Precision Medicine, CRISPR, and Genome Engineering: Moving from Association to Biology and Therapeutics PDF
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Advances in Experimental Medicine and Biology 1016 Stephen H. Tsang Editor Precision Medicine, CRISPR, and Genome Engineering Moving from Association to Biology and Therapeutics Advances in Experimental Medicine and Biology Editorial Board: IRUN R. COHEN, The Weizmann Institute of Science, Rehovot, Israel ABEL LAJTHA, N.S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA JOHN D. LAMBRIS, University of Pennsylvania, Philadelphia, PA, USA RODOLFO PAOLETTI, University of Milan, Milan, Italy NIMA REZAEI, Tehran University of Medical Sciences, Tehran, Iran More information about this series at http://www.springer.com/series/5584 Stephen H. Tsang Editor Precision Medicine, CRISPR, and Genome Engineering Moving from Association to Biology and Therapeutics Foreword by George M. Church Editor Stephen H. Tsang Departments of Ophthalmology, Pathology & Cell Biology and Biomedical Engineering Institute of Human Nutrition Columbia Stem Cell Initiative Herbert Irving Comprehensive Cancer Center Graduate Program in Neurobiology & Behavior Columbia University New York, NY, USA Jonas Children’s Vision Care Edward S. Harkness Eye Institute New York-Presbyterian Hospital New York, NY, USA Foreword by George M. Church Department of Genetics Harvard Medical School Boston, MA, USA Wyss Institute for Biologically Inspired Engineering Harvard University Boston, MA, USA ISSN 0065-2598 ISSN 2214-8019 (electronic) Advances in Experimental Medicine and Biology ISBN 978-3-319-63903-1 ISBN 978-3-319-63904-8 (eBook) DOI 10.1007/978-3-319-63904-8 Library of Congress Control Number: 2017954398 © Springer International Publishing AG 2017 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 Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Foreword All of life is encoded in the four letters of DNA, ATGC. Recent advances in genome engineering now enable us to manipulate, customize, and reprogram our genomes, thus empowering us to rewrite our fate. Transplanting genetically altered cells and organs into humans, helping prevent and cure cancers, and reversing aging would once have been miracles and are suddenly now within our reach. This comprehensive new text on genome engineering and the CRISPR revolution comes at a perfect time in the evolution of the field. The growth in new publications, techniques, and discoveries is exponential, and keeping pace with the ever-expanding applications of genome engineering can prove difficult. This book provides a general introduction to the field and to the mechanics of CRISPR, the most recent advance in genome engineering. The text subsequently presents CRISPR’s applications in a variety of model systems, from cells to agricul- ture to animal models. It concludes with a presentation of the future applications and ethical considerations of genome engineering. Suitable for novices and experts alike, this book will serve as a gateway for making original research publications in the field more accessible by providing a broad overview of genome engineering applications in a variety of contexts. We are at a unique time in history where we have the unprecedented ability to play an active role in our own evolution. This book will equip readers with the knowledge to determine in which direction we should take it. H arvard University George M. Church Boston, MA, USA v Contents Part I Introduction to the CRISPR Revolution 1 Viral Vectors, Engineered Cells and the CRISPR Revolution . . . . . . . 3 James E. DiCarlo, Anurag Deeconda, and Stephen H. Tsang 2 Combining Engineered Nucleases with Adeno- associated Viral Vectors for Therapeutic Gene Editing . . . . . . . . . . . . . . . . . . . . . . 29 Benjamin E. Epstein and David V. Schaffer Part II CRISPR in Model Systems 3 From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering . . . . . . . . . . . . . . 45 Rebecca K. Delker and Richard S. Mann 4 A Transgenic Core Facility’s Experience in Genome Editing Revolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Celvie L. Yuan and Yueh-Chiang Hu 5 Genome Editing to Study Ca2+ Homeostasis in Zebrafish Cone Photoreceptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 Susan E. Brockerhoff 6 CRISPR: From Prokaryotic Immune Systems to Plant Genome Editing Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Anindya Bandyopadhyay, Shamik Mazumdar, Xiaojia Yin, and William Paul Quick vii viii Contents Part III The Future of CRISPR 7 Target Discovery for Precision Medicine Using High-Throughput Genome Engineering . . . . . . . . . . . . . . . . . . . . . . . . . 123 Xinyi Guo, Poonam Chitale, and Neville E. Sanjana 8 CRISPR in the Retina: Evaluation of Future Potential . . . . . . . . . . . . 147 Galaxy Y. Cho, Sally Justus, Jesse D. Sengillo, and Stephen H. Tsang 9 The Future of CRISPR Applications in the Lab, the Clinic and Society . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 Soren H. Hough and Ayokunmi Ajetunmobi About the Authors Stephen H. Tsang For years, Stephen H. Tsang has been culturing embryonic stem (ES) cells and created the first mouse model for a recessive form of retinitis pigmentosa by applying homologous recombination to ES cell technology. Two ele- ments define his laboratory. First, by leveraging his genetics clinical practice, in which over 1000 retinal patients are cared for, he brings an array of clinical resources to his research, including stem cells and live imaging data. Second, he and his stu- dents are recognized authorities in a broad array of state-of-the-art technologies. Most recently, he was invited as a Moderator for the Gene Editing/Rewriting the Genome session during the 65th American Society of Human Genetics Annual Meeting. George M. Church, professor at Harvard and MIT, coauthor of 425 papers, 95 patent publications, and the book Regenesis, developed methods used for the first genome sequence (1994) and millionfold cost reductions since (via NGS and nano- pores), plus barcoding, DNA assembly from chips, genome editing, writing, and recoding. He co-initiated the BRAIN Initiative (2011) and Genome Projects (1984, 2005) to provide and interpret the world’s only open-access personal precision med- icine datasets. ix Part I Introduction to the CRISPR Revolution Chapter 1 Viral Vectors, Engineered Cells and the CRISPR Revolution James E. DiCarlo, Anurag Deeconda, and Stephen H. Tsang Abstract Over the past few decades the ability to edit human cells has revolution- ized modern biology and medicine. With advances in genome editing methodolo- gies, gene delivery and cell-based therapeutics targeted at treatment of genetic disease have become a reality that will become more and more essential in clinical practice. Modifying specific mutations in eukaryotic cells using CRISPR-Cas sys- tems derived from prokaryotic immune systems has allowed for precision in cor- recting various disease mutations. Furthermore, delivery of genetic payloads by employing viral tropism has become a crucial and effective mechanism for deliver- ing genes and gene editing systems into cells. Lastly, cells modified ex vivo have tremendous potential and have shown effective in studying and treating a myriad of diseases. This chapter seeks to highlight and review important progress in the realm of the editing of human cells using CRISPR-Cas systems, the use of viruses as vectors for gene therapy, and the application of engineered cells to study and treat disease. Keywords CRISPR/Cas • Ophthalmology • Genome Surgery • Gene Therapy J.E. DiCarlo, Ph.D. (*) • A. Deeconda Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA Department of Pathology and Cell Biology, Institute of Human Nutrition, College of Physicians, Columbia University, New York, NY, USA Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA e-mail: [email protected]; [email protected] S.H. Tsang, M.D., Ph.D. (*) Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA Department of Ophthalmology, Columbia University, New York, NY, USA Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA Department of Pathology and Cell Biology, Columbia University, New York, NY, USA e-mail: [email protected] © Springer International Publishing AG 2017 3 S.H. Tsang (ed.), Precision Medicine, CRISPR, and Genome Engineering, Advances in Experimental Medicine and Biology 1016, DOI 10.1007/978-3-319-63904-8_1
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