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M E T H O D S I N M O L E C U L A R M E D I C I N ETM CCeelliiaacc DDiisseeaassee MMeetthhooddss aanndd PPrroottooccoollss EEddiitteedd bbyy MMiicchhaaeell NN.. MMaarrsshh,, ,, ,, MMDD DDSScc FFRRCCPP HHuummaannaa PPrreessss Celiac Disease M E T H O D S I N M O L E C U L A R M E D I C I N ETM Celiac Disease Methods and Protocols Edited by Michael N. Marsh , MD, DSc, FRCP Department of Medicine, University of Manchester, Salford, UK Humana Press Totowa, New Jersey © 2000 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. Methods in Molecular Medicine™is a trademark of The Humana Press Inc. All authored papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. (cid:39) ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Cover design by Patricia F. Cleary Due diligence has been taken by the publishers, editors, and authors of this book to assure the accuracy of the information published and to describe generally accepted practices. The contributors herein have carefully checked to ensure that the drug selectionsand dosages set forth in this text are accurate and in accord with the standards accepted at the time of publication. Notwithstanding, as new research, changes in government regulations, and knowledge from clinical experience relating to drug therapy and drug reactions constantly occurs, the reader is advised to check the product information provided by the manufacturer of each drug for any change in dosages or for additional warnings and contraindications. This is of utmost importance when the recommended drug herein is a new or infrequently used drug. It is the responsibility of the treating physician to determine dosages and treatment strategies for individual patients. Further, it is the responsibility of the health care provider to ascertain the Food and Drug Administration status of each drug or device used in their clinical practice. 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For those organizations that have been granted a photocopy license from the CCC, a separate system of payment has been arranged and is acceptable to Humana Press Inc. The fee code for users of the Transactional Reporting Service is: [0-89603-650-2/00 $10.00 + $00.25]. Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 TO COME FROM Library of Congress Cataloging in Publication Data LIB. OF CONGRESS Main entry under title: Methods in molecular medicine™. Celiac disease: methods and protocols / edited by Michael N. Marsh. p. cm. -- (Methods in molecular medicine™ ) Includes index. ISBN 0-89603-650-2 (alk. paper) 1. XXXXXXX--Laboratory manuals. I. Marsh, Michael N. II. Series. [DNLM: 1. XXXXXX. 2. XXXXX. QXXXXX 2000] QXXXXX 2000 DNLM/DLC 00-4625 for Library of Congress CIP Preface Research into gluten sensitivity has never been more popular nor more exciting. Thus a call for a new book, Celiac Disease: Methods and Protocols, devoted entirely to techniques and technology seemed a most appropriate undertaking. I am therefore grateful to Professor J. M. Walker for inviting me to complete this task for Humana Press. To do this would have been impos- sible without the contributions of friends and colleagues from around the world who have devoted so much interest to the project. It has also been necessary for them to master the unique chapter-writing skills required of every manu- script published in this series of laboratory monographs. With regard to gluten sensitivity we are in a period of great change, occasioned by the introduction of reproducible methods for cloning lymphocytes, the application of physical methods to identify gluten sequences as T-cell antigens, the study of peptide responses in vitro and in vivo by either jejunal or rectal challenge, elucidating the locations of other genes concerned in pathogenesis, or the use of elegant immunohistocytochemical and mRNA probing techniques for analyzing the finer points of the mucosal inflamma- tory response to gluten. Never was a detailed laboratory handbook, of the quality assembled here through its contributing experts, so necessary as at this time! It has been a privilege to put together Celiac Disease: Methods and Pro- tocols and it is offered in the hope that its pages will contain the necessary information for any newcomer to this field to get himself or herself organized quickly with the least technical hindrance. Michael N. Marsh, MD, DSc, FRCP v Dedication This book is dedicated to the memory of Professor Anne Ferguson, whose un- timely death has deprived gastrointestinal science of one of its most renowned and prolific investigators. Although our pro- fessional lives had almost run concur- rently, she and I met only rarely, usually transiently at various international meet- ings or gatherings. It was her earlier work with Delphine Parrott in Glasgow, and subsequently with Thomas MacDonald and Allan Mowat in Edinburgh, that provided the initial evidence that mucosal T lymphocytes influence mucosal architecture, and hence may play a fundamental role in the immunopathogenesis of celiac disease. Indeed, the most recent studies with cloned mucosal T lymphocytes have con- firmed such pioneering work and affirmed that lymphocytic sensitization to gluten, and subsequent antigen-induced activation, does result in the spec- trum of mucosal changes that has now been identified across the ever- widening perception of what, today, should be known as gluten sensitivity, rather than by its restrictive 1970s clinical designation as “celiac disease.” Anne's later contributions to the measurement, and diagnostic use, of inflam- matory/immunologic mediators in intestinal lavage fluid are further novel applications of her approach to the understanding of gastrointestinal disease: these studies have been brought together by her colleagues for publication in this volume. Anne's name will go down in the history of gluten sensitivity along with those of Dicke, Shiner, Rubin, and Crosby. May she forever rest in peace. Michael N. Marsh vi Contents Preface .............................................................................................................v Dedication........................................................................................................vi Contributors.....................................................................................................ix 1 Celiac Disease: A Brief Overview Debbie Williamson and Michael N. Marsh .........................................1 2 Genotyping Methodologies Stephen Bevan and Richard S. Houlston.........................................11 3 From Linkage to Genes: Positional Cloning, Stephen Bevan and Richard S. Houlston.........................................21 4 Linkage and the Transmission Disequilibrium Test in Complex Traits: Celiac Disease as a Case Study Stephen Bevan and Richard S. Houlston.........................................33 5 Extraction, Separation, and Purification of Wheat Gluten Proteins and Related Proteins of Barley, Rye, and Oats Arthur S. Tatham, Simon M. Gilbert, Roger J. Fido, and Peter R. Shewry.......................................................................55 6 Structure Elucidation of Gluten-Derived Peptides by Tandem Mass Spectrometry Peter A. van Veelen, Jan W. Drijfhout, and Frits Koning ..............75 7 Synthetic Peptide Libraries for T-Cell Epitope Identification Hoebert S. Hiemstra, Jan W. Drijfhout, and Frits Koning..............89 8 Characterization of HLA–DQ-Specific Peptide-Binding Motifs Yvonne van de Wal, Reinout Amons, and Frits Koning.................97 9 Studies of Gliadin-Specific T Cells in Celiac Disease Øyvind Molberg, Stephen N. McAdam, Knut E. A. Lundin, and Ludvig M. Sollid ...................................................................105 10 Morphometric Analysis of Intestinal Mucosa: The Measurement of Volume Compartments and Cell Volumes in Human Intestinal Mucosa Michael N. Marsh, Peter T. Crowe, Kieran J. Moriarty, and Arzu Ensari ....................................................................................125 vii viii Contents 11 Morphometry of Rectal Mucosa Arzu Ensari, Michael N. Marsh, Peter T. Crowe, and Kieran J. Moriarty..................................................................147 12 Organ Culture of Rectal Mucosa: In Vitro Challenge with Gluten in Celiac Disease Guiseppe Mazzarella, Franco Paparo, Maria Maglio, and Riccardo Troncone........................................................................163 13 In Situ Hybridization Conrad G. Beckett and Paul Ciclitira..............................................175 14 Quantification of Cytokine mRNA Expression by Quantitative Polymerase Chain Reaction in Studies of Celiac Disease Ellen M. Nilsen, Finn-Eirik Johansen, and Per Brandtzaeg ........185 15 Immunohistochemistry in Research and Diagnosis of Celiac Disease Per Brandtzaeg and Frode L. Jahnsen .........................................203 16 Immunoassay for Detection of IgA Antitissue Transglutaminase in Patients with Celiac Disease Walburga Dieterich, Ernst Otto Riecken, and Detlef Schuppan.241 17 Antiendomysial and Antigliadin Antibody Tests and Diagnosis of Celiac Disease David J. Unsworth ............................................................................247 18 Whole Gut Lavage Fluid Analysis: A Minimally Invasive Method for Study of Mucosal Immunity and Inflammation Subrata Ghosh, Anna Dahele, Hazel E. Drummond, Syed S. Hoque, Kenneth Humphreys, and Ian D. R. Arnott ...257 Index .........................................................................................................279 Contributors REINOUT AMONS • Department of Immunohaematology and Bloodbank, University of Leiden, Leiden, The Netherlands IAN D. R. ARNOTT • Department of Gastroenterology, Western General Hospital, Edinburgh, UK CONRAD G. BECKETT • Department of Gastroenterology, Bradford Royal Informary, Bradford, West Yorkshire, UK STEPHEN BEVAN • Institute of Cancer Research, Sutton, Surrey, UK PER BRANDTZAEG •Laboratory for Immunohistochemistry and Immunopathology (LIIPAT), Institute of Pathology, The National Hospital, Oslo, Norway PAUL J. CICLITIRA • Department of Gastroenterology, The Rayne Institute, St. Thomas' Hospital, London, UK PETER T. CROWE • University Department of Medicine, Hope Hospital, Salford, UK ANNA DAHELE • Department of Gastroenterology, Western General Hospital, Edinburgh, UK WALBURGA DIETERICH • Medical Clinic I, University of Erlangen, Erlangen, Germany JAN W. DRIJFHOUT • Department of Immunohaematology and Bloodbank, University of Leiden, Leiden, The Netherlands HAZEL E. DRUMMOND •Department of Gastroenterology, Western General Hospital, Edinburgh, UK ARZU ENSARI • Department of Pathology, University of Ankara Medical School, Ankara, Turkey ROGER J. FIDO • Department of Agricultural Sciences, IACR-Long Ashton Research Station, Long Ashton, Bristol, UK SUBRATA GHOSH • Department of Gastroenterology, Western General Hospital, Edinburgh, UK SIMON M. GILBERT • Department of Agricultural Sciences, IACR-Long Ashton Research Station, Long Ashton, Bristol, UK HOEBERT S. HIEMSTRA • Department of Immunohaematology and Bloodbank, University of Leiden, Leiden, The Netherlands ix