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Genetic Susceptibility to Infectious Diseases PDF

464 Pages·2008·3.02 MB·English
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Genetic Susceptibility to Infectious Diseases This page intentionally left blank Genetic Susceptibility to Infectious Diseases Edited by Richard A. Kaslow Janet M. McNicholl Adrian V.S. Hill 1 2008 1 Oxford University Press, Inc., publishes works that further Oxford University’s objective of excellence in research, scholarship, and education. Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Copyright ª 2008 by Oxford University Press, Inc. Published by Oxford University Press, Inc. 198 Madison Avenue, New York, New York 10016 www.oup.com Oxford is a registered trademark of Oxford University Press 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, without the prior permission of Oxford University Press. Library of Congress Cataloging-in-Publication Data Kaslow, Richard A. Genetic susceptibility to infectious diseases = Richard Kaslow, Janet McNicholl, Adrian Hill. p. cm. Includes bibliographical references. ISBN 978-0-19-517490-8 1. Communicable diseases—Genetic aspects. 2. Infection—Genetic aspects. 3. Disease susceptibility—Genetic aspects. I. McNicholl, Janet. II. Hill, Adrian. III. Title. [DNLM: 1. Communicable Diseases—genetics. 2. Genetic Predisposition to Disease. 3. Variation (Genetics)—immunology. QZ 50 K19b 2007] RC112.K27 2007 616.9042—dc22 2007008576 9 8 7 6 5 4 3 2 1 Printed in the United States of America on acid-free paper Preface The twentieth century was filled with triumph in pose of this volume is to organize existing knowledge of preventing and controlling infectious diseases. Much those influences into a foundation for future inquiry. of that success was achieved through a combination of The book was conceived early in 2001 in the sanitation (simple alterations of the physical environ- ‘‘pregenomic’’ era, a few months before the first draft ment), antimicrobials (painstaking discovery and test- sequence of the human genome was available and ing of compounds to inactivate or destroy etiologic before the International HapMap Project was even agents), and immunization (elegant manipulation of designed. Beyond gathering in one place the infor- the agents or their products to stimulate protective host mation that a reader would otherwise be forced to ex- immunity). Of the three approaches, only immuniza- cavate from many sites, this collection is intended to tion depended on the genetically mediated host im- accomplish a secondary goal: to ‘‘cross-fertilize’’ the mune responses—and even then only indirectly and work of basic scientists, clinicians, and others who may often imperceptibly. Numerous vaccines with im- be more familiar with genetics or infection but not pressive efficacies of 70–90% or higher—the most re- both. It is thus meant to be a blend of the general and cent example being the remarkable human papillo- the specific—containing aspects of critical review, mavirus vaccine—were developed with little or no systematic progress report, clinical application, and attention to the principles of human genetics. In short, prospectus. throughout decades of progress, our meager knowledge In the gestational period between conception of the of host genes and genetic variation was largely irrele- text and delivery of the manuscript to the publisher, vant to the many landmark victories. many new candidate genes with probable influence on During that same period, numerous assaults on infection and immunity have surfaced, and previously infectious disease faltered, with grave consequences. quiescent or unrecognized infections of major public The quarter-century-long explosion of HIV-1 infec- health consequence such as West Nile virus infection tion, the resurgence of tuberculosis both with and and corona virus–associated severe acute respiratory without HIV=AIDS, the unshakable persistence of distress syndrome (SARS) have emerged. Meanwhile, malaria, and biological threats such as anthrax con- revolutionary advances in the knowledge and tech- tinue to remind us of the inadequacy of previously nology of genetics have continued to sweep through effective strategies. Those ‘‘failures’’ as much as any- every corner of the biomedical research enterprise. In thing have refocused attention on the origins of in- the midst of such dynamic changes, we have tried to fectious diseases in their full complexity. There has maintain as much currency as the constraints of space been increasing recognition that strategies for con- and time allowed. trolling these diseases will likely require insights at the To assist the diverse audience, we have divided the deeper level of human and microbial genetics—a book into three parts that mirror that diversity in ori- thorough understanding of the influences of host ge- entation and knowledge base. Part I describes the netic variation on infection and immunity. The pur- current methods for generating information about vi PREFACE genetic variation in populations of humans and ani- Part III reveals notable unevenness in current mals. Part II highlights families of genes whose varia- knowledge among the diseases of interest. Chapter 18 tion is known or likely to contribute to susceptibility to encompasses uncommon immune deficiencies due to human infectious disease, and part III covers the major derangements of immunoglobulin genes and others infectious diseases on which the influences of host showing classic Mendelian inheritance. Subsequent genetic variation are stronger or better established. chapters cover some diseases of major public health Sections of individual chapters in parts II and III importance. Some other conditions of comparable conform roughly to a general outline. General topic impact on populations, such as dengue fever and hu- headings and the structure of certain tables correspond man papillomavirus infection, are mentioned in the more closely across chapters; however, the inherent appropriate places in part II but not covered explicitly disparity in knowledge of each individual gene or in their own right. For most of the disorders included, disease limited further standardization. investigation of susceptibility due to genetic polymor- We have made no attempt to catalogue every tech- phism has yielded relatively convincing evidence, but nique, gene, or disease with some connection to the the diseases and the genes examined vary considerably title theme; that encyclopedic approach was beyond in that regard. Malaria, HIV=AIDS, and tuberculosis the scope of the endeavor. At the risk of diluting or show definitive relationships with variable gene con- omitting, we have tried to be rather more selective, to tent or allelic polymorphisms in numerous chromo- create an anthology with accessibility to readers in a somal regions. The work on malaria has been thorough broad set of disciplines. Chapters in part I provide enough to devote a separate chapter in part II to the more perspective than specifics. Including sections on profound impact of red blood cell genes and a chapter such topics as bioinformatics tools and applications, in part III to the disease itself. the latest strategies for genomewide association studies, Interest and information on genetic determinants whole-genome sequencing or expression microarray of variable response to vaccines for preventing infec- analysis, proteomics, and alternative animal models tions and to drugs for treating them are expanding. might have added more specialized material of interest Aside from space limits, a simple reason explains our to some but are well reviewed elsewhere. deliberate decision to include a chapter on the former Part II covers 14 families of genes whose variation is but not the latter. Vaccines are biological products—in known to contribute to differential susceptibility. The some cases actually replicating organisms—to which relevant polymorphisms of those selected range widely genetically mediated responses may well parallel re- in the degree of certainty of their involvement and in sponses to the naturally occurring pathogen. Accord- their importance in terms of population frequency. ingly, observations about variable vaccine response are For some gene families (e.g., those encoding certain quite likely to inform studies of infection and vice complement components or immunoglobulin recep- versa. On the other hand, anti-infective pharmaceuti- tors), clinically significant variation is well established cals are transported and metabolized along pathways but relatively uncommon. Different chapters reflect whose regulation, for the most part, involves a very varying perspectives among authors in accepting the different set of genes with more tenuous involvement validity or relevance of polymorphisms reported to in immunity or susceptibility. alter immune function or disease susceptibility. For Although we could not continue beyond a point example, although experimental or epidemiologic to update the text with every new gene family, disease, studies of various inflammatory diseases have impli- or genotype–phenotype relationship to susceptibility cated the genes encoding MHC class I polypeptide– whenever potentially relevant information appeared, related sequence (MICA and MICB) and the Toll-like two efforts have been made to maintain its currency receptors (TLRs), the chapters on those gene clusters during production. One effort resulted in an appendix reflect considerable skepticism that published associ- containing a list of particularly informative Web sites ations of infectious diseases with specific alleles rep- among the many devoted to ‘‘postgenomic’’ activities. resent effects that are functionally significant and in- Compiling such a compendium was a challenge—one dependent of alleles in close linkage disequilibrium that is likely to grow as Web sites proliferate even with unknown variants. Other chapters are more lib- further, but an exercise worth the effort because it will eral in including reported relationships. not be long before these and subsequent electronic PREFACE v i i sources will be providing rich and continuously timely this coevolutionary contest between human and mi- information beyond the scope of this volume. crobial life have forged remarkable patterns of poly- The other updating effort followed our decision morphism that remain with us—many probably per- to use current nomenclature and conventions of the sisting long after the pathogens responsible for driving U.S. National Center for Biotechnology Information the particular variation have ceased to colonize our (NCBI) as universally as possible. Names of genes are species. However, the patterns in our DNA do not intended to follow official NCBI designations uni- constitute mere ‘‘fossil record’’ of these encounters. formly. Wherever possible, and with a few exceptions Our genetic legacy continues to exert its force and, as for those likely to be confusing in context, the NCBI in the past, will inevitably shape reemergent and newly gene symbol has been systematically substituted for the recognized transmissible microorganisms into agents historical or more common abbreviation, often with a of future epidemics. The difference between the past parenthetic reference to the older, familiar one. By and the future is that we have recently crossed a thresh- convention, symbols that refer to a human gene rather old into the promise of a postgenomic world. There we than to its product or to its specific alleles are meant to can envision far more powerful observational and ex- be capitalized and italicized; a symbol for a human perimental research that will accelerate the translation gene accompanied by one or more of its alleles is also of discovery about human genetic susceptibility into usually capitalized but not italicized. Although the effective measures of disease control. We hope that in latter convention has not been widely adopted, we some small way this text will equip each reader to have tried for the most part to conform to it. For HLA contribute to that goal. genes and alleles, the more exacting nomenclature is explained in the text. Genes of nonhuman species may or may not be capitalized but are italicized. Acknowledgments As the mining of the human genome for suscepti- bility genes gathers pace, with greatly improved tech- Every text is ultimately more than the sum of its pub- nologies and larger study populations, the relevance of lished parts. This one represents the collective, orga- this work to public health will expand. The number of nized wisdom of the authors and the product of con- susceptibility gene discoveries that have so far gener- tinuous editorial exchange about content and form. ated new intervention strategies is still small but likely However, other contributions were essential. At the to grow rapidly, particularly for the major killers that earliest conceptual stages, three individuals with dif- have proved most refractory to more traditional ap- ferent orientations understood the theme of genetic proaches. New susceptibility profiles will have appli- susceptibility to infection and were of common mind cation to risk assessment, to prioritization of individu- as they envisioned something like this text. Jeffrey als for prophylaxis, and to selection of alternative House, the Oxford University Press representative for treatments. Equally important, pathways identified many years; Emil Skamene, the eminent McGill through the recognition of novel susceptibility genes University immunobiologist and physician; and Muin have already suggested unexpected mechanisms with Khoury, the Centers for Disease Control and Preven- candidate molecular targets. tion genetic epidemiologist and public health expo- Research on genetic susceptibility to infectious nent, deserve our special gratitude for encouraging us diseases has often taken place at the interface between to convert our shared vision into reality. Throughout the science of evolutionary biology and the real world the process that followed, we have relied on others be- of treatment and prevention. The text summarizes the hind the scenes to inspire, encourage, facilitate, tol- scientific discoveries of more than half a century in a erate, restrain, revive, and (still) love us for what we series of stories about an ancient, ongoing struggle were trying to do. To them—our families, friends, between host and pathogen. Victories on both sides of colleagues—we owe our profound gratitude. This page intentionally left blank Contents Contributors xi 8. Red Blood Cell Genes and Malaria 107 David Weatherall I METHODS AND TOOLS 9. Immunoglobulin (Fc) and Related 1. Genetic Epidemiology of Infectious Disease 3 Receptor Genes 120 Priya Duggal & Terri H. Beaty Jennifer A. Croker & Robert P. Kimberly 2. Laboratory Analysis of Genetic Variation 18 10. Mannose-Binding Lectin Genes 137 Meredith Yeager, Robert A. Welch, Richard Bellamy & Stephen J. Chanock 11. Complement Genes 151 3. Mouse Models for Genetic Susceptibility Keith D. Crawford & Chester A. Alper to Infection in Humans 32 Anny Fortin, Ellen Buschman, & Emil Skamene 12. Toll-Like Receptor Genes 165 Bruce Beutler II IMMUNE RESPONSE GENES AND INFECTION 13. Metal Transport Genes 175 Jean-Franc¸ois Marquis, John R. Forbes, 4. MHC Class I and Related Genes 47 Franc¸ois Canonne-Hergaux, Cynthia Horth, Henry A. F. Stephens & Philippe Gros 5. MHC Class II and Related Genes 62 14. Tumor Necrosis Factor and Janet M. McNicholl, Peter E. Jensen, Related Genes 190 & Jeremy M. Boss Grant Gallagher, Milton O. Moraes, & Juan-Manuel Anaya 6. MHC Class I Polypeptide–Related Sequence A and B (MICA and MICB) 15. Cytokine Genes I: IL10, IL6, IL4, and the Genes 83 IL1 Family 208 Seiamak Bahram Milton O. Moraes, Janet M. McNicholl, Tom W. J. Huizinga, & Tom H. M. Ottenhoff 7. Killer Immunoglobulin-Like Receptor and Related Genes 89 16. Cytokine Genes II: IL12, IFNG, and Their Maureen P. Martin, M. Tevfik Dorak, Receptor Genes 227 & Mary Carrington Margje H. Haverkamp & Stephen M. Holland

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