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METABOLIC PROFILING: ITSROLE IN BIOMARKER DISCOVERYAND GENE FUNCTION ANALYSIS
METABOLIC PROFILING: ITS ROLE IN BIOMARKER DISCOVERY AND GENE FUNCTION ANALYSIS
edited by
George G. Harrigan Pharmacia Corporation Chesterfield, MO 63198
U.S.A.
Royston Goodacre Department of Chemistry, UM/Sr, PO Box 88, Manchester, M60 1 QD,
United Kingdom.
~.
" SPRINGER SCIENCE+BUSINESS MEDIA, LLC
Library of Congress CataIoging-in-Publication Data
Metabolie profiling : its role in biomarker discovery and gene function analysis / edited by George G. Harrigan, Royston Goodacre.
p.;cm. Includes bibliographical references and index. ISBN 978-1-4613-5025-5 ISBN 978-1-4615-0333-0 (eBook)
DOI 10.1007/978-1-4615-0333-0
1. Metabolites 2. Metabolie profile tests 3. Biochemical markers 4. Proteomics 5. Genetic regulation.!. Harrigan, George G. 11. Goodacre, Royston.
QP171 .M37752003 612.3'9--dc21
Copyright © 2003 Springer Science+Business Media New York Originally published by Kluwer Academic Publisher in 2003 Softcover reprint of the hardcover 1 st edition 2003
All rights reserved. No part of this work may be reproduced, stored in a retrleval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without the written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.
Permission for booles published in Europe: [email protected] Permissions for books published in the United States of America: [email protected]
Printed on acid-free paper.
TO BETH, SEAN AND EVAN andTO ELIZABETH, TAMARA AND PICKLES
Contents
Contributors ix
Preface Xlll
1. IntroductionGeorge G. Harrigan and Royston Goodacre
2. Metabolome And Proteome Profiling For MicrobialCharacterization 9Seetharaman Vaidyanathan and Royston Goodacre
3. Can 18 NMR Derived Metabolic Profiles Contribute ToProteomic Analyses? 39Julian L. Griffin and Elizabeth Sang
4. Application OfMetabonomics In The PharmaceuticalIndustry 69Alan P. Breau and Glenn H. Cantor
5. Metabolic Profiling In Tumors By In Vivo And In VitroNMR Spectroscopy 83Yeun-Li Chung, Marion Stubbs and John R. Griffiths
6. Raman Spectroscopy For Whole Organism And TissueProfiling 95Sarah Clarke and Royston Goodacre
VIII
7. Metabolic Fingerprinting With Fourier TransformInfrared SpectroscopyDavid I. Ellis, George G. Harrigan and Royston Goodacre
8. Metabolomic Analysis With Fourier Transform IonCyclotron Resonance Mass SpectrometryDayan Goodenowe
9. Stable Isotope-Based Dynamic Metabolic Profiling InDisease And HealthLaszlo G. Boros, Marta Cascante and Wai-Nang Paul Lee
10. The Role OfMetabolomics In Systems BiologyJan van der Greef, Eugene Davidov, Elwin Verheij,Jack Vogels, Rob van der Heijden, Aram S. Adourian,Matej Oresic, Edward W. Marple and Stephen Naylor
11. Use OfMetabolomics To Discover Metabolic PatternsAssociated With Human DiseasesOliver Fiehn and Joachim Spranger
12. Bioactive Lipids In Reproductive DiseasesJaideep Chaudhary, Tim Compton and JeffA. Parrott
13. Evolutionary Computation For The Interpretation OfMetabolomic DataRoyston Goodacre and Douglas B. Kell
14. Dynamic Profiling And Canonical ModelingEberhard O. Voit and Jonas Almeida
15. Databases, Data Modeling And SchemasNigel Hardy and Helen Fuell
16. Databases And Visualization ForMetabolomicsX. Jing Li, Olga Brazhnik, Aejaaz Kamal, Dianjing Guo,Christine Lee, Stefan Hoops and Pedro Mendes
17. The Human MetabolomeChris W.W. Beecher
Index
Contents
111
125
141
171
199
217
239
257
277
293
311
321
Contributors
Aram S. Adourian. Beyond Genomics Inc., 40 Bear Hill Road, Waltham,MA 02451, USA
Jonas Almeida. Department of Biometry and Epidemiology and Departmentof Biochemistry and Molecular Biology, Medical University of SouthCarolina, Charleston, SC 29435, USA
Christopher W. W. Beecher. Paradigm Genetics, 108 TW Alexander Dr.,Research Triangle, NC 27709, USA
Laszlo G. Boros. Harbor-UCLA Research and Education Institute, 1124West Carson Street RBI, Torrance, CA 90502, USA
Olga Brazhnik. Virginia Bioinforrnatics Institute, Virginia Tech(0477),1880 Pratt Dr., Blacksburg, VA 24061, USA
Alan P. Breau. Global Drug Metabolism, Pharrnacia Corporation, 4901Searle Parkway, Skokie, IL 60077, USA
Glenn H. Cantor. Investigative Toxicology, Pharrnacia Corporation, 301Henrietta St., Kalamazoo, MI 49007, USA
Marta Cascante. Department of Biochemistry and Molecular Biology,University of Barcelona, Marti/I Franques 1, Barcelona 08028, Catalonia,Spain
x Contributors
Jaideep Chaudhary. Atairgin Technologies, 101 Theory, Irvine, CA 92612,USA
Yeun-Li Chung. Cancer Research UK Biomedical Magnetic ResonanceResearch Group, Department of Biochemistry and Immunology, St.George's Hospital Medical School, London, SWl7 ORE, UK
Sarah Clarke. Institute of Biological Sciences, University of Wales,Aberystwyth, SY23 3DD, UK
Tim Compton. Atairgin Technologies, 101 Theory, Irvine, CA 92612, USA
Eugene Davidov. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA02451, USA
David I. Ellis. Institute of Biological Sciences, University of Wales,Aberystwyth, SY23 3DD, UK
Oliver Fiehn. Max-Planck-Institute of Molecular Plant Physiology, 14424PotsdamlGolm, Germany
Helen Fuell. Department of Computer Sciences, University of Wales,Aberystwyth, SY23 3DB, UK.
Royston Goodacre. Department of Chemistry, University of ManchesterInstitute of Science and Technology, PO Box 88, Sackville St.,Manchester, M60 1QD, UK
Dayan Goodenowe. Phenomenome Discoveries Inc., 204-407 DowneyRoad, Saskatoon SK S7N 4L8, Canada
Julian L. Griffin. Division of Biomedical Sciences, Imperial College ofScience, Technology and Medicine, London, SW7 2AZ, UK
John R. Griffiths. Cancer Research UK Biomedical Magnetic ResonanceResearch Group, Department of Biochemistry and Immunology, St.George's Hospital Medical School, London, SW17 ORE, UK
Dianjing Guo. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880Pratt Dr., Blacksburg, VA 24061, USA
Contributors XI
Nigel Hardy. Department of Computer Sciences, University of Wales,Aberystwyth, SY23 3DB, UK
George G. Harrigan. Global HTS, Pharmacia Corporation, 700Chesterfield Parkway, Chesterfield, MO 63198, USA
Stefan Hoops. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880Pratt Dr., Blacksburg, VA 24061, USA
Aejaaz Kamal. Virginia Bioinformatics Institute, Virginia Tech (0477),1880 Pratt Dr., Blacksburg, VA 24061, USA
Douglas B. Kell. Department of Chemistry, University of ManchesterInstitute of Science and Technology, PO Box 88, Sackville St.,Manchester, M60 1QD, UK
Christine Lee. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880Pratt Dr., Blacksburg, VA 24061, USA
Wai-Nang Paul Lee. Harbor-UCLA Research and Education Institute, 1124West Carson Street RBI, Torrance, CA 90502, USA
X. Jing Li. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880Pratt Dr., Blacksburg, VA 24061, USA
Edward W. Marple. Beyond Genomics Inc., 40 Bear Hill Road, Waltham,MA 02451, USA
Pedro Mendes. Virginia Bioinformatics Institute, Virginia Tech (0477),1880 Pratt Dr., Blacksburg, VA 24061, USA
Stephen Naylor. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA02451, USA
Matej Oresic. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA,02451, USA
Jeff A. Parrott. Atairgin Technologies, 101 Theory, Irvine, CA 92612, USA
Elizabeth Sang. Department of Biochemistry, Oxford University, Oxford,OXI 3QV, UK
xii Contributors
Joachim Spranger. Gennan Instiute of Human Nutrition (DitE), 14558Bergholz-Rehbriicke, Gennany
Marion Stubbs. Cancer Research UK Biomedical Magnetic ResonanceResearch Group, Department of Biochemistry and Immunology, St.George's Hospital Medical School, London, SWI7 ORE, UK
Seetharaman Vaidyanathan. Instiute of Biological Sciences, University ofWales, Aberystwyth, SY23 3DD, UK
Jan van der Greef. Beyond Genomics Inc., 40 Bear Hill Road, Waltham,MA 02451, USA, TNO Phanna, PO Box 22152031 CE, Zemikedreff 9,2333 CK, Leiden, Netherlands and Leiden University/Amsterdam Centerfor Drug Research, Division of Analytical Sciences, NL-2300 RA Leiden,Netherlands
Rob van der Heijden. Leiden University/Amsterdam Center for DrugResearch, Division of Analytical Sciences, NL-2300 RA Leiden,Netherlands
Elwin Verheij. TNO Phanna, PO Box 22152031 CE, Zemikedreff9, 2333CK, Leiden, Netherlands
Jack Vogels. TNO Phanna, PO Box 2215 2031 CE, Zemikedreff 9, 2333CK, Leiden, Netherlands
Eberhard O. Voit. Department of Biometry and Epidemiology, MedicalUniversity of South Carolina, Charleston, SC 29435, USA
Preface
An impressive amount of data has emerged from genomics andproteomics ventures yet this has often served more to highlight thecomplexity of cellular regulation than to elucidate mechanism. It is alsoevident that biochemical control is not strictly hierarchical and thatintermediary metabolism can contribute to control of regulatory pathways.Metabolic studies are therefore increasingly contributing to gene functionanalyses, and an increased interest in metabolites as biomarkers for diseaseprogression or response to therapeutic intervention is also evident in thepharmaceutical industry. Front Line Strategic Consulting recently stated(September, 2002) that, worldwide, the metabolomics industry is anticipatedto grow at a compound rate of over 40% over the next five years and thatthe market for metabolomic technology sales will exceed $255 million by2007.The purpose of this book is to offer guidelines as to the technology
currently available for such pursuits and the bioinformatics and databasestrategies now being developed. We present evidence that metabolicprofiling is a valuable addition to genomics and proteomics strategiesdevoted to drug discovery and development, and believe that metabolicprofiling may be seen to offer numerous advantages, as will be highlighted inthis volume.There has been a number of recent literature reviews devoted to metabolic
profiling and an increasing number of related conferences, including the FirstInternational Congress of Plant Metabolomics (Wageningen, 2002) and theSysteomics Conference (San Francisco, 2002). The genesis of this book canbe traced to the First Annual Cambridge HealthTech Institute Conference onMetabolic Profiling (Chapel Hill, 2001) and a subsequent conference report
XIV Preface
published in Drug Discovery Today. There has, however, been no definitivevolume that describes progress in this area, particularly in the health carearena, and this book aims to address this. It is not, however, intended as acomplete review of all that is going on in pharmaceutically directedmetabolic profiling. We have not addressed in silico modeling, for example,and of course there has already been several excellent volumes on metaboliccontrol/regulation and the technological impact thereof.We hope that the book will be of interest to researchers in the
pharmaceutical industries (Big Pharma and small venture capital endeavors),academe-industry technology transfer organizations and academicresearchers. The bias of the book is to healthcare and the pharmaceuticalindustry but metabolic profiling has been extensively applied in theagriculture and microbiological arenas. Some of the book contributors havedeveloped their expertise in these areas and have much to offer ourcolleagues in biomedicine. We are of course greatly indebted to ourcontributors without whom this volume would not have been possible. Theyhave succeeded in ensuring a volume of high scientific merit and quality.Finally, we would like to acknowledge our colleagues who contributed
valuable comments and support, and helped in proofreading. RoxanneLaPlante and Elizabeth Coliantes diligently proofread many chapters andhelped with manuscript preparation. They, along with Margann Wideman,Ying Ping Zhang, Nancy Wall and Gilles Goetz, have made valuablecontributions to the development of metabolic profiling at Pharmacia. Wealso thank David Lester for valuable suggestions at the onset of this book.We would like to thank the University of Wales, Aberystwyth and the UKBBSRC and UK EPSRC for allowing us the academic freedom and financialassistance to investigate metabolic profiling, and look forward to continuingthis research in the University of Manchester Institute of Science andTechnology (UMIST).
George G. Harrigan
Royston Goodacre