pharmacogenomics the search for individualized therapies

Julio Licinio, Ma-Li Wong (Editors) Pharmacogenomics The Search for Individualized Therapies Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) Pharmacogenomics The Search for Individualized Therapies Edited by Julio Licinio and Ma-Li Wong Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) Editors Julio Licinio Ma-Li Wong Interdepartmental Clinical Pharmacology Center UCLA Neuropsychiatric Institute and School of Medicine Gonda Center 3357A 695 Charles Young Drive So. Los Angeles, CA 90095-1761 USA e-mails: licinio@ucla.edu mali@ucla.edu Library of Congress Card No.: applied for British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Die Deutsche Bibliothek – CIP-Cataloguing-in- Publication Data A catalogue record for this publication is available from Die Deutsche Bibliothek © WILEY-VCH Verlag GmbH Weinheim (Germany), 2002 All rights reserved (including those of translation in other languages). No part of this book may be reproduced in any form – by photoprinting, mi- crofilm, or any other means – nor transmitted or translated into machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law. printed in the Federal Republic of Germany printed on acid-free paper Composition K+V Fotosatz GmbH, Beerfelden Printing Strauss Offsetdruck GmbH, Mörlenbach Bookbinding J. Schäffer GmbH & Co. KG, Grünstadt ISBN 3-527-30380-4 n This book was carefully produced. Nevertheless, editors, authors and publisher do not warrant the information contained therein to be free of er- rors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate. Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) We dedicate this book to our parents Áurea and João, and Yin Shen and Kwok Keung. VPharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) We acknowledge the exceptional role of Barbara A. Levey, M.D., in bringing us into the field of clinical pharmacology, of which pharmacogenomics is a new fron- tier. We are very fortunate to have worked with Karin Dembowsky at WILEY-VCH whose enthusiasm, expertise, and dedication greatly contributed to this project. Professor Boris Vargaftig’s generous invitation for one of us (J. L.) to join the Sci- entific Committee of the Euroconference “Pharmacogenetics and Pharmacogen- omics” (Institut Pasteur, Paris, France, October 12–13, 2000) greatly contributed to enhance our understanding of the state-of-the-art in pharmacogenomics. Acknowledgements Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) In this book leading experts provide the state-of-the-art in the emerging and excit- ing field of pharmacogenomics. The multitude of ways that pharmacogenomics can be approached and applied reflects the possibilities brought about by the wealth of data generated by the Human Genome Project, in conjunction with par- allel advances in bioinformatics and biotechnology. Procedures that are now rou- tine were a decade ago thought to be impossible. We now study the simultaneous expression of thousands of genes and test thousands of discrete gene variations (single nucleotide polymorphisms) in one sample. To clinicians and researchers pharmacogenomics is powerfully attractive. Individ- ualized treatment is the Holy Grail of medical practice. However, unlike medieval knights who would leave family and country behind in their adventurous quest, we must stay firmly grounded in the reality of clinical practice and ethics as we search the rich minefields of genomic data for the sequences that will bring about a new era in individualized therapeutics. The quest for the Grail of pharmacogen- omics is irresistible and enthralling. The promise of novel, individualized, more efficacious treatments with minimal or no adverse reactions is almost within reach. Given the fact that key diseases are complex and of unknown cause, the ex- pectation of better treatments is extremely appealing. However, is such hope real or a mirage? Will the popular saying “too good to be true” apply to this new area of biomedical research? Each chapter in this book contributes a piece of the puzzle that will reveal not only the possibilities, but also the complexities of the field. The final picture is still evolving, but our perception as we complete the editing of this volume is that we are witnessing the beginning of an eruption that will unleash revolutionary changes in patient-oriented research and in data processing and integration. It is hoped that this will directly impact on disease treatments, but to achieve such a goal there will be a need to overcome multiple challenges. We will need to devel- op analytical tools to deal with high volumes of data, data mining, and data inte- gration. New strategies are required to bridge genomics and proteomics and new tools are needed to understand complex information, including behavioral data. Moreover, as the progress of pharmacogenomics is brought to the clinic, it be- comes necessary to address increasingly complex ethical issues in patient-oriented research and in treatment design and delivery. VII Preface Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) Pharmacogenomics represents a paradigm shift in medicine. In the 21st cen- tury the search to understand overwhelming complexity replaces the reductionis- tic approach to science that was a hallmark of the 20th century. Until recently sci- entific thinking led investigators to approach a topic by controlling conditions and studying one or few aspects of the problem. In this new century we fully acknowl- edge the complexity of biology, and the challenge is now one of feasibility. We need to discover what will the smallest unit of pharmacogenomic data be that will support final conclusions. This book provides chapters on the latest updates on genomic science, related methodological issues, and the application of genomics to biological systems and to therapeutics of diseases that are public health problems worldwide. These are followed by chapters on ethical considerations. We conclude with a chapter on the role of vascular proteomics in individualized treatment. Many of the chapters start with a discussion of what pharmacogenomics is and its distinction from pharma- cogenetics. Rather than edit out those – at times conflicting and redundant – para- graphs we thought it would be in the reader’s best interest to leave those in, so that different individual perspectives could be presented. As this is such a new and emerging field, concepts and definitions are still evolving. While we person- ally believe that the term “pharmacogenomics” will eventually replace “pharmaco- genetics,” or be used interchangeably, others have a more strict view of the dis- tinction between these concepts. We opted to have each author introduce the field in her/his chapter for readers to appreciate the diversity of views and the evolu- tion of the field. Our goal when we first conceptualized this project was to bring together in one volume the current level of development in pharmacogenomics. We are delighted that leading experts have participated in this endeavor and we are very grateful to them for having made that goal a reality. Los Angeles, January 2002 Julio Licinio and Ma-Li Wong PrefaceVIII Preface VII List of Contributors XXIII Color Plates XXXI 1 Introduction to Pharmacogenomics: Promises, Opportunities, and Limitations 1 Urs A. Meyer Abstract 1 1.1 Pharmacogenetics – The Roots of Pharmacogenomis 1 1.2 Pharmacogenomics – It is Not just Pharmacogenetics 3 1.2.1 Genetic Drug Response Profiles 3 1.2.2 The Effect of Drugs on Gene Expression 4 1.2.3 Pharmacogenomics in Drug Discovery and Drug Development 5 1.3 Pharmacogenomics – Hopfe or Hype? 5 1.4 References 7 2 The Human Genome 9 Samuel Broder, G. Subramanian and J. Craig Venter Abstract 9 2.1 Introduction 9 2.2 Expressed Sequence Tags (ESTs) and Computational Biology: The Foundation of Modern Genomic Science 10 2.3 Microbial Genomics 12 2.3.1 Computational Analysis of Whole Genomes 13 2.3.2 Comparative Genome Analysis 13 2.4 Genomic Differences that Affect the Outcome of Host-Pathogen Interactions: A Template for the Future of Whole-Genome-Based Pharmacologic Science 18 2.5 More Lessons from the Human Genome 22 2.5.1 Protein-Coding Genes 22 2.5.2 Repeat Elements 23 IX Contents Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co. KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) 2.5.3 Genome Duplication 24 2.5.4 Analysis of the Proteome 25 2.5.5 DNA Variation 26 2.6 Biological Complexity and the Role of Medicine in the Future of the Genome 28 2.7 Conclusion 29 2.8 References 29 3 Turning SNPs into Useful Markers of Drug Response 35 Jeanette J. McCarthy Abstract 35 3.1 Introduction 35 3.2 Two Approaches for Employing SNPs in Pharmacogenomics 36 3.2.1 Candidate Gene Studies 36 3.2.2 Whole Genome Linkage Disequilibrium Mapping Studies 38 3.2.3 Comparison of Candidate Gene and Whole Genome LD Mapping 40 3.3 How Many SNPs are Needed and What Kind are Useful for Pharmacogenomic Studies 41 3.3.1 Location 42 3.3.2 Frequency 43 3.3.3 Haplotype Analysis 44 3.3.4 Number of SNPs Required for Whole Genome LD Mapping Studies 46 3.4 Study Designs for Pharmacogenomic Analysis 46 3.4.1 Challenges Unique to Pharmacogenomics 46 3.4.2 Clinical Trials, Case-Control and Cohort Studies 47 3.5 Analytical Issues is Pharmacogenomic Studies 48 3.5.1 Effect of LD on Sample Size 48 3.5.2 Multiple Hypothesis Testing 49 3.5.3 Gene–Drug Interaction 50 3.6 Development of Pharmacogenomic Markers 51 3.7 Conclusion 52 3.8 References 53 4 Association Studies in Pharmacogenomics 57 Laurent Essioux, Benoit Destenaves, Philippe Jais and François Thomas Abstract 57 4.1 Introduction 57 4.2 Variability and ADR in Drug Response: Contribution of Genetic Factors 58 4.3 Multiple Inherited Genetic Factors Influence the Outcome of Drug Treatments 60 4.3.1 Background 60 4.3.2 Liver Metabolism Enzymes 60 4.3.3 Transporters 62 ContentsX 4.3.4 Plasma Binding Proteins 62 4.3.5 Drug Targets 62 4.4 Association Studies in Pharmacogenomics 64 4.4.1 The Principles of Association Studies 64 4.4.2 Study Design 64 4.4.3 Direct Approach: A Hypothesis-Driven Strategy 66 4.4.4 Indirect Approach: A Hypothesis-Generating Strategy 67 4.5 SNP Assembly into Maps 68 4.6 Strategies for Pharmacogenomic Association Studies 69 4.6.1 Candidate Genes 69 4.6.2 Genome-Wide Scan 71 4.7 Expected Benefits of Pharmacogenomics in Drug R & D 72 4.7.1 Background 72 4.7.2 Identification of New Targets 72 4.7.3 Pre-Clinical Development Phase 74 4.7.4 Pre-Marketing Clinical Trials 74 4.7.5 Post-Marketing Phase IV 75 4.7.6 Targeting Drugs to the Individual 76 4.8 Conclusion 76 4.9 References 77 5 Genomics Applications that Facilitate the Understanding of Drug Action and Toxicity 83 L. Mike Furness Abstract 83 5.1 Platform Technologies 83 5.1.1 Genomics 83 5.1.2 Proteomics 85 5.1.3 Bioinformatics 86 5.2 The Pharmaceutical Process 89 5.3 Application to the Pharmaceutical Industry 91 5.3.1 Understanding Biology and Disease 92 5.3.2 Target Identification and Validation 101 5.3.3 Drug Candidate Identification and Optimization 103 5.3.4 Safety and Toxicology Studies 106 5.4 Application to the Medical Research Community 108 5.5 Conclusions 109 5.6 References 110 6 The Role of Pharmacogenetics in Drug Discovery and Therapeutics 127 Klaus Lindpaintner 6.1 Introduction 127 6.2 Definition of Terms 127 6.2.1 Pharmacogenomics 127 6.2.2 Pharmacogenetics 128 Contents XI [...]... Contents 15 Pharmacogenomics of the Blood–Brain Barrier 311 15.3 15.3.1 15.3.2 15.3.2.1 15.3.2.2 15.4 15.5 Jean-Michel Scherrmann Abstract 311 Basic Concepts Underlying the Pharmacogenomics of the Blood–Brain Barrier 312 The Two Barriers 312 Constituents of the Blood–Brain Barrier 313 Endothelial Cells in the Blood–Brain Barrier 313 Pericytes in the Blood–Brain Barrier 315 Astrocytes in the Blood–Brain... segments (1–6) The segment 4 of each of the domains acts as the voltage sensor, physically moving out in response to depolarization resulting in activation of the sodium channel The channel is inactivated rapidly by the linker region between III and IV docking on to the acceptor site formed by the cytoplasmic ends of S5 and S6 of domain IV The b-subunits have a common structure, with the b1 non-covalently... Mechanism of Action of Existing Treatments and New Directions for Drug Therapy 454 Classifying Smokers According to the Molecular Basis for their Habit 455 Accurate Determination of Dosage for Therapeutic Interventions 455 “Minimum SNP Set“ for Tobacco Dependence and Need for High-Throughput Genotyping 455 Conclusion 457 References 457 23 Pharmacogenomics of Opioid Systems 23.1 Terry Reisine Abstract... to the a-channel (adapted from [4]) The S5/S6 and the segment linking them (P-loop) are believed to constitute the most of the pore of the channel Specific mutations in the P-loop are associated with loss of selectivity of the channel Mutations identified in generalized epilepsy with febrile seizures plus are denoted by red dots, while those in severe myoclonic epilepsy of infancy with black dots The. .. neurogenesis C57BL/6 mice were treated with lithium for 14 days, and then received once daily BrdU injections for 12 consecutive days while lithium treatment continued 24 hours after the last injection, the brains were processed for BrdU immunohistochemistry Cell counts were performed in the hippocampal dentate gyrus at three levels along the dorsoventral axis in all the animals BrdU-positive cells were counted... CB2 3DD UK Chapter 7 Pharmacogenomics: The Search for Individualized Therapies Edited by J Licinio and M.-L Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) Color Plates Fig 5.2 In vitro microarray data from xenobiotic treatment XXXI XXXII Color Plates Mutation of Thr164 to Ile (cyan) in the fourth transmembrane region of the b2-adrenergic... Junctions, Receptors and Cell Cross-Talk at the Blood–Brain Barrier 326 Pharmacogenomics of the Blood–Brain Barrier 328 Objectives for Pharmacogenomics of the Blood–Brain Barrier 328 Current Experimental Approaches and Their Limitations 328 In vitro Pharmacogenomic Studies 329 In vivo Pharmacogenomic Studies 330 Conclusion 331 References 332 16 Pharmacogenomics and the Treatment of Neurological Disease 16.1... Enzymes 449 Future Targets for Candidate Gene Studies 450 Genome Scans to Investigate Tobacco Dependence 450 Genomic Areas Linked with Susceptibility to Nicotine Dependence 451 Biallelic or Multiallelic Markers for Linkage Studies? 451 Genome Scans in the Future 452 Evidence for the Genomic Basis of Nicotine Addiction from Animal Models 452 Applying Pharmacogenomics to Therapy for Nicotine Addiction 454... Barrier 315 Astrocytes in the Blood–Brain Barrier 317 Basement Membrane at the Blood–Brain Barrier 317 The Main Gene and Protein Targets for Pharmacogenomics of the Blood–Brain Barrier 319 Drug-Metabolizing Enzymes at the Blood–Brain Barrier 319 Drug-Carrier Transporters at the Blood–Brain Barrier 321 Mono- or Bidirectional Transporters for Small Compounds 321 Peptide and Protein Transporters 323 A New Generation... Index 541 525 531 Pharmacogenomics: The Search for Individualized Therapies Edited by J Licinio and M.-L Wong Copyright © 2002 Wiley-VCH Verlag GmbH & Co KGaA ISBNs: 3-527-30380-4 (Paper); 3-527-60075-2 (Electronic) List of Contributors * corresponding author Simon D Ahorvon National Neuroscience Institute 11 Jalan Tan Tock Seng Singapore 308433 Chapter 16 Israel Alvarado Laboratory of Pharmacogenomics . Julio Licinio, Ma-Li Wong (Editors) Pharmacogenomics The Search for Individualized Therapies Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright. 3-527-60075-2 (Electronic) Pharmacogenomics The Search for Individualized Therapies Edited by Julio Licinio and Ma-Li Wong Pharmacogenomics: The Search for Individualized Therapies. Edited by J contributed to enhance our understanding of the state-of -the- art in pharmacogenomics. Acknowledgements Pharmacogenomics: The Search for Individualized Therapies. Edited by J. Licinio and M L. Wong Copyright