Genomics: Applications in Human Biology G E N O M I C S Applications in Human Biology Sandy B. Primrose Senior Partner, Business & Technology Management, High Wycombe, UK Richard M. Twyman Department of Biology, University of York, York, UK Managing Director, Write Science, York, UK © 2004 by Blackwell Science Ltd a Blackwell Publishing company 350 Main Street, Malden, MA 02148-5020, USA 108 Cowley Road, Oxford OX4 1JF, UK 550 Swanston Street, Carlton, Victoria 3053, Australia The right of Sandy B. Primrose and Richard M.
Twyman to be identified as the Authors of this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher. Library of Congress Cataloging-in-Publication Data Primrose, S.
Genomics : applications in human biology / Sandy B. Primrose and Richard Twyman. 042— dc21 2003007541 A catalogue record for this title is available from the British Library. Set in 91/2 /12pt Photina by Graphicraft Limited, Hong Kong Printed and bound in the United Kingdom by TJ International Ltd, Padstow, Cornwall For further information on Blackwell Publishing, visit our website: http://www.com Brief Contents Full Contents vii Preface xi Acknowledgments xiii CHAPTER ONE Biotechnology and genomics in medicine 1 CHAPTER TWO An overview of genomics 20 CHAPTER THREE Genomics and the challenge of infectious disease 60 CHAPTER FOUR Analyzing and treating genetic diseases 90 CHAPTER FIVE Diagnosis and treatment of cancer 112 CHAPTER SIX The large scale production of biopharmaceuticals 131 CHAPTER SEVEN Genomics and the development of new chemical entities 157 CHAPTER EIGHT Gene and cell therapies 178 Index 205 Full Contents CHAPTER ONE: Biotechnology and genomics in medicine 1 Introduction 1 Recombinant DNA technology 2 The central importance of cloning 2 Identification and cloning of specific genes 5 Functional characterization of cloned genes 9 From recombinant DNA to molecular medicine 10 The use of DNA sequences as diagnostic tools 11 The production of therapeutic proteins 11 Gene medicine 14 Disease models 15 The impact of genomics on medicine 15 The new molecular medicine 17 Outline of this book 18 Further reading 19 CHAPTER TWO: An overview of genomics 20 Introduction 20 A review of progress: the Human Genome Project 21 Breakthroughs in genetic mapping 23 Breakthroughs in physical mapping 25 Sequencing strategies 28 Genome annotation 31 The future: functional genomics 35 Sequence comparison and comparative genomics 37 Transcriptomics: global analysis of mRNA 40 Proteomics: global analysis of proteins 45 Technology platforms for proteome separation 47 Protein characterization by mass spectrometry 49 viii Full Contents Applications of expression proteomics 51 Technology platforms for interaction proteomics 51 Mutational genomics 55 Further reading 57 CHAPTER THREE: Genomics and the challenge of infectious disease 60 Microorganisms causing disease 60 Where do new diseases come from? 63 Identifying the causative agent of a disease 65 Molecular epidemiology 68 Host resistance to infection 70 Understanding bacterial pathogenicity 70 Pathogenicity islands 72 Comparative genomics and genome plasticity 73 Combating infectious disease 75 Novel routes to vaccines 76 Genomics and the development of new antibacterial agents 78 Combating fungal infections 81 Progress in tackling protozoan diseases 82 Developing antiviral drugs 86 Further reading 89 CHAPTER FOUR: Analyzing and treating genetic diseases 90 Genetic disease in context 90 Detecting single gene disorders 91 Treating single gene disorders 96 Finding genes for monogenic diseases and determining gene function 98 Positional cloning 99 The candidate gene approach 100 Analysis of polygenic disorders 102 Model-free linkage analysis 102 Linkage disequilibrium mapping 103 Haplotypes 105 The major histocompatibility complex 106 Individual responses to drugs (pharmacogenomics) 109 Further reading 110 CHAPTER FIVE: Diagnosis and treatment of cancer 112 Introduction 112 The molecular basis of cancer 112 The impact of genomics on cancer research 116 Full Contents ix New methods for the diagnosis of cancer 119 New approaches to cancer therapy 122 Radiotherapy 122 Chemotherapy 123 Biotherapy 127 New therapeutic targets 129 Further reading 129 CHAPTER SIX: The large scale production of biopharmaceuticals 131 Overview 131 The generation of monoclonal antibodies 132 Radioimmunotherapy and diagnostic imaging 135 Other modified antibodies 137 The large scale culture of microorganisms 137 The large scale culture of animal cells 140 Expression systems 144 Downstream processing 145 Using gene manipulation to facilitate downstream processing of biopharmaceuticals 148 The quality of biopharmaceuticals 149 Good manufacturing practice 153 Alternative production systems 154 Further reading 155 CHAPTER SEVEN: Genomics and the development of new chemical entities 157 Introduction: how drugs are developed 157 High-throughput screening 159 Target validation and animal models 163 Combinatorial chemistry 167 Dynamic combinatorial libraries 170 Virtual screening 171 Combinatorial biosynthesis and chemobiosynthesis 172 Drug metabolism 174 Toxicogenomics 175 Further reading 176 CHAPTER EIGHT: Gene and cell therapies 178 Introduction 178 Gene therapy 179 Gene delivery strategies 181 Gene delivery mechanisms 182 Case studies 186 x Full Contents Nucleic acids as drugs 190 Antisense drugs 190 Ribozyme drugs 191 The potential of short interfering RNAs 191 Aptamer drugs 193 Gene medicine for infectious diseases: HIV 193 DNA vaccines 194 Disease models 195 Models of single gene disorders 195 Models of complex disorders 199 Cell therapy 199 Stem cells and cloning 200 Organ transplants 202 Further reading 203 Preface Fifty years ago, Watson and Crick detailed for us the structure of DNA and showed how it could be replicated faithfully from generation to generation.
The impact of this discovery on medicine was barely considered. Rather, biologists wanted to know about the structure of genes and the genetic code. Twenty-five years ago the biotechnology revolution was underway following the development of recombin- ant DNA technology, which permitted the in vitro production of human proteins on a large scale. Then the vision for biotechnology was no more than factories producing recombinant molecules.
Pharmaceutical biotechnology, as it then was known, was a very narrow subject. Today we are in the midst of the genomics revolution, which was spearheaded by international projects aiming to sequence the complete genomes of organisms ranging from bacteria to mammals, including humans. Many of the genes in these organisms have been identified and good progress is being made towards under- standing the roles of these genes in health and disease. As a consequence, there is almost no aspect of medicine and drug development that has not been affected.
For example, we now have a good understanding of the genes involved in microbial pathogenicity and this is facilitating the development of new diagnostics, new vac- cines, and new antibiotics. Similarly, we are rapidly dissecting the genetic basis of inherited diseases and cancer, which again is leading to new diagnostics and new treatments. The development of these new pharmaceuticals is being facilitated by the introduction of novel screening methodologies that are themselves based on recombinant DNA technology and genomics. When Watson and Crick announced their momentous discovery almost all pharmaceuticals were small molecules, although insulin was a notable exception.
Following the advent of recombinant DNA technology this drug repertoire was expanded to include a much wider range of natural human proteins including interferons, blood products, and further hormones. Today the diversity of drug molecules has expanded further, to include engineered proteins that are unlike any produced naturally, humanized antibodies, and even nucleic acids. Furthermore new medical procedures are being developed, such as gene therapy, cell therapy, and tissue therapy. xii Preface Given the pace at which the above developments are taking place it is not surpris- ing that students and their academic mentors have difficulty in seeing the whole picture.
This book has been written to provide them with the necessary overview, covering technologic developments, applications, and (where necessary) the eth- ical implications. The book is divided into three sections. The first section (Chapters 1 and 2) introduces the role of biotechnology and genomics in medicine and sets out some of the technologic advances that have been the basis of recent medical break- throughs. The second section (Chapters 3–5) takes a closer look at how biotech- nology and genomics are influencing the prevention and treatment of different categories of disease.
Finally, in the third section (Chapters 6–8), we describe the contribution of biotechnology and genomics to the development of different types of therapy, including conventional drugs, recombinant proteins, and gene/cell therapies. Throughout the book, the level of detail has been selected so that the reader can grasp what has been achieved without falling victim to “not seeing the wood for the trees.” A basic understanding of genetics and molecular biology has been assumed so we can avoid the obligatory chapters on DNA structure, gene expression, etc. that appear in most larger biology textbooks regardless of their actual focus. Readers requiring more detail of the recombinant DNA and genomics techniques should consult our more advanced textbooks on these subjects: Principles of Gene Manipulation (POGM) and Principles of Genome Analysis and Genomics (POGA), also published by Blackwell Publishing.
References to appropriate sections in these two books are included at the end of each chapter (with the relevant acronym indicating the book), plus a short bibliography mostly comprising review papers that have been selected for their clarity of presentation. The reader will also find the text con- tains several categories of boxed text, which include history boxes (describing the origins and development of particular technologies or treatments), molecular boxes (which describe the molecular basis of diseases or treatments in more detail), and ethics boxes (which discuss the ethical implications of technology development and new therapies). Finally, we would like to thank the people who provided invaluable assistance in the preparation of the manuscript, particularly Sue Goddard and her team in the library at CAMR and Alistair Fitter at the Department of Biology, University of York. Richard Twyman would like to dedicate this book to his parents, Peter and Irene, his children, Emily and Lucy, and to Hannah, Joshua, and Dylan.
Primrose and Richard M. Twyman References Primrose SB, Twyman RM (2003) Principles of Genome Analysis and Genomics, 3rd edn. Blackwell Publishing, Oxford. Primrose SB, Twyman RM, Old RW (2001) Principles of Gene Manipulation, 6th edn.
Blackwell Science, Oxford. Acknowledgments Some figures and tables have been used from other sources. We thank the various authors and publishers for permission to use this material, which has come from the following sources: Figures are extensively drawn from the following publications by the authors: Primrose SB (1991) Molecular Biotechnology, 2nd edn. Blackwell Science, Oxford.
Primrose SB, Twyman RM (2003) Principles of Genome Analysis and Genomics, 3rd edn. Blackwell Publishing, Oxford. Primrose SB, Twyman RM, Old RW (2001) Principles of Gene Manipulation, 6th edn. Blackwell Science, Oxford.
Specific tables and figures have been taken from the following sources: Fig.4: Coulson A, Sulston J, Brenner S et al. (1986) Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci USA 83, 7821–7825.8: EnsEMBL human genome browser www.9: Veculescu VE et al. (1997) Characterization of the yeast transcriptome.12 inset: Görg A, Postel W, Baumer M, Weiss W (1992) Two-dimensional polyacrylamide gel electrophoresis, with immobilized pH gradients in the first dimension, of barley seed proteins: discrimination of cultivars with different mating grades.4: Courtesy of Catherine Arnold, UK Health Protection Agency.3: Behr et al.4: Nussbaum RL, McInnes RR, Willard HF (2001) Genetics in Medicine, WB Saunders, Philadelphia, figure 4.
Original photograph courtesy of P. Wray, Hospital for Sick Children, Toronto.6: Nussbaum RL, McInnes RR, Willard HF (2001) Genetics in Medicine, WB Saunders, Philadelphia. xiv Acknowledgments Fig.7: Thomson G (2001) Mapping of disease loci. In: Kalow W, Meyer UA, Tyndale R, eds.
Marcel Dekker, New York.9: Judson R, Stephens JC, Windemuth A (2000) The predictive power of haplotypes in clinical response.10: Nussbaum RL, McInnes RR, Willard HF (2001) Genetics in Medicine, WB Saunders, Philadelphia, figure 4.11: Johnson JA, Evans WE (2002) Molecular diagnostics as a predictive tool: genetics of drug efficacy and toxicity. Trends Mol Med 8, 300–305.