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中国生物工程杂志

China Biotechnology
China Biotechnology  2012, Vol. 32 Issue (07): 113-119    DOI:
    
The Types of siRNA Off-target Effects and the Strategies for Mitigation
TANG De-ping1, MAO Ai-hong2, LIAO Shi-qi2, XUE Lin-gui1, ZHANG Bing-lin1
1. The School of Chemical & Biological Engineering, Lanzhou Jiaotong University, lanzhou 730070, China;
2. Institute of Gansu Medical Science Research, lanzhou 730050, China
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Abstract  Small interfering RNAs (siRNAs) can specific silence target genes,and are widely used to elucidate gene function,indentify drug targets and develop more specific therapeutics than are currently available. Off-target effects (OTEs) can complicate the interpretation of phenotypic effects in gene-silencing experiments and can potentially lead to unwanted toxicities. siRNAs OTEs include microRNA-like off-target effects, immune stimulation and saturation of the RNAi machinery. The types of off-target effects of siRNAs and methods to mitigate them was focused, to help enable effective application of RNAi technology.

Key wordsRNAi      siRNA      Off-target effects      MicroRNA-like off-target effects     
Received: 21 February 2012      Published: 25 July 2012
ZTFLH:  Q522  
Cite this article:

TANG De-ping, MAO Ai-hong, LIAO Shi-qi, XUE Lin-gui, ZHANG Bing-lin. The Types of siRNA Off-target Effects and the Strategies for Mitigation. China Biotechnology, 2012, 32(07): 113-119.

URL:

https://manu60.magtech.com.cn/biotech/     OR     https://manu60.magtech.com.cn/biotech/Y2012/V32/I07/113

[1] Tuschl T,Zamore P D,Lehmann R,et al. Targeted mRNA degradation by doubl stranded RNA in vitro. Genes & Dev, 1999, 13(24): 3191-3197.
[2] Richard W C, Erik J. Origins and mechanisms of miRNAs and siRNAs. Cell, 2009, 136(4): 642-655.
[3] Elbashir S M, Martinez J, Patkaniowska A, et al. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J, 2001, 20(23): 6877-6888.
[4] Jackson A L, Linsley P S, Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nature Rev Drug Discov, 2010, 9(1): 57-67.
[5] Jackson A L, Bartz S R, Schelter J, et al. Expression profiling reveals off-target gene regulation by RNAi. Nature Biotech, 2003, 21(6): 635-637.
[6] Jackson A L, Burchard J, Schelter J, et al. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA, 2006(7), 12: 1179-1187.
[7] Wang Y L, Juranek S, Li H T, et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature, 2008, 456(7724): 921-926.
[8] Lin X Y, Ruan XA, Anderson M G, et al. siRNA-mediated off-target gene silence triggered by a 7nt complementation. Nucleic Acid Res, 2005, 33(14): 4527-4535.
[9] Burchard J, Jackson A L, Malkov V, et al. MicroRNA-like off-target transcript regulation by siRNAs is species specific. RNA, 2009, 15(2): 308-315.
[10] Cullen B R. Enhancing and confirming the specificity of RNAi experiments. Nature Methods, 2006, 3(9): 677-681.
[11] Echeverri C J, Beachy P A, Baum B, et al. Minimizing the risk of reporting false positives in large-scale RNAi screens. Nature Methods, 2006, 3(10): 777-779.
[12] Kittler R, Pelletier L, Ma C L, et al. RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells. Proc Natl Acad Sci, 2005, 102(7): 2396-2401.
[13] Grimson A, Farh K K H, Johnston W K, et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell, 2007, 27(1): 91-105.
[14] Kittler R, Surendranath V, Heninger A K,et al. Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nature Methods, 2007, 4(4): 337-344.
[15] Jackson A L, Burchard J, Leake D, et al. Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA, 2006, 12(7): 1197-1205.
[16] Caffrey D R, Zhao J, Song Z L, et al. siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS ONE, 2011, 6(7): e21503.
[17] Lu X Z, Yang G D, Zhang J, et al. The sense strand pre-cleaved RNA duplex mediates an efficient RNA interference with less off-target and immune response effects. Applied Microbiology and Biotechnology, 2011, 90(2): 583-589.
[18] Vaish N, Chen F, Seth S, et al. Improved specificity of gene silencing by siRNAs containing Unlocked nucleobase analogs. Nucleic Acids Research, 2011, 39(5): 1823-1832.
[19] Petri S, Dueck A, Lehmann G, et al. Increased siRNA duplex stability correlates with reduced off-target and elevated on-target effects. RNA, 2011, 17(4): 551-554.
[20] Boudreau R L, Spengler R M, Davidson B L. Rational design of therapeutic siRNAs:minimizing off-targeting potential to improve the safety of RNAi therapy for huntington’s disease. Molecular Therapy, 2011, 19(9):2169-2177.
[21] Persengiev S P, Zhu X C, Green M R. Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA, 2004, 10(1): 12-18.
[22] Klinghoffer R A, Magnus J, Schelter J, et al. Reduced seed region-based off-target activity with lentivirus-mediated RNAi. RNA, 2010, 16(5): 879-884.
[23] Elbashir S M, Harborth J, Lendecke W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 2001, 411(6836): 494-498.
[24] Robbins M, Judg A, MacLachlan I. siRNA and innate immunity. Oligonucleotides, 2009, 19(2):89-102.
[25] Hornung V, Biller M G, Bourquin C, et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nature Med, 2005, 11(3): 263-270.
[26] Judge A D, Sood V, Shaw J R, et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nature Biotechnol, 2005, 23(4): 457-462.
[27] Diebold S S, Kaisho T, Hemmi H, et al. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. Science, 2004, 303(5663): 1529-1531.
[28] Heil F, Hemmi H, Hochrein H, et al. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science, 2004, 303(5663): 1526-1529.
[29] Forsbach A, Nemorin J G, Montino C, et al. Identification of RNA sequence motif stimulating sequence-specific TLR8-dependent immune responses. J Immunol, 2008, 180(6): 3729-3738.
[30] Goodchild A, Nopper N, King A, et al. Sequence determinants of innate immune activation by short interfering RNAs. BMC Immunol, 2009, 10: 40.
[31] Robbins M,Judge A,Ambegia E,et al. Misinterpreting the therapeutic effects of siRNA caused by immune stimulation. Hum Gene Ther, 2008, 19(10): 991-999.
[32] Kleinman M E, Yamada K, TakedaA, et al. Sequence-and target-independent angiogenesis suppression by siRNA via TLR3. Nature, 2008, 452(7187): 591-597.
[33] Armstrong M E, Gantier M, Li L L, et al. Small interfering RNAs induce macrophage migration inhibitory factor production and proliferation in breast cancer cell via a double-stranded RNA-dependent protein kinase-dependent mechanism. J Immunol, 2008, 180(11): 7125-7133.
[34] Eberle F, Gieβler K, Deck C, et al. Modifications in small interfering RNA that separate immunostimulation from RNA interference. J Immunol, 2008, 180(5): 3229-3237.
[35] Braasch D A, Corey D R. Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol, 2001, 8(1): 1-7.
[36] Judge A D, Bola G, Lee A C H, et al. Design of noninflammatory synthetic siRNA mediating potent gene silencing in vivo. Mol Ther, 2006, 13(3): 494-505.
[37] Robbins M, Judge A, Liang L, et al. 2'-O-methyl-modified RNAs act as TLR7 antagonists. Mol Ther, 2007, 15(9): 1663-1669.
[38] Sioud M. Induction of inflammatory cytokines and interferon responses by double-stranded and single-stranded siRNAs is sequence-dependent and requires endosomal localization. J Mol Biol, 2005, 348(5): 1079-1090.
[39] Yi R, Doehle B P, Qin Y, et al. Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNA and microRNAs. RNA, 2005, 11(2): 220-226.
[40] Grimm D, Streetz K L, Jopling C L, et al. Fatality in mice due to over saturation of cellular microRNA/short hairpin RNA pathways. Nature, 2006, 441(7092): 537-541.
[41] Bitko V, Musiyenko A, Shulyayeva O, et al. Inhibition of respiratory viruses by nasally administered siRNA. Nature Med, 2004, 11(1): 50-55.
[42] Hutvagner G, Simard M J, Mello C C, et al. Sequence-specific inhibition of small RNA function. PLoS Biology, 2004, 2(4): E98.
[43] John M, Constien R,Akinc A, et al. Effective RNAi-mediated gene silencing without interruption of the endogenous microRNA pathway. Nature, 2007, 449(7163): 745-747.
[44] Khan A A, Betel D, Miller M L, et al. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nature Biotechnol, 2009, 27(6): 549-555.
[45] Lares M R, Rossi J J,Ouellet D L,RNAi and small interfering RNAs in human disease therapeutic applications. Trends in Biotechnology, 2010, 28(11): 570-579.
[46] Ulrich W, Inga N, Mehmet K T, et al. Targeted delivery of short interfering RNAs -strategies for in vivo delivery. Recent Patents on Anti-Cancer Drug Discovery, 2009, 4(1): 1-8.
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