to place genes in immune pathways, (2)multi’omic platforms for deep mechanistic characterization of gene function,(3) developing mouse models to discern gene function in the context of complex pathologicalresponses in vivo, and (4) identification of novel targets for therapeutic development. Collectively, hiswork has contributed to the understanding of inflammatory signal transduction pathways that elicitinnate effector mechanisms (oxidative burst, natural cytotoxicity) and acquisition of adaptiveimmunity (antigen presentation, T cell differentiation). Ongoing efforts aim to shed light on thecoordinated interactions between the innate and adaptive immune systems within the gut mucosa.

Daniel Graham Broad InstituteBostonUSA

Session 4Day 2: Thursday

11th February

16

The genetic landscape of monogenic forms of inflammatory bowel disease

Holm Uhlig is an Associate Professor and Honorary Consultant in PaediatricGastroenterology, Children’s Hospital Oxford and the TranslationalGastroenterology Unit, University of Oxford. He completed medicalresidency in pediatrics and pediatric gastroenterology at the University ofLeipzig (Germany) and obtained a DPhil in mucosal immunology at the SirWilliam Dunn School of Pathology in Oxford (UK). Holm investigates raremonogenic disorders that are associated with very early onset ofinflammatory bowel disease. Holm contributed to the functionalcharacterisation of several genetic defects that can cause intestinalinflammation. He investigates patients by whole exome sequencingtranslating genetic information and immunologic understanding intoindividualised patient care.

Holm Uhlig Nuffield Department of MedicineExperimental Medicine DivisionUniversity of OxfordUK


11th February

17

Role of CARD14 in psoriasis pathogenesis

Anne Bowcock is Professor and Chair in Cancer Genomics at ImperialCollege London. She obtained a PhD from the University of Witwatersrandin South Africa and was a postdoctoral fellow at Stanford Universityworking with Professor Luigi Cavalli-Sforza. She held faculty positions at theUniversity of Texas Southwestern Medical Center at Dallas and WashingtonUniversity School of Medicine in Saint Louis. Among her researchachievements are demonstrating the use of DNA markers in reconstructinghuman evolution, identifying proteins interacting with the early onset breastcancer gene BRCA1 and identifying a gene commonly mutated in highlymetastatic uveal melanoma. She has studied the genetics of psoriasis andpsoriatic arthritis for over twenty years and her recent achievements in this field have been inidentifying a familiar form of psoriasis and psoriatic arthritis and functional consequences of thedisease causing mutations. She is also searching for additional rare and highly penetrant geneticchanges that lead to psoriasis and psoriatic arthritis, their role in disease susceptibility and ways ofcombatting their effects.

Anne Bowcock National Heart and Lung InstituteImperial College LondonUK


11th February

18

A functional SNP associated with atopic dermatitis controlscell type-specific methylation of the immunecheckpoint gene SIRL-1

Linde Meyaard finished her undergraduate studies in Biomedical Sciences atLeiden University in 1990. She subsequently studied T cell function in HIV-1infection at Sanquin in Amsterdam with Prof. Frank Miedema, where shegraduated in 1995 (Cum Laude). She started studying immune inhibitoryreceptors at DNAX research institute in Palo Alto, CA in the laboratory of ProfLewis Lanier and Joseph Phillips, where she cloned the inhibitory receptorLAIR-1. Upon return to the Netherlands she continued her work on LAIR-1initially as a post-doc with Prof Hans Clevers and later as an independent group leader at theUniversity Medical Center in Utrecht. She was the first to identify collagens and collagen-like proteinsas the natural ligands for LAIR-1.

She extended her research towards other inhibitory receptors that are able to control collateraldamage by the immune system and discovered SIRL-1 as a novel inhibitory receptor able to regulatethe function of neutrophils and monocytes. Currently, she focuses on studying the control of immune-mediated collateral tissue damage through inhibitory receptors. She introduced mouse models in herlab, which allowed her to establish an essential role for CD200R in the control of sex-biased immune-mediated damage upon viral infections. Furthermore, she formed a translational research team withclinician Prof Louis Bont, studying regulation of neutrophilic airway inflammation and the potential totherapeutically exploit inhibitory receptors.

Meyaard was appointed full Professor of Immune Regulation in Utrecht in 2007. Her work issupported by several prestigious grants, such as a fellowship of the Royal Dutch Academy of Sciences(1999-2001) and personal grants from the Dutch society for Scientific Research (2001, 2002 and2015) and by grants from the Dutch Arthritis Foundation, Dutch Cancer Society, AICR and others.

In addition, the growing global interest in targeting inhibitory receptors therapeutically resulted inconsultancies, collaborations and invitations for seminars in pharmaceutical companies opening uppossibilities for clinical application of her work. Professor Meyaard serves on multiple scientific boardsof and was secretary general of the Dutch Society of Immunology from 2008-2014.

Linde Meyaard Department of Immunology, University Medical Centre UtrechtThe Netherlands


11th February

19

20

Sequencing in a specific population for recessive variants

Professor Trembath trained in Medicine at Guy's Hospital Medical School,undertook postgraduate studies in genetics at the Institute of Child Health inLondon and moved to the University of Leicester in 1992, being appointed tothe Foundation Chair of Medical Genetics in Leicester in 1998, before movingto King’s in the summer of 2005 where he held the role of Head of Divisionof Genetics & Molecular Medicine and as the founding Director of theNational Institute for Health Research Comprehensive Biomedical ResearchCentre in association with Guy's & St Thomas' NHS Foundation Trust.

Professor Trembath moved to QMUL in 2011 where he held the position of Vice-Principal for Healthand Executive Dean of the Barts and The London School of Medicine and Dentistry. In this roleProfessor Trembath led a major period of change, strengthening cross faculty working, developingmodels of support for development of the early stages of academic careers, driving forward QMULnew Life Sciences Initiative and partnership working at scale, as an Executive and Board member ofthe academic health science centre, UCL Partners.

He is Fellow of the Academy of Medical Sciences and a former Senior Investigator for the NationalInstitute of Health Research.

Professor Trembath's research interests include the identification and characterisation of genes and themolecular pathways underlying a range of human common and rare disorders. Working withcolleagues at the University of Cambridge and the Wellcome Trust Sanger Institute, he is the Principalinvestigator and Co-Director of a major population genomics programme, known as East LondonGenes and Health.

Richard Trembath Division of Genetics & Molecular Medicine King’s College LondonUK


11th February

21

Levels of Genomic and Functional Diversity in the Human Intestinal Microbiota

Trevor's research investigates the mechanisms that underlie how micro-organisms on mucosal surfaces (gut, nasopharnyx, uro-gential tract)interact with their host during periods of health and disease. In particularhe seeks to develop novel ways to treat diseases that are associated withunwanted imbalances in the micro-organism communities.

Trevor uses high-throughput genome sequencing to investigate themicrobial communities contained on and within host organisms that areassociated with health and disease. He uses clinical samples and mousemodels to identify the pathogen and host factors that are linked to disease and infectivity.

Trevor obtained his PhD from the University of Alberta, Canada, where he studied the mechanismsthat pathogenic bacteria use to disseminate antibiotic resistance genes. Dr Diane Taylor and DrLaura Frost were his supervisors. His PhD thesis culminated in 2004 with him receiving the 'GoldAward' (Graduate Student of the Year) from the Canadian Society of Microbiologists.

After his PhD Trevor was awarded a Canadian Institutes of Health Research post-doctoralfellowship to work in the Laboratory of Professor Stanley Falkow and Dr Denise Monack atStanford University, USA, where he studied the impact of antibiotic treatment on Salmonelladisease and transmission. In 2007 Trevor received a Royal Society of London Award - sponsored byProfessor Gordon Dougan - to start a research programme on Clostridium difficile disease andtransmission within the Microbial Pathogenesis group at the Wellcome Trust Sanger Institute.

In 2010, Trevor was appointed as a Career Development Fellow in the Sanger Institute Faculty andwas promoted to Group Leader in 2014. He receives funding from the Medical Research Council.

Trevor Lawley Trevor Lawley Sanger InstituteCambridgeUK


11th February

22

23

Single cell technologies

Dr Alka Saxena studied medicine at Shivaji University in India and after 7years of clinical practice, completed her PhD at the Murdoch Children’sResearch Institute at the University of Melbourne in Australia.

Alka then went on to work on monogenic disorders, first on DuchenneMuscular Dystrophy at the Australian Neuromuscular Research Institute inPerth, Australia as a Muscular Dystrophy Association (MDA) Research Fellowand later on Rett Syndrome as an NH& MRC postdoctoral Research Fellow atthe University of Western Australia, where she received the Barry MarshallAward for her work, before becoming an Assistant Professor.

Alka continued her work on Rett Syndrome through Advanced Genomics Technologies at the RIKENOmics Science Centre in Japan as an international JSPS research Fellow, where she also participated inthe FANTOM 5 project, learned new methods for next generation sequencing of RNAs and studiedpromoters, non-coding RNAs, small RNAs, piRNAs and iPS cells in the context of human disease. AtRIKEN, Alka developed special skills for generating and sequencing RNA libraries from minisculeamounts of input RNA.

Alka relocated to the UK in 2013, where she is the Head of the Genomics Research Platform at theBRC at Guy's and St Thomas' NHS Foundation Trust and an Honorary Senior Research Fellow at King’sCollege London. In this role, Alka and her team are not only providing more than 15 different typesof library preparation and sequencing services but also pushing the boundaries of science throughtechnology development for Single Cell Genomics.

Peer reviewed recent publications:

1. Kaudewitz D, Skroblin P, Bender LH, Barwari T, Willeit P, Pechlaner R, Sunderland NP, Willeit W, Morton A, Armstrong PC, Chan MV, LuR, Yin X, Gracio F, Dudek D, Langley S, Zampetaki A, de Rinaldis E, Ye S, Warner T, Saxena A, Kiechl S, Storey R, Mayr M, Association ofMicroRNAs and YRNAs with platelet function, Circ Res 2015 Dec 8 Epub

2. Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P; Remodelingof retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors, EpigeneticsChromatin 2015 14;8:55. Epub 2015 Dec 14.

3. Arner E et al Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells, Science 2015 Feb12;347(6225):1010-4. Epub 2015 Feb 12.

4. Francescatto M, Vitezic M, Heutink P, Saxena A; Brain-specific noncoding RNAs are likely to originate in repeats and may play a role in up-regulating genes in cis. Int J Biochem Cell Biol 2014 Sep 30;54:331-7. Epub 2014 Jun 30.

5. Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, FagioliniM, Forrest ARR, Carninci P, Saxena A, CAGE-defined promoter regions of the genes implicated in Rett Syndrome BMC Genomics 201424;15:1177. Epub 2014 Dec 24.

6. Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong C, Hoon M,Andersson R, Sandelin A, Suzuki H, Wei C, Koseki H, Hasegawa Y, Forrest ARR & Carninci P, Deep transcriptome profiling of mammalianstem cells supports a key regulatory role for retrotransposon in pluripotency maintenance, Nat Genet 2014 Jun 28;46(6):558-66.Epub 2014 Apr 28.

7. Forrest ARR, et al A promoter-level mammalian expression atlas, Nature 2014 Mar;507(7493):462-70

8. Durand S, Patrizi S, Quast K, Hachigian L, Pavlyuk R, Saxena A, Carninci P, Hensch TK and Fagiolini M; NMDA Receptor RegulationPrevents Regression of Visual Cortical Function in the Absence of Mecp2, Neuron 2012, 76(6) 1078-1090

9. Saxena A*, Tang D and Carninci P; piRNAs warrant investigation in Rett Syndrome: an Omics perspective; Disease Markers 2012,10.3233/DMA-2012-0932, *corresponding author

10. Francia S, Michelini F, Saxena A, Viviana A, Tang D, Dobreva M, Mione M, Carninci P and d'Adda di Fagagna F; DICER and DROSHA RNAproducts control the DNA damage response; Nature, 2012, doi:10.1038/nature 11179

Alka Saxena NIHR-BRC at Guy’s and St Thomas’ NHS Foundation Trust LondonUK


11th February

(continued overleaf)

24

Session 5


(continued)

11. Saxena A*, Wagatsuma A*, Noro Y, Kuji T, Watahiki A, Gurnot C, Fagiolini M, Hensch T and Carninci P; Trehalose-enhanced isolation ofspecific neuron sub-types from adult mouse brain, BioTechniques, 2012, (*shared first authorship)

12. Cernilogar F, Onoratti MC, O’ Kothe G, Burroughs A, Parsi KM, Breiling A, lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi M, Carninci P,Gilmour D, Corona D, and Orlando V; Chromatin associated RNAi components control transcriptional regulation in Drosophila,Nature 2011 doi: 10.1038/nature10492

13. Saxena A and Carninci P, Long Non coding RNA modifies Chromatin; Bioessays 2011, DOI: 10.1002/bies.201100084

14. Saxena A and Carninci P; Whole transcriptome analysis: What are we still missing? 2010; Advanced Reviews, WIRES; Systems Biologyand Medicine, Pubmed id:21197667; Doi 10.1002/wbsm.135

25

Abstracts

A3 Eric Schordan : miRNA profiling usingHTG-Edgeseq platform predicts response toanti-TNFα therapy in rheumatoid arthritis

AuthorsE. Schordan, G. Bilger, M. Coq, S. Danilin, M.Schumacher, H. Firat.

AffiliationFiralis SAS, Huningue, France

Abstract text

Millions of patients suffering Rheumatoid Arthritis (RA)are treated with agents inhibiting TNF-α, however,response rate is low (30 to 40%) and no tool exists topredict the treatment response. Using the HTG-Edgeseqplatform, an innovative combination of nucleaseprotection assay and next generation sequencing, weidentified sets of miRNAs that discriminate respondersfrom non-responders to anti TNF-α therapy.

Sixty-seven patients diagnosed with RA, eligible fortreatment with 1st line anti-TNFα and for whom DMARDtherapy had failed were enrolled in the study. Twelve to14 weeks after anti-TNFα therapy, patients werecategorized as responders or non-responders based onDAS28 index. Patients’ miRNA profile was establishedfrom 15µl of plasma using HTG-Edgeseq WholeTranscriptome Assay (WTA) miRNA panel (2256 miRNA).Results were normalized based on the median of thesample and Random forest was used as the classificationmodel. For 8 patients, miRNA were also analyzed withthe qPCR Exiqon miRNA panel V4 to determine HTG-Edgeseq accuracy. Method reproductibility was assessedby analyzing 4 times an independent sample on differentsites, with different instruments/days/operators.

Results obtained from both HTG-Edgeseq and qPCRmethods showed an overall correlation of 0.63 for the341 miRNA common between those 2 kits, andcorrelations factors between the 4 independentexperiments ranged from 0.993 to 0.999. Statisticalanalysis of patients’ miRNA profile identified 2 panels of6 and 52 miRNAs with significant predictive power todiscriminate responders from non-responders (sensitivitywas 0.898 and 0.918, and AUC 0.773 and 0.824respectively).

In conclusion, miRNA profiling in RA patients usingHTG-EdgeSeq allowed us to build 2 predictive models forresponse to anti-TNF-α drugs. Moreover, we showed thatHTG-Edgeseq platform offers accurate and sensitive RNAexpression measurement. Its low sample inputrequirement and compatibility with all biological materialmakes it an invaluable tool for biomarkers discovery.

A4 Chris Odhams : Discovering SLEcandidate genes and mechanisms by eQTLanalysis using RNA-Seq

AuthorsChris Odhams, Deborah Cunninghame Graham, DavidMorris, Andrea Cortini, Tim Vyse .

AffiliationKing’s College London Department of Medical & MolecularGenetics

Abstract text

Background: Integration of expression quantitative traitloci (eQTL) mapping with Genome-wide association studies(GWAS) allow for the functional interpretation of diseasesusceptibility loci by prioritizing candidate genes andrefining causal variants. The majority of existing studiesimplement 3′ targeted microarrays to profile geneexpression and are thus limited in their ability to accuratelyquantify transcriptional output and target the full array ofexpressed isoforms. Large eQTL mapping studies usingRNA-Sequencing (RNA-Seq) are now accessible and havethe potential to reveal novel disease-associated eQTLs andthe accompanying pathogenic mechanism.

Aims & Methods: In this study we functionally annotateSLE associated loci through integration of cis-eQTL dataderived from microarray and RNA-Seq experiments in LCLsand whole blood with results from the largest currentGWAS in SLE to compare the ability of both quantificationmethods to discover eQTLs. We consider only eQTLs thatshow evidence of a shared causal variant between diseaseand eQTL signal by applying a conditional andcolocalisation analysis pipeline.

Results: We detect eight SLE candidate causal cis-eQTLsusing microarray (modulating expression of twelveeGenes), eleven using gene-level RNA-Seq (nineteeneGenes), and fourteen using exon-level RNA-Seq (thirty-four eGenes); demonstrating the benefits of increasedaccuracy and resolution in eQTL detection. We provide adetailed example of annotation of novel susceptibilitylocus, 2q34, which appeared quiescent using microarrayanalysis but with RNA-Seq unearthed a putative causalsplicing mechanism (replicated with qPCR) in IKZF2, a T-regrestricted transcription factor.

Discussion: We have emphasised the need to employRNA-Seq to increase elucidation of GWAS results and, indoing so, have pointed to targeted follow-up studies. Weshall increase our understanding of the genetic control ofgene and isoform expression in the genetic architecture ofcomplex disease once RNA-Seq eQTL cohorts becomeavailable across a wider range of ex vivo cell types andconditions.

26

Abstracts

A5 Angela Hodges : AD-associated TREM2variants lead to fewer microglia expressingHLA-DP, DQ, DR in the hippocampus of post-mortem human brains

Authors:Yau Mun Lim1, Anaelle Dumas1, Andrew King1, ClaireTroakes1, Christina Murray2 Kuang Lin1, Safa Al-Sarraj1,Lawrence Sivakumar1, Tammaryn Lashley2, and AngelaHodges1

Affiliation:1 King's College London, Institute of Psychiatry,

Psychology & Neuroscience, London, SE5 8AF, UK

2 University College London, Institute of Neurology,London, WC1N 3BG, UK

Abstract text:

Recent research revealed the triggering receptorexpressed on myeloid cells 2 (TREM2) gene is a risk genefor Alzheimer’s disease (AD) and related dementias. Genevariants appear to cause a loss-of-function of normalTREM2 function. TREM2 is crucial for the functioning ofmicroglia, the cells that mediate immune function andrespond to damage in the brain. We set out toinvestigate the effects of TREM2 variants in post-mortemhuman brain sections by labelling microglia with theestablished microglial markers CD68 and Iba-1 (proteinsinvolved in phagocytosis, a process of internalising debrisand unwanted substances) and HLA-DP, DQ, DR(henceforth called HLA, a set of proteins involved inrecognising misfolded and pathogenic proteins and thusappearing to mediate adaptive immune responses in thebrain. We compared the abundance of microglia with thedifferent markers in the CA1 and CA4 hippocampalregions between AD cases with suspected pathogenicTREM2 variants (TREM2+) and AD and Control caseswithout TREM2 variants (TREM2-). AD/TREM2+ caseswere found to have significantly fewer HLA-stainedmicroglia, marginally lower CD68-stained microglia butno difference in Iba-1-stained microglia compared toAD/TREM2- cases. Our results suggest that TREM2variants inhibit the activation of resident resting microgliabut not the overall number of microglia as we did notdetect differences between Iba-1-stained microglia inAD/TREM2+, AD/TREM2- and Control/TREM2- groups.This may lead to the inability of microglia to respondappropriately to pathology that arise in AD and thusresult in a susceptibility for individuals with TREM2variants to develop AD.

27

Altered B cell signaling orchestrates loss oftolerance and systemic autoimmunity

Dr. David Rawlings is Chief of the Division of Immunology at SeattleChildren’s Hospital, the major Pacific Northwest referral center forimmunodeficiency patients; and Director for Center for Immunity andImmunotherapies (CIIT) at Seattle Children's Research Institute (SCRI)pursuing translational research focused on human immune disorders. Heco-directed the NIH roadmap-supported, Northwest Genome EngineeringConsortium (NGEC) and currently co-directs the Seattle Children’sProgram for Cell and Gene Therapy (PCGT). His primary research hasfocused on altered immune cell function leading to immunodeficiency,autoimmunity or lymphoid malignancies, and the development of genetherapy or gene repair for these disorders.

David Rawlings Division of immunologySeattle Children’s HospitalWashingtonUSA


11th February

28

Stephen McMahon Sherrington Professor of Physiology, King's College Londonand Director, London Pain Consortium UK

Pain – why does it hurt so much?

Stephen McMahon is Sherrington Professor of Physiology at King’s CollegeLondon, and Director of the London Pain Consortium. He is aneuroscientist who trained with Patrick Wall in the 1980s. He is principallyinterested in somatosensory systems and actively engaged in work rangingfrom molecular biology to electrophysiology to human psychophysicalstudies. He has published more than 290 original research articles, manyhighly rated (H-index 92) and is co-editor of the Textbook of Pain. His workhas been published in leading scientific journals including, Nature, NatureMedicine, Science, Nature Neuroscience, Cell, Neuron and Brain.He is theholder of a Wellcome Trust Senior Investigator Award and a Fellow of theAcademy of Medical Sciences.

His major interest is in pain mechanisms. He was the principal investigator on a major grant fromthe Wellcome Trust in 2002 to establish the London Pain Consortium (LPC), of which he is theScientific Director. Further funding from the Wellcome Trust, in the form of a 5 year StrategicAward, in May 2008, on which he was again the principal investigator, supported further researchactivity and a 4-year PhD training programme. He is the principal investigator on a recentStrategic award (awarded 2014) from the Wellcome Trust entitled “Defining pain circuitry in healthand disease”. He is also the academic lead of an EU consortium, Europain, which is a private-public partnership funded under the Innovative Medicines Initiative (IMI) scheme. This bringstogether a large group of academic scientists working in Europe with a group of pharmaceuticalcompanies with an interest in analgesic drug development. Europain receives €6m support fromthe EU and €13.5m from industry and is undertaking precompetitive clinical and preclinicalresearch aimed at improving understanding and treatment of chronic pain.

Both of these collaborations (the London Pain Consortium and Europain) involve a series ofinterlinked and mutually supportive programmes of experimental research, underpinned andsupported by a coordinated training and bioinformatics facility. There are considerable synergiesbetween the programmes. About half of the research activity is focused on the study of pain inpreclinical models, with the major aims of: identifying novel pain mediators; elucidating theperipheral and central nervous system changes contributing to pain; improving and refining animalmodels of pain and the measurement of pain in these models. The other half of the researchactivity explores pain mechanisms in humans, with the major aims of: establishing and validatingmechanism-based pain models in human volunteers; finding objective measures of spontaneouspain; collecting detailed phenotypic data on chronic pain patients; and determining psychosocial,genetic and clinical risk factors for development of chronic pain.


11th February

29

30

Mesenchymal causalities in chronic inflammation

George Kollias is a full member of the Academy of Athens, Professor ofExperimental Physiology at the Medical School of the University of Athensand Director of the Immunology Division at the Biomedical SciencesResearch Center "Alexander Fleming", where he served as President andScientific director from 2002-2010. In 2005 he founded the first CRO-biotech spin-off of BSRC Fleming, Biomedcode Hellas SA.

Professor Kollias has pioneered genetic approaches to study the function ofcytokine signaling, with specific focus on Tumor Necrosis Factor (TNF), inanimal models of human diseases. His lab is highly cited for a series ofdiscoveries on molecular and cellular mechanisms driving chronicinflammation and autoimmunity and for proof of principle studies that provided the preclinicalrationale and drove the development of the first biological anti-TNF therapies for rheumatoidarthritis in the clinic. His laboratory is supported by several competitive grants from the EuropeanCommission and National sources, as well as by the pharmaceutical industry. He was recentlygranted an Advanced ERC grant to study the role of mesenchymal cells in tissue homeostasis andpathophysiology. In 2014, he was awarded the Carol-Nachman Award for Rheumatology.

George Kollias Alexander Fleming Biomedical Sciences Research CentreAthensGreece


11th February

31

A6 Miranda Houtman : Investigation of theassociated PTPN2 locus in rheumatoidarthritis: importance of long non-coding RNA

AuthorsM. Houtman, K. Shchetynsky & L. Padyukov

AffiliationRheumatology Unit, Department of Medicine Solna,Karolinska Institute and Karolinska University Hospital,Stockholm, Sweden

Abstract text

Background: Rheumatoid arthritis (RA) is a commonchronic autoimmune disorder that has a strong geneticcomponent. Over 100 risk loci have been confirmed ingenome-wide association studies and the major riskfactor are the HLA-DRB1 shared epitope (SE) alleles.Outside the HLA-DRB1 region, one of the recentlyidentified candidate genes for RA is protein tyrosinephosphatase non-receptor type 2 (PTPN2). However, thefunctional consequences of genetic variations in thePTPN2 region remain undefined. We aimed tounderstand the functional mechanisms that connectvariations in the PTPN2 region with the risk of RAdevelopment.

Methods: We conducted an association study in theRACI cohort (6573 seropositive RA cases and 15870controls), computed gene-gene interactions usingattributable proportion for SE alleles with 11 SNPs in thePTPN2 region, analyzed DNA methylation data (354seropositive RA cases and 337 controls), and performedRNA expression analysis for PTPN2 and genes in its closeproximity in samples from 179 RA patients and 175healthy controls.

Results: The interaction analysis between SNPs withinPTPN2 and SE alleles pointed to the RA-associated SNPrs657555 (meta-analysis in RACI cohort, p = 3.35e-06;OR = 1.1352; Q = 0.3993). The expression of totalPTPN2 and PTPN2 splice variants, did not varysignificantly in individuals with different rs657555genotypes. In addition, the expression of other protein-coding genes from the locus within 1 Mb from rs657555were not different in relation to genotypes in our andpublicly available data. We detected that the rs657555risk allele is strongly associated with changes in DNAmethylation at four CpG sites 7 kb downstream of PTPN2and with changes in expression of the long non-codingRNA LOC100996324.

Conclusion: These results provide a new insight into themechanism driving the increased RA risk at the PTPN2region and suggest LOC100996324 for future studies of RA.

A7 Olfa Khalifa : New genes in the Xchromosome associated with RheumatoidArthritis

AuthorsOlfa KHALIFA1,2, Isabelle Duroux-Richard 1, NathalieBALANDRAUD3,4, Nathalie LAMBERT3, Isabelle AUGER3,Jean ROUDIER3,4, Audrey SÉNÉCHAL5, DavidGENEVIÈVE1,2,6, Christophe PICARD7, Gérard LEFRANC2,8 ,Isabelle TOUITOU1,2,9, Bakridine M'MADI MRENDA10,Etienne PARDOUX10, Anne-laure GAGEZ11 , Yves-MariePERS1,2,12, Christian JORGENSEN1,2,12, Touhami MAHJOUB13

and Florence APPARAILLY1,2

Affiliation

1 Inserm, U1183, Institute for Regenerative Medicineand Biotherapies, CHU Saint Eloi, 80 Avenue AugustinFliche, 34295 Montpellier cedex 5, France

2 University of Montpellier, Boulevard Henri IV, 34090Montpellier, France

3 Inserm UMRs 1097, Aix-Marseille University, Marseille,France

4 APHM, Rhumatology department, Marseille, France

5 Inserm, U1051, University Hospital Saint Eloi, Institutefor Neurosciences Montpellier, France

6 Department of Clinical Genetics, University Hospital ofMontpellier, France

7 Aix-Marseille Université, CNRS, EFS, ADES UMR 7268,13916, Marseille, France

8 Laboratoire d'Immuno Génétique Moléculaire, UPR1142 CNRS, Institute of Human Genetics, Montpellier,France

9 Department of Molecular Genetics, University Hospitalof Montpellier, France

10 Aix-Marseille University, CNRS, Centrale Marseille, I2M,UMR 7373 13453 Marseille, France

11 CNRS UMR 5235, Université de Montpellier,Montpellier, France

12 Clinical department for Osteoarticular diseases andBiotherapy, University Hospital, Lapeyronie, 34295Montpellier, France.

13 Laboratory of Human Genome and Multifactorialdiseases, University of Monastir, Faculty of Pharmacy,Monastir, Tunisie.

Abstract text

Objective: Among risk genes associated with rheumatoidarthritis (RA) susceptibility, the Xq28 region was the firstreported and is thus of importance given the femalepredominance of the disease. The X chromosome is alsoencoding sixty-seven micro-RNAs (miRNA). Here, we aimedat investigating the association between 3 genepolymorphisms (rs13397, rs1059702 and rs1059703) and12 miRNAs in the X chromosome in Tunisian and Frenchpopulation.

Abstracts

Continued on next page

32

Abstracts Continued

A8 Klementy Shchetynsky : Discovery of NewCandidate Genes for Rheumatoid Arthritis byIntegration of Genetic Association Data withExpression Pathway Analysis

Authors:K Shchetynsky, LM Diaz-Gallo, L Folkersen, AH Hensvold, AICatrina, L Berg, L Klareskog, L Padyukov

Affiliation:Rheumatology Unit, Department of Medicine, KarolinskaInstitutet/Karolinska University Hospital, Stockholm,Sweden

Abstract text:

Combining data from genetic association studies withgene expression analysis may help us to expand ourunderstanding of genetic background of rheumatoidarthritis (RA). We performed RNA-seq based expressionanalysis of 377 genes from previously-verified RA-associated loci in blood cells from 5 newly diagnosed, non-treated RA patients, 7 patients with treated RA and 12healthy controls. Our focus was on differentially expressedgenes sharing a similar expression pattern in the RA sub-groups. 11 qualifying genes were selected for pathwayanalysis and grouped into 2 functional protein networks,containing 29 and 27 additional “connector” molecules.The expression of genes, corresponding to connectormolecules was then also tested in our RNA-seq data.ERBB2, TP53 and THOP1 showed similar expressiondifference in both treated and non-treated RA patients andadditional nine genes were differentially expressed in atleast one patient’s group compared to healthy controlgroup. ERBB2, TP53 and THOP1 expression profile wassuccessfully replicated in RNA-seq data from peripheralblood mononuclear cells from healthy controls and non-treated RA patients in an independent material. In summary, an integration of RNA-seq data with findingsfrom association studies, and consequent pathway analysisimplicate new candidate genes, ERBB2, TP53, and THOP1in the pathogenesis of RA.

Methods: A case–control study of 408 RA women and471 healthy age-matched women was conducted inTunisian and French subjects. The genotype distribution,haplotype analysis, and linkage disequilibrium (LD) wereanalyzed using Bayesian statistical method, PLINK 1.07 andHaploview 4.2 softwares, respectively. Total RNA wasextracted from PBMC (Peripheral blood mononuclear cell)of 20 RA patients, as well as sex- and age-matchedcontrols. miRNAs expression levels were quantified usingRT-qPCR.

Results: The TMEM187 rs13397 G and IRAK1 rs1059703T major alleles were significantly increased in RA patientscompared with controls in both Tunisian and Frenchwomen. The two variants were in strong LD in theTunisian, but not in the French cohort. The GTC haplotypedisplayed a protective effect against RA, while the ATC,GCC and GTT haplotypes conferred significant risk for RAin the French population. All the 4 detected haplotypesdisplayed however neutral effect in the Tunisianpopulation. Analyses of 12 miRNAs expression levels areongoing.

Conclusion: These data further support the involvement ofX chromosome in RA susceptibility, evidencing howeverethnicities differences.

33

Using hiCLIP to identify long-range loops in RNAs

Following a degree in Natural Sciences at Jesus College, University ofCambridge (1993-1996), Nick studied for a Ph.D. with Janet Thornton atUCL (1996-2000) on the basis for specificity of DNA-binding proteins. Hethen moved to Yale University, USA, as an Anna Fuller Postdoctoral Fellowwith Mark Gerstein (2000-2005), where he shifted research focus togenomics with a particular emphasis on yeast transcriptional regulation. Hewas a Group Leader at the EMBL-European Bioinformatics Institute (2005-2012) in Cambridge and built a computational biology laboratory with anemphasis on genomics and gene regulation. During this time, he joinedthe Okinawa Institute of Science & Technology as an Adjunct Faculty toestablish a small group focused on developmental regulation (2011-present).He recently returned to UCL as a Chair in Computational Biology in the UCLGenetics Institute and holds a joint appointment as a Senior Group Leader atthe Cancer Research UK London Research Institute. His laboratory joined theFrancis Crick Institute in 2015.

Nicholas LuscombeCancer Research UK London Research InstituteUniversity College LondonUK


11th February

34

High-resolution maps of regulatory DNA cell-type activity profiles improve the discoveryof risk alleles for autoimmune diseases andtheir interpretability

Dr Aviv Madar is a computational biologist with a broad backgroundencompassing engineering, biology, mathematics, statistics, and computerscience. He is currently a postdoc jointly advised by Prof. Alon Keinan(Department of Biological Statistics and Computational Biology) and Prof.Andrew Clark (Department of Molecular Biology and Genetics)laboratories, at Cornell University. During his Ph.D., Aviv contributed to thefield of cellular network inference and quantitative model building in systems biology. For example,Statistical methods he developed were selected as best performers in two consecutive internationalDREAM network inference competitions (2008 and 2009).

Building upon his Ph.D. work, Aviv developed a data-integrative network inference pipeline thatwas used to characterize a high-accuracy regulatory network of T helper-17 cell differentiation inmice, a key T cell contributor to multiple autoimmune diseases (Cell, 2012). His current work isaimed at leveraging the growing volume and accuracy of regulatory annotation of the humangenome toward detecting and interpreting non-coding sequence variants that contribute tocomplex traits, focusing on autoimmune diseases.

Aviv MadarDepartment of Biological Statistics and Computational BiologyCornell UniversityNew YorkUSA


11th February

35

eQTL analyses and systems biology in MS and dementia

Dr. Philip De Jager is an Associate Professor of Neurology at HarvardMedical School and Director of the Program in TranslationalNeuroPsychiatric Genomics within the Ann Romney Center for NeurologicDiseases in the Department of Neurology at Brigham and Women’sHospital. He is the first incumbent of the Steven R. and Kathleen P. HaleyDistinguished Chair for the Neurosciences. He is a practicing clinicalneuroimmunologist.

The goal of Dr. De Jager’s work as a clinician-scientist is to apply modernmethods of neuroimmunology, statistical genetics and computational biology to first delineate andthen intervene in the sequence of events leading from health to neurodegenerative diseases.

Phil de JagerBrigham & Women's HospitalHarvard Medical SchoolBoston USA


11th February

36

Genes, ancestry and prevalence in SLE

David’s work involves statistical analysis of genetic data arising from Lupusstudies. He has extensive experience in association studies, quantitativetrait analysis, copy number variation analysis and genetic imputation (SNPsand HLA genotype). He gained experience in DNA expression analysis andBayesian Statistics during his PhD which was entitled ‘Bayesian Analysis ofMicroarray data’. During this time he worked closely with the industrialsponsor Pfizer. He is joint first author of the largest ever genome wideassociation study (GWAS) on SLE, which has increased the number ofassociated loci by 50%. He led the statistical analysis of the current GWAS,a large MHC meta-analysis, a sub-phenotype analyses of SLE Europeandata and a large collaboration with two Chinese groups for a meta-analysis of GWAS data acrosspopulations. He also has experience in modelling biological processes with multistate capture-recapture methods applied to a brown Trout population.

David Morris Genetics and Modular MedicineKing’s College LondonUK

Session 8Day 3: Friday12th February

37

Investigating immune endophenotypes in healthy human carriers of autoimmune disease-associated risk haplotypes in BLK and TNIP1

Kim Simpfendorfer is an Institute Scientist at the Feinstein Institute forMedical Research. Prior to joining the Feinstein Institute as a post-doctoralfellow in Peter Gregersen’s group in 2010, Kim completed her PhD in theDepartment of Microbiology and Immunology at the University ofMelbourne, studying the contribution of mucosal antibodies to susceptibilityto type I diabetes in the Non-Obese Diabetic mouse model (1). Additionally,Kim was involved in research into the innate immune defense againstSalmonella Typhimurium infection as well as pathogen transmission (2).

Since joining The Feinstein Institute for Medical Research, Dr. Simpfendorfer’s research has focused onthe functional analysis of immune-related genes associated with human autoimmune disease,including lupus and rheumatoid arthritis (3, 4, 5, 6). Her research has contributed to understanding howautoimmune risk alleles influence the functional diversity of cells in the human immune system,particularly human B cells. Her work has emphasized the value of defining endophenotypes in healthyhuman carriers of specific risk genes, including BLK, TNIP1 and PTPN22. In addition to fundamentalinsights into autoimmune pathogenesis, her work may lead to improved diagnostic criteria forpersonalized medicine and potentially identifying healthy patients at risk of developing autoimmunity.

Peer reviewed recent publications - see overleaf:

(1) Simpfendorfer KR, Strugnell RA, Brodnicki TC, Wijburg OLC. 2015. “Hitchhiking” genomic intervals in pIgR-deficient NOD mice confirmand localize Idd5.4, a susceptibility locus for autoimmune diabetes. PlosOne

(2) Wijburg OL, Uren TK, Simpfendorfer K, Johansen FE, Brandtzaeg P, Strugnell RA. 2006. Innate secretory antibodies protect against naturalSalmonella typhimurium infection. Journal of Experimental Medicine

(3) Simpfendorfer KR, Olsson LM, Manjarrez Orduno N, Khalili H, Simeone AM, Katz MS, Lee AT, Diamond B, Gregersen PK. 2012. Theautoimmunity-associated BLK haplotype exhibits cis-regulatory effects on mRNA and protein expression that are prominently observed in Bcells early in development. Human Molecular Genetics

(4) Simpfendorfer KR, Armstead BE, Shih A, Li W, Curran M, Manjarrez-Orduño N, Lee AT, Diamond B and Gregersen PK. 2015. Autoimmunedisease associated haplotypes of BLK exhibit lowered thresholds for B-cell activation and expansion of immunoglobulin class switched B-cells. Accepted at Arthritis & Rheumatology

(5) Gregersen PK, Klein G, Keogh M, Kern M, DeFranco M, Simpfendorfer KR, Kim SJ, Diamond B. 2015. The Genotype and Phenotype (GaP)registry: a living biobank for the analysis of quantitative traits. Immunologic Research

(6) Gregersen PK, Kosoy R, Lee AT, Lamb J, Sussman J, McKee D, Simpfendorfer KR, Pirskanen-Matell R, Piehl F, Pan-Hammarstrom Q,Verschuuren JJ, Titulaer MJ, Niks EH, Marx A, Strobel P, Tackenberg B, Putz M, Maniaol A, Elsais A, Tallaksen C, Harbo HF, Lie BA,Raychaudhuri S, de Bakker PI, Melms A, Garchon HJ, Willcox N, Hammarstrom L, Seldin MF. 2012. Risk for myasthenia gravis maps to a(151) Pro-->Ala change in TNIP1 and to human leukocyte antigen-B*08. Annals of Neurology

Kim Simpfendorfer The Feinstein Institute for Medical Research New YorkUSA


38

39

A genomic analysis of susceptibility to systemic autoimmunity

Edward K. Wakeland, Ph.D., an internationally recognized immunologist, hasbeen a faculty member at UT Southwestern Medical Center since 1998 andChair of the Department of Immunology since 2007.

An expert on the genetic basis for susceptibility to autoimmune disease, Dr.Wakeland’s labs have made significant advances in the study of lupus, achronic, debilitating disease that affects more than a million Americans.Among his many professional activities, he is a past Chair of the GeneticsInitiative Planning Committee, Alliance for Lupus Research, and a pastmember of the American Cancer Society's National Scientific Advisory Committee for Immunology.

Dr. Wakeland has been an invited speaker at dozens of meetings and workshops around the worldand is the author of more than 175 published scientific papers. He currently serves on the editorialboards or review boards of several leading immunology publications, including Current Opinion inImmunology and the Journal of Immunology.

An experienced educator, Dr. Wakeland has mentored nearly 50 doctoral students and postdoctoralfellows now serving in various capacities at academic institutions and research facilities in the UnitedStates, Europe, and Asia.

In addition to leading the Department of Immunology, Dr. Wakeland is also Director of the Walter M.and Helen D. Bader Center for Research on Arthritis and Autoimmune Diseases at UT Southwestern,as well as Director of the Genomics Core Facility.

Ward Wakeland The University of Texas Southwestern Medical CenterDallasUSA


40

Dissecting the structure and phenotypic consequences of HLA genomic variation

Gil McVean is Professor of Statistical Genetics at the University of Oxfordand Acting Director of Oxford’s Big Data Institute within the Li Ka ShingCentre for Health Information and Discovery. After an undergraduatetraining in Zoology, he worked in Cambridge and Edinburgh onevolutionary genetics before joining Oxford in 2000. His research focuseson understanding the molecular and evolutionary processes that shapegenetic variation in populations and the relationship between geneticvariation and phenotype. He has made contributions to our understandingof areas including recombination hotspots, historical patterns of naturalselection, the male mutation rate, human genetic variation, the role of HLA in complex disease andgenealogical processes. He has played a leading role in the HapMap and 1000 Genomes Projectsand currently works on organisms from HIV to malaria.

Gil McVeanThe University of Texas Southwestern Medical CenterDallasUSA


41

Dissecting the structure and phenotypic consequences of HLA genomic variation

Marc did his undergraduate degree at Yale University in Mathematics andPhysics. He then went on to do a PhD at the University of California, Berkeley,under the supervision of Professor Richard Harland, where he diddevelopmental genetics on mice. After his PhD, Marc moved to apostdoctoral position at Stanford University, where he worked in thelaboratory of Professor David Schneider to develop systems to analyse thehost genetic contribution to bacterial infections using Drosophilamelanogaster as a model host.

Marc moved to King’s College London to begin his own group in 2007; they have continued thiswork, with a focus on the interaction of bacterial pathogenesis with host metabolic regulation. Thegroup have developed ways to integrate in vivo functional screening with computational functionalpredictions to reveal new mechanisms of immune-metabolic interaction and pathology driven byinfection and inflammation. In 2015, Marc moved his laboratory to the Department of Life Sciencesand the MRC Centre for Molecular Bacteriology and Infection at Imperial College London.

Marc Dionne MRC Centre for Molecular Bacteriology and Infection Imperial College LondonUK


42

Using zebrafish to unpick the interactions between biomechanics and genes in making,shaping and maintaining a joint

After studying Biochemistry at the University of Oxford, Chrissy swappedfields into Developmental Biology for her PhD in Simon Hughes’ lab at King’sCollege London. Her PhD was studying the origins of the dermomyotome,during which she developed an enduring love of zebrafish. After a short stintas postdoc at the Royal Veterinary College working on chick skeletaldevelopment, she was awarded an EMBO fellowship to identify novel genescontrolling bone development in Stefan Schulte-Merker’s lab at theHubrecht Institute in the Netherlands. After 3 years in the flatlands, she attempted to put her workon muscle, cartilage and bone together and was awarded an Arthritis Research UK fellowship tostudy joint development in zebrafish. Her lab now focuses on understanding the interaction betweengenes and biomechanics using zebrafish as a model organism.

Chrissy HammondSchool of Physiology and PharmacologyUniversity of BristolUK


43

Positioning and analysis of the major genes controlling arthritis in rats

PhD 1985, MD 1987, professor Lund university 19932008, guest professor atFinnish Academy Turku 1987-2011 and Southern medical university,Guangzhou 2011-, professor Karolinska Institutet 2008-

Member of the Nobel Assembly. Member of the governmental advisory boardfor gene technology in Sweden

Receiver of the Swedish Göran Gustafsson prize (1994), the EuropeanDescartes prize (2002), the Nordic SalusAnsvar prize (2003) and the NordicAnders Jahre prize (2015)

Main supervisor for 37 PhD and assistant supervisor for additional 11.

Publication summary: 536 publications (436 peer reviewed original articles, 60 peer reviewedoverviews, 26 books/book chapters, 12 patents, 1 thesis, 1 popular press) + more than 300abstracts/conference proceedingsThomson: 16917 citations, h-index 70. Google Scholar: 22293citations, h-index 81

Some key research achievements:

• The identification of the major gene associated with animal models for rheumatoid arthritis (Aq)and its human functional homologue (DRB1*0401) using humanized mice

• The identification of a glycopeptide within the type II collagen molecule as binding DR4 and Aqand being a major T cell recognition peptide in CIA and RA

• The identification of the major gene regions associated with disease in mouse and rat models forMS and RA

• The cloning of the Ncf1 gene responsible for a major locus associated with arthritis (Pia4) andthereby discovery of a new pathway for how oxidative radicals regulate the adaptive immunesystem

• Demonstration of pathogenicity and molecular interaction of antibodies specific for citrullinatedproteins, of critical importance in rheumatoid arthritis

Currently he is leading a research laboratory (Medical Inflammation research) (www.inflam.mbb.ki.se)with a focus on complex genetics and immunology of chronic inflammatory diseases. The mainemphasis is on autoimmune diseases, using models for arthritis as a prototype disease. Identifiedgenes are investigated through their molecular pathogenic pathway and therapy is developed with theaim to transfer the knowledge into clinical use.

Key references:

1. Vingsbo-Lundberg C, Nordquist N, Olofsson P, Sundvall M, Saxne T, Pettersson U, Holmdahl R: Genetic control of arthritis onset, severityand chronicity in a model for rheumatoid arthritis in rats. Nature Genetics 20, 401-404. 1998.

2. Olofsson P, Holmberg J, Tordsson J, Lu S, Åkerström B, Holmdahl R: Positional identification of Ncf1 as a gene that regulates arthritisseverity in rats. Nature Genetics 33, 25-32. 2003.

3. Gelderman KA, Hultqvist M, Holmberg J, Olofsson P, Holmdahl R: T cell surface redox levels determine T cell reactivity and arthritissusceptibility. Proc Natl Acad Sci U S A; 103, 12831-6, 2006.

4. Rintisch, C., Ameri, J., Olofsson, P., Luthman, H. and Holmdahl, R., Positional identification of the V lambda gene and its association withrheumatoid factor production and eosinophilic inflammation in rats. Proc Natl Acad Sci U S A 2008. 105:14005-10.

Rikard Holmdahl Department of Medical Biochemistry and Biophysics (MBB)Division of Medical Inflammation ResearchKarolinska InstituteSweden


continued on next page

44

Session 9

Day 3: Friday 12th February

(continued)

5. Kraaij, M. D., Savage, N. D. L., van der Kooij, S. W., Koekkoek, K., Wang, J., van den Berg, J. M., Ottenhoff, T. H. M., Kuijpers, T. W.,Holmdahl, R., van Kooten, C., and Gelderman, K. A., Induction of regulatory T cells by macrophages is dependent on ROS generated bythe NADPH-oxidase. Proc Natl Acad Sci U S A 2010;107(41):17686-91.

6. Hultqvist, M., Sareila, O., Vilhardt, F., Norin, U., Olsson, L. M., Olofsson, P., Hellman, U. and Holmdahl, R., Positioning of a PolymorphicQuantitative Trait Nucleotide in the Ncf1 Gene Controlling Oxidative Burst Response and Arthritis Severity in Rats. Antioxid Redox Signal2011;14(12):2373-83.

7. Tuncel J, Haag S, Carlsén S, Yau ACY, Lu S, Burkhardt H and Holmdahl R. MHC class II-restricted Response to Collagen type XI regulatesthe Chronic development of Arthritis in rats. Arthritis Rheum. 2012 Mar 5.

8. Schiavone S, Jaquet V, Sorce S, Dubois-Dauphin M, Hultqvist M, Bäckdahl L, Holmdahl R, Colaianna M, Trabace L and Krause KH. NADPHoxidase elevations in pyramidal neurons drive psychosocial stress-induced neuropathology. Transl Psych 2012;2:e111.

9. Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R: Identification of candidate risk gene variations by whole-genome sequence offour rat strains commonly used in inflammation research. BMC Genomics. 2014;15:391.

10. Tuncel J, Haag S, Yau ACY, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg J, Ekman D, Thordardottir S, Johannesson M, Gillett A,Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J and Holmdahl R: Natural Polymorphisms in Tap2Influence Negative Selection and CD4:CD8 Lineage Commitment in the Rat. PLoS Genet. 2014 Feb 20;10(2):e1004151. doi:10.1371/journal.pgen.1004151. PMID: 24586191

11. Haag S, Jonatan Tuncel J, Thordardottir S, Mason DE, Yau ACY, Dobritzsch D, Bäcklund J, Peters EC, Holmdahl R: Positional identificationof RT1-B (HLA-DQ) as susceptibility locus for autoimmune arthritis. J Immunol 2015 Mar 15;194(6):2539–50.

12. Holmdahl R, Sareila O, Olsson L, Bäckdahl L, Wing K: Ncf1 polymorphism reveals oxidative regulation of autoimmune chronicinflammation, Immunol Rev 2015 (in press)

45

Making progress in MS

Stephen Sawcer is Professor of Neurological Genetics at the University ofCambridge and an Honorary Consultant Neurologist at Addenbrooke'sHospital. He completed a BSc in Physics at Liverpool University and went tomedical school (MB ChB) at Birmingham University. After completing MRCPin 1991 he undertook Neurology specialist training in Manchester andCambridge and became FRCP in 2010. His PhD (A linkage genome screen inmultiple sclerosis, 1997) was undertaken at the University of Cambridge,supervised by Professor Alastair Compston and Professor Peter Goodfellowand examined by Professor Martin Bobrow and Professor Kay Davies.Professor Sawcer has worked on the genetics of multiple sclerosis for morethan 20 years with a main focus on genomewide approaches. He is a member of the InternationalMultiple Sclerosis Genetics Consortium (IMSGC) and the Wellcome Trust Case Control Consortium(WTCCC).Key MS genetics references

a) IMSGC. (2005) A high-density screen for linkage in multiple sclerosis. Am J Hum Genet 77, 454-67.

b) IMSGC (2007) Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study. N Engl J Med 357, 851-62.

c) IMSGC and WTCCC2. (2011) Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 476, 214-9.

d) IMSGC. (2013) Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 45, 1353-60.

Stephen SawcerDepartment of Clinical NeurosciencesUniversity of CambridgeUK


46

Abstracts

A9 Michelle Krishnan : Investigation ofbiological pathways involved in braindevelopment in preterm neonates using amultivariate phenotype and sparse regression

AuthorsMichelle L Krishnan1, James Boardman2, Matt Silver3,Gareth Ball1, Serena Counsell1, Andrew J Walley4, A DavidEdwards1, Giovanni Montana5

Affiliation1Centre for the Developing Brain, King’s College London;2Neonatology, Royal Infirmary of Edinburgh; 3LondonSchool of Hygiene and tropical Medicine; 4Institute ofMedical & Biomedical Education (IMBE), St. George'sUniversity of London; 5Department of BiomedicalEngineering, King's College London

Abstract text

BackgroundThe incidence of preterm birth is increasing, with a highproportion of survivors experiencing adverse motor,cognitive and psychiatric sequelae. Diffusion tensorimaging (DTI) provides measures of white mattermicrostructure that are correlated withneurodevelopmental outcome and highly heritable. Jointmodelling of multivariate imaging and genetic data, usingprior biological knowledge of functional pathways,increases power to detect associations in complex disease.We aim to identify biological pathways through whichpremature birth impacts the microstructure of whitematter in neonates.Methods3-Tesla MR images and saliva were acquired for 72 preterminfants (mean gestational age (GA) 28+4 weeks, meanpostmenstrual age (PMA) at scan 40+3 weeks). FA mapswere constructed from 15-direction DTI, and Tract BasedSpatial Statistics was used to obtain a group white matterskeleton varying with degree of prematurity, adjusting forPMA and GA at scan. Salivary DNA was extracted andgenotyped using Illumina HumanOmniExpress-12 arrays.Pathways sparse reduced- rank regression (PsRRR) [1] wasused to jointly model the voxel-wise effects of genome-wide SNPs grouped into 186 KEGG pathways.ResultsLipid pathways were significantly over-represented in thetop ranking pathways adjusted for PMA (p≤0.005) and theempirical selection frequency of the most highly rankedlipid pathway (peroxisome proliferator-activated receptor(PPAR) signaling) increased from 0.09 to 0.2 withadjustment for GA. The highest ranked pathways havecorresponding low selection probabilities in the nullmodel. Two of the top three pathways (PPAR metabolismand alpha-linoleic acid metabolism) include the gene fattyacid desaturase (FADS2), which has been recentlyassociated with changes in brain microstructure in acandidate study with this cohort [2].

ConclusionsBiological pathways associated with a quantitativemultivariate imaging endophenotype of prematurity suggestan important role for lipid metabolism. FADS2 might bedriving pathway selection as it is a member of two highlyranked, relatively small pathways involving lipid metabolism.

[1] Silver, M., Janousova E., Hua X., Thompson, P.M., Montana,G.: Identification of gene pathways implicated in Alzheimer'sdisease using longitudinal imaging phenotypes with sparseregression. Neuroimage, 63(3): 1681-1694 (2012)

[2] Boardman, J.P., Walley, A., Ball, G., Takousis, P., Krishnan,M.L., Hughes-Carre, L., Aljabar, P., Serag, A., King, C.,Merchant, N., Srinivasan, L., Froguel, P., Hajnal, J., Rueckert,D., Counsell, S., Edwards, A.D.: Common Genetic Variantsand Risk of Brain Injury After Preterm Birth. Pediatrics,133(6): e1655-e1663 (2014)

47

A10 Gisela Orozco : Capture Hi-C reveals anovel causal gene, IL20RA, in the pan-autoimmune genetic susceptibilityregion 6q23

AuthorsAmanda McGovern1, Stefan Schoenfelder2, Paul Martin1,Jonathan Massey1, Kate Duffus1, Darren Plant3, Arthur GPratt4, Amy E Anderson4, John D Isaacs4, Julie Diboll4,Nishanthi Thalayasingam4, Caroline Ospelt5, Peter Fraser2,Anne Barton1,3, Jane Worthington1,3, Stephen Eyre1, GiselaOrozco1

Affiliation1 Arthritis Research UK Centre for Genetics and Genomics.Centre for Musculoskeletal Research. Institute ofInflammation and Repair. Faculty of Medical and HumanSciences. Manchester Academic Health Science Centre. TheUniversity of Manchester. Stopford Building. Oxford Road.M13 9PT Manchester, UK. 2 Nuclear Dynamics Programme,The Babraham Institute, Cambridge CB22 3AT, UK. 3 NIHRManchester Musculoskeletal BRU, Manchester AcademicHealth Sciences Centre, Central Manchester FoundationTrust, Manchester, UK. 4 Institute of Cellular Medicine(Musculoskeletal Research Group), Newcastle University,Newcastle upon Tyne, NE2 4HH, UK. 5 Center ofExperimental Rheumatology Department of Rheumatology,University Hospital of Zurich, Wagistrasse 14, CH-8952Schlieren, Switzerland.

Abstract text

The majority of genetic variants that predispose to complexdiseases map to non-coding enhancer regions, which mayregulate transcription through long-range interactions withtheir target genes. The 6q23 locus is associated with anumber of autoimmune diseases. Associated SNPs lie a largedistance from any gene. The aim of this work was to identifycausal disease genes at the locus by studying long rangechromatin interactions using capture Hi-C in T and B celllines.

The disease intergenic region and all promoters within500kb of associated SNPs were targeted. The diseaseassociated intergenic SNPs interacted with IL20RA, IFNGR1and lncRNAs downstream of TNFAIP3. IL20RA interacts withthese lncRNAs and the promoter of TNFAIP3. TNFAIP3 alsodemonstrated interactions with the same lncRNAs.

The lead SNP in the 6q23 region is in tight LD with eightother SNPs. The most plausible causal SNP seems to bers6927172, as it maps to an enhancer in B and T cells, is in aDNase hypersensitivity cluster and shows transcription factorbinding. We used human primary T cell gene expression datato examine expression eQTLs. The risk allele was associatedwith an increased expression of IL20RA. LCLs carrying the riskallele of rs6927172 showed a higher frequency ofinteractions between this SNP and IL20RA. Chromatinimmunoprecipitation demonstrated enriched binding ofchromatin marks of active enhancers (H3K4me1 andH3K27ac) and the transcription factor NFκB to rs6927172risk allele in Jurkat cells.

Abstracts

In conclusion, we have compelling evidence that theautoimmune risk variant, rs6927172, is within a complex generegulatory region, involving IL20RA, TNFAIP3 and regulatoryelements, such as lncRNAs. These results show that CHi-C canhelp identify GWAS causal genes and suggest novel therapeutictargets; indeed, anti-IL-20 monoclonal antibody therapy hasrecently been shown to be effective in the treatment ofrheumatoid arthritis.

48

Type I Diabetes

John Todd FRS, FMedSci, FRCP Hons, PhD is Professor of Medical Genetics atCambridge University, Director of the JDRF/Wellcome Trust Diabetes andInflammation Laboratory (DIL) in the University’s Cambridge Institute forMedical Research and a Senior Investigator of the National Institute for HealthResearch. Todd researches type 1 diabetes (T1D) genetics and diseasemechanisms with an aim of clinical intervention. Previously, Todd wasProfessor of Human Genetics at Oxford University and a Wellcome TrustPrincipal Research Fellow. Todd helped pioneer genome-wide genetic studies,first in mice and then in humans. He then went on to study the associationsbetween mapped genomic disease-associated regions and phenotypes byfounding and deploying the Cambridge BioResource. His research in genetics and diabetes hasreceived several awards and prizes.

In the latest phase of his research, to translate basic genetic and immunological knowledge totreatment and prevention, the DIL has now completed its first mechanistic, statistically adaptive, drugdose-finding trial in T1D patients, establishing new and effective methods of trial design, governance,conduct and patient recruitment. The DIL has a major role in training and mentoring others inpatient/people-based research, promoting data/sample access and sharing, and can advise otherlaboratories and industrial partners in immunotherapeutics and experimental medicine.

Todd has supervised 29 PhD students with five in progress. h-index 89, total citations 33,681 (Nov 2014).

John Todd Cambridge Institute for Medical ResearchUniversity of CambridgeUK


49

P2 Elena Carnero-Montero : Epigenome-wide analysis of myeloid:lymphoid ratios inwhole blood

AuthorsElena Carnero-Montoro1, Vivek Naranbhai2, Ben Fairfax2,Tim D. Spector1, Jordana T. Bell1

Affiliation1Department of Twin Research and Genetic Epidemiology,King’s College London, London, United Kingdom; 2 Wellcome Trust Centre for Human Genetics, NuffieldDepartment of Medicine, University of Oxford, Oxford,United Kingdom

Abstract text

Recent studies have shown that peripheral bloodmonocyte:lymphocyte (ML) and neutrophils:lymphocyte(NL) ratios are better predictors of cellular transcriptionalprofiles and of infectious, cardiovascular and malignantdiseases than peripheral blood leukocyte subset counts ontheir own. Functional genomic studies of myeloid:lymphoidratios can add important insights into the biology of whiteblood cells and the mechanisms behind immune responses.Because the methylome of different white blood cell typesis unique and is related to cell origin and function, wehypothesized that ML and NL ratios may be linked tochanges in DNA methylation profiles that can explain someof the observed transcriptional and physiological changes.

We tested whether myeloid-lymphoid ratios associatewith DNA methylation at CpG sites assayed by 450KIllumina Infinium methylation array in 877 whole bloodsamples from female participants in TwinsUK. Wecalculated myeloid-lymphoid ratios using cell proportionspredicted by the DNA methylation age calculator andadjusted the analysis for family structure, smoking, age,batch effects, and predicted cell proportions. We usedgranulocyte proportion as a surrogate measure ofneutrophils.

Our preliminary genome-wide results show that ML andNL ratios are associated with DNA hypomethylation effectsat 770 and 219 CpG sites respectively, after Bonferroni andgenomic inflation correction. Interestingly, multiple keyimmune-, cancer- and transcriptional-related pathways aresignificantly enriched in hypomethylated genes. Theseinclude leukocyte extravasation signaling, NF-kB activationby viruses and integrin signaling for ML, and cell cycleregulation and apoptosis-, ceramida- and HIPPO-signalingpathways for NL. We also found significant enrichment forhypomethylated genes to be under transcriptional controlof ID3, mir-17-5p, TGFB1, TNF, CD3 and actin.

Altogether our findings suggest that DNA methylationdynamics could explain previous associations foundbetween myeloid-lymphoid ratios, transcriptional changesand immune responses; and show the potential of DNAmethylation profiling to identify new genes involved inpathological outcomes and develop new predictivemarkers.

P1 Aggelos Banos : Transcriptome Analysisof Hematopoietic Stem Cells (HSCs) inSystemic Lupus Erythematosus (SLE)

AuthorsBanos A.1*, Grigoriou M.1, Verginis P.1, Pavlidis P.2, BertsiasG.3, Boumpas DT.1,4

Affiliation1. Biomedical Research Foundation of the Academy of

Athens, Athens, Greece2. Institute of Molecular Biology and Biotechnology

(IMBB), Foundation of Research and Technology-Hellas,Heraklion, Crete, Greece

3. Medical School, University of Crete, Heraklion, Greece4. Joint Academic Rheumatology Program, Medical

School, National and Kapodistrian University of Athens,Athens, Greece

Abstract text

Hematopoietic Stem Cells (HSCs) give rise to all blood celllineages, which have been implicated in the pathogenesis ofSystemic Lupus Erythematosus (SLE). We reasoned that thefundamental immune aberrations in SLE –genetic orepigenetic- may be more facile to be traced back to the HSCpopulation.

HSCs were isolated from either healthy C57/BL6 orNZBxNZW/F1 lupus prone mice bone marrow (n=15±5). Theselection markers used are Lin-Sca-1+c-Kit+ for LSKcompartment, including both long and short term HSCs.Flow cytometry cell sorting of the aforementionedpopulations was utilized for enumeration, RNA extraction andcell cultures. Finally, paired-end RNA-sequencing analysis wasperformed with HiSeq 2000 platform.

We identified significantly increased frequencies (~3%pre-diseased vs ~5% diseased, p<0.05) as well as absolutenumbers (80-100×103 pre-diseased vs 100-150×103

diseased, p<0.05) of HSCs in the BM of lupus NZBxNZW/F1mice with established disease as compared to young pre-diseased NZBxNZW/F1 or control C57/BL6 mice. Bonemarrow populations such as hematopoietic stem progenitorscells (HSPCs), lymphoid and myeloid lineages differed inhomogeneity depending upon either age or disease,suggesting alterations in HSC potential under inflammatoryconditions. Accordingly, serum from F1 young micepromoted healthy HSCs to proliferation and skewed theirdifferentiation towards to myeloid lineage. Transcriptomeanalysis by RNA-seq of HSCs from lupus mice revealed variousdifferentially expressed genes (DEGs) (FC>1.5, q<0.05) indiseased lupus mice compared to pre-diseased. DEGs showenrichment in transcription factors involved in hematopoiesis(Arid3a, Runx2), regulation of immune responses duringinflammation and autoimmune diseases (Irf4, Maf) and HSCfunction and homeostasis (Cxcl2, Vegfa, Fbxw7).

These data provide initial insights in the fundamentalchanges and the molecular identity of HSCs in lupus withinthe inflammatory milieu of the disease, regulated by acomplex transcriptional network.

Posters

50

Posters

P3 Lingyan Chen : Genetic Risk and GeneExpression in Systemic Lupus Erythematosus

AuthorsLingyan Chen, David L Morris, and Timothy J Vyse

AffiliationKing’s College London

Abstract text

Systemic lupus erythematosus (SLE) is a chronicautoimmune disease with marked clinical heterogeneity.The genetic basis of SLE remains largely undetermined dueto its complexity, involving multiple genetic andenvironmental factors. Although genome-wide associationstudies (GWAS) have identified many common risk variantsunderlying susceptibility to SLE, there is scant and oftenconflicting information on how these variants modifynormal lymphocyte signalling and predispose toautoimmunity.

The promising findings from the largest European SLEGWAS and trans-ancestry meta-analysis of Chinese andEuropean GWAS (in review) provide an opportunity toexplain the genetics of SLE. eQTL mapping, whichintegrates the genetic variants and the gene expressionphenotype, may functionally annotate GWAS signals, thusproviding evidence for further causality inference. My studyaims to use genome-wide gene expression datasets onmultiple ex vivo cell types from microarray or exon-arraysources to identify if the SLE associated variants are cis- ortrans- eQTLs and infer the underlying causal genes. Inaddition, joint analysis across populations/tissues in thecurrent available datasets applying a Bayesian Framework(eQTLBMA) is performed to get higher statistical power, aswell as formally estimate the best models of combinationsof subgroups.

P4 Fiona Clarke : The protein tyrosinephosphatase PTPN22 negatively regulates Fc�receptor signalling in dendritic cells

AuthorsFiona Clarke, Cristina Sanchez-Blanco and Andrew Cope

AffiliationAcademic Department of Rheumatology, Centre forMolecular and Cellular Biology of Inflammation, Faculty ofLife Sciences and Medicine, King’s College London, UnitedKingdom

Abstract text

PTPN22 is a non-receptor tyrosine phosphatase, expressedin hematopoietic cells. A single nucleotide polymorphism inthe gene confers an arginine to a tryptophan substitutionat position 620 of the human protein. This is associatedwith an enhanced susceptibility to multiple autoimmunediseases including type 1 diabetes and rheumatoid arthritis.

PTPN22 dephosphorylates Src family kinases and Sykand is known to negatively regulate T cell receptor (TCR)signalling. Despite also being expressed in other immunecell types, its role in these cells has been less well studied.This project aims to investigate the role of PTPN22 in Fcγreceptor (FcγR) signalling in dendritic cells (DCs). Wehypothesise that PTPN22 dampens down FcγR signalling asits targets Src family kinases and Syk are downstream of thereceptors. In addition, the majority of the autoimmunediseases associated with the variant protein have anautoantibody component. FcγRs recognise the Fc regionsof IgGs and are expressed on most innate immune cells.The immune system utilises both activating and inhibitoryFcγRs to modulate its response to foreign antigens. Thebound IgGs crosslink the activating FcγRs, leading todownstream signalling, resulting in DC maturation,cytokine production and antigen presentation.

Using bone marrow derived dendritic cells (BMDCs)from wild type (WT) and PTPN22-/- mice, we have foundthat PTPN22 is dispensable for binding and uptake ofovalbumin:anti-ovalbumin immune complexes (ICs) viaFcγRs. However, PTPN22-/- BMDCs stimulated withovalbumin ICs upregulate MHCII and costimulatorymolecules CD80 and CD86 to a greater extent than WTBMDCs. These cells also secrete higher levels of IL-12/23p40after IC stimulation. When these IC-pulsed PTPN22-/- BMDCsare cocultured with ovalbumin-specific WT CD4+ T cells,they cause enhanced T cell proliferation and augmentedsecretion of IL-17. These results suggest that PTPN22negatively regulates signalling downstream of FcγRs indendritic cells.

51

Posters

P5 Georgina Cornish : PTPN22 negativelyregulates effector T cell migration.

AuthorsGeorgina Cornish1, Garth L. Burn1, Rose Zamoyska2, LenaM. Svensson3 and Andrew P. Cope1.

Affiliation1Academic Department of Rheumatology, Centre forMolecular and Cellular Biology of Inflammation, Faculty ofLife Sciences and Medicine, King’s College London, UnitedKingdom. 2Institute of Immunology and InfectionResearch, Centre for Immunity, Infection and Evolution,University of Edinburgh, Edinburgh, UnitedKingdom.3Department of Experimental Medical Science,Lund University, Lund, Sweden.

Abstract text

PTPN22/Lyp is a protein phosphatase known to negativelyregulate Src-family kinases Lck and Zap-70 down stream of Tcell receptor signaling. These src kinases also signaldownstream of affinity matured LFA-1 integrin. This studyaimed to investigate PTPN22 driven regulation of Lck andZap-70 on engagement of LFA-1 with ligand ICAM-1 duringT cell migration. LFA-1 is a β2 integrin highly expressed onlymphocytes and is thought to mediate effector T cell trans-endothelial cell migration from the blood stream intoinflamed tissue. The Lyp-R620W mutation is known to effectphosphatase activity of PTPN22 and is associated withmultiple autoimmune diseases including RheumatoidArthritis, Graves disease, Type1 Diabetes and Lupus. Ourresults show that loss of PTPN22/Lyp expression, orexpression of the autoimmune disease associated Lyp-R620W mutant is associated with hyper-phosphorylation ofLck and Zap-70, increased T cell motility and integrin-mediated adhesion under static and shear flow conditions.These data suggest loss of PTPN22 function differentiallyregulates integrin signaling in T lymphocytes.

P6 Kate Duffus : Characterising the causalmechanism at the 5q11 suceptibility locusassociated with rheumatoid arthritis

AuthorsKate McAllister1, Gisela Orozco1 Stephen Eyre1

Affiliation1Arthritis Research UK Centre for Genetics and Genomics,University of Manchester

Abstract text

IntroductionRheumatoid arthritis (RA) has a strong genetic componentwith over 100 loci associated with disease suceptibility,however for the majority the causal genes and mechanismremain unknown. The third strongest association in RA liesintronic to the ANKRD55 gene, on chromosome 5q11. Theobjective was to further characterise the 5q11 risk locususing genetic, bioinformatic and functional approaches.

MethodsGenetic fine mapping of 60 single nucleotidepolymorphisms (SNPs) was carried out at the 5q11 locus in11,475 cases and 15,870 controls. Bioinformatic toolswere used to prioritise SNPs based on their regulatorypotential. Prioritised SNPs were then correlated withexpression of nearby genes in whole blood (n=67), CD4+(n=185) and CD8+ T cell subsets (n=23). Additionally inB and T cell lines capture Hi-C, in order to identify long-range DNA interactions and chromatinimmunoprecipitation (ChIP) for histone markers ofenhancers was carried out.

ResultsFine-mapping refined the association at the 5q11 locus tors71624119 (p = 5.59E-20). Bioinformatic prioritisationimplicated 2 SNPs, rs10065637 and rs6859219 withstrong evidence of regulatory potential. The risk SNPscorrelated with expression of ANKRD55 in whole blood (p=3.85E-05) and both ANKRD55 (p = 6.21E-11) and IL6ST(p = 6.54E-04) in CD4+. Preliminary capture Hi-C data in Tand B cell lines identified that the disease-associated SNPsphysically interact with the promoters of both ANKRD55and IL6ST. ChIP data was suggestive of enrichment for thehistone marks of enhancer activity, H3K4me1 andH3K27ac.

ConclusionThe 5q11 locus contains multiple gene candidates forcausality, however preliminary findings implicate the SNPsare located in an intronic enhancer element stronglyregulating expression of ANKRD55, and to a lesser extentIL6ST in CD4+ T cells. It is crucial to further dissect thefunctional mechanism at this locus in order to illuminatenovel pathways and therapeutic targets in disease.

52

Posters

P7 Isabelle Duroux-Richard : Microrna inSystemic Lupus Erythematosus

AuthorsDuroux-Richard I1,2, Cuenca J3, Ponsolles C1,2, Roubert C4,Jorgensen C1,2,5, Figueroa F3, Khoury M3, Apparailly F1,2,5

Affiliation1 INSERM, U1183, University Hospital Saint Eloi, 80 rueAugustin Fliche, 34295 Montpellier, France

2 University of Medicine, Boulevard Henri IV, 34090Montpellier, France

3 University de Los Andes, Las condes, San carlos deApoquindo 2200, 73000 Santiago, Chile

4 Exploratory Unit, Sanofi R & D, 371 rue du professeur J.Blayac, 34184 Montpellier, France

5 Clinical department for osteoarticular diseases, Universityhospital Lapeyronie, 371 Avenue Gaston Giraud, 34295Montpellier, France

Abstract text

Several micro(mi)RNAs have been related to B celldifferentiation and functions, known to participate in thepathogenesis of systemic lupus erythematosus (SLE).However, a common miRNA signature has not emerged inSLE, since published arrays from patients exhibit variablepatterns due to variability in genetic background, severityand type of disease, as well as to the limitation ofperforming gene expression studies in unfractionated,heterogeneous cell populations. Here, we aimed atidentifying a miRNA-based signature of disease severity in apopulation unexplored so far using purified B cells. Bloodsamples were obtained from healthy controls (HC) with nohistory of autoimmune diseases and SLE patients with orwithout severe lupus nephritis (LN), and ethnichomogeneity for chilean population. Naive and memory Bcells were sorted using CD27 surface marker. The genome-wide miRNA expression study was perfomed using theTaqMan® Human MicroRNA Array Cards v3.0 (AppliedBiosystems). TLDA analyses of naive and memory B cellsfrom HC and 2 subsets of SLE patients revealed twocategories of miRNA-based signatures. The first signaturerepresents miRNAs with potential as diagnostic biomarkers: 11 miRNAs discriminating all SLE patients from HC, and 8miARNs discriminating patient subsets (SLE versus SLE-LN).Clustering analyses of TLDA datasets evidenced that themain differences in miRNA expression profilings betweenSLE patients were between naive and memory B cells,independently of disease severity. Among these, we foundmiR-223 that was previously reported as deregulated inSLE, as well as in other autoimmune disorders and B cellleukemia. Array data were further validated on individualsamples (n=6). Overall, the present work identified twotypes of miRNA-based signatures in circulating B cellsisolated from Chilean SLE patients, providing promisingbiomarkers in molecular diagnostics for disease severity aswell as potential new targets for therapeutic intervention in SLE.

53

Desig

ned and produced by AYA-Creative w

ww.aya-creative.co

.uk

© Guy’s an

d St Th

omas’ N

HS Fo

undation Trust / Feb

ruary 2016

BTCURE EU IMI ProgrammeNIHR/Biomedical Research Centre at Guy’s and St Thomas’

NHS Foundation Trust and King’s College London

Documents

Functional - Be The Curebtcure.eu/wp-content/uploads/Functional-Genomics-Workshop... · Plenary 7 Holm Uhlig (University of Oxford, UK): The genetic landscape of monogenic forms of