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Precision Medicine, CRISPR, and Genome Engineering - Moving from Association to Biology and Therapeutics
Foreword
5
Contents
6
About the Authors
8
Part I: Introduction to the CRISPR Revolution
9
Chapter 1: Viral Vectors, Engineered Cells and the CRISPR Revolution
10
1.1 Introduction
11
1.2 CRISPR-Cas Genome Manipulation
12
1.2.1 A Brief Overview of Genome Modification Using Endonucleases
12
1.2.2 CRISPR-Cas Systems
14
1.2.3 CRISPR Tools in Biology
14
1.3 Gene Therapy Using Viruses
15
1.3.1 Retroviral Vectors
15
1.3.2 Modifications and Implementation of Retroviral Vectors
16
1.3.3 Translational and Clinical Progress Using Retroviral Vectors
17
1.4 Adenoviral Vectors
17
1.4.1 Modifications and Implementation of Adenoviral Vectors
18
1.4.2 Translational and Clinical Progress Using Adenoviral Vectors
19
1.5 Adenoviral-Associated Viral Vectors
20
1.5.1 Modifications and Implementation of Adeno-associated Viral Vectors
21
1.5.2 Translational and Clinical Progress Using Adeno-associated Viral Vectors
22
1.6 Ex Vivo CRISPR Therapies
23
1.6.1 CAR T-Cell Therapy
23
1.6.2 iPSCs
25
1.7 Conclusion
27
References
27
Chapter 2: Combining Engineered Nucleases with Adeno-associated Viral Vectors for Therapeutic Gene Editing
35
2.1 Introduction
36
2.2 Therapeutic Gene Editing
37
2.2.1 AAV
40
2.2.2 Nucleases and AAV for Therapeutic Gene Editing
41
2.2.3 Challenges
42
2.3 Conclusion
45
References
45
Part II: CRISPR in Model Systems
49
Chapter 3: From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering
50
3.1 Introduction and Historical Context
50
3.2 CRISPR Genome Editing in Brief
53
3.3 A Genomics Perspective
54
3.3.1 Gene Network Analysis with CRISPR GE
55
3.3.2 Mapping and Understanding Regulatory DNA Within the Genomic Context with CRISPR GE
57
3.4 An Epigenomics Perspective
60
3.4.1 Manipulating DNA and Histone Modifications with CRISPR GE
61
3.4.2 Tracking 3D Genomic Structure with CRISPR GE
63
3.5 A Cellular Perspective
65
3.5.1 Lineage Tracing with CRISPR GE
66
3.5.2 CRISPR GE and Ex Vivo Organogenesis
69
3.5.3 Final Thoughts
71
References
71
Chapter 4: A Transgenic Core Facility’s Experience in Genome Editing Revolution
80
4.1 Pronuclear Microinjection
81
4.2 ES Cell Injection
82
4.3 Cytoplasmic Microinjection
82
4.4 A New Era of Animal Model Production by the CRISPR/Cas9 Technology
83
4.5 Guide RNA Activity is the Key
84
4.6 Design of the CRISPR/Cas9-Mediated Targeting
85
4.7 Conclusion and Perspectives
91
References
92
Chapter 5: Genome Editing to Study Ca2+ Homeostasis in Zebrafish Cone Photoreceptors
96
5.1 Introduction
96
5.2 Ca2+ Homeostasis in Photoreceptors
97
5.3 Genome Editing in Zebrafish
99
References
102
Chapter 6: CRISPR: From Prokaryotic Immune Systems to Plant Genome Editing Tools
106
6.1 Introduction
107
6.2 What Is CRISPR?
108
6.3 History of CRISPR
110
6.4 Cas9 and Cpf1: The Lead Players in CRISPR-Based Genome Editing
111
6.5 Modification of the CRISPR System in Plants
114
6.6 Application of CRISPR in Plants
116
6.6.1 Model Plants
116
6.6.2 Application in Crop Plants
119
6.6.3 Off-Target Effects
120
6.7 Future Prospects of Genome Editing in Plants
120
References
122
Part III: The Future of CRISPR
126
Chapter 7: Target Discovery for Precision Medicine Using High-Throughput Genome Engineering
127
7.1 Introduction
127
7.2 Technologies for CRISPR Screens
128
7.2.1 From Gene Editing to Pooled Screens
128
7.2.2 Types of CRISPR Screens
135
7.3 CRISPR Screen Applications: Genetic Mechanisms of Human Disease and Therapeutic Development
137
7.3.1 CRISPR Screens in Cancer for Synthetic Lethality and Drug Resistance
137
7.3.1.1 Identifying Cancer-Specific Vulnerabilities
137
7.3.1.2 Understanding Mechanisms of Drug Resistance
138
7.3.1.3 Examining Noncoding Regulators of Cancer Gene Expression
139
7.3.2 CRISPR Screens in Infectious Disease
140
7.3.3 CRISPR Screens for Understanding and Treating Inborn Genetic Disorders
141
7.4 Conclusion and Future Perspectives
143
References
143
Chapter 8: CRISPR in the Retina: Evaluation of Future Potential
150
8.1 Introduction: CRISPR and the Retina
151
8.2 “Is There Anything You Can Do for Me?”
152
8.3 Research Highlights
153
8.3.1 Limitations and Imprecision Medicine
153
8.3.2 Future Strategies
154
References
155
Chapter 9: The Future of CRISPR Applications in the Lab, the Clinic and Society
159
9.1 The Scientific Community Debates Somatic and Germline Genome Modification
161
9.2 The Somatic-Germ Line Barrier
163
9.3 A New Paradigm for Genomic Medicine
166
9.4 Converging Technologies to Democratize CRISPR
166
9.5 The Impact of CRISPR on Human Biodiversity
168
9.6 Editing the Ecosystem
170
9.7 CRISPR Calls for a Conversation
171
References
174
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