Advanced Textbook on Gene Transfer, Gene Therapy and Genetic Pharmacology

Principles, Delivery and Pharmacological and Biomedical Applications of Nucleotide-Based Therapies

Daniel Scherman

• Publisher: WSPC (EUROPE)
• Year: 2019
• ISBN:
  9781786346896
• Edition: 2
• Topic: Biological Sciences
• Subtopic: Molecular Biology
• Index: Biological Sciences

This unique advanced textbook provides a clear and comprehensive overview of gene delivery, gene therapy and genetic pharmacology, with descriptions of the main gene transfer vectors and a set of selected therapeutic applications, along with safety considerations. The second edition features new groundbreaking material on genome editing using the recently discovered CRISPR/Cas9 system and on cancer immunotherapy by CAR-T cells. It also presents the historical milestone of gene therapy application in the field of severe combined immunodeficiency, and other fields of gene therapy and molecular medicine.

The use of gene transfer is exponentially growing in the scientific and medical communities for day-to-day cell biology experiments and swift development of gene therapy, which is already revolutionizing medicine. In this advanced textbook, more than 30 leading scientists come together to explore these topics.

This educational introduction provides the background material needed to further explore the subject as well as relevant research literature. It is an invaluable resource to Master, PhD or MD students, post-doctoral scientists or medical doctors, as well as any scientist wishing to deliver a gene or synthetic nucleotide or develop a gene therapy strategy. The second edition's simple and synthetic content will be of value to any reader interested in the biological and medical revolution derived from the elucidation of the human genome.

Contents:

• Basic Definitions and Principles:
  • Introduction (Thierry VandenDriessche)
  • Basic Definitions and General Principles (Daniel Scherman)
  • History of Gene Therapy (Serge Braun)
  • Genetic Pharmacology Using Synthetic Deoxyribonucleotides (Jean-Christophe François and Carine Giovannangeli)
  • Principles of RNAi Trigger Expression for Gene Therapy (Lisa J Scherer and John J Rossi)
  • On Demand Alternative Splicing for Gene Rescue (Stéphanie Lorain and Luis Garcia)
  • Nuclease-Mediated Targeted Genetic Correction (Dieter C Gruenert, Hamid Emamekhoo and R Geoffrey Sargent)
  • Genome Engineering and Genome Editing Using CRISPR/Cas9–RNA-Guided Nuclease (Daniel Scherman and Jean-Louis Mandel)
• Vectors and Gene Delivery Techniques:
  • γ-Retrovirus- and Lentivirus-Derived Vectors for Gene Transfer and Therapy (Caroline Duros and Odile Cohen-Haguenauer)
  • Adenovirus Vectors (Stefan Kochanek)
  • Adeno-Associated Virus (AAV) Vectors (Aurélie Ploquin, Hildegard Büning and Anna Salvetti)
  • Herpes Simplex Virus (HSV-1)-Based Vectors: Applications for Gene Transfer, Gene Therapy, Cancer Virotherapy and Vaccination (Matias E Melendez, Aldo Pourchet, Anna Greco and Alberto L Epstein)
  • Non-Viral DNA Vectors (Martin Schleef)
  • Macromolecular Conjugates for Non-Viral Nucleic Acid Delivery (Mark Ericson, Kevin Rice and Guy Zuber)
  • Auto-Associative Lipid-Based Systems for Non-Viral Nucleic Acid Delivery (Virginie Escriou, Nathalie Mignet and Andrew Miller)
  • Hydrodynamic-Pressure-Based Non-Viral Nucleic Acid Delivery (Takeshi Suda, Kenya Kamimura, Guisheng Zhang and Dexi Liu)
  • Electrotransfer/Electroporation for Non-Viral Nucleic Acid Delivery (Pascal Bigey, Richard Heller and Daniel Scherman)
  • Imaging of Gene Delivery (Georges Vassaux, Peggy Richard-Fiardo, Béatrice Cambien and Philippe Franken)
• Therapeutic Applications:
  • Oncolytic Adenoviruses for Cancer Gene Therapy (Gunnel Hallden, Yaohe Wang, Han-Hsi Wong and Nick R Lemoine)
  • Progress in DNA Vaccine Approaches for Cancer Immunotherapy (Geoffrey D Hannigan and David B Weiner)
  • Adoptive Immunotherapy and CAR-T Cells: A Revolutionary Cell/Gene Therapy to Treat Cancer (Daniel Scherman)
  • Gene Therapy for Severe Combined Immunodeficiencies (SCID) (Salima Hacein-Bey-Abina, Alain Fischer and Marina Cavazzana)
  • Gene Therapy of the β-Hemoglobinopathies (Emmanuel Payen, Charlotte Colomb, Olivier Negre, Marina Cavazzana Calvo, Salima Hacein-Bey Abina, Yves Beuzard and Philippe Leboulch)
  • Gene Therapy for Hemophilia A and B (Nisha Nair, Marinee Chuah and Thierry VandenDriessche)
  • Experimental and Clinical Ocular Gene Therapy (Alexis-Pierre Bemelmans and José-Alain Sahel)
  • Gene Therapy of Neurological Diseases (Lisa M Stanek, Lamya S Shihabuddin and Seng H Cheng)
  • Genetic Therapy of Muscle Diseases: Duchenne Muscular Dystrophy (Takis Athanasopoulos, Susan Jarmin, Helen Foster, Keith Foster, Jagjeet Kang, Taeyoung Koo, Alberto Malerba, Linda Popplewell, Daniel Scherman and George Dickson)
  • New Genetic Approaches to Treating Cystic Fibrosis (Stephen L Hart, Amy Walker and Patrick T Harrison)
  • Induced Pluripotent Stem Cells and Gene Targeting for Regenerative Medicine (Jizhong Zou and Linzhao Cheng)
• Gene Vector Production:
  • Production and Purification of Viral Vectors and Safety Considerations Related to Their Use (Otto-Wilhelm Merten, Matthias Schweizer, Parminder Chahal and Amine Kamen)
  • Production and Purification of Plasmid Vectors (Martin Schleef)

Readership: Master, PhD or MD students, post-doctoral scientists or medical doctors, and any scientists using gene transfer techniques or implementing gene therapy strategies.Gene Transfer;Gene Therapy;Gene Delivery;Genetic Pharmacology;Genetic Diseases;Vectors;Nucleotide;Therapy00

PART I

BASIC DEFINITIONS AND PRINCIPLES

1

INTRODUCTION

Thierry VandenDriessche^a

Gene therapy offers unprecedented opportunities to treat or cure disease and alleviate human suffering. It has been more than ten years now since the first clinical successes in gene therapy were first reported for the treatment of severe combined immunodeficiency (SCID-X1). The recurrent opportunistic and life-threatening infections in patients suffering from these types of hereditary diseases are like a sword of Damocles that constantly reminds them of their tragic fate. The majority of the infants that were afflicted by this devastating disease and that were subsequently treated by gene therapy can now essentially lead normal lives. These remarkable and historic achievements formally prove that gene therapy, moving forward, can be a realistic and successful medical intervention. Most importantly, these successes offer new therapeutic options for patients who are currently untreatable.

Convincing evidence continues to emerge that gene therapy is effective in patients suffering from other hereditary diseases besides the congenital immune deficiencies (e.g., hemophilia, epidermolysis bullosa, and β-thalassemia) but also from more common disorders like cancer, neurodegenerative or cardiovascular disorders. Even patients (including children) suffering from an inborn genetic disease that is not life-threatening but causes blindness can finally start to see following gene therapy. These few selected recent examples of clinical advances in gene therapy clearly indicate that the momentum in this field is building up. In the absence of effective drugs or alternative therapies, the advances in gene therapy technology clearly represent the best hope for the many patients and families that are blighted by these various diseases. Given the current global economic challenges it is even more important than ever to find sustainable solutions to treat diseases of high unmet medical need. The potential for a one-time curative treatment by gene therapy should be offset against the high costs of continuous therapeutic interventions for the treatment of chronic diseases. The current demographic trends will only worsen the overall burden on our already overstretched health care system. To reduce the economic burden it is absolutely essential to further consolidate this vision and to take into account the mid- and long-term sustainable benefits of gene therapy relative to the initial investments made.

Despite the advances in gene therapy on the clinical and preclinical fronts, clinical progress has been slower than originally anticipated. As detailed in Chapter 3 dedicated to the history of gene therapy, technical obstacles have been compounded with some safety concerns related primarily to unexpected immune complications or insertional oncogenesis due to integrating vectors. However, significant progress has recently been made to improve the safety profiles and risk:benefit ratios in gene therapy. It is particularly reassuring that the gene therapy vectors used today are much safer and/or efficient than some of the vectors used in the first gene therapy trials. Indeed, some of the recent progress in gene and cell therapy could be ascribed to the continuous improvement in gene transfer technologies.

Whereas the earlier gene therapy trials based on the use of genetically modified hematopoietic stem cells (HSCs) relied on γ-retroviral vectors, subsequent trials involved lentiviral vectors instead. It is truly ironic that the human immunodeficiency virus that devastates the immune system during AIDS progression has now been converted into a relatively safe vector for the potential treatment of hereditary diseases by gene therapy, including congenital immunodeficiencies and even AIDS itself. Virus non semper maleficum est. Some of the most compelling clinical trial data thus far obtained using lentiviral vectors were based on a phase I/II study for adrenoleukodystrophy (ALD) and β-thalassemia. In addition, adeno-associated viral (AAV) vectors have shown promise for many in vivo gene therapy approaches targeting a wide variety of different organs (including liver, heart, skeletal muscle, and brain) and diseases. The emergence of new gene-transfer technologies based on non-viral vectors that rely on chemical and physical gene delivery paradigms also show remarkable progress both in preclinical studies and in clinical trials. For instance, the oligonucleotide-based exon skipping approach for the treatment of Duchenne muscular dystrophy underscores this vision. In addition, the prevailing assumption that non-viral gene delivery could not be used to stably deliver genes into HSCs has recently been challenged through the use emerging transposon-based gene delivery technologies.

Despite the progress in clinical trials and preclinical studies, there is still no gene therapy product on the market that has been approved by the regulatory authorities. Nevertheless, many experts agree that this is likely to happen in the near future. Some of the challenges faced by gene therapists are not unique to the field but are inherent to translational research at the forefront of medical innovation. Though the high hopes for gene therapy in the early 1990s did not immediately translate into clinical success, it is important to recognize that these initial expectations were not realistic, and created the false impression of slow progress.

In many ways, the development of gene therapy mirrors that of therapeutic monoclonal antibodies or clinical bone marrow transplantation. These biomedical and biotechnological innovations took over 25 years to perfect and have now become life-saving therapies for hundreds of thousands of patients suffering from many different diseases, thanks largely to the perseverance and commitments of many academic, medical, and industrial stakeholders. The road to clinical trials and product registration takes 10–15 years in conventional drug development, gene- and cell-therapeutics being no exception. More basic science was required; now that some emerging technologies are becoming real options, the time has come for clinical translation making use of cutting edge technology. It is important to take these realistic timelines into consideration when assessing the overall progress in the field. Sustained funding of both high-quality science and clinical trials is required to guarantee successful clinical developments and the expansion of the pharmaceutical sector, based on genuine innovation and technology transfer securing further phases of clinical development. The continued interactions of gene therapy stakeholders from academia, industry, patient organizations, and regulatory authorities are thereby essential to move this field forward.

While gene therapists continue to perfect the gene delivery vectors from the clinical standpoint of safety and efficacy, several biomedical disciplines are harvesting the fruits of these emerging technologies.

Indeed, gene therapy has fueled the fields of biology and medicine with technologies that allow hypothesis-driven research questions to be addressed. Furthermore, there are also key emerging fields where insights and technologies from the gene therapy community are playing increasingly important roles. In particular, the emerging fields of RNA interference, microRNA and antisense therapies benefit from advances in gene therapy, since safe and efficient delivery of these RNA-based therapeutics is once again the key issue. Furthermore, targeted genomic integration using engineered nucleases not only reduces the risk of insertional oncogenesis associated with random integration but also paves the way towards improved gene targeting and functional genomics approaches in various model systems. Moreover, the recent development of induced pluripotent stem cells (iPS) for regenerative medicine by “genetic reprogramming” is intimately linked to the transfer of genes encoding reprogramming factors into somatic cells and can be considered as a bona fide spin-off of the gene therapy field.

The remarkable progress made in vector development and manufacturing, preclinical studies, and clinical gene therapy trials is highlighted in this excellent monograph. Thanks to the leadership of Professor Daniel Scherman as editor and the valuable contributions of the authors of the various chapters, each of them leaders in their respective disciplines, it adequately captures the state-of-the-art developments in the field of gene therapy. It serves as a testimony to the dedication and perseverance of gene therapists across the globe that made this remarkable progress possible. I have no doubt it will provide a valuable and inspiring resource to foster future developments in this exciting field at the forefront of biomedical innovation.

^aDepartment of Gene Therapy & Regenerative Medicine, Free University of Brussels, Center for Molecular & Vascular Biology, University of Leuven, Belgium
Email: [email protected]

2

BASIC DEFINITIONS AND GENERAL PRINCIPLES

Daniel Scherman^a

2.1Definitions

Genetic pharmacology refers to the use of short synthetic oligonucleotides to manipulate gene expression. This can be principally achieved by the so-called antisense, antigene, or RNA-interfering strategies, which will be discussed in Chapters 4 and 5. Other applications of short nucleotide sequences for mRNA exon skipping or for gene targeting and repair are described in Chapters 6 and 7.

The specificity of genetic pharmacology, as compared to classical “small-chemical drug” pharmacology, is that the short single-strand oligonucleotide pharmacological agent recognizes its cognate target through base pairing. The length of the oligonucleotide sequence necessary to ensure target specificity is around 20 bases. The single-strand oligonucleotide generally binds to another single-strand DNA or mRNA target through Watson–Crick hydrogen bonds, but it can also form a triple helix with DNA duplexes by Hoogsteen base pairing. Except for this mechanism of action based on base-pair recognition, genetic pharmacology cannot be distinguished from the more classical small-drug pharmacology, which is based on receptor–ligand molecular recognition (the “lock and key” concept of Paul Ehrlich).

FIGURE 2.1

While chemical drugs classically target proteins (except in the case of anticancer cytotoxic compounds), small-chemical oligonucleotides used in genetic pharmacology generally target DNA and/or RNA, with the exception of aptamers (Chapter 4). Gene therapy consists of administering a gene-expressing cassette (promoter — gene — polyadenylation signal) to the cells.

Gene therapy more specifically refers to the cell delivery of a gene-expressing cassette, namely a transcribed DNA sequence flanked at its 5′ end by a eukaryotic promoter and at its 3′ end by a polyadenylation signal. This promotes the transcription of an RNA which either by itself displays a therapeutic intracellular effect, or which encodes a missing protein or any protein or peptide allowing a therapeutic or vaccination effect. The distincti...