Advanced Delivery and Therapeutic Applications of RNAi
1. Edition May 2013
534 Pages, Hardcover
Wiley & Sons Ltd
Short Description
Commonly used by researchers to develop technologies for modifying and studying genetic process, RNA interference (RNAi) has many potential uses in medicine, biotechnology, and functional genomics. This book covers all essential aspects involved in the development of RNAi therapeutics, providing detailed guidance on the challenges and opportunities of bringing RNAi technologies from bench to clinic. It explores the design and mechanism of RNAi molecules, delivery strategies, and therapeutic applications in various diseases. Preclinical, regulatory, market, and intellectual aspects of RNAi technologies are also covered.
ISBN:
978-1-119-97686-8
John Wiley & Sons
RNA interference (RNAi) is a process in living cells whereby small double stranded RNA interferes with the expression of specific genes with complementary nucleotide sequence. Like many nucleic acid-based therapies, RNAi has great potential in treating various life-threatening diseases. However, the poor stability and cellular uptake of RNAi molecules remain considerable barriers to their efficient delivery which is paramount to a successful therapy. This book provides a comprehensive introduction to RNAi delivery, then goes on to discuss different delivery strategies, and concludes with current applications in various diseases. It covers:
* Mechanisms, Barriers, and Analysis of RNAi Delivery
* Nonclinical Safety Assessments and Clinical Pharmacokinetics: A Regulatory Perspective
* Bioconjugation of siRNA for Site Specifi c Delivery
* Nanoscale Delivery Systems for RNAi
* Environmentally-Responsive Delivery Systems for RNAi
* Light-sensitive RNAi
* Viral-Mediated Delivery of shRNA and miRNA
* RNAi applications in Cancer Therapy, Liver Diseases, Hepatitis B, and Ocular Disease
* miRNA as therapeutic agents and targets
Advanced Delivery and Therapeutic Applications of RNAi combines the essential aspects of developing RNAi therapeutics from bench to clinic, and is invaluable for researchers working on RNAi, drug discovery and delivery, biomedical engineering, biomaterials, molecular biology, and biotechnology.
Preface xvii
Contributors xix
About the Editors xxiii
Part 1 Introduction and Basics of RNAi 1
1 Mechanisms and Barriers to RNAi Delivery 3
Jiehua Zhou and John J. Rossi
1.1 Introduction 3
1.2 Barriers to Systemic RNAi Delivery 5
1.3 Rational Design to Improve RNAi Efficacy 6
1.4 Chemical Modifications to Enhance siRNA Stability and Reduce Immune Response 7
1.5 Cellular Uptake and Intracellular Release of siRNA 7
1.6 Combinatorial Targeting for Targeted RNAi Delivery 8
1.7 Cell-Specific Aptamer-Functionalized Nanocarriers for RNAi Delivery 9
1.8 The Clinical Development and Challenges of siRNAs Therapeutics 10
1.9 Conclusion and Perspectives 12
References 12
2 Analysis of siRNA Delivery Using Various Methodologies 19
Yi Pei
2.1 Introduction 19
2.2 Checkpoints for Analyzing siRNA Delivery 20
2.2.1 Circulation Checkpoint 22
2.2.2 Organ or Tissue Checkpoint 22
2.2.3 Cellular Checkpoint 22
2.2.4 RISC Checkpoint 23
2.2.5 Target mRNA Knockdown (Indirect Checkpoint) 24
2.2.6 Protein and Outcome (Indirect Checkpoint) 25
2.2.7 Safety (Indirect Checkpoint) 26
2.3 Methods for Analysis of siRNA 26
2.3.1 General Considerations 26
2.3.2 Hybridization-Based (Non-Imaging) Methods 28
2.3.3 Non-Hybridization-Based (Non-Imaging) Methods 34
2.3.4 Imaging-Based (Non-Hybridization) Methods 35
2.3.5 Imaging-Based (Hybridization) Methods 37
2.4 Case Study for siRNA Delivery Analysis 38
References 39
3 Challenges and Opportunities in Bringing RNAi Technologies from Bench to Bed 45
Sandesh Subramanya and Lance Ford
3.1 Introduction 45
3.2 RNAi Mediator (siRNA or shRNA) 45
3.2.1 siRNA 45
3.2.2 Vector-derived shRNA 47
3.2.3 miRNAs 49
3.3 Safety Issues of RNAi Mediators 50
3.3.1 Immune Stimulation 50
3.3.2 RNAi Over expression 52
3.4 Efficacy of RNAi Mediators 52
3.4.1 Therapeutic Response 52
3.5 RNAi Mediators in Clinical Trials 53
3.6 Conclusion 54
References 55
Nonclinical Safety Assessments and Clinical Pharmacokinetics for Oligonucleotide Therapeutics: A Regulatory Perspective 63
Shwu-Luan Lee, Paul Brown, Jian Wang and Robert T. Dorsam
4.1 Introduction 63
4.2 Unique Properties of Oligonucleotide-based Therapeutics 63
4.3 Regulation of Oligonucleotide-Based Therapeutics 65
4.3.1 Submission to the FDA 65
4.3.2 Review Process for Non-clinical Studies 67
4.3.3 Regulatory Issues 74
4.3.4 Clinical Pharmacokinetics 76
4.4 Conclusion 79
Disclaimer 79
Appendix 79
References 80
Role of Promoters and MicroRNA Backbone for Efficient Gene Silencing 83
Feng Li and Ram I. Mahato
5.1 Introduction 83
5.2 Promoters for shRNA Expression 84
5.2.1 Constitutive Promoters 84
5.2.2 Inducible Promoters 87
5.2.3 Site Specific Promoters 93
5.3 miRNA-based shRNAs 96
5.3.1 miRNA-based shRNA Enhances Gene Silencing 96
5.3.2 miRNA-based shRNA Reduces Toxicities 97
5.3.3 Application of miRNA-based shRNA for Combination Gene Therapy 98
5.4 Concluding Remarks 100 References 101
Part 2 RNAi Delivery Strategies 109
6 Bioconjugation of siRNA for Site-specific Delivery 111
Bin Qin, Wei Jin and Kun Cheng
6.1 Introduction 111
6.2 Conjugation Strategy 112
6.2.1 RNA Chemical Modification 112
6.2.2 Site of Conjugation 114
6.2.3 Conjugation Chemistry 115
6.3 Bioconjugates for Site-specific Delivery 120
6.3.1 Antibody-siRNA Bioconjugates 120
6.3.2 Aptamer-siRNA Bioconjugates 122
6.3.3 Peptide-siRNA Bioconjugates 124
6.3.4 Lipid-siRNA Bioconjugates 126
6.3.5 Others 128
6.4 Conclusion 129
References 129
7 Multifunctional RNAi Delivery Systems 137
China Malakondaiah Kummitha, Anthony S. Malamas and Zheng-Rong Lu
7.1 Introduction 137 7.1.1 Chapter Objectives 139
7.2 Lipid-Based Delivery Systems 139
7.2.1 Cationic Lipids 139
7.2.2 Ionizable Cationic Lipids 140
7.2.3 Lipid-Like Materials 140
7.2.4 pH-sensitive Surfactants as Multifunctional siRNA Carriers 142
7.3 Polymeric Multifunctional siRNA Delivery Systems 150
7.3.1 Polyethylenimine 150
7.3.2 Chitosan 151
7.3.3 Cyclodextrins 152
7.3.4 Dendrimers 152
7.3.5 Polyalkylacrylic Acid-based pH-sensitive Polymers 153
7.3.6 Other pH-sensitive Polymers 156
7.4 Conclusion 157
References 157
8 Dendrimers in RNAi Delivery 163
Jose Luis Jimenez Fuentes, Paula Ortega, Sara Ferrando-Mart?nez, Rafael Gomez, Manuel Leal, Javier de la Mata and MaAngeles Munoz-Fernandez
8.1 Introduction 163
8.2 Challenges in RNAi Delivery 164
8.3 Dendrimers as Non Viral Vectors 166
8.3.1 Dendritic Architectures 166
8.3.2 Synthesis of Dendrimers 168
8.3.3 Types of Dendrimers in Drug Delivery 169
9 Development of Pharmaceutically Adapted Mesoporous Silica Nanoparticles for siRNA Delivery 187
Wilson X. Mai, Tian Xia and Huan Meng
9.1 Introduction 187
9.2 Mesoporous Silica Nanoparticles as Novel Inorganic Nanocarriers for siRNA Delivery 188
9.2.1 Discovery and Synthesis 188
9.2.2 Surface Modification of MSNP for Nucleic Acid Delivery 190
9.2.3 MSNP for Dual siRNA and Drug Delivery 191
9.2.4 Improving in vivo Implementation of MSNP-Based Delivery Platform 196
9.2.5 Design of Pharmaceutically Adapted MSNP via the Knowledge Generated by Discoveries at the Nano/Bio Interface 197
9.3 Safety Assessment of Nanocarrier and Design of Safe MSNP Carrier 199
9.3.1 Safety of Nanocarriers 199
9.3.2 Safe Design of MSNP Carrier 201
References 179
9.4 Summary References 202
10 Environmentally-Responsive Nanogels for siRNA Delivery 207
Atsushi Tamura and Yukio Nagasaki
10.1 Introduction 207
10.1.1 siRNA Delivery System 207
10.1.2 Crosslinked Nanogels for siRNA Delivery 208
10.2 Reductive Environment-Responsive Disulfide Crosslinked Nanogels 209
10.3 Temperature-Responsive Nanogels 211
10.4 pH-Responsive Nanogels 212
10.4.1 Acid-degradable Nanogels for Intracellular Release of siRNA 212
10.4.2 Design of pH-Responsive PEGylated Nanogels with Endosomal Escape Ability 212
10.4.3 Cytoplasmic Delivery of PEGylated Nanogel/siRNA Complexes 214
10.5 PEGylated and Partially Quaternized Polyamine Nanogels 216
10.5.1 Design of Quaternized Polyamine Nanogels 216
10.5.2 Enhanced Cellular Uptake of siRNA by Quaternized Polyamine Nanogels 216
10.5.3 Enhanced Gene-Silencing Activity of Quaternized Polyamine Nanogel/siRNA Complexes 219
10.6 Conclusions 220
References 220
11 Viral-Mediated Delivery of shRNA and miRNA 225
Fredric P. Manfredsson
11.1 Introduction 225
11.2 RNAi - A Brief Overview 226
11.3 shRNA or miRNA? 226
11.4 Rational Design 227
11.5 Viral Vectors 227
11.5.1 Recombinant Adeno-associated Virus (rAAV) 229
11.5.2 Retrovirus (RV) 230
11.5.3 Lentivirus (LV) 230
11.5.4 Adenovirus (AD) 231
11.5.5 Herpes Simplex Virus (HSV) 231
11.5.6 Baculovirus (BV) 232
11.5.7 Poxvirus 232
11.6 Tissue-specific Transduction 233
11.6.1 CNS 233
11.6.2 Ocular 234
11.6.3 Respiratory System 235
11.6.4 Liver 236
11.6.5 Skeletal Muscle 237
11.6.6 Heart 237
11.6.7 Systemic 238
11.6.8 Ex Vivo 238
11.6.9 Cell Culture 238
11.6.10 Transcription Cassettes 239
11.7 Applications of Virally Expressed shRNAs 241
11.7.1 Virally Mediated "Knockouts" 241
11.7.2 Concomitant Expression of Therapeutic Genes 241
11.8 Viral Gene Therapy in the Clinic 241
11.9 Conclusion 242
References 242
12 The Control of RNA Interference with Light 255
Simon H. Friedman
12.1 Introduction 255 12.2 The Importance of Gene Expression 255
12.3 Light Control of Gene Expression 257
12.4 Why Use RNA Interference as a Basis for Light Control of Gene Expression? 258
12.5 Light Activated RNA Interference (LARI), the work of Friedman and Co-Workers 259
12.6 Work of McMaster and Co-Workers, 50 Antisense Phosphate Block 262
12.7 Work of Heckel and Co-Workers, Nucleobase Block 263
12.8 Use of 20 FsiRNA, work of Monroe and Co-Workers 264
12.9 Photochemical Internalization 265
12.10 Future Directions and Conclusions 266
Acknowledgments 267
References 267
Part 3 Applications of RNAi in Various Diseases 269
13 RNAi in Cancer Therapy 271
Cristian Rodriguez-Aguayo, Arturo Chavez-Reyes, Gabriel Lopez-Berestein and Anil K. Sood
13.1 Introduction 271
13.2 Therapeutic Opportunities for Noncoding RNAs 274
13.3 RNAs as Drugs 277
13.4 Overcoming Anatomical and Physiologic Barriers 278
13.4.1 Intravascular Degradation 279
13.4.2 Tissue and Intracellular Delivery 280
13.4.3 Immune-mediated Toxic Effects 281
13.4.4 Nanocarrier-mediated Toxic Effects 282
13.5 Advanced Delivery 283
13.5.1 Localized siRNA Delivery 285
13.5.2 Systemic siRNA Delivery 288
13.5.3 Targeted siRNA Delivery 291
13.5.4 Monitoring Delivery and Therapeutic Response 293
13.6 Clinical Experience 294
13.7 The Next Steps 298
Acknowledgments 298
References 298
14 Adenovirus-mediated siRNA Delivery to Cancer 309
Chae-Ok Yun
14.1 Introduction 309
14.1.1 shRNA-expressing Vectors 310
14.1.2 Adenovirus Vectors 311
14.2 shRNA-expressing Adenoviruses: Cancer Biological Studies and Therapeutic Implications 312
14.2.1 Oncogene-targeted shRNA-expressing Ads 312
14.2.2 shRNA-expressing Adenoviruses that Target Anti-apoptotic Genes 314
14.3 Exploiting Oncolytic Adenovirus for siRNA Expression 315
14.4 Current Limitations of Adenovirus-mediated siRNA Therapy and Future Directions: Smart Adenovirus Nanocomplexes Expressing siRNA for Systemic Administration 318
14.5 Conclusion 320
References 321
15 RNAi in Liver Diseases 327
Jiang Li, Jianqin Lu, Yifei Zhang, Mohammed Ghazwani, Peng Zhang, Xiang Gao and Song Li
15.1 Introduction 327
15.2 RNAi in Viral Hepatitis 327
15.2.1 Hepatitis B 328
15.2.2 RNAi of HBV Infection via siRNA/shRNA 329
15.2.3 RNAi of HBV Infection via miRNAs 330
15.2.4 Hepatitis C 332
15.2.5 RNAi of HCV Infection via siRNA/shRNA 333
15.2.6 RNAi of HCV Infection via miRNAs 335
15.3 RNAi in Hepatocellular Carcinoma 336
15.3.1 RNAi of HCC via siRNA/shRNA 337
15.3.2 RNAi of HCC via miRNAs 338
15.4 RNAi in Liver Fibrosis 340
15.4.1 RNAi of Liver Fibrosis via siRNA/shRNA 341
15.4.2 RNAi of Liver Fibrosis via miRNAs 343
15.5 Delivery Systems in RNAi 345
15.5.1 Liver Anatomy 346
15.5.2 Viral Delivery Systems 346
15.5.3 Non-Viral Delivery Systems 347
15.5.4 Cell-specific Targeting Strategies 348
15.5.5 Cellular Events after the Uptake of Nucleic Acid-Carrier Complexes 349
15.5.6 Lipid-based Delivery Systems 350
15.5.7 Polymer-Based Systems 350
15.5.8 Calcium Phosphate-Lipid Hybrid System 351
15.5.9 Hydrophobitized Nucleic Acid Derivatives 351
15.5.10 Targeted Delivery to Tumor Blood Vessels 351
15.6 Conclusion 352
Acknowledgments 353
References 353
16 Approaches to Delivering RNAi Therapeutics that Target Hepatitis B Virus 367
Carol Crowther, Mohube Betty Mowa, Abdullah Ely and Patrick Arbuthnot
16.1 Introduction 367
16.1.1 RNAi Therapeutics 368
16.1.2 Hepatitis B Virus as a Target for RNAi-based Gene Silencing 369
16.2 Vectors Suitable for Hepatic Delivery of HBV Gene Silencers 369
16.2.1 Viral Vectors 370
16.2.2 Nonviral Vectors 377
16.3 Conclusions 381
Acknowledgments 382
References 382
17 RNAi in Respiratory Diseases 391
Ciara Kelly, Awadh B. Yadav, Paul J. McKiernan, Catherine M. Greene and Sally-Ann Cryan
17.1 Introduction 391
17.2 Respiratory Disease and RNA Interference 392
17.2.1 RNAi in Lung Cancer 393
17.2.2 RNAi to Treat Respiratory Infections 393
17.2.3 RNAi in Inflammatory Lung Disease 394
17.3 Delivery and Development of RNAi Therapies for Respiratory Disease 397
17.3.1 Inhalation of RNA-medicines 397
17.3.2 Chemical Modifications of siRNA 399
17.3.3 RNAi Vectors 400
17.3.4 RNAi Therapy In Vivo 405
17.4 Conclusions 408
Acknowledgements 408 References 408
18 RNAi in Ocular Diseases 417
Andrey Turchinovich, Georg Zoidl and Rolf Dermietzel
18.1 Introduction 417
18.2 The Principle of RNAi 418
18.3 In vivo Delivery of siRNA 419
18.4 Delivery of siRNA into the Eye 420
18.4.1 Routes for Ocular Delivery of siRNA 420
18.4.2 Delivery of Naked siRNA 421
18.4.3 Delivery of siRNA Using Carriers 425
18.4.4 Viral Delivery of shRNA 429
18.5 Conclusions 431
Abbreviations 432
References 432
19 micro RNAs as Therapeutic Agents and Targets 439
D.S. Karolina and K. Jeyaseelan
19.1 Introduction 439
19.2 miRNA Therapeutics 440
19.2.1 Therapeutic miRNA Inhibition 443
19.2.2 Therapeutic miRNA Mimicry 446
19.3 MicroRNAs and Cancer 447
19.4 MicroRNAs in Stroke 450
19.5 MicroRNAs in Heart Diseases 452
19.6 MicroRNAs in Diabetes Mellitus 454
19.7 MicroRNAs in Liver Diseases 457
19.8 MicroRNAs and Ocular Diseases 461
19.9 MicroRNAs and Respiratory Diseases 462
19.10 MicroRNAs and Stem Cell Research 465
19.11 Conclusion 468
References 469
20 Delivery of Micro RNA Sponges for Interrogation of MicroRNA Function In Vitro and In Vivo 483
Jiakai Lin and Shu Wang
20.1 MicroRNA Loss-of-Function Studies 483
20.2 Considerations in MicroRNA Sponge Design 486
20.2.1 Vector 486
20.2.2 Promoter 487
20.2.3 Reporter Gene 488
20.2.4 MicroRNA Binding Sites 488
20.3 Advantages and Limitations of MicroRNA Sponge over Other MicroRNA Loss-of-Function Strategies 489
20.4 Interrogating MicroRNA Function via Transient MicroRNA Sponge Expression 493
20.5 Interrogating MicroRNA Function via Stable MicroRNA Sponge Expression 494
20.5.1 MicroRNA and Cell Differentiation 494
20.5.2 MicroRNAs in Disease Development 495
20.6 Utility of MicroRNA Sponge in Living Organisms 496
20.6.1 MicroRNA Knockdown in Plants 496
20.6.2 MicroRNA Knockdown in Mouse 497
20.6.3 MicroRNA Knockdown in Drosophila Melanogaster 498
20.7 Future Perspectives 498
References 499
Index 505
Contributors xix
About the Editors xxiii
Part 1 Introduction and Basics of RNAi 1
1 Mechanisms and Barriers to RNAi Delivery 3
Jiehua Zhou and John J. Rossi
1.1 Introduction 3
1.2 Barriers to Systemic RNAi Delivery 5
1.3 Rational Design to Improve RNAi Efficacy 6
1.4 Chemical Modifications to Enhance siRNA Stability and Reduce Immune Response 7
1.5 Cellular Uptake and Intracellular Release of siRNA 7
1.6 Combinatorial Targeting for Targeted RNAi Delivery 8
1.7 Cell-Specific Aptamer-Functionalized Nanocarriers for RNAi Delivery 9
1.8 The Clinical Development and Challenges of siRNAs Therapeutics 10
1.9 Conclusion and Perspectives 12
References 12
2 Analysis of siRNA Delivery Using Various Methodologies 19
Yi Pei
2.1 Introduction 19
2.2 Checkpoints for Analyzing siRNA Delivery 20
2.2.1 Circulation Checkpoint 22
2.2.2 Organ or Tissue Checkpoint 22
2.2.3 Cellular Checkpoint 22
2.2.4 RISC Checkpoint 23
2.2.5 Target mRNA Knockdown (Indirect Checkpoint) 24
2.2.6 Protein and Outcome (Indirect Checkpoint) 25
2.2.7 Safety (Indirect Checkpoint) 26
2.3 Methods for Analysis of siRNA 26
2.3.1 General Considerations 26
2.3.2 Hybridization-Based (Non-Imaging) Methods 28
2.3.3 Non-Hybridization-Based (Non-Imaging) Methods 34
2.3.4 Imaging-Based (Non-Hybridization) Methods 35
2.3.5 Imaging-Based (Hybridization) Methods 37
2.4 Case Study for siRNA Delivery Analysis 38
References 39
3 Challenges and Opportunities in Bringing RNAi Technologies from Bench to Bed 45
Sandesh Subramanya and Lance Ford
3.1 Introduction 45
3.2 RNAi Mediator (siRNA or shRNA) 45
3.2.1 siRNA 45
3.2.2 Vector-derived shRNA 47
3.2.3 miRNAs 49
3.3 Safety Issues of RNAi Mediators 50
3.3.1 Immune Stimulation 50
3.3.2 RNAi Over expression 52
3.4 Efficacy of RNAi Mediators 52
3.4.1 Therapeutic Response 52
3.5 RNAi Mediators in Clinical Trials 53
3.6 Conclusion 54
References 55
Nonclinical Safety Assessments and Clinical Pharmacokinetics for Oligonucleotide Therapeutics: A Regulatory Perspective 63
Shwu-Luan Lee, Paul Brown, Jian Wang and Robert T. Dorsam
4.1 Introduction 63
4.2 Unique Properties of Oligonucleotide-based Therapeutics 63
4.3 Regulation of Oligonucleotide-Based Therapeutics 65
4.3.1 Submission to the FDA 65
4.3.2 Review Process for Non-clinical Studies 67
4.3.3 Regulatory Issues 74
4.3.4 Clinical Pharmacokinetics 76
4.4 Conclusion 79
Disclaimer 79
Appendix 79
References 80
Role of Promoters and MicroRNA Backbone for Efficient Gene Silencing 83
Feng Li and Ram I. Mahato
5.1 Introduction 83
5.2 Promoters for shRNA Expression 84
5.2.1 Constitutive Promoters 84
5.2.2 Inducible Promoters 87
5.2.3 Site Specific Promoters 93
5.3 miRNA-based shRNAs 96
5.3.1 miRNA-based shRNA Enhances Gene Silencing 96
5.3.2 miRNA-based shRNA Reduces Toxicities 97
5.3.3 Application of miRNA-based shRNA for Combination Gene Therapy 98
5.4 Concluding Remarks 100 References 101
Part 2 RNAi Delivery Strategies 109
6 Bioconjugation of siRNA for Site-specific Delivery 111
Bin Qin, Wei Jin and Kun Cheng
6.1 Introduction 111
6.2 Conjugation Strategy 112
6.2.1 RNA Chemical Modification 112
6.2.2 Site of Conjugation 114
6.2.3 Conjugation Chemistry 115
6.3 Bioconjugates for Site-specific Delivery 120
6.3.1 Antibody-siRNA Bioconjugates 120
6.3.2 Aptamer-siRNA Bioconjugates 122
6.3.3 Peptide-siRNA Bioconjugates 124
6.3.4 Lipid-siRNA Bioconjugates 126
6.3.5 Others 128
6.4 Conclusion 129
References 129
7 Multifunctional RNAi Delivery Systems 137
China Malakondaiah Kummitha, Anthony S. Malamas and Zheng-Rong Lu
7.1 Introduction 137 7.1.1 Chapter Objectives 139
7.2 Lipid-Based Delivery Systems 139
7.2.1 Cationic Lipids 139
7.2.2 Ionizable Cationic Lipids 140
7.2.3 Lipid-Like Materials 140
7.2.4 pH-sensitive Surfactants as Multifunctional siRNA Carriers 142
7.3 Polymeric Multifunctional siRNA Delivery Systems 150
7.3.1 Polyethylenimine 150
7.3.2 Chitosan 151
7.3.3 Cyclodextrins 152
7.3.4 Dendrimers 152
7.3.5 Polyalkylacrylic Acid-based pH-sensitive Polymers 153
7.3.6 Other pH-sensitive Polymers 156
7.4 Conclusion 157
References 157
8 Dendrimers in RNAi Delivery 163
Jose Luis Jimenez Fuentes, Paula Ortega, Sara Ferrando-Mart?nez, Rafael Gomez, Manuel Leal, Javier de la Mata and MaAngeles Munoz-Fernandez
8.1 Introduction 163
8.2 Challenges in RNAi Delivery 164
8.3 Dendrimers as Non Viral Vectors 166
8.3.1 Dendritic Architectures 166
8.3.2 Synthesis of Dendrimers 168
8.3.3 Types of Dendrimers in Drug Delivery 169
9 Development of Pharmaceutically Adapted Mesoporous Silica Nanoparticles for siRNA Delivery 187
Wilson X. Mai, Tian Xia and Huan Meng
9.1 Introduction 187
9.2 Mesoporous Silica Nanoparticles as Novel Inorganic Nanocarriers for siRNA Delivery 188
9.2.1 Discovery and Synthesis 188
9.2.2 Surface Modification of MSNP for Nucleic Acid Delivery 190
9.2.3 MSNP for Dual siRNA and Drug Delivery 191
9.2.4 Improving in vivo Implementation of MSNP-Based Delivery Platform 196
9.2.5 Design of Pharmaceutically Adapted MSNP via the Knowledge Generated by Discoveries at the Nano/Bio Interface 197
9.3 Safety Assessment of Nanocarrier and Design of Safe MSNP Carrier 199
9.3.1 Safety of Nanocarriers 199
9.3.2 Safe Design of MSNP Carrier 201
References 179
9.4 Summary References 202
10 Environmentally-Responsive Nanogels for siRNA Delivery 207
Atsushi Tamura and Yukio Nagasaki
10.1 Introduction 207
10.1.1 siRNA Delivery System 207
10.1.2 Crosslinked Nanogels for siRNA Delivery 208
10.2 Reductive Environment-Responsive Disulfide Crosslinked Nanogels 209
10.3 Temperature-Responsive Nanogels 211
10.4 pH-Responsive Nanogels 212
10.4.1 Acid-degradable Nanogels for Intracellular Release of siRNA 212
10.4.2 Design of pH-Responsive PEGylated Nanogels with Endosomal Escape Ability 212
10.4.3 Cytoplasmic Delivery of PEGylated Nanogel/siRNA Complexes 214
10.5 PEGylated and Partially Quaternized Polyamine Nanogels 216
10.5.1 Design of Quaternized Polyamine Nanogels 216
10.5.2 Enhanced Cellular Uptake of siRNA by Quaternized Polyamine Nanogels 216
10.5.3 Enhanced Gene-Silencing Activity of Quaternized Polyamine Nanogel/siRNA Complexes 219
10.6 Conclusions 220
References 220
11 Viral-Mediated Delivery of shRNA and miRNA 225
Fredric P. Manfredsson
11.1 Introduction 225
11.2 RNAi - A Brief Overview 226
11.3 shRNA or miRNA? 226
11.4 Rational Design 227
11.5 Viral Vectors 227
11.5.1 Recombinant Adeno-associated Virus (rAAV) 229
11.5.2 Retrovirus (RV) 230
11.5.3 Lentivirus (LV) 230
11.5.4 Adenovirus (AD) 231
11.5.5 Herpes Simplex Virus (HSV) 231
11.5.6 Baculovirus (BV) 232
11.5.7 Poxvirus 232
11.6 Tissue-specific Transduction 233
11.6.1 CNS 233
11.6.2 Ocular 234
11.6.3 Respiratory System 235
11.6.4 Liver 236
11.6.5 Skeletal Muscle 237
11.6.6 Heart 237
11.6.7 Systemic 238
11.6.8 Ex Vivo 238
11.6.9 Cell Culture 238
11.6.10 Transcription Cassettes 239
11.7 Applications of Virally Expressed shRNAs 241
11.7.1 Virally Mediated "Knockouts" 241
11.7.2 Concomitant Expression of Therapeutic Genes 241
11.8 Viral Gene Therapy in the Clinic 241
11.9 Conclusion 242
References 242
12 The Control of RNA Interference with Light 255
Simon H. Friedman
12.1 Introduction 255 12.2 The Importance of Gene Expression 255
12.3 Light Control of Gene Expression 257
12.4 Why Use RNA Interference as a Basis for Light Control of Gene Expression? 258
12.5 Light Activated RNA Interference (LARI), the work of Friedman and Co-Workers 259
12.6 Work of McMaster and Co-Workers, 50 Antisense Phosphate Block 262
12.7 Work of Heckel and Co-Workers, Nucleobase Block 263
12.8 Use of 20 FsiRNA, work of Monroe and Co-Workers 264
12.9 Photochemical Internalization 265
12.10 Future Directions and Conclusions 266
Acknowledgments 267
References 267
Part 3 Applications of RNAi in Various Diseases 269
13 RNAi in Cancer Therapy 271
Cristian Rodriguez-Aguayo, Arturo Chavez-Reyes, Gabriel Lopez-Berestein and Anil K. Sood
13.1 Introduction 271
13.2 Therapeutic Opportunities for Noncoding RNAs 274
13.3 RNAs as Drugs 277
13.4 Overcoming Anatomical and Physiologic Barriers 278
13.4.1 Intravascular Degradation 279
13.4.2 Tissue and Intracellular Delivery 280
13.4.3 Immune-mediated Toxic Effects 281
13.4.4 Nanocarrier-mediated Toxic Effects 282
13.5 Advanced Delivery 283
13.5.1 Localized siRNA Delivery 285
13.5.2 Systemic siRNA Delivery 288
13.5.3 Targeted siRNA Delivery 291
13.5.4 Monitoring Delivery and Therapeutic Response 293
13.6 Clinical Experience 294
13.7 The Next Steps 298
Acknowledgments 298
References 298
14 Adenovirus-mediated siRNA Delivery to Cancer 309
Chae-Ok Yun
14.1 Introduction 309
14.1.1 shRNA-expressing Vectors 310
14.1.2 Adenovirus Vectors 311
14.2 shRNA-expressing Adenoviruses: Cancer Biological Studies and Therapeutic Implications 312
14.2.1 Oncogene-targeted shRNA-expressing Ads 312
14.2.2 shRNA-expressing Adenoviruses that Target Anti-apoptotic Genes 314
14.3 Exploiting Oncolytic Adenovirus for siRNA Expression 315
14.4 Current Limitations of Adenovirus-mediated siRNA Therapy and Future Directions: Smart Adenovirus Nanocomplexes Expressing siRNA for Systemic Administration 318
14.5 Conclusion 320
References 321
15 RNAi in Liver Diseases 327
Jiang Li, Jianqin Lu, Yifei Zhang, Mohammed Ghazwani, Peng Zhang, Xiang Gao and Song Li
15.1 Introduction 327
15.2 RNAi in Viral Hepatitis 327
15.2.1 Hepatitis B 328
15.2.2 RNAi of HBV Infection via siRNA/shRNA 329
15.2.3 RNAi of HBV Infection via miRNAs 330
15.2.4 Hepatitis C 332
15.2.5 RNAi of HCV Infection via siRNA/shRNA 333
15.2.6 RNAi of HCV Infection via miRNAs 335
15.3 RNAi in Hepatocellular Carcinoma 336
15.3.1 RNAi of HCC via siRNA/shRNA 337
15.3.2 RNAi of HCC via miRNAs 338
15.4 RNAi in Liver Fibrosis 340
15.4.1 RNAi of Liver Fibrosis via siRNA/shRNA 341
15.4.2 RNAi of Liver Fibrosis via miRNAs 343
15.5 Delivery Systems in RNAi 345
15.5.1 Liver Anatomy 346
15.5.2 Viral Delivery Systems 346
15.5.3 Non-Viral Delivery Systems 347
15.5.4 Cell-specific Targeting Strategies 348
15.5.5 Cellular Events after the Uptake of Nucleic Acid-Carrier Complexes 349
15.5.6 Lipid-based Delivery Systems 350
15.5.7 Polymer-Based Systems 350
15.5.8 Calcium Phosphate-Lipid Hybrid System 351
15.5.9 Hydrophobitized Nucleic Acid Derivatives 351
15.5.10 Targeted Delivery to Tumor Blood Vessels 351
15.6 Conclusion 352
Acknowledgments 353
References 353
16 Approaches to Delivering RNAi Therapeutics that Target Hepatitis B Virus 367
Carol Crowther, Mohube Betty Mowa, Abdullah Ely and Patrick Arbuthnot
16.1 Introduction 367
16.1.1 RNAi Therapeutics 368
16.1.2 Hepatitis B Virus as a Target for RNAi-based Gene Silencing 369
16.2 Vectors Suitable for Hepatic Delivery of HBV Gene Silencers 369
16.2.1 Viral Vectors 370
16.2.2 Nonviral Vectors 377
16.3 Conclusions 381
Acknowledgments 382
References 382
17 RNAi in Respiratory Diseases 391
Ciara Kelly, Awadh B. Yadav, Paul J. McKiernan, Catherine M. Greene and Sally-Ann Cryan
17.1 Introduction 391
17.2 Respiratory Disease and RNA Interference 392
17.2.1 RNAi in Lung Cancer 393
17.2.2 RNAi to Treat Respiratory Infections 393
17.2.3 RNAi in Inflammatory Lung Disease 394
17.3 Delivery and Development of RNAi Therapies for Respiratory Disease 397
17.3.1 Inhalation of RNA-medicines 397
17.3.2 Chemical Modifications of siRNA 399
17.3.3 RNAi Vectors 400
17.3.4 RNAi Therapy In Vivo 405
17.4 Conclusions 408
Acknowledgements 408 References 408
18 RNAi in Ocular Diseases 417
Andrey Turchinovich, Georg Zoidl and Rolf Dermietzel
18.1 Introduction 417
18.2 The Principle of RNAi 418
18.3 In vivo Delivery of siRNA 419
18.4 Delivery of siRNA into the Eye 420
18.4.1 Routes for Ocular Delivery of siRNA 420
18.4.2 Delivery of Naked siRNA 421
18.4.3 Delivery of siRNA Using Carriers 425
18.4.4 Viral Delivery of shRNA 429
18.5 Conclusions 431
Abbreviations 432
References 432
19 micro RNAs as Therapeutic Agents and Targets 439
D.S. Karolina and K. Jeyaseelan
19.1 Introduction 439
19.2 miRNA Therapeutics 440
19.2.1 Therapeutic miRNA Inhibition 443
19.2.2 Therapeutic miRNA Mimicry 446
19.3 MicroRNAs and Cancer 447
19.4 MicroRNAs in Stroke 450
19.5 MicroRNAs in Heart Diseases 452
19.6 MicroRNAs in Diabetes Mellitus 454
19.7 MicroRNAs in Liver Diseases 457
19.8 MicroRNAs and Ocular Diseases 461
19.9 MicroRNAs and Respiratory Diseases 462
19.10 MicroRNAs and Stem Cell Research 465
19.11 Conclusion 468
References 469
20 Delivery of Micro RNA Sponges for Interrogation of MicroRNA Function In Vitro and In Vivo 483
Jiakai Lin and Shu Wang
20.1 MicroRNA Loss-of-Function Studies 483
20.2 Considerations in MicroRNA Sponge Design 486
20.2.1 Vector 486
20.2.2 Promoter 487
20.2.3 Reporter Gene 488
20.2.4 MicroRNA Binding Sites 488
20.3 Advantages and Limitations of MicroRNA Sponge over Other MicroRNA Loss-of-Function Strategies 489
20.4 Interrogating MicroRNA Function via Transient MicroRNA Sponge Expression 493
20.5 Interrogating MicroRNA Function via Stable MicroRNA Sponge Expression 494
20.5.1 MicroRNA and Cell Differentiation 494
20.5.2 MicroRNAs in Disease Development 495
20.6 Utility of MicroRNA Sponge in Living Organisms 496
20.6.1 MicroRNA Knockdown in Plants 496
20.6.2 MicroRNA Knockdown in Mouse 497
20.6.3 MicroRNA Knockdown in Drosophila Melanogaster 498
20.7 Future Perspectives 498
References 499
Index 505