RNA interference (RNAi)

Transcription

1 RN interference (RNi) Natasha aplen ene Silencing Section Office of Science and Technology Partnerships Office of the Director enter for ancer Research National ancer Institute

2 Plants RN silencing. elegans Napoli et al., Plant ell (990) Van der Krol et al., Plant ell (990) 2 29 Fungi Double stranded RN dsrn processing Fire et al., Nature (998) Drosophila Romano & Macino Mol. Microbiol (992) S. pombe s Small interfering RNs (SiRNs) Misquitta & Paterson PNS (999) Kennerdell & arthew ell (998) Mammals Volpe et al., Science (2003) RN induced silencing complex RIS Elbashir et al., Nature (200) aplen et al., PNS (200)

3 RN interference (RNi) & its associated pathways Endogenous mechanism(s) controlling gene expression via silencing Requires double stranded RN (dsrn) or dsrn domain containing molecules ssociated with a number of conserved proteins containing dsrn binding domains Biological roles include: ontrol of endogenous gene expression from protein encoding mrns Heterochromatin formation Silencing of selfish genetic material ntiviral response

4 RNi Down regulation mediated by RNi can occur at a: DN, RN or protein level Determined by: haracteristics of the dsrn trigger The proteins incorporated with the RNi mediating RN protein complex The interaction of the small RN molecule and the target sequence

5 DN Nucleus Modified Short hairpin RNs (shrn mir) ytoplasm Transcription DR8 Pasha Drosha Processing I Precursor mirn Export Pre mirn Pre mirn Exportin5 Primary mirn Pri mirn Heterchromatin DN dsrn Heterochromatin RNs Dicer K9 methylated H3 RIST rgonaute Proteins Short hairpin RNs Processing II leavage sirn duplexes sirn omplex Formation Dicer Dicer rgonaute Proteins ytoplasmic (P ) bodies Repression RIS Mature mirn RNi associated pathways

6 RNi via transcript cleavage or protein blockade Sequence alignment is of importance in determining the mode (cleavage versus repression) and degree (efficacy of cleavage and/or repression) leavage Target 5 3 Repression 2 nt alignment Maximum cleavage 2 7 nt alignment 3 5 Necessary & sufficient for minimal (but potentially functionally relevant) cleavage Target 5 3 X/2 nt alignment Maximum repression 5/7 nt alignment 3 5 Minimal (but potentially functionally relevant) repression

7 Endogenous triggers of RNI: MicroRNs naturally occurring small species of ssrn, ~22 (7 24) nts in size Precursor and mature mirns interact with many of the same proteins as exogenous small RNs (sirns) that mediate RNi Interaction with target mrn decreases protein levels mirn RN induced silencing complex (RIS) interaction with a transcript may induce (a) Translational repression (b) RN cleavage Epigenetic regulation of gene expression through mirn: transcript interactions appears to be critical for multiple cellular process including essential roles in development and differentiation

8 Exogenous triggers of RNs: shrns and sirns ntisense (guide) strand Huppi, Martin, aplen Molecular ell (2005) 7 0

9 Two principal RNi effectors Synthetic sirns and short hairpin RNs Synthetic sirns Double strand oligonucleotides Sense r(n9)dtdt, antisense r(n9)dxdy Short hairpin RNs Single strand molecule requiring intracellular processing an be expressed intracelluarly

10 pplications of RNi Functional genomic analysis up to whole genome Drug: target characterization Novel cellular model systems Transgenic animals Experimental studies of RNi as a therapeutic

11 Therapeutic potential of RNi: ancer Brummelkamp et al., Stable suppression of tumorigenicity by virusmediated RN interference. ancer ell (2002) RS genes are frequently mutated in human cancers, e.g. 85% of pancreatic cancers, 40% or colon carcinomas harbor mutations. Ras genes are guanine nucleotide binding proteins and act as intracellular a signaling proteins and are required for regulation of cell proliferation, differentiation and survival. Therapeutic intervention requires specific elimination of the product from the mutant oncogenic allele Stable & selective loss of tumorigenicity by a retroviral vector that targets the K RSV2 oncogene

12 Therapeutic potential of RNi: Dominant enetic Disease RNi suppresses polyglutamine induced neurodegeneration in a model of spinocerebellar ataxia Xia et al., Nature Medicine (2004) 0,

13 Therapeutic potential of RNi: HIV infection Novina et al., sirn directed inhibition of HIV infection Nature Medicine (2002) p24 sirn inhibits viral replication in HeLa D4 cells. D4 sirn inhibits HIV entry and infection in Magi R5 cells.

14 RNi and issues related to therapy Effects on the normal cellular role of RNi RNi effects on non targeted transcripts ctivation of non specific dsrn cellular responses The establishment of resistance through mutation

15 Effects on the normal cellular role of RNi an the RNi machinery be saturated? Utilization of multiple shrns Transcriptome & proteome analysis mirn expression profiling Functional analysis (e.g. Differentiation)

16 RNi effects on non targeted transcripts Optimization of RNi effector Microarray expression profiling Bioinformatics Functional analysis

17 Optimization of the RNi effector symmetric loading using small RN thermodynamics can be used to favor RIS loading of the antisense (guide) strand Delta nt 5 NTISENSE ss sirn 3

18 Microarray expression profiling Expression profiling reveals off target gene regulation by RNi Jackson et al., Nat. Biotech. (2003) Multiple additional studies show that though the predominate interaction may be the targeted one there can be a significant background of off target interactions.

19 n NME2 Directed sirn Reduces NME Transcript Levels

20 RNi via transcript cleavage or protein blockade Sequence alignment is of importance in determining the mode (cleavage versus repression) and degree (efficacy of cleavage and/or repression) leavage Target 5 3 Repression 2 nt alignment Maximum cleavage 2 7 nt alignment 3 5 Necessary & sufficient for minimal (but potentially functionally relevant) cleavage Target 5 3 X/2 nt alignment Maximum repression 5/7 nt alignment 3 5 Minimal (but potentially functionally relevant) repression

21 RNi non specific effects: Bioinformatic analysis T 6 T T shi target ND ND: calcium channel, voltage dependent, L type, alpha D subunit NM_000720

22 RNi non specific effects: Bioinformatic analysis T T shi target TMPRSS6 TMPRSS6: Transmembrane protease, serine 6 NM_53609

23 RNi non specific effects: Functional analysis Do cells remain functional intact?

24 RNi and activation of non specific dsrn cellular responses ellular responses to dsrn part of anti viral response Frequently result in non specific decrease in protein translation and cell death Size and concentration may play significant role Some sequence motifs within small dsrns may be more potent than others as stimulators of dsrn cellular respones Key proteins include PKR, OS, and Toll 3 receptor

25 RNi and the establishment of resistance through mutation Single nucleotide changes can eliminate RNi Selective pressures could lead to resistance as a result of single nucleotide changes Of more signficance with respect to efficacy

26 Overview RNi is a potent mediate of gene silencing RNi has been successful exploited as a functional genomic tool The move to a clinical application will be determined by the ability to assess the realistic implications of any effects on the RNi machinery, any effects on other cellular transcripts and minimization of non specific effects