RNAi - technologies, markets and companies

Table of Contents

0. Executive Summary

1. Technologies for suppressing gene function

• Introduction
• DNA transcription
• RNA
• Non-coding RNA
• RNA research and potential applications
• Role of RNA in regulation of the dihydrofolate reductase gene
• Gene regulation
• Post-transcriptional regulation of gene expression
• Alternative RNA splicing
• Technologies for gene suppression
• Antisense oligonucleotides
• Transcription factor decoys
• Aptamers
• Ribozymes
• Aptazymes
• RNA aptamers vs allosteric ribozymes
• RNA Lasso
• Peptide nucleic acid
• PNA-DNA chimeras
• Locked nucleic acid
• Gene silencing
• Post-transcriptional gene silencing
• TargeTron™ technology for gene knockout
• Definitions and terminology of RNAi
• RNAi mechanisms
• Non-promoter-associated small RNAs
• Piwi-interacting RNAs in germ cell development
• Relation of RNAi to junk DNA
• RNA editing and RNAi
• Historical landmarks in the development of RNAi

2. RNAi Technologies

• Introduction
• Comparison of antisense and RNAi
• Advantages of antisense over siRNAs
• Advantages of siRNAs over antisense
• RNA aptamers vs siRNA
• RNA Lassos versus siRNA
• Concluding remarks on antisense vs RNAi
• Antisense vs DNP-ssRNA and DNP-siRNA
• LNA and RNAi
• LNA for gene suppression
• Comparison of LNA and RNAi
• Use of siLNA to improve siRNA
• RNAi versus small molecules
• RNAi in vivo
• Cre-regulated RNAi in vivo
• RNAi kits
• ShortCut™ RNAi Kit
• HiScribe™ RNAi Transcription Kit
• pSUPER RNAi system
• Si2 Silencing Duplex
• Techniques for measuring RNAi-induced gene silencing
• Application of PCR in RNAi
• Real-time quantitative PCR
• Assessment of the silencing effect of siRNA by RT-PCR
• Bioinformatics tools for design of siRNAs
• Random siRNA design
• Rational siRNA design
• The concept of pooling siRNAs
• Criteria for rational siRNA design
• BLOCK-iT RNAi Designer
• QIAGEN' s 2-for-Silencing siRNA Duplexes
• Designing vector-based siRNA
• iRNAChek for designing siRNA
• TROD: T7 RNAi Oligo Designer
• siDirect: siRNA design software
• Prediction of efficacy of siRNAs
• Algorithms for prediction of siRNA efficacy
• siRNA databases
• Production of siRNAs
• Chemical synthesis of short oligonucleotides
• In vitro transcription
• Generation of siRNA in vivo
• siRNA:DNA hybrid molecules
• Chemical modifications of siRNAs
• Sugar modifications of siRNA
• Phosphate linkage modifications of siRNA
• Modifications to the siRNA overhangs
• Modifications to the duplex architecture
• Applications of chemical modification of siRNAs
• Synthetic RNAs vs siRNAs
• Specificity of siRNAs
• Asymmetric interfering RNA
• Genome-wide data sets for the production of esiRNAs
• ddRNAi for inducing RNAi
• ddRNAi technology
• Advantages of ddRNAi over siRNA
• Short hairpin RNAs
• siRNA versus shRNA
• Expressed interfering RNA
• RNA-induced transcriptional silencing complex
• Inhibition of gene expression by antigene RNA
• RNAi vs mRNA modulation by small molecular weight compounds

3. MicroRNA

• Introduction
• miRNA and RISC
• Role of the microprocessor complex in miRNA
• miRNAs compared to siRNAs
• miRNA and stem cells
• Influence of miRNA on stem cell formation and maintenance
• Role of miRNAs in gene regulation during stem cell differentiation
• miRNA databases
• Sanger miRBase miRNA sequence database
• Mapping miRNA genes
• A database of ultraconserved sequences and miRNA function
• A database for miRNA deregulation in human disease
• An database of miRNA-target interactions
• Role of miRNA in gene regulation
• Control of gene expression by miRNA
• miRNA-mediated translational repression involving Piwi
• Transcriptional regulators of ESCs control of miRNA gene expression
• Mechanism of miRNAs-induced silencing of gene expression
• miRNA diagnostics
• Biochemical approach to identification of miRNA
• Computational approaches for the identification of miRNAs
• LNA probes for exploring miRNA
• Microarrays for analysis of miRNA gene expression
• Microarrays vs quantitative PCR for measuring miRNAs
• miRNAs as biomarkers of hepatotoxicity
• Modification of in situ hybridization for detection of miRNAs
• Nuclease Protection Assay to measure miRNA expression
• Real-time PCR for expression profiling of miRNAs
• Targeting of miRNAs with antisense oligonucleotides
• Silencing miRNAs by antagomirs
• miRNA-regulated lentiviral vectors
• miRNAs as drug targets
• miRNAs as targets for antisense drugs
• Challenges facing use of miRNAs as drug targets
• Target specificity of miRNAs
• Prediction of miRNA targets
• Role of miRNA in human health and disease
• Role of miRNAs in regulation of hematopoiesis
• Role of miRNA depletion in tissue regeneration
• Role of miRNA in regulation of aging
• Role of miRNA in inflammation
• Role of miRNAs in regulation of immune system
• Role of miRNA in the cardiovascular system
• Role of miRNAs in development of the cardiovascular system
• Role of miRNAs in angiogenesis
• Role of miRNAs in cardiac hypertrophy and failure
• Role of miRNAs in conduction and rhythm disorders of the heart
• miRNA-based approach for reduction of hypercholesterolemia
• miRNA-based approach for restenosis following angioplasty
• miRNAs as therapeutic targets for cardiovascular diseases
• Concluding remarks and future prospects of miRNA in the cardiovascular system
• Role of miRNAs in the nervous system
• miRNAs as biomarkers of Alzheimer' s disease
• miRNA and schizophrenia
• miRNAs and retinal neurodegenerative disorders
• Role of miRNA in viral infections
• Role of miRNA in HSV-1 latency
• miRNA and autoimmune disorders
• miRNA in systemic lupus erythematosus
• miRNA and skin disorders
• Role of miRNA in inflammatory skin disorders
• Role of miRNAs in cancer
• Linking miRNA sequences to cancer using RNA samples
• Role of miRNAs in viral oncogenesis
• miRNA genes in cancer
• miRNAs, embryonic stem cells and cancer
• miRNAs and cancer metastases
• Role of miRNAs in cancer diagnosis
• Cancer miRNA signature
• miRNA biomarkers in cancer
• Diagnostic value of miRNA in cancer
• miRNAs as basis of cancer therapeutics
• Antisense oligonucleotides targeted to miRNA
• Role of miRNAs in adoptive immunotherapy of cancer
• Restoration of tumor suppressor miRNA may inhibit cancer
• Role of miRNAs in various cancers
• miRNA and brain cancer
• miRNA and breast cancer
• miRNA and colorectal cancer
• miRNA and hematological malignancies
• miRNA and hepatocellular carcinoma
• miRNA and lung cancer
• miRNA and nasopharyngeal carcinoma
• miRNA and ovarian cancer
• miRNA and pancreatic cancer
• miRNA and prostatic cancer
• miRNA and thyroid cancer
• Future prospects of miRNA
• Companies involved in miRNA

4. Methods of delivery in RNAi

• Introduction
• Methods of delivery of oligonucleotides
• Oral and rectal administration
• Pulmonary administration
• Targeted delivery to the CNS
• High flow microinfusion into the brain parenchyma
• Intracellular guidance by special techniques
• Biochemical microinjection
• Liposomes-mediated oligonucleotide delivery
• Polyethylenimine-mediated oligonucleotide delivery
• Delivery of TF Decoys
• Biodegradable microparticles
• Microparticles
• Nanoparticles
• siRNA delivery technologies
• Local delivery of siRNA
• In vivo delivery of siRNAs by synthetic vectors
• Intracellular delivery of siRNAs
• Protamine-antibody fusion proteins for delivery of siRNA to cells
• Protein transduction domains
• MPG-based delivery of siRNA
• Delivery of siRNAs with aptamer-siRNA chimeras
• Phosphorothioate stimulated cellular delivery of siRNA
• Targeted delivery of siRNAs by lipid-based technologies
• Systemic in vivo delivery of lipophilic siRNAs
• NeoLipid™ technology
• siFECTamine™
• Delivery of siRNA-lipoplexes
• Lipidoids for delivery of siRNAs
• Electroporation
• Nucleofactor technology
• Intravascular delivery of siRNA
• 27mer siRNA duplexes for improved delivery and potency
• TransIT-TKO®
• DNA-based plasmids for delivery of siRNA
• Convergent transcription
• PCR cassettes expressing siRNAs
• Genetically engineered bacteria for delivery of shRNA
• Viral vectors for delivery of siRNA
• Adenoviral vectors
• Adeno-associated virus vectors for shRNA expression
• Baculovirus vector
• Lentiviral vectors
• Retroviral delivery of siRNA
• Transkingdom RNAi delivery by genetically engineered bacteria
• Delivery of siRNA without a vector
• Cell-penetrating peptides for delivery of siRNAs
• Role of nanobiotechnology in siRNA delivery
• Chitosan-coated nanoparticles for siRNA delivery
• Delivery of gold nanorod-siRNA nanoplex to dopaminergic neurons
• Lipidic aminoglycoside as siRNA nanocarrier
• Lipid nanoparticles-mediated siRNA delivery
• Nanosize liposomes for delivery of siRNA
• PAMAM dendrimers for siRNA delivery
• Polyethylenimine nanoparticles for siRNA delivery
• Polycation-based nanoparticles for siRNA delivery
• Quantum dots to monitor siRNA delivery
• Targeted delivery of siRNAs to specific organs
• siRNA delivery to the CNS
• siRNA delivery to the liver
• siRNAdelivery to the lungs
• Control of RNAi and siRNA levels
• siRNA pharmacokinetics in mammalian cells
• Mathematical modeling for determining the dosing schedule of siRNA
• Assessing siRNA pharmacodynamics in animal models
• Research on siRNA delivery funded by the NIH
• Companies involved in delivery technologies for siRNA

5. RNAi in Research

• Introduction
• Basic RNAi research
• Genes and lifespan
• Antiviral role of RNAi in animal cells
• Silencing snoRNA genes
• Profiling small RNAs
• Study of signaling pathways
• RNAi for research in neuroscience
• Use of RNAi to study insulin action
• Detection of cancer mutations
• Loss-of-function genetic screens
• Inducible and reversible RNAi
• Combination of siRNA with green fluorescent protein
• RNAi and environmental research
• Applied RNAi research
• RNAi for gene expression studies
• Microarrays for measuring gene expression in RNAi
• RNAi for functional genomic analysis
• RNAi studies on C. elegans
• RNAi studies on Drosophila
• RNAi in planaria
• Testing the specificity of RNAi
• Tissue-specific RNAi
• siRNA-mediated gene silencing
• RNAi libraries
• Universal plasmid siRNA library
• pDual library using plasmid vector
• pHippy plasmid vector library
• siRNA libary including miRNAs
• siRNA libraries using pRetroSuper vector
• siRNA produced by enzymatic engineering of DNA
• shRNA libraries
• Enzymatic production of RNAi library
• RNAi and alternative splicing
• RNAi in animal development
• RNAi for creating transgenic animals
• RNAi for creating models of neurological disorders
• Research support for RNAi in US
• RNAi for toxicogenomics
• Role of RNAi in the US biodefense research
• The RNAi Consortium
• Research support for RNAi in Europe
• European Union for RNA Interference Technology
• Research support of RNAi
• Role of RNAi in MitoCheck project
• Genome-Wide RNAi Global Initiative

6. RNAi in drug discovery

• Basis of RNAi for drug discovery
• Use of siRNA libraries to identify genes as therapeutic targets
• Role of siRNAs in drug target identification
• Use of a genome-wide, siRNA library for drug discovery
• Use of arrayed adenoviral siRNA libraries for drug discovery
• RNAi as a tool for assay development
• Targeting human kinases with an siRNAi library
• Challenges of drug discovery with RNAi
• Express TrackSM siRNA Drug Discovery Program
• Genome-wide siRNA screens in mammalian cells
• Natural antisense and ncRNA as drug targets
• RNAi for target validation
• Delivering siRNA for target validation in vivo
• Off-target effects of siRNA-mediated gene silencing
• Bioinformatic approach to off-target effects
• Validation of oncology targets discovered through RNAi screens
• Selection of siRNA versus shRNA for target validation
• Application of RNAi to the druggable genome
• Application of siRNA during preclinical drug development
• siRNAs vs small molecules as drugs
• siRNAs vs antisense drugs
• RNAi technology in plants for drug discovery and development
• Application of RNAi to poppy plant as source of new drugs

7. Therapeutic applications of RNAi

• Introduction
• Potential of RNAi-based therapies
• In vitro applications of siRNA
• In vivo applications of RNAi
• RNAi and cell therapy
• Gene inactivation to study hESCs
• RNAi and stem cells
• Cell therapy for immune disorders
• RNAi gene therapy
• Drug-inducible systems for control of gene expression
• Potential side effects of RNAi gene therapy
• Systemic delivery of siRNAs
• In vivo RNAi therapeutic efficacy in animal models of human diseases
• Virus infections
• RNAi approaches to viral infections
• Delivery of siRNAs in viral infections
• RNAi applications in HIV
• Anti-HIV shRNA for AIDS lymphoma
• Aptamer-mediated delivery of anti-HIV siRNAs
• Bispecific siRNA constructs
• Role of the nef gene during HIV-1 infection and RNAi
• siRNA-directed inhibition of HIV-1 infection
• Synergistic effect of snRNA and siRNA
• Targeting CXCR4 with siRNAs
• Targeting CCR5 with siRNAs
• Concluding remarks on RNAi approach to HIV/AIDS
• Influenza
• Inhibition of influenza virus by siRNAs
• Delivery of siRNA in influenza
• Challenges and future prospects of siRNAs for influenza
• Respiratory syncytial and parainfluenza viruses
• Coronavirus/severe acute respiratory syndrome
• Herpes simplex virus 2
• Hepatitis B
• Hepatitis C virus
• Cytomegalovirus
• siRNA vs antisense oligonucleotides for viral infections
• siRNA against methicillin-resistant S. aureus
• RNAi-based rational approach to antimalarial drug discovery
• Inhibiting the growth of malarial parasite by heme-binding DNA aptamers
• siRNA-based antimalarial therapeutics
• RNAi applications in oncology
• Inhibition of oncogenes
• RNAi approach to study TRAIL
• Modification of alternative splicing in cancer
• Allele-specific inhibition
• siRNAs for anticancer drug discovery
• siRNAs for inhibition of angiogenesis
• siRNA targeting the R2 subunit of ribonucleotide reductase
• siRNA for cancer chemoprevention
• Onconase
• Drug delivery issues in managing cancer by RNAi approach
• siHybrids vs siRNAs as anticancer agents
• Nanobiotechnology-based delivery of siRNAs
• Lipid nanoparticle-based delivery of anticancer siRNAs
• Minicells for targeted delivery of nanoscale anticancer therapeutics
• Nanoimmunoliposome-based system for targeted delivery of siRNA
• Polymer nanoparticles for targeted delivery of anticancer siRNA
• RNA nanotechnology for delivery of cancer therapeutics
• RNAi-based treatment of various cancer types
• RNAi-based therapy of brain cancer
• RNAi in breast cancer
• Enhancing efficacy of hyperthermia/chemotherapy in cervical cancer
• RNAi and colorectal cancer
• RNAi and Ewing' s sarcoma
• RNAi and leukemias
• RNAi and lung cancer
• RNAi and melanoma
• RNAi and pancreatic cancer
• RNAi and prostate cancer
• Overcoming drug resistance in cancer
• Targeting fusion proteins in cancer
• Increasing chemosensitivity by RNAi
• Genetic disorders
• Pachyonychia congenita
• Neurological disorders
• RNAi for neurodegenerative disorders
• Alzheimer' s disease
• Parkinson' s disease
• Amyotrophic lateral sclerosis
• Prion diseases
• Polyglutamine-induced neurodegeneration
• Fragile X syndrome and RNAi
• RNAi-based therapy for Huntington' s disease
• Combination of RNAi and gene therapy to prevent neurodegenerative disease
• siRNA for relief of neuropathic pain
• siRNA for dystonia
• Role of RNAi in repair of spinal cord injury
• Role of RNAi in treatment of multiple sclerosis
• siRNA for Duchenne muscular dystrophy
• RNAi in ophthalmology
• Age related macular degeneration
• Current treatment of AMD
• RNAi-based treatments for AMD
• Diabetic retinopathy
• Retinitis pigmentosa
• RNAi and metabolic disorders
• RNAi and obesity
• Genes and regulation of body fat
• RNAi and diabetes
• Use of siRNAs to study glucose transporter
• Use of RNAi to study genes in animal models of diabetes
• RNAi for drug discovery in diabetes
• A miRNA that regulates insulin secretion
• RNAi in hematology
• Stem cell-based gene therapy and RNAi for sickle cell disease
• RNAi and disorders of the immune system
• siRNA applications in immunology
• Use of RNAi in transplantation
• RNAi for cardiovascular disorders
• RNAi for hypercholesterolemia
• siRNA targeting NADPH oxidase in cardiovascular diseases
• siRNA for study and treatment of ischemia-reperfusion injury
• RNAi in respiratory disorders
• siRNA for cystic fibrosis
• siRNA for asthma
• RNAi for musculoskeletal disorders
• RNAi for rheumatoid arthritis
• RNAi for bone disorders
• Future prospects of RNAi
• Clinical trials of RNAi-based therapies
• Improving efficacy of siRNAs for clinical trials by improved delivery
• Role of RNAi in development of personalized medicine
• Challenges for the development of RNAi-based therapeutics

8. Safety, regulatory and patent issues

• Introduction
• Limitations and drawbacks of RNAi
• Adverse effects of RNAi
• Effect of siRNAs on interferon response
• Detection of interferon response
• Prevention of the interferon response in RNAi
• Overcoming the innate immune response to siRNAs
• Regulatory issues relevant to RNAi
• RNAi patents
• Companies with strong patent position
• Alnylam
• Benitec
• Intradigm
• Sirna Therapeutics

9. Markets for RNAi Technologies

• Introduction
• Current and future market potential for RNAi technologies
• RNAi reagents
• RNAi-based drug discovery and target validation
• RNAi-based development of therapeutics
• RNAi market potential according to therapeutic areas
• Market for viral infections
• Market for cancer
• Market for age related macular degeneration
• Unmet needs in RNAi
• Strategies for marketing RNAi
• Choosing optimal indications
• Strategies according to the trends in healthcare in the next decade
• Concluding remarks

10. Companies involved in RNAi Technologies

• Introduction
• Major players in RNAi
• Profiles of companies
• Collaborations

11. References

Tables

• Table 1 1: Historical landmarks in the evolution of RNAi
• Table 2 1: RNAi versus small molecules
• Table 2 2: Providers of software for siRNA design
• Table 2 3: Methods for the production of siRNAs
• Table 2 4: Advantages and limitations of methods of shRNA-derived siRNA knockdown
• Table 2 5: Comparison of eiRNA with siRNA
• Table 3 1: Methods for miRNA target prediction
• Table 3 2: Dysregulation of miRNA expression in epithelial cancers
• Table 3 3: Companies involved in miRNA diagnostics and therapeutics
• Table 4 1: Methods of delivery of oligonucleotides
• Table 4 2: Methods of delivery of siRNA
• Table 4 3: Companies developing siRNA delivery technologies
• Table 5 1: RNAi libraries
• Table 6 1: Delivery of siRNAs in vivo for target validation
• Table 6 2: Selection of siRNA versus shRNA for target validation
• Table 7 1: RNAi-based therapeutic approaches
• Table 7 2: In vivo RNAi therapeutic efficacy in animal models of human diseases
• Table 7 3: Inhibition of viral replication by RNAi
• Table 7 4: Cancer-associated genes that can be targeted by RNAi
• Table 7 5: Neurological disorders that have been studied by using RNAi
• Table 7 6: Clinical trials of RNAi-based therapeutics
• Table 9 1: RNAi markets according to technologies and reagents 2008-2018
• Table 9 2: Markets for RNAi therapy for selected diseases: years 2008-2018
• Table 10 1: RNAi reagent, technology and service companies
• Table 10 2: Pharmaceutical companies using RNAi for drug discovery and development
• Table 10 3: Biotechnology companies using RNAi for drug discovery and development
• Table 10 4: Companies developing RNAi-based therapeutic products
• Table 10 5: Major players in RNAi
• Table 10 6: RNAi products of Benitec
• Table 10 7: Proprietary reagents of ImuThes
• Table 10 8: Product pipeline of Silence Therapeutics
• Table 10 9: Collaborations in RNAi technologies

Figures

• Figure 1 1: Relationship of DNA, RNA and protein in the cell
• Figure 1 2: Schematic of suppression of gene expression by RNAi
• Figure 2 1: Overview of ShortCut RNAi Kit
• Figure 2 2: Gene silencing by RNAi induced with ddRNAi
• Figure 3 1: A schematic miRNA pathway
• Figure 3 2: Molecular mechanisms of miRNA generation
• Figure 7 1: Targeting disease by RNAi
• Figure 7 2: Role of RNAi in personalized medicine
• Figure 8 1: Problems with use of synthetic siRNAs and measures to prevent them
• Figure 9 1: Unmet needs in RNAi technologies