Antibody Phage Display: Methods and Protocols

391 Pages·2002·2.362 MB·English

by  Hennie R. Hoogenboom (auth.), Philippa M. O’Brien, Robert Aitken (eds.)

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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™
Antibody Phage
Display
Methods and Protocols
Edited by
Philippa M. O’Brien
and
Robert Aitken
University of Glasgow, Glasgow, Scotland, UK
Humana Press Totowa, New Jersey
©2002 Humana Press Inc.
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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
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
v
Contents
Preface .......................................................................................................... v
Contributors.................................................................................................. xi
1 Overview of Antibody Phage-Display Technology and Its Applications
Hennie R. Hoogenboom.....................................................................1
2 Standard Protocols for the Construction of Fab Libraries
Michelle A. Clark...............................................................................39
3 Standard Protocols for the Construction of scFv Libraries
Simon Lennard..................................................................................59
4 Broadening the Impact of Antibody Phage Display Technology:
Amplification of Immunoglobulin Sequences from Species
Other than Humans or Mice
Philippa M. O’Brien and Robert Aitken..........................................73
5 Construction of Large Naïve Fab Libraries
Hans J. W. de Haard.........................................................................87
6 Construction of Polyclonal Antibody Libraries Using Phage Display
Jacqueline Sharon, Seshi R. Sompuram, Chiou-Ying Yang,
Brent R. Williams, and Stefanie Sarantopoulos.....................101
7 Antigen-Driven Stimulation of B-Lymphocytes In Vitro
Zhiwei Hu.........................................................................................113
8 The Recovery of Immunoglobulin Sequences from Single Human
B Cells by Clonal Expansion
Ruud M. T. de Wildt and René M. A. Hoet....................................121
9 Panning of Antibody Phage-Display Libraries: Standard Protocols
David W. J. Coomber......................................................................133
10 Selection of Antibodies Against Biotinylated Antigens
Patrick Chames, Hennie R. Hoogenboom,
and Paula Henderikx..................................................................147
11 Isolation of Anti-Hapten Specific Antibody Fragments
from Combinatorial Libraries
Keith A. Charlton and Andrew J. Porter......................................159
12 Blocking Immunodominant Epitopes by Competitive Deselection
Roberto Burioni...............................................................................173
vii
viii Contents
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 Antibvodi´es 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
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 Antibody Fragments in Saccharomyces cerevisiae
HH
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
YVELISE BARRIOS • Department of Immunotechnology, Lund University,
Lund, Sweden
ROBERTO BURIONI • Istituto di Microbiologia, Facoltà di Medicina, Università
di Ancona, Ancona, Italy
SILVANA CANEVARI • Istituto Nazionale per lo Studio e la Cura dei Tumori,
Department of Experimental Oncology, Unit of Molecular Therapies,
Milano, Italy
PATRICK CHAMES • Department of Pathology, Maastricht University and
University Hospital, Maastricht, The Netherlands
KEITH A. CHARLTON • Remedios Ltd., Aberdeen, Scotland, UK
PARTHA S. CHOWDHURY • Human Genome Sciences, Rockville, MD
MICHELLE A. CLARK • St. Vincent’s Hospital, Sydney, Australia
PASCALE A. COHEN • Faculté de Pharmacie, Université Montpellier I,
Montpellier, France
GREGORY COIA•CRC for Diagnostic Technologies at CSIRO Health Sciences
and Nutrition, Parkville, Victoria, Australia
DAVID W. J. COOMBER • Department of Surgery and Molecular Oncology,
Ninewells Hospital and Medical School, University of Dundee, Scotland, UK
MICHELLE DE GRAAF • Division of Gene Therapy, Department of Medical
Oncology, Vrije University, Amsterdam, The Netherlands
HANS J. W. DE HAARD • Department of Functional Biomolecules, Unilever
Research Laboratorium Vlaardingen, Vlaardingen, The Netherlands
RUUD M. T. DE WILDT• MRC Laboratory of Molecular Biology, Cambridge, UK
HENRIK J. DITZEL • Department of Immunology, The Scripps Research
Institute, La Jolla, CA
SOLDANO FERRONE • Department of Immunology, Roswell Park Cancer
Institute, Buffalo, NY
MARIANGELA FIGINI • Istituto Nazionale per lo Studio e la Cura dei Tumori,
Department of Experimental Oncology, Unit of Molecular Therapies,
Milano, Italy
HIDDE J. HAISMA • Department of Medical Oncology, Division of Gene
Therapy, Vrije University, Amsterdam, The Netherlands
PAULA HENDERIKX • Dyax sa, Lie`ge, Belgium
xi
xii Contributors
RENÉ M. A. HOET • Dyax sa, Lie`ge, Belgium
PHILIPP HOLLIGER • MRC Laboratory of Molecular Biology, Cambridge, UK
HENNIE R. HOOGENBOOM • Dyax sa, Lie`ge, 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
PETER 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
ROBERT A. IRVING • CRC for Diagnostic Technologies at CSIRO Health
Sciences and Nutrition, Parkville, Victoria, Australia
KUNIHIKO ITOH • Department of Pharmaceutical Science, Akita University
Hospital, Akita, Japan
PERNILLA JIRHOLT • Department of Immunotechnology, Lund University,
Lund, Sweden
SERGEY M. KIPRIYANOV • Affimed Therapeutics AG, Ladenburg, Germany
YOSHIKAZU KUROSAWA • Institute for Comprehensive Medical Science, Fujita
Health University, Toyoake, Japan
JOHAN LANTTO • Department of Immunotechnology, Lund University, Lund,
Sweden
SIMON LENNARD • Cambridge Antibody Technology, The Science Park,
Melbourn, Cambridgeshire, UK
ANN-CHRISTIN MALMBORG • Department of Immunotechnology, Lund
University, Lund, Sweden
PIERRE MARTINEAU • CNRS, Faculté de Pharmacie, Montpellier, France
CHIE MIYAZAKI • Toyota Central R&D Laboratories, Nagakute, Japan
NINA NILSSON • Department of Immunotechnology, Lund University, Lund,
Sweden
ELVYRA J. NORONHA • Department of Microbiology, Hammer Health Science
Center, Columbia University, New York, NY
PHILIPPA M. O’BRIEN • University of Glasgow, Glasgow, Scotland, UK
MATS OHLIN•Department of Immunotechnology, Lund University, Lund,
Sweden
JANE K. OSBOURN • Cambridge Antibody Technology, The Science Park,
Melbourn, Cambridgeshire, UK
HERBERT M. PINEDO • Division of Gene Therapy, Department of Medical
Oncology, Vrije Universiteit, Amsterdam, The Netherlands
ANDREW J. PORTER • Department of Molecular and Cell Biology, Institute of
Medical Science, University of Aberdeen, Aberdeen, Scotland, UK
KATARINA RADOSvEVIC´• Department of Immunology, Erasmus University
Rotterdam/University Hospital Rotterdam-Dijkzigt, Rotterdam,
The Netherlands