Antibody Phage Display Methods and Protocols - part 1 docx

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O’Brien and Robert Aitken University of Glasgow, Glasgow, Scotland, UK Humana Press Totowa, New Jersey M E T H O D S I N M O L E C U L A R B I O L O G Y™ ©2002 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com 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 Biology ™ is a trademark of The Humana Press Inc. The content and opinions expressed in this book are the sole work of the authors and editors, who have warranted due diligence in the creation and issuance of their work. The publisher, editors, and authors are not responsible for errors or omissions or for any consequences arising from the information or opinions presented in this book and make no warranty, express or implied, with respect to its contents. 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Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging in Publication Data Antibody phage display : methods and protocols / edited by Philippa M. O’Brien and Robert Aitken. p. cm. (Methods in molecular biology ; v. 178) Includes bibliographical references and index. ISBN 0-89603-906-4 (alk. paper) (hardcover) ISBN 0-89603-711-8 (comb) 1. Monoclonal antibodies Research Methodology. 2. Bacteriophages. I. O’Brien, Philippa M. II. Aitken, Robert, 1960- III. Methods in molecular biology (Clifton, N.J.) ; v. 178. QR186.85 .A585 2002 616.07'98 dc21 2001039568 v ´ v Preface The closing years of the 19th century and the start of the 20th century witnessed the emergence of microbiology and immunology as discrete scien- tific disciplines, and in the work of Roux and Yersin, perhaps the first benefits of their synergy—immunotherapy against bacterial infection. As we advance into the new millennium, microbiology and immunology again offer a con- ceptual leap forward as antibody phage display gains increasing acceptance as the definitive technology for monoclonal production and unleashes new op- portunities in immunotherapy, drug discovery, and functional genomics. In assembling Antibody Phage Display: Methods and Protocols, we have aimed to produce a resource of real value for scientists who have followed the development of phage display technology over the past decade. The founding principles of phage display have always held an elegant simplicity. We hope that readers will find similar clarity in the technical guidance offered by the book’s contributors. In meeting our objectives, we have tried to cover the broad scope of the technology and the key areas of library construction, screen- ing, antibody modification, and expression. Of course, the technology contin- ues to advance apace, but we trust that readers will be able to gage the potential of phage display from our coverage, that some of its subtleties will emerge, and that our selection of methods will prove appealing. We are indebted to all the contributing authors for sharing their expertise with the wider scientific community. We also thank the Beatson Institute for Cancer Research, the Association for International Cancer Research (PO’B), the Caledonian Research Foundation, and the Scottish Hospitals Endowment Research Trust for their funding during the preparation of this book. Finally, we are grateful to our friend and colleague Professor M. Saveria Campo who has encouraged and supported our ventures into phage display. Philippa M. O’Brien Robert Aitken 13 Rescue of a Broader Range of Antibody Specificities Using an Epitope-Masking Strategy Henrik J. Ditzel 179 14 Screening of Phage-Expressed Antibody Libraries by Capture Lift Jeffry D. Watkins 187 15 Antibody-Guided Selection Using Capture-Sandwich ELISA Kunihiko Itoh and Toshio Suzuki 195 16 Proximity-Guided (ProxiMol) Antibody Selection Jane K. Osbourn 201 17 Isolation of Human Monoclonal Antibodies Using Guided Selection with Mouse Monoclonal Antibodies Mariangela Figini and Silvana Canevari 207 18 Selecting Antibodies to Cell-Surface Antigens Using Magnetic Sorting Techniques Don L. Siegel 219 19 Isolation of Human Tumor-Associated Cell Surface Antigen-Binding scFvs Elvyra J. Noronha, Xinhui Wang, and Soldano Ferrone 227 20 Subtractive Isolation of Single-Chain Antibodies Using Tissue Fragments Katarina Radosevic and Willem van Ewijk 235 21 Selection of Antibodies Based on Antibody Kinetic Binding Properties Ann-Christin Malmborg, Nina Nilsson, and Mats Ohlin 245 22 Selection of Functional Antibodies on the Basis of Valency Manuela Zaccolo 255 23 Two-Step Strategy for Alteration of Immunoglobulin Specificity by In Vitro Mutagenesis Yoshitaka Iba, Chie Miyazaki, and Yoshikazu Kurosawa 259 24 Targeting Random Mutations to Hotspots in Antibody Variable Domains for Affinity Improvement Partha S. Chowdhury 269 25 Error-Prone Polymerase Chain Reaction for Modification of scFvs Pierre Martineau 287 26 Use of Escherichia coli Mutator Cells to Mature Antibodies Robert A. Irving, Gregory Coia, Anna Raicevic, and Peter J. Hudson 295 27 Chain Shuffling to Modify Properties of Recombinant Immunoglobulins Johan Lantto, Pernilla Jirholt, Yvelise Barrios, and Mats Ohlin 303 v viii Contents ´ Contents ix 28 Generation of Bispecific and Tandem Diabodies Sergey M. Kipriyanov 317 29 High-Level Periplasmic Expression and Purification of scFvs Sergey M. Kipriyanov 333 30 Periplasmic Expression and Purification of Recombinant Fabs Robert L. Raffaï 343 31 Expression of Antibody Fragments in Pichia pastoris Philipp Holliger 349 32 Expression of V HH Antibody Fragments in Saccharomyces cerevisiae J. Marcel van der Vaart 359 33 Intrabodies: Targeting scFv Expression to Eukaryotic Intracellular Compartments Pascale A. Cohen 367 34 Expression of scFvs and scFv Fusion Proteins in Eukaryotic Cells Michelle de Graaf, Ida H. van der Meulen-Muileman, Herbert M. Pinedo, and Hidde J. Haisma 379 35 Expression of Antibody Fab Fragments and Whole Immunoglobulin in Mammalian Cells Pietro P. Sanna 389 Index 397 Contributors ROBERT AITKEN • University of Glasgow, Glasgow, Scotland, UK Y VELISE BARRIOS • Department of Immunotechnology, Lund University, Lund, Sweden R OBERTO BURIONI • Istituto di Microbiologia, Facoltà di Medicina, Università di Ancona, Ancona, Italy S ILVANA CANEVARI • Istituto Nazionale per lo Studio e la Cura dei Tumori, Department of Experimental Oncology, Unit of Molecular Therapies, Milano, Italy P ATRICK CHAMES • Department of Pathology, Maastricht University and University Hospital, Maastricht, The Netherlands K EITH A. CHARLTON • Remedios Ltd., Aberdeen, Scotland, UK P ARTHA S. CHOWDHURY • Human Genome Sciences, Rockville, MD M ICHELLE A. C LARK • St. Vincent’s Hospital, Sydney, Australia PASCALE A. COHEN • Faculté de Pharmacie, Université Montpellier I, Montpellier, France G REGORY COIA • CRC for Diagnostic Technologies at CSIRO Health Sciences and Nutrition, Parkville, Victoria, Australia D AVID W. J. COOMBER • Department of Surgery and Molecular Oncology, Ninewells Hospital and Medical School, University of Dundee, Scotland, UK M ICHELLE DE GRAAF • Division of Gene Therapy, Department of Medical Oncology, Vrije University, Amsterdam, The Netherlands H ANS J. W. DE HAARD • Department of Functional Biomolecules, Unilever Research Laboratorium Vlaardingen, Vlaardingen, The Netherlands R UUD M. T. DE WILDT • MRC Laboratory of Molecular Biology, Cambridge, UK H ENRIK J. DITZEL • Department of Immunology, The Scripps Research Institute, La Jolla, CA S OLDANO FERRONE • Department of Immunology, Roswell Park Cancer Institute, Buffalo, NY M ARIANGELA FIGINI • Istituto Nazionale per lo Studio e la Cura dei Tumori, Department of Experimental Oncology, Unit of Molecular Therapies, Milano, Italy H IDDE J. HAISMA • Department of Medical Oncology, Division of Gene Therapy, Vrije University, Amsterdam, The Netherlands P AULA H ENDERIKX • Dyax sa, Liege, Belgium xi ` xii Contributors RENÉ M. A. HOET • Dyax sa, Liege, Belgium P HILIPP HOLLIGER • MRC Laboratory of Molecular Biology, Cambridge, UK H ENNIE R. HOOGENBOOM • Dyax sa, Liege, Belgium ZHIWEI HU • Cancer Research Institute, Hunan Medical University, Changsha, Hunan, China; Current address: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT P ETER J. HUDSON • CRC for Diagnostic Technologies at CSIRO Health Sciences and Nutrition, Parkville, Victoria, Australia YOSHITAKA IBA • Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan R OBERT A. IRVING • CRC for Diagnostic Technologies at CSIRO Health Sciences and Nutrition, Parkville, Victoria, Australia K UNIHIKO ITOH • Department of Pharmaceutical Science, Akita University Hospital, Akita, Japan P ERNILLA JIRHOLT • Department of Immunotechnology, Lund University, Lund, Sweden SERGEY M. KIPRIYANOV • Affimed Therapeutics AG, Ladenburg, Germany Y OSHIKAZU KUROSAWA • Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan J OHAN LANTTO • Department of Immunotechnology, Lund University, Lund, Sweden S IMON LENNARD • Cambridge Antibody Technology, The Science Park, Melbourn, Cambridgeshire, UK ANN-CHRISTIN MALMBORG • Department of Immunotechnology, Lund University, Lund, Sweden P IERRE MARTINEAU • CNRS, Faculté de Pharmacie, Montpellier, France C HIE MIYAZAKI • Toyota Central R&D Laboratories, Nagakute, Japan N INA NILSSON • Department of Immunotechnology, Lund University, Lund, Sweden E LVYRA J. NORONHA • Department of Microbiology, Hammer Health Science Center, Columbia University, New York, NY P HILIPPA M. O’BRIEN • University of Glasgow, Glasgow, Scotland, UK M ATS O HLIN • Department of Immunotechnology, Lund University, Lund, Sweden JANE K. OSBOURN • Cambridge Antibody Technology, The Science Park, Melbourn, Cambridgeshire, UK H ERBERT M. PINEDO • Division of Gene Therapy, Department of Medical Oncology, Vrije Universiteit, Amsterdam, The Netherlands A NDREW J. PORTER • Department of Molecular and Cell Biology, Institute of Medical Science, University of Aberdeen, Aberdeen, Scotland, UK K ATARINA RADOSEVIC´• Department of Immunology, Erasmus University Rotterdam/University Hospital Rotterdam-Dijkzigt, Rotterdam, The Netherlands v ` ` [...]... 2 Antibody Phage Display 2 .1 The Phage- Display Principle The power of the phage- display system is illustrated in Fig 1 DNA encoding millions of variants of certain ligands (e.g., peptides, proteins, or fragments From: Methods in Molecular Biology, vol 17 8: Antibody Phage Display: Methods and Protocols Edited by: P M O’Brien and R Aitken © Humana Press Inc., Totowa, NJ 1 2 Hoogenboom Fig 1 Phage- display. .. (15 4 15 8), combinations of the two (15 9 ,16 0), a separate group of highly constrained protease inhibitors (97 ,16 1 ,16 2), proteins based on a single immunoglobulin fold (16 3 16 5) or on the eight-strand β-barrel of the lipocalins (16 6) or green fluorescent protein (16 7) Since secreted, as well as cytoplasmic and nuclear, proteins have been displayed on phage (15 1), display on phage is often the first strategy... sites (11 13 ) so that the scFv or other ligand may be fused at the N-terminus of the mature gene III protein (6 ,12 ) or at the N-terminus of a truncated pIII lacking the first two N-terminal domains (11 ,14 ) They may also be formatted for direct secretion of the unfused Ab fragment without subcloning (12 ) Many phagemids utilize the lacZ promoter to drive expression of the antibody- pIII fusion (12 ,14 ,15 ),... Science References 1 Smith, G P (19 85) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface Science 228, 13 15 13 17 2 Winter, G., Griffiths, A D., Hawkins, R E., and Hoogenboom, H R (19 94) Making antibody by phage display technology Ann Rev Immunol 12 , 433–455 3 Hoogenboom, H R and Chames, P (2000) Natural and designer binding sites made by phage display technology... of this G-protein-coupled 7-TM receptor One other early study (14 1) has addressed phage- mediated triggering of 7-TM receptors: in that study, the melanocortin receptor was triggered by using one of the receptor’s natural ligands displayed on phage It should thus be feasible to isolate receptor-specific ligands from phage libraries using panning on cells that overexpress the target receptor and to screen... library, and eventually subjected to more detailed analysis The success of ligand phage display hinges on the synthesis of large combinatorial repertoires on phage and the combination of display and enrichment 2.2 Filamentous Phage Biology and Display Although other display systems have been described (see Subheading 3.4.), the most popular vehicle for display remains the filamentous bacteriophage The... filamentous phage, fd, or M13, infects strains of E coli containing the F conjugative plasmid Phage particles attach to the tip of the F pilus encoded by genes on the plasmid and the phage genome, a circular singlestranded DNA molecule, is translocated into the cytoplasm The genome is replicated involving both phage- and host-derived proteins and packaged by the infected cell into a rod-shaped particle,... ligand being presented on the phage surface; its genetic material resides within the phage particle This connection between ligand genotype and phenotype allows the enrichment of specific phage, e.g., using selection on an immobilized target Phage that Ab Phage- Display Technology Overview 3 display a relevant ligand will be retained, but nonadherent phage will be washed away Bound phage can be recovered from... nonimmunogenic, and toxic Ags (20,22,47) The affinity of Abs selected from a naïve library is proportional to the size of the library, ranging from 10 6–7 M 1 for a small library of 3 × 10 7 clones (20,22) to 10 8 10 M 1 for a large repertoire of 10 10 clones made by brute-force cloning (47) This finding is in line with theoretical considerations ( 51) Other large naïve human scFv libraries (6.7 × 10 9 clones) (52) and. .. specific phage (% input) Panning on cells in suspension 10 ,000 2–5 Panning on glass slide-mounted cryosections Injection of phage into tumor interstitium Injection of phage into the tail vein 80 0.025 10 0.005 none 0.0 01 aMixtures of an excess of control phage compared to specific (anti-epithelial glycoprotein–2) phage were selected on a number of different target materials Since Ag-specific and control phage . Marilena Aquino de Muro and Ralph Rapley, 2002 17 8. Antibody Phage Display: Methods and Protocols, edited by Philippa M. O’Brien and Robert Aitken, 2002 17 7. Two-Hybrid Systems: Methods and Protocols, edited. 17 9 14 Screening of Phage- Expressed Antibody Libraries by Capture Lift Jeffry D. Watkins 18 7 15 Antibody- Guided Selection Using Capture-Sandwich ELISA Kunihiko Itoh and Toshio Suzuki 19 5 16 . Italy 1 From: Methods in Molecular Biology, vol. 17 8: Antibody Phage Display: Methods and Protocols Edited by: P. M. O’Brien and R. Aitken © Humana Press Inc., Totowa, NJ 1 Overview of Antibody Phage- Display