Methods in Molecular Biology 1701 Michael Hust Theam Soon Lim Editors Phage Display Methods and Protocols M ETHODS IN M OLECULAR B IOLOGY Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Phage Display Methods and Protocols Edited by Michael Hust Technische Universit€at Braunschweig, Braunschweig, Germany Theam Soon Lim Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia Editors Michael Hust Theam Soon Lim Technische Universit€at Braunschweig Institute for Research in Molecular Medicine Braunschweig, Germany Universiti Sains Malaysia Minden, Penang, Malaysia ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-7446-7 ISBN 978-1-4939-7447-4 (eBook) DOI 10.1007/978-1-4939-7447-4 Library of Congress Control Number: 2017956713 © Springer Science+Business Media LLC 2018 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media, LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Preface Antibodies have emerged from humble beginnings over a century ago when Emil von Behring and Shibasaburo Kitasato first witnessed the unique ability of antibodies in sera (first called “Anti-toxine”) from immunized rabbits to neutralize toxins. Since then, anti- bodies have emerged to become the most important biologicals. In the mid-1970s, Ko¨hler and Milstein revolutionized the application of antibodies not only in basic research and diagnostics but also in the biomedical field with their work on hybridoma technology. This was a turning point for many medical approaches applied at that time. The inherent ability to produce monospecific antibodies was a game changer in the pharmaceutical industry, but these antibodies were still mainly murine antibodies which can cause side effects. The evolution of DNA technology coupled with a deeper understanding of molecular biology and immunology allowed for the successive growth of antibody technology. The groundbreaking discovery by Smith on M13 phage display allowed for the presentation of a specific peptide on the surface of bacteriophages. This work was then further enhanced with the presentation of antibody fragments on the surface of bacteriophage which was indepen- dently developed around 1990 at the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg, Germany, at the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, and at the Scripps Research Institute in La Jolla, USA. The advancement in technologies allowed the selection of fully human antibodies from antibody phage display libraries. The plethora of different types of phage display libraries and applications of phage display highlights the robustness and durability of the method for antibody generation and became a key technology for the generation of therapeutic antibodies. Antibody phage display was also the technology to develop the first human antibody, Adalimumab, and best sold biological. This book provides examples of the generation of different forms of antibody libraries including libraries from different hosts. Many research groups share their expertise and experience in this book. A comprehensive list of different antibody libraries as well as novel approaches for antibody discovery is covered in this book. The chapters in this book can be divided into four sections: the first focuses on the construction of antibody libraries, followed by selection strategies for antibodies, complementary approaches for antibody selection, and finally epitope mapping and biomarker identification. This book provides a comprehensive list of antibody phage display technologies and applications. On a personal note, the ability to carry out intercontinental collaborative efforts was the essence of this book. This book showcases a collection of works from researchers from various countries across the globe. The experience of producing this edition when we were physically located in two different continents, in Europe and Asia, has helped to strengthen our resolve in our quest to contribute further in science. The work on this book has also helped strengthen the relationship and exchange between our laboratories not just on a research level but also more importantly on a personal level. Many new friendships and ideas have been developed over the course of this book that holds well for cross-border collabo- rative initiatives. Although a comprehensive list of topics has been covered in this book, there are still many more chapters that can still be written considering so much activity in all the antibody laboratories in the world. As the antibody business is a multibillion dollar industry, rapid v vi Preface technological developments as well as the emergence of new laboratories are expected. The new kid on the block in this book is the antibody technology program at the Institute for Research in Molecular Medicine (INFORMM), which is the brainchild of the Malaysian Ministry of Higher Education under the Higher Institution Centre of Excellence (HICoE) program together with Universiti Sains Malaysia (USM). It is our aim that this book can provide technical assistance to new start-ups that are venturing into the field of antibody phage display. We also hope this book will help spur interest and ideas in the field while expanding our growing family of enthusiastic antibody researchers. We would like to thank the authors whose contributions to this volume have allowed it to be a comprehensive guide to the processes involved in antibody phage display. We would also like to thank Prof. John M. Walker for his guidance and assistance throughout the editorial process. Our scientific career would not be possible without our great mentors Erhard Rhiel, Thomas Reinard, and Stefan Dubel€ and Zolta`n Konthur and Jo¨rn Glo¨kler. On a personal note, we would like to thank our families Dagmar, Noah Joris, and Lenja Marie and Poi Hong, Hayley, and Hayden for their patience while preparing this book and all our other projects. Braunschweig, Germany Michael Hust Penang, Malaysia Theam Soon Lim Contents Preface . ................................................................... v Contributors................................................................. xi PART ICONSTRUCTION OF ANTIBODY PHAGE DISPLAY LIBRARIES 1 Construction of Human Immune and Naive scFv Libraries . ............... 3 Jonas Kugler,€ Florian Tomszak, Andre´ Frenzel, and Michael Hust 2 Construction of Naive and Immune Human Fab Phage-Display Library ....... 25 Noorsharmimi Omar and Theam Soon Lim 3 Construction of Synthetic Antibody Phage-Display Libraries . ............... 45 Johan Nilvebrant and Sachdev S. Sidhu 4 Modular Construction of Large Non-Immune Human Antibody Phage-Display Libraries from Variable Heavy and Light Chain Gene Cassettes . ............................................. 61 Nam-Kyung Lee, Scott Bidlingmaier, Yang Su, and Bin Liu 5 Construction of Macaque Immune-Libraries . .............................. 83 Arnaud Avril, Sebastian Miethe, Michael Hust, and Thibaut Pelat 6 Construction of Bovine Immunoglobulin Libraries in the Single-Chain Fragment Variable (scFv) Format ............................. 113 Ulrike S. Diesterbeck 7 Construction of Rabbit Immune Antibody Libraries . ....................... 133 Thi Thu Ha Nguyen, Jong Seo Lee, and Hyunbo Shim 8 Generation of Semi-Synthetic Shark IgNAR Single-Domain Antibody Libraries . .................................................... 147 Julius Grzeschik, Doreen Ko¨nning, Steffen C. Hinz, Simon Krah, Christian Schro¨ter, Martin Empting, Harald Kolmar, and Stefan Zielonka 9 Construction of High-Quality Camel Immune Antibody Libraries ............ 169 Ema Roma˜o, Vianney Poignavent, Ce´cile Vincke, Christophe Ritzenthaler, Serge Muyldermans, and Baptiste Monsion 10 Construction of Chicken Antibody Libraries . .............................. 189 Jeanni Fehrsen, Susan Wemmer, and Wouter van Wyngaardt ® 11 Construction and Selection of Affilin Phage Display Libraries ............... 205 Florian Settele, Madlen Zwarg, Sebastian Fiedler, Daniel Koscheinz, and Eva Bosse-Doenecke 12 Construction of a Synthetic Antibody