Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919)
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Jennifer E. Van Eyk and Michael J. Dunn (Editors)Proteomic and Genomic Analysis of Cardiovascular DiseaseProteomic and Genomic Analysis of Cardiovascular Disease.Edited by Jennifer E. van Eyk, Michael J. DunnCopyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 3-527-30596-3Related Titles from Wiley-VCH:Stefan Lorkowski and Paul Cullen (Eds.)Analysing Gene ExpressionA Handbook of Methods.
Possibilities and Pitfalls(2 Volumes)2002ISBN 3-527-30488-6Reiner Westermeier, Tom NavenProteomics in PracticeA Laboratory Manual of Proteome Analysis2002ISBN 3-527-30354-5ProteomicsThe premier international source for information in the field of proteomics(Journal with 12 issues a year)ISSN 1615-9853http://www.wiley-vch.de/home/proteomicsProteomic and Genomic Analysisof Cardiovascular DiseaseEdited by:Jennifer E. Van Eyk and Michael J. DunnEditors:Jennifer E.
Van EykDepartment of PhysiologyQueen’s University429 Botterell HallKingston, Ontario K7L 2N6CanadaMichael J. DunnDepartment of NeuroscienceKing’s CollegeDe Crespigny ParkLondon, SE5 8AFUKn This book was carefully produced. Nevertheless,authors and publisher do not warrant the information contained therein to be free of errors.Readers are advised to keep in mind that statements, data, illustrations, procedural details orother items may inadvertently be inaccurate.Each section in this book is the exclusive responsibility of the authors of that section.Library of Congress Card No.: applied forBritish Library Cataloguing-in-Publication DataA catalogue record for this book is available fromthe British Library.Bibliographic information publishedby Die Deutsche BibliothekDie Deutsche Bibliothek lists this publicationin the Deutsche Nationalbibliografie; detailedbibliographic data is available in the Internet at<http://dnb.ddb.de>© 2003 WILEY-VCH Verlag GmbH & Co.
KGaA,WeinheimAll rights reserved (including those of translationin other languages). No part of this book may bereproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted ortranslated into machine language without writtenpermission from the publishers. Registerednames, trademarks, etc. used in this book, evenwhen not specifically marked as such, are not tobe considered unprotected by law.Printed in the Federal Republic of GermanyPrinted on acid-free paperComposition K+V Fotosatz GmbH, BeerfeldenPrinting Druckhaus Darmstadt GmbH,DarmstadtBookbinding Litges & Dopf Buchbinderei,HeppenheimISBN3-527-30596-3VPrefaceOver the last several years, the increased level of interest in and recognition of thepower and potential of genomics and proteomics has been astonishing.
The useof these approaches for the study of complex disease is accelerating and is especially applicable to cardiovascular disease, the number one cause of death in theworld.This is the first book in which leaders in the fields of genomics and proteomicsaddress current issues about their applications to cardiovascular disease. By exploring the various strategies and technical aspects of both, using examples fromcardiac or vascular biology, the limitations and the potential of these methods canbe clearly seen. The book is divided into three sections: the first focuses on genomics, the second on proteomics, and the third provides an overview of the importance of these two scientific disciplines in drug and diagnostic discovery. The goalof this book is the transfer of their hard-earned lessons to the growing number ofcardiovascular researchers using these techniques, with the hope of saving timeand accelerating the pace of discovery.The study of genomics most often entails the quantification of the transcriptome – the many thousands of messenger RNA’s associated with the cellular response to stress and disease.
Chapters by M. Schinke, L. Riggi, A. J. Butte and S.Izumo; C. C. Liew provide wonderful overviews of large-scale expression profilingin several chronic cardiac diseases. The strategic choices and decisions required tocreate a valid genomic study are described by M. Krenz, G. Schwartzbauer and J.Robbins – and emphasizes that physiology and genomics complement one another.
Equally eloquent is the chapter by T. T. Tuomisto and S. Ylä-Herttuala inwhich they examine the use of genomics to study atherosclerosis and plaque formation – an area not yet influenced by proteomics. Although genomic analysis isoften focused on chronic heart failure (e.g., S. Arab, M. Husain and P. Liu), it canalso be applied to more acute settings, such as myocardial protection (E.
Murphy,C. A. Afshari, J. G. Petranka and C. Steenbergen) and the stress response of thepulmonary vascular system (S.-F. Ma, S. Q. Ye and J. G. N. Garcia); these chaptersprovide insight into these distinct but clinically relevant issues.Most genomic chapters focus on DNA microarrays; however, the use of subtractive hybridization in gene profiling is highlighted in the chapter by C. Depre.Throughout these powerful chapters on genomics and transcriptomics are theProteomic and Genomic Analysis of Cardiovascular Disease.Edited by Jennifer E. van Eyk, Michael J.
DunnCopyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 3-527-30596-3VIPrefacehard-learned lessons; one such cautionary and sobering tale is retold (A. C. Alpinand C. E. Murry) which also underscores the chapter entitled the skeptic‘s viewpoint (L. Adams, R. E. Bumgarner and S. M. Schwartz). Overall, the chapters balance the advantages and limitations of genomics, and outline the remaining challenges while acknowledging the enormous quantity of information that can begleaned by this approach.Proteomics, the study of the proteome, is still in its infancy. Its technical side isbenefiting from new approaches and strategies based on previous studies.
Technically, proteomics essentially consists of protein separation, identification and characterization (co- and post-translational modifications, function, cell localization,structure and binding partners). Although straightforward in theory, the technologies utilized in proteomics are challenging in practice.
This is, in part, a reflectionof the complexity of the proteome – a result of the complex chemical nature ofproteins, each with its unique amino acid sequence, as well as their many (over100) possible co- and post-translational modifications, modifications that changetheir chemical properties. Thus, separation and identification of these extremelycomplex protein mixtures require skill, fortitude, and patience (of both the investigator and the granting agency).The classical, broad-based screening approach based on two-dimensional gelelectrophoretic separation of proteins coupled with their identification by massspectrometry is highlighted by one of the major founders of proteomics in cardiacdisease (E.
McGregor and M. J. Dunn). The underlying technologies of 2-DE andmass spectrometry are still the most commonly used methods for studyingchanges within the proteome; as such, mass spectrometry is vital. An overview ofthe evolution of mass spectrometry and its diverse roles in proteomics (H. L.Byers and M.A. Ward) is complemented by the chapter by M.
E. Wright and R. Aebersold writing on ICAT, the first robust method for differential quantification ofmass spectrometry data, and that by R. E. Jenkins and S. R. Pennington on theapplication of new protein chip/mass spectrometry techniques. This is followedby a series of chapters focusing on subproteomics – the detailed study of specificgroups of proteins within cardiac and vascular cells. Subproteomic analysis can bebased on: investigation of discrete cellular organelles (R. A.
Gottlieb and H. He);dynamic signaling cascades (J. A. MacDonald and T. A. J. Haystead; T. M. Vondriska, J. Zhang and P. Ping); functional groups either within cells (J. A. Simpson, S.Iscoe and J. E. Van Eyk) or external to cells, as with the study of secreted proteinsand peptides (Z.-G., Jin, D.-F. Liao, C. Yan and B. C. Berk). Collectively, thesechapters describe strategies that allow detailed insights into the dynamics of thecell.Translating the identification of a gene or protein change in disease to an approved commercial product – either a diagnostic marker or therapeutic drug – is along and difficult process.
The final two chapters by A. J. Marion and M. H. Gollob and by S. T. Rapundalo explore this process and the promise of genomics andproteomics, respectively, with regard to drug discovery. Both provide an interesting and insightful perspective on the use of these scientific disciplines in thebroader scheme of clinical and commercial application. The detailed knowledgePrefacethat can be obtained from proteomics and genomics should provide a greaterprobability of success.Genomics and proteomics are two sides of the same coin. The link betweenthese two disciplines, however, has yet to be fully appreciated and exploited; thisshould occur in the next few years.The chapters in this book collectively provide an overview of the current statusof genomics and proteomics in the cardiovascular field.
When looked at in its entirety, one obtains tantalizing glimpses into the incredible complexity of cellularfunction – the complexity that drives the cell’s adaptation to stress and its environment, and how disease alters its normal physiological response, whether compensatory or pathological. New and exciting discoveries based on genomic and proteomic strategies provide insight into cardiovascular disease, information that mayaid in development of new diagnostic markers and therapeutic approaches for itscontrol and treatment.
While editors regularly express the sentiment that “the future holds unlimited potential,” the examples provided herein are a testament tothe fact that this potential is already being realized. What remains to be determined is the magnitude of their influence in shaping future scientific discoveryand how this will impact on clinical treatment of cardiovascular disease.Jennifer E. Van Eyk and Michael J. DunnKingston (Canada) and London (UK)December 2002VIIIXContentsPrefaceVList of ContributorsXIXSection 1Genomics1Large Scale Expression Profiling in Cardiovascular Disease Using Microarrays:Prospects and Pitfalls 31.11.1.11.1.21.21.2.11.2.21.2.31.2.41.31.41.522.12.22.32.42.52.62.71Martina Schinke, Lauren Riggi, Atul J. Butte, and Seigo IzumoDNA Microarray Technologies 3cDNA Microarrays or Oligonucleotide Arrays? 3Designing Meaningful Experiments 9Computational Analysis of Microarray Data 11Raw Data Analysis 11Comparing Expression Data 13Clustering Algorithms 16Data Sharing 19Potential Use of this Technology in UnderstandingComplex Heart Disease 20Acknowledgements 23References 24Global Genomic Analyses of Cardiovascular Disease:A Potential Map or Blind Alley? 27Maike Krenz, Gary Schwartzbauer, and Jeffrey RobbinsBlindly Searching for Structure-Function 27The Starting Line: Garbage In – Garbage Out? 29Is the Mouse a Valid Model for Human-Based DiseaseTranscriptome Studiese? 32Arrays and Cardiovascular Disease 33Filtering the Transcriptome: Enhancing the Value 35Concluding Remarks 39References 40Proteomic and Genomic Analysis of Cardiovascular Disease.Edited by Jennifer E.
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