Note: Advanced Delivery and Therapeutic Applications of RNAi -- Contents -- Preface -- Contributors -- About the Editors -- Part 1: Introduction and Basics of RNAi -- 1 Mechanisms and Barriers to RNAi Delivery -- 1.1 Introduction -- 1.2 Barriers to Systemic RNAi Delivery -- 1.3 Rational Design to Improve RNAi Efficacy -- 1.4 Chemical Modifications to Enhance siRNA Stability and Reduce Immune Response -- 1.5 Cellular Uptake and Intracellular Release of siRNA -- 1.6 Combinatorial Targeting for Targeted RNAi Delivery -- 1.7 Cell-Specific Aptamer-Functionalized Nanocarriers for RNAi Delivery -- 1.8 The Clinical Development and Challenges of siRNAs Therapeutics -- 1.9 Conclusion and Perspectives -- References -- 2 Analysis of siRNA Delivery Using Various Methodologies -- 2.1 Introduction -- 2.2 Checkpoints for Analyzing siRNA Delivery -- 2.2.1 Circulation Checkpoint -- 2.2.2 Organ or Tissue Checkpoint -- 2.2.3 Cellular Checkpoint -- 2.2.4 RISC Checkpoint -- 2.2.5 Target mRNA Knockdown (Indirect Checkpoint) -- 2.2.6 Protein and Outcome (Indirect Checkpoint) -- 2.2.7 Safety (Indirect Checkpoint) -- 2.3 Methods for Analysis of siRNA -- 2.3.1 General Considerations -- 2.3.2 Hybridization-Based (Non-Imaging) Methods -- 2.3.3 Non-Hybridization-Based (Non-Imaging) Methods -- 2.3.4 Imaging-Based (Non-Hybridization) Methods -- 2.3.5 Imaging-Based (Hybridization) Methods -- 2.4 Case Study for siRNA Delivery Analysis -- References -- 3 Challenges and Opportunities in Bringing RNAi Technologies from Bench to Bed -- 3.1 Introduction -- 3.2 RNAi Mediator (siRNA or shRNA) -- 3.2.1 siRNA -- 3.2.2 Vector-derived shRNA -- 3.2.3 miRNAs -- 3.3 Safety Issues of RNAi Mediators -- 3.3.1 Immune Stimulation -- 3.3.2 RNAi Overexpression -- 3.4 Efficacy of RNAi Mediators -- 3.4.1 Therapeutic Response -- 3.5 RNAi Mediators in Clinical Trials -- 3.6 Conclusion -- References. , 4 Nonclinical Safety Assessments and Clinical Pharmacokinetics for Oligonucleotide Therapeutics: A Regulatory Perspective -- 4.1 Introduction -- 4.2 Unique Properties of Oligonucleotide-based Therapeutics -- 4.3 Regulation of Oligonucleotide-Based Therapeutics -- 4.3.1 Submission to the FDA -- 4.3.2 Review Process for Non-clinical Studies -- 4.3.3 Regulatory Issues -- 4.3.4 Clinical Pharmacokinetics -- 4.4 Conclusion -- Disclaimer -- Appendix -- References -- 5 Role of Promoters and MicroRNA Backbone for Efficient Gene Silencing -- 5.1 Introduction -- 5.2 Promoters for shRNA Expression -- 5.2.1 Constitutive Promoters -- 5.2.2 Inducible Promoters -- 5.2.3 Site Specific Promoters -- 5.3 miRNA-based shRNAs -- 5.3.1 miRNA-based shRNA Enhances Gene Silencing -- 5.3.2 miRNA-based shRNA Reduces Toxicities -- 5.3.3 Application of miRNA-based shRNA for Combination Gene Therapy -- 5.4 Concluding Remarks -- References -- Part 2: RNAi Delivery Strategies -- 6 Bioconjugation of siRNA for Site-specific Delivery -- 6.1 Introduction -- 6.2 Conjugation Strategy -- 6.2.1 RNA Chemical Modification -- 6.2.2 Site of Conjugation -- 6.2.3 Conjugation Chemistry -- 6.3 Bioconjugates for Site-specific Delivery -- 6.3.1 Antibody-siRNA Bioconjugates -- 6.3.2 Aptamer-siRNA Bioconjugates -- 6.3.3 Peptide-siRNA Bioconjugates -- 6.3.4 Lipid-siRNA Bioconjugates -- 6.3.5 Others -- 6.4 Conclusion -- References -- 7 Multifunctional RNAi Delivery Systems -- 7.1 Introduction -- 7.1.1 Chapter Objectives -- 7.2 Lipid-Based Delivery Systems -- 7.2.1 Cationic Lipids -- 7.2.2 Ionizable Cationic Lipids -- 7.2.3 Lipid-Like Materials -- 7.2.4 pH-sensitive Surfactants as Multifunctional siRNA Carriers -- 7.3 Polymeric Multifunctional siRNA Delivery Systems -- 7.3.1 Polyethylenimine -- 7.3.2 Chitosan -- 7.3.3 Cyclodextrins -- 7.3.4 Dendrimers. , 7.3.5 Polyalkylacrylic Acid-based pH-sensitive Polymers -- 7.3.6 Other pH-sensitive Polymers -- 7.4 Conclusion -- References -- 8 Dendrimers in RNAi Delivery -- 8.1 Introduction -- 8.2 Challenges in RNAi Delivery -- 8.3 Dendrimers as Non Viral Vectors -- 8.3.1 Dendritic Architectures -- 8.3.2 Synthesis of Dendrimers -- 8.3.3 Types of Dendrimers in Drug Delivery -- References -- 9 Development of Pharmaceutically Adapted Mesoporous Silica Nanoparticles for siRNA Delivery -- 9.1 Introduction -- 9.2 Mesoporous Silica Nanoparticles as Novel Inorganic Nanocarriers for siRNA Delivery -- 9.2.1 Discovery and Synthesis -- 9.2.2 Surface Modification of MSNP for Nucleic Acid Delivery -- 9.2.3 MSNP for Dual siRNA and Drug Delivery -- 9.2.4 Improving in vivo Implementation of MSNP-Based Delivery Platform -- 9.2.5 Design of Pharmaceutically Adapted MSNP via the Knowledge Generated by Discoveries at the Nano/Bio Interface -- 9.3 Safety Assessment of Nanocarrier and Design of Safe MSNP Carrier -- 9.3.1 Safety of Nanocarriers -- 9.3.2 Safe Design of MSNP Carrier -- 9.4 Summary -- References -- 10 Environmentally-Responsive Nanogels for siRNA Delivery -- 10.1 Introduction -- 10.1.1 siRNA Delivery System -- 10.1.2 Crosslinked Nanogels for siRNA Delivery -- 10.2 Reductive Environment-Responsive Disulfide Crosslinked Nanogels -- 10.3 Temperature-Responsive Nanogels -- 10.4 pH-Responsive Nanogels -- 10.4.1 Acid-degradable Nanogels for Intracellular Release of siRNA -- 10.4.2 Design of pH-Responsive PEGylated Nanogels with Endosomal Escape Ability -- 10.4.3 Cytoplasmic Delivery of PEGylated Nanogel/siRNA Complexes -- 10.5 PEGylated and Partially Quaternized Polyamine Nanogels -- 10.5.1 Design of Quaternized Polyamine Nanogels -- 10.5.2 Enhanced Cellular Uptake of siRNA by Quaternized Polyamine Nanogels. , 10.5.3 Enhanced Gene-Silencing Activity of Quaternized Polyamine Nanogel/siRNA Complexes -- 10.6 Conclusions -- References -- 11 Viral-Mediated Delivery of shRNA and miRNA -- 11.1 Introduction -- 11.2 RNAi - A Brief Overview -- 11.3 shRNA or miRNA? -- 11.4 Rational Design -- 11.5 Viral Vectors -- 11.5.1 Recombinant Adeno-associated Virus (rAAV) -- 11.5.2 Retrovirus (RV) -- 11.5.3 Lentivirus (LV) -- 11.5.4 Adenovirus (AD) -- 11.5.5 Herpes Simplex Virus (HSV) -- 11.5.6 Baculovirus (BV) -- 11.5.7 Poxvirus -- 11.6 Tissue-specific Transduction -- 11.6.1 CNS -- 11.6.2 Ocular -- 11.6.3 Respiratory System -- 11.6.4 Liver -- 11.6.5 Skeletal Muscle -- 11.6.6 Heart -- 11.6.7 Systemic -- 11.6.8 Ex Vivo -- 11.6.9 Cell Culture -- 11.6.10 Transcription Cassettes -- 11.7 Applications of Virally Expressed shRNAs -- 11.7.1 Virally Mediated "Knockouts" -- 11.7.2 Concomitant Expression of Therapeutic Genes -- 11.8 Viral Gene Therapy in the Clinic -- 11.9 Conclusion -- References -- 12 The Control of RNA Interference with Light -- 12.1 Introduction -- 12.2 The Importance of Gene Expression -- 12.3 Light Control of Gene Expression -- 12.4 Why Use RNA Interference as a Basis for Light Control of Gene Expression? -- 12.5 Light Activated RNA Interference (LARI), the work of Friedman and Co-Workers -- 12.6 Work of McMaster and Co-Workers, 50 Antisense Phosphate Block -- 12.7 Work of Heckel and Co-Workers, Nucleobase Block -- 12.8 Use of 20 FsiRNA, work of Monroe and Co-Workers -- 12.9 Photochemical Internalization -- 12.10 Future Directions and Conclusions -- Acknowledgments -- References -- Part 3 Applications of RNAi in Various Diseases -- 13 RNAi in Cancer Therapy -- 13.1 Introduction -- 13.2 Therapeutic Opportunities for Noncoding RNAs -- 13.3 RNAs as Drugs -- 13.4 Overcoming Anatomical and Physiologic Barriers -- 13.4.1 Intravascular Degradation. , 13.4.2 Tissue and Intracellular Delivery -- 13.4.3 Immune-mediated Toxic Effects -- 13.4.4 Nanocarrier-mediated Toxic Effects -- 13.5 Advanced Delivery -- 13.5.1 Localized siRNA Delivery -- 13.5.2 Systemic siRNA Delivery -- 13.5.3 Targeted siRNA Delivery -- 13.5.4 Monitoring Delivery and Therapeutic Response -- 13.6 Clinical Experience -- 13.7 The Next Steps -- Acknowledgments -- References -- 14 Adenovirus-mediated siRNA Delivery to Cancer -- 14.1 Introduction -- 14.1.1 shRNA-expressing Vectors -- 14.1.2 Adenovirus Vectors -- 14.2 shRNA-expressing Adenoviruses: Cancer Biological Studies and Therapeutic Implications -- 14.2.1 Oncogene-targeted shRNA-expressing Ads -- 14.2.2 shRNA-expressing Adenoviruses that Target Anti-apoptotic Genes -- 14.3 Exploiting Oncolytic Adenovirus for siRNA Expression -- 14.4 Current Limitations of Adenovirus-mediated siRNATherapy and Future Directions: Smart Adenovirus Nanocomplexes Expressing siRNA for Systemic Administration -- 14.5 Conclusion -- References -- 15 RNAi in Liver Diseases -- 15.1 Introduction -- 15.2 RNAi in Viral Hepatitis -- 15.2.1 Hepatitis B -- 15.2.2 RNAi of HBV Infection via siRNA/shRNA -- 15.2.3 RNAi of HBV Infection via miRNAs -- 15.2.4 Hepatitis C -- 15.2.5 RNAi of HCV Infection via siRNA/shRNA -- 15.2.6 RNAi of HCV Infection via miRNAs -- 15.3 RNAi in Hepatocellular Carcinoma -- 15.3.1 RNAi of HCC via siRNA/shRNA -- 15.3.2 RNAi of HCC via miRNAs -- 15.4 RNAi in Liver Fibrosis -- 15.4.1 RNAi of Liver Fibrosis via siRNA/shRNA -- 15.4.2 RNAi of Liver Fibrosis via miRNAs -- 15.5 Delivery Systems in RNAi -- 15.5.1 Liver Anatomy -- 15.5.2 Viral Delivery Systems -- 15.5.3 Non-Viral Delivery Systems -- 15.5.4 Cell-specific Targeting Strategies -- 15.5.5 Cellular Events after the Uptake of Nucleic Acid-Carrier Complexes -- 15.5.6 Lipid-based Delivery Systems -- 15.5.7 Polymer-Based Systems. , 15.5.8 Calcium Phosphate-Lipid Hybrid System.