Dongsheng Duan Jerry R. Mendell Editors Muscle Gene Therapy Second Edition Muscle Gene Therapy Dongsheng Duan • Jerry R. Mendell Editors Muscle Gene Therapy Second Edition Editors Dongsheng Duan Jerry R. Mendell Department of Molecular Microbiology Department of Pediatrics and Immunology Nationwide Children’s Hospital School of Medicine and Research Institute University of Missouri The Ohio State University Columbia, MO, USA Columbus, OH, USA Department of Neurology Department of Neurology School of Medicine Nationwide Children’s Hospital University of Missouri and Research Institute Columbia, MO, USA The Ohio State University Columbus, OH, USA Department of Biomedical Sciences College of Veterinary Medicine University of Missouri Columbia, MO, USA Department of Bioengineering University of Missouri Columbia, MO, USA ISBN 978-3-030-03094-0 ISBN 978-3-030-03095-7 (eBook) https://doi.org/10.1007/978-3-030-03095-7 Library of Congress Control Number: 2019931907 © Springer Nature Switzerland AG 2010, 2019 This work is subject to copyright. 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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. Cover illustration: Top panels (from left to right): (1) AAV1 gene therapy restored α-sarcoglycan expression in a type 2D limb girdle muscular dystrophy patient; (2) Nominal α-sarcoglycan was detected in patient’s muscle before AAV1 gene therapy; (3) AAV9 micro-dystrophin gene therapy improved muscle histology in the dog model of Duchenne muscular dystrophy; (4) Untreated dystrophic dog muscle showed degeneration, necrosis, inflammation and fibrosis. Bottom panel background: Transmission electron microscope image of purified recombinant adeno-associated virus (AAV) particles. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland To patients and their families and friends who have fought fiercely to defeat muscle diseases To investigators who work diligently to develop gene therapy for neuromuscular diseases Preface “It is like watching a car crash in slow motion. Your child is inside the car. You are outside the car and there is nothing you can do about it”— the frustration on the lack of a curative therapy from a mother whose child is suffering from muscular dystrophy. Jen Portnoy, Hope for Javier, April 10, 2017 It is estimated that approximately seven million people are affected by neuromuscu- lar diseases worldwide. Majority affected are children. Almost all neuromuscular diseases are caused by genetic mutations. According to the gene table of neuromus- cular disorders (www.musclegenetable.fr/), among ~900 neuromuscular diseases, nearly 500 disease genes have been identified. Contemporary gene therapy technol- ogy brings in a hope of treating these diseases at their genetic roots by correcting the mutated gene or introducing a normal one to replace the defective gene. The first disease gene for a neuromuscular disease was discovered in 1987 by Louis Kunkel and colleagues. This gene was called the DMD gene because its mutations cause Duchenne muscular dystrophy (DMD), the most common child- hood lethal muscle disease. The DMD gene encodes dystrophin, an essential muscle survival protein. In the absence of dystrophin, muscle undergoes degeneration and necrosis. The discovery of the DMD gene immediately generated euphoria and excitement among patients, their families and friends, researchers, and the general public. Optimism for a DMD cure by gene therapy appeared to be a realistic expec- tation. However, early attempts to transfer the DMD gene did not bring an immedi- ate cure. To review the lessons learned from these early studies, the first edition of Muscle Gene Therapy was published in 2010. This was the first book entirely dedi- cated to muscle gene therapy. At the time of the publication of the first edition, the proof of principle for neuromuscular disease gene therapy had been demonstrated in rodent models, and a few clinical trials had just been initiated to test the safety and feasibility of directly administering a candidate muscle gene therapy vector to human patients. Yet, there was no gene therapy drug approved by a regulatory agency for any inherited disease, not to mention neuromuscular diseases. This situ- ation is changed now. Gene therapy drugs have been marketed, including one gene expression modification therapy (exon skipping) for DMD and gene replacement therapies to treat a rare inherited lipid disease (lipoprotein lipase deficiency), a form vii viii Preface of blindness affecting children and adults (Leber congenital amaurosis). Cell-based gene therapies have also been approved to treat acute lymphoblastic leukemia and non-Hodgkin lymphoma. The field of gene therapy has entered a new phase and begun to produce measurable clinical benefits for some patients, including patients suffering from certain neuromuscular disorders. New approaches have been devel- oped to expand the scope of neuromuscular disease gene therapy from the original gene replacement to gene knockdown, gene expression modulation, gene therapy with noncoding sequences (such as microRNA), gene therapy with disease- modifying genes, and, more recently, with the CRISPR technology-based gene edit- ing. Creative new gene therapy strategies and encouraging animal study results are emerging targeting neuromuscular diseases. Preclinical rodent studies are now being scaled up in large animal models. New vector production and purification technologies are developed to meet the ever-increasing needs for both preclinical and clinical studies. Several promising bodywide therapies are on the horizon and in clinical trials for treating spinal muscular atrophy, X-linked myotubular myopa- thy, and DMD. In view of these advances in translational science, this new edition of Muscle Gene Therapy provides a comprehensive review of recent developments and ongoing progress. In the second edition of Muscle Gene Therapy, we have structured the book into three major sections. Part I provides a review of the foundation for muscle gene therapy; Part II describes the importance of preclinical studies in the development of muscle gene therapy for clinical translation; Part III demonstrates the essence of translation by illustrating examples of progress from preclinical to clinical muscle gene therapy. In Part I of the book, we start with an overview of muscle biology and physiology, then a chapter on the molecular basis of neuromuscular diseases and a chapter on animal models. In subsequent four chapters, stem cells, microRNA, and immunology in muscle disease and gene therapy are discussed. The success of gene therapy hinges on our understanding of the gene delivery vector. Hence, five chap- ters are devoted to this topic. These include one chapter on the design of the muscle gene therapy expression cassette, one chapter on nonviral vectors, one chapter on viral vectors, and two chapters on vectors based on adeno-associated virus (AAV). AAV vectors are currently the most promising gene delivery platform for muscle gene therapy. Strategies that can improve the existing AAV vector system and AAV manufacture methods are essential to bring muscle gene therapy to every patient. Hence, one of the AAV chapters is on the development of the next-generation AAV vectors and the other on large-scale clinical grade AAV production. Outcome mea- sures for testing efficacy of muscle gene therapy are addressed in three chapters, including one devoted to histological and biochemical evaluation of muscle gene therapy, another on biomarkers, and a chapter devoted to the newly developed imag- ing technology called optical polarization tractography. Part I of the book is wrapped up with a chapter dedicated to the use of genome editing to treat neuromuscular diseases. Most chapters in the first edition of Muscle Gene Therapy focus on preclinical development of muscle gene therapy for various neuromuscular diseases. In the second edition, all preclinical animal studies are grouped in Part II. The design and Preface ix implementation of a preclinical muscle gene therapy study are a very important but rarely discussed topics in the literature. As a unique feature of the new edition, we introduce Part II of the book with a chapter on preclinical study considerations. The DMD gene was the first neuromuscular disease gene discovered. Consistently, DMD is also the most studied disease in muscle gene therapy. Seven chapters are devoted to different aspects of DMD gene therapy including gene replacement, exon skipping, genome editing, and gene therapy approaches to treat brain dysfunction in DMD. Two chapters are given to innovative approaches, one for alternative transla- tion initiation and one for sarcolipin knockdown. Remaining chapters in Part II of the book review the latest gene therapy developments for treating other neuromus- cular diseases such as dysferlinopathy, dystroglycanopathies, facioscapulohumeral muscular dystrophy, myotonic dystrophy, myotubular myopathy, mitochondrial myopathy, Charcot-Marie-Tooth inherited neuropathy, and other dominantly inher- ited muscular dystrophies and myopathies. Since sarcolemma weakness/damage is a common feature in many types of muscular dystrophies, we include one chapter to specifically discuss therapies based on muscle cell membrane repair. The last chap- ter of Part II discusses muscle as a target for genetic vaccination. The ultimate goal of muscle gene therapy research is to benefit patients. In the first edition of the book, only a single chapter was devoted to clinical translation consistent with limited numbers of clinical trials largely focused on proof-of- principle studies. Recently, the field has made a quantum leap forward with highly promising clinical data from bodywide systemic AAV therapy in patients with type I spinal muscular atrophy. For the first time in history, a gene therapy has signifi- cantly changed the disease course, reduced symptoms, improved quality of life, and increased survival in a neuromuscular disease. Conditional approval of an exon- skipping therapy drug for DMD by the FDA, though still being hotly debated, marks another important milestone as the first molecular-based genetic modifying therapy approved by a regulatory agency. There is no doubt that many more candidate mus- cle gene therapy drugs will progress from bench to bedside in the upcoming years. In the view of the editors of the second edition of the book, there is a need to bring researchers, trainees, funding agencies, and the patient community up to date on the clinical progress of neuromuscular disease gene therapy. There is also a need to review and reflect on experiences and lessons learned from completed and ongoing trials. With this backdrop, we devote nine chapters in Part III of the book to clinical muscle gene therapy. We start this section of the book with a chapter on patient and family perspective. This is followed with two chapters on clinical trial design. Of particular interest is the discussion on the practical and regulatory issues pivotal to the development of a muscle gene therapy product from the initial hypothesis to early preclinical studies, investigative new drug application, clinical trials, and regu- latory approval. One chapter provides a comprehensive discussion on magnetic resonance imaging (MRI). The noninvasive and quantitative nature of this imaging technology makes it especially appealing for monitoring neuromuscular disease gene therapy. The next three chapters are devoted to clinical gene therapy trials for DMD and limb-girdle muscular dystrophy, with a special focus on gene replacement therapy and exon skipping. These chapters touch on important issues encountered in x Preface human studies such as the immune response and expression levels of the therapeutic protein. This is followed by a chapter on clinical gene therapy trials for the meta- bolic glycogen storage disease type II, commonly referred to as Pompe disease. The final chapter of the book explores muscle-directed gene therapy for treating alpha-1 antitrypsin deficiency. The first edition of the book has a total of 16 chapters. In the second edition, we have a total of 45 chapters. The book is not only expanded greatly in its length but also on its quality and content. We are very grateful to chapter authors for their out- standing contributions. We would like to thank Springer for giving us the opportu- nity to compile this new edition. We would also like to thank Michael Nance for his assistance in the preparation of this book. Special thanks are extended to dedicated basic scientists and clinical researchers, the patient community, and funding agen- cies for taking neuromuscular disease gene therapy from a paper concept to a reality for patients. We would also like to acknowledge the support from the National Institutes of Health; Department of Defense; Parent Project Muscular Dystrophy; Jesse’s Journey, The Foundation for Gene and Cell Therapy; the Jackson Freel DMD Research Fund; the Muscular Dystrophy Association; Hope for Javier; Coalition to Cure Calpain 3; Solid Biosciences; and Sarepta Therapeutics and Avexis, Inc., for funding our neuromuscular gene therapy studies. Columbia, MO, USA Dongsheng Duan Columbus, OH, USA Jerry R. Mendell Disclosures DD is a member of the scientific advisory board for Solid Biosciences and an equity holder of Solid Biosciences. The Duan lab has received research support from Solid Biosciences. JRM serves as a consultant for Sarepta Therapeutics, AveXis, Inc. (Novartis), Myonexus Therapeutics, Exonics Therapeutics, and Milo Biotechnology. He holds no equity in any product that has been licensed from Nationwide Children’s Hospital or is currently in clinical trial. xi