This is a presentation slide about cellular RNA interference process and RNA interference technology. Contains basic information about biology of cellular RNA interference processes and its discovery, and RNA interference technology. Also gives you the history and development of in-vitro and in-vivo technologies for applicability of RNA interference technology. siRNA synthesis, siRNA libraries, siRNA delivering techniques, Electroporation, viral transfection methods, Advantages and disadvantages of RNA interference technology. details about the preliminary and pre-clinical experiments of RNA interference as well as clinical trials of RNA interference.

1. 1
K. Ashok
M.Sc. Medical Biochemistry,
JAWAHARLAL INSTITUTE OF POST GRADUATE MEDICAL
EDUCATION AND RESEARCH (JIPMER),
RNA
INTERFERENCE
TECHNOLOGY

2. CONTENTS
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RNA INTERFERENCE
Introduction
Discovery of RNAi
Proteins involved in RNAi
RNAi pathway
Sources of siRNAs
Amplification of RNAi
RNAi TECHNOLOGY
Introduction
siRNA libraries
siRNA designing & delivery
Applications of RNAi tech
Advantages & limitations
Summary

3. RNA INTERFERENCE - INTRODUCTION
• Sequence specific post-transcriptional gene silencing.
• Observed in fungi, protozoa, insects and vertebrates.
• Protects the genetic code.
• Defense mechanism against viruses and transposons.
• Degrade mRNA & Inhibit translation.
• Highly conserved process.
• It is probably an eukaryotic innovation.
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4. THE DISCOVERY OF RNAi
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• Aim: To prove chalcone synthase (CS) is the rate-limiting enzyme.
• They overexpressed CS gene.
• Levels of mRNA was 50-fold decreased.
• The process is named as “co-suppression”.
1990: Napoli and Jorgensen
studied anthocyanin biosynthesis. Petunia Flowers

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1992
• Romano and Macino: similar phenomenon in N.crassa (quelling).
1995
• Guo & Kemphues: sense or antisense RNA results in degradation
of mRNA (sense or antisense RNA inhibition).
1998
• The explanation provided by Andrew Fire & Craig Mello through
RNA interference (RNAi).
2006
• Nobel Prize awarded to A. Fire & C. Mello for discovery of
RNAi.

6. 6
Proteins involved in RNAi
Dicer RISC RdRP RNAi

7.  dsRNA specific endonuclease
 Dual Rnase III: Cleaves RNA strands
 PAZ Domain: Holds 3’ overhang
 dsRNA binding Domain: Binds to dsRNA
 N terminal Helicase Domain
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Dicer (type III RNase)

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Catalytic activity of Dicer
siRNA (21 nucleotiodes)
3’ overhang region
3’ overhang region

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RISC loading complex

10.  RISC promotes unwinding of siRNA.
 Passenger strand excluded from RISC (active).
 The antisense strand guides active RISC.
 Proteins: Argonaute.
Vasa intronic gene protein.
RNA dependent RNA Polymerase (RdRP).
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RISC (RNA induced silencing complex)

11. RNAse H: Slicer
 N domain: Helicase
 PAZ domain: 3’ RNA binding domain
 MID domain: 5’ phosphate engaging
 PIWI domain: Endonuclease activity
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ARGONAUTE: The catalytic Engine of RISC

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Sources of siRNA
Transposon
Viral
RNA Transposon miRNA shRNA

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Biogenesis of miRNA

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Steps of RNAi pathway
dsRNA cleavage
Silencing complex formation
Silencing complex activation
Silencing effect

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RNAi pathways

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Silencing mechanisms

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Mechanism of Translatinal Repression

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siRNA amplification
RdRP acts on passenger strand
Generation of secondary siRNAs
Secondary siRNAs loaded to RISC
Amplification of RNAi

19.  Ability to down-regulate almost any gene.
 Exploits cellular RNAi system for gene knockdown.
 Suppression of unwanted genes.
 A key tool in functional genomics.
 Manipulation of RNAi is more biological approach.
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RNA INTERFERENCE TECHNOLOGY

20.  Synthetic siRNA libraries: targets whole genomes.
 Provides database: siRNAs specific to target genes.
 Human siRNA libraries available as individual siRNAs.
 siRNA libraries: Human Kinase siRNA Library,
Human Phosphatase siRNA Library,
Apoptosis siRNA library etc,.
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siRNA libraries

21.  siRNAs acts based on its sequence.
 Synthesized as 21-mer RNA.
 Central 19 bp duplex region.
 2-base 3’ overhangs on both ends.
 Dicer-substrate RNAs: 27-mer RNA duplexes.
 2’-O-methyl RNA residues prevents IFN responses.
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Synthesis of siRNA & designing strategies

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siRNA delivering techniques
Viral transfection
Lipofection
microinjection
Electroporation
• Microinjection
• Electroporation
• Hydrodynamic delivery
Physical
methods
• Lipofection
• Calcium phosphate
• DEAE-dextran
Chemical
methods
• Adenovirus
• Retrovirus
• Vacciniavirus
Viral
transfection

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Inserting genetic materials to mammalian cells.Transfection

24. Introducing genetic materials to cells using a pulse of electricity.
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Electroporation

25.  Cationic Cell Penetrating Peptides.
 Polymeric & Dendrimeric Carriers.
 siRNA Bioconjugates:
Lipid-Based Carriers: - liposomes
- micelles
- microemulsions
- solid lipid nanoparticles 25
siRNA carriers

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 Overcome electrostatic repulsion.
 Neutralizing the charge of siRNA.
 Delivers siRNA cargo into cytoplasm.
 Increases plasma half life of siRNAs.
Liposome formulated siRNA

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Cholesterol conjugated siRNA
 Receptor mediated endocytosis.
 Systemic delivery of siRNAs.
Antibody-protamine complexed siRNA
 Increases tissue-specific delivery.
 Targeting siRNAs by exploiting tissue-specificity
yields promising systemic siRNA delivery solutions.

28. Delivery Immunogenicity Effect Biosafety required Cost
Viral transfection + Slow + High
Lipofection +/- Fast - Low
Electroporation - Fast - Moderate
Microinjection - Fast - High
Calcium phosphate - Fast - Low
DEAE-dextran - Fast - Low
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Comparison of siRNA delivery methods

29.  Gene knockdown: Human diseases may be modelled in animals by the
inhibition of key regulatory proteins.
 Functional genomics: To study individual genes & genome-wide screening.
 Transgenic animals: RNAi is used to rapidly create transgenic mice.
 Inhibits viral replication: Targeting Protein coding genes of HBV & HIV
inhibits its replication.
 RNAi therapeutics: Disruption of signaling pathways suppress tumor.
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Applications

30. DRUG TARGET DISEASE STATUS
EZN-2968 HIF-1, survivin Advanced solid tumor/lymphoma Phase I
FANG vaccine Furin & GM-CSF Solid tumors Phase I
SYL040012 β2 adrenergic receptor Glaucoma Active Phase II
SPC3649 miR-122 Hepatitis C Active Phase II
AGN211745 VEGFR1 Age-related macular degeneration Active Phase III
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RNAi Therapeutics

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Advantages
• Offers different siRNA design & delivery strategies.Convenient:
• Ability to silence any gene using custom libraries.Comprehensive:
• 1-3 siRNAs for complete silencing of a gene (amplification).High potency:
• Sequence specific binding & degradation of mRNA.High specificity:
• Ability to determine the duration of silencing effect.Customizable:
• siRNAs meticulously designed for maximum potency & specificity.Effective:
• Silencing effect is amplified through secondary siRNAs.Amplifiable:

32.  Off-target silencing: As little as 11 nucleotides match with mRNAs other
than target results in off-target knockdown.
 Transfectors may influence expression profiles independent of the siRNA.
 5′-GUCCUUCAA-3′ sequence can be recognized by TLR3, TLR7, TLR8
in the dendritic cells and activate IFN responses.
 Certain transfecting agents are immunogenic.
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Limitations

33.  RNAi is an intracellular process of gene silencing.
 dsRNAs are Dicer substrates (RNAse III).
 Dicer products binds to Argonaute (RNAse H).
 RISC carries guide strand and discards passenger strand.
 RISC can either breaks down target mRNA or prevents translation.
 RNAi amplification: polymerization of passenger strand by RdRP.
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SUMMARY

34.  RNAi technology utilizes cellular RNAi system to accomplish silencing.
 Custom siRNA libraries available for targeting whole genome.
 Appropriate designing of siRNA increases specificity & efficiency.
 Systemic siRNA delivery strategies provide convenient gene silencing.
 RNAi technology is the robust tool to temporarily silence any gene.
 Limitations: off-target silencing & IFN responses.
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SUMMARY

35.  Molecular Biology. David P. Clark. 2nd Edition.
 Genes XI. Lewin. 11th edition.
 A brief history of RNAi: the silence of the genes. George L. Sen, Helen M. Blau. The
FASEB Journal . Review. 20, 1293–1299, 2006.
 RNA interference-significance and applications. Justyna Stanisławska and Waldemar
L. Olszewski. Arch Immunol Ther Exp, 2005, 53, 39–46 .
 RNA interference revolution. Archana Thakur. Electronic Journal of Biotechnology
ISSN: 0717-3458, Vol.6 No.1, April 15, 2003.
 RNA Interference: Endogenous siRNAs Derived from Transposable Elements. Darren
J. Obbard and David J. Finnegan. Current Biology, Vol 18, No 13, R562.
 Review of the Application of RNA Interference Technology in the Pharmaceutical
Industry. Henny M. Martineu, Ian T. Pyrah. Toxicologic pathology; 35:327–336; 2007.
 RNA interference. Gregory J. Hannon. Nature, Vol 418, 11 July 2002.
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REFERENCES

36.  RNA Interference – A fine tuner of gene regulation: a Review. S.K. Dash, Sushil K.
Mohapatra and H.N. Malik. Int. J. Biotechnol. Mol. Biol. Res: Vol. 6(5) pp. 35-39,
June 2015.
 RNA Interference and its Role in Cancer Therapy. Behzad Mansoori, Siamak
Sandoghchian Shotorbani, Behzad Baradaran. Adv Pharm Bull, 2014, 4(4), 313-321.
 Mammalian RNAi: a practical guide Peter Sandy, Andrea Ventura, and Tyler Jacks.
BioTechniques 39:215-224: August 2005.
 RNAi therapeutics: Principles, prospects and challenges. Lars Aagaard, John J.
Rossi. Advanced Drug Delivery Reviews 59:75–86, 2007.
 Current prospects for RNA interference-based therapies. Beverly L. Davidson and
Paul B. McCray. Nature reviews, genetics. Volume 12, May 2011.
 Gene Therapy Using RNAi. Yang Yu-Lin1, Chang Wen-Teng and Shih Yuan-Wei.
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REFERENCES

37. THANK YOU!
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