Strategies to Antagonize miRNA Functions In Vitro and In Vivo

References

• Ambros V . MicroRNAs and developmental timing. Curr. Opin. Genet. Dev.21 (4), 511–517 (2011).
   PubMed Web of Science ®Google Scholar
• Kim VN , HanJ, SiomiMC. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol.10 (2), 126–139 (2009).
   PubMed Web of Science ®Google Scholar
• Krol J , LoedigeI, FilipowiczW. The widespread regulation of microRNA biogenesis, function and decay. Nat. Rev. Genet.11 (9), 597–610 (2010).
   PubMed Web of Science ®Google Scholar
• Nathans R , ChuCY, SerquinaAK, LuCC, CaoH, RanaTM. Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol. Cell34 (6), 696–709 (2009).
   PubMed Web of Science ®Google Scholar
• Rodriguez A , Griffiths-JonesS, AshurstJL, BradleyA. Identification of mammalian microRNA host genes and transcription units. Genome Res.14 (10A), 1902–1910 (2004).
   PubMed Web of Science ®Google Scholar
• Carthew RW , SontheimerEJ. Origins and mechanisms of miRNAs and siRNAs. Cell136 (4), 642–655 (2009).
   PubMed Web of Science ®Google Scholar
• Murchison EP , HannonGJ. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr. Opin. Cell Biol.16 (3), 223–229 (2004).
   PubMed Web of Science ®Google Scholar
• Chu CY , RanaTM. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol.4 (7), e210 (2006).
   PubMed Web of Science ®Google Scholar
• Li Z , RanaTM. Molecular mechanisms of RNA-triggered gene silencing machineries. Acc. Chem. Res.45 (7), 1122–1131 (2012).
   PubMed Web of Science ®Google Scholar
• Rana TM . Illuminating the silence: understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell Biol.8 (1), 23–36 (2007).
   PubMed Web of Science ®Google Scholar
• Bagga S , BrachtJ, HunterSet al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell122 (4), 553–563 (2005).
   PubMed Web of Science ®Google Scholar
• Fabian MR , SonenbergN, FilipowiczW. Regulation of mRNA translation and stability by microRNAs. Annu. Rev. Biochem.79, 351–379 (2010).
   PubMed Web of Science ®Google Scholar
• Guo H , IngoliaNT, WeissmanJS, BartelDP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature466 (7308), 835–840 (2010).
   PubMed Web of Science ®Google Scholar
• Friedman RC , FarhKK, BurgeCB, BartelDP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res.19 (1), 92–105 (2009).
   PubMed Web of Science ®Google Scholar
• Betel D , WilsonM, GabowA, MarksDS, SanderC. The microRNA.org resource: targets and expression. Nucleic Acids Res.36 (Database issue), D49–D153 (2008).
   Google Scholar
• Griffiths-Jones S , SainiHK, Van DongenS, EnrightAJ. miRBase: tools for microRNA genomics. Nucleic Acids Res.36 (Database issue), D154–D158 (2008).
   PubMed Web of Science ®Google Scholar
• Lall S , GrunD, KrekAet al. A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol.16 (5), 460–471 (2006).
   PubMed Web of Science ®Google Scholar
• Chi SW , ZangJB, MeleA, DarnellRB. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature460 (7254), 479–486 (2009).
   PubMed Web of Science ®Google Scholar
• Hafner M , LandthalerM, BurgerLet al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell141 (1), 129–141 (2010).
   PubMed Web of Science ®Google Scholar
• Baigude H , Ahsanullah, Li Z, ZhouY, RanaTM. miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew. Chem. Int. Ed. Engl.51 (24), 5880–5883 (2012).
   PubMed Web of Science ®Google Scholar
• Park CY , ChoiYS, McManusMT. Analysis of microRNA knockouts in mice. Hum. Mol. Genet.19 (R2), R169–175 (2010).
   PubMedGoogle Scholar
• Ebert MS , SharpPA. MicroRNA sponges: progress and possibilities. RNA16 (11), 2043–2050 (2010).
   PubMed Web of Science ®Google Scholar
• Kota J , ChivukulaRR, O'DonnellKAet al. Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell137 (6), 1005–1017 (2009).
   PubMed Web of Science ®Google Scholar
• Henry JC , Azevedo-PoulyAC, SchmittgenTD. MicroRNA replacement therapy for cancer. Pharm. Res.28 (12), 3030–3042 (2011).
   PubMed Web of Science ®Google Scholar
• Hamilton MP , RajapaksheK, HartigSMet al. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat. Commun.4, 2730 (2013).
   PubMed Web of Science ®Google Scholar
• Munker R , CalinGA. MicroRNA profiling in cancer. Clin. Sci. (Lond.)121 (4), 141–158 (2011).
   PubMed Web of Science ®Google Scholar
• Chang TC , YuD, LeeYSet al. Widespread microRNA repression by Myc contributes to tumorigenesis. Nat. Genet.40 (1), 43–50 (2008).
   PubMed Web of Science ®Google Scholar
• Croce CM . Causes and consequences of microRNA dysregulation in cancer. Nat. Rev. Genet.10 (10), 704–714 (2009).
   PubMed Web of Science ®Google Scholar
• Volinia S , CalinGA, LiuCGet al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc. Natl Acad. Sci. USA103 (7), 2257–2261 (2006).
   PubMed Web of Science ®Google Scholar
• Landgraf P , RusuM, SheridanRet al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell129 (7), 1401–1414 (2007).
   PubMed Web of Science ®Google Scholar
• Pundhir S , GorodkinJ. MicroRNA discovery by similarity search to a database of RNA-seq profiles. Front. Genet.4, 133 (2013).
   PubMedGoogle Scholar
• Brown M , SuryawanshiH, HafnerM, FaraziTA, TuschlT. Mammalian miRNA curation through next-generation sequencing. Front. Genet.4, 145 (2013).
   PubMedGoogle Scholar
• Garzon R , MarcucciG, CroceCM. Targeting microRNAs in cancer: rationale, strategies and challenges. Nat. Rev. Drug Discov.9 (10), 775–789 (2010).
   PubMed Web of Science ®Google Scholar
• Montgomery RL , Van RooijE. Therapeutic advances in MicroRNA targeting. J. Cardiovasc. Pharmacol.57 (1), 1–7 (2011).
   PubMed Web of Science ®Google Scholar
• Esau C , DavisS, MurraySFet al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab.3 (2), 87–98 (2006).
   PubMed Web of Science ®Google Scholar
• Krutzfeldt J , RajewskyN, BraichRet al. Silencing of microRNAs in vivo with ‘antagomirs’. Nature438 (7068), 685–689 (2005).
   PubMed Web of Science ®Google Scholar
• Elmen J , LindowM, SchutzSet al. LNA-mediated microRNA silencing in non-human primates. Nature452 (7189), 896–899 (2008).
   PubMed Web of Science ®Google Scholar
• Jopling CL , YiM, LancasterAM, LemonSM, SarnowP. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science309 (5740), 1577–1581 (2005).
   PubMed Web of Science ®Google Scholar
• Pedersen IM , ChengG, WielandSet al. Interferon modulation of cellular microRNAs as an antiviral mechanism. Nature449 (7164), 919–922 (2007).
   PubMed Web of Science ®Google Scholar
• Lanford RE , Hildebrandt-EriksenES, PetriAet al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science327 (5962), 198–201 (2010).
   PubMed Web of Science ®Google Scholar
• Najafi-Shoushtari SH , KristoF, LiYet al. MicroRNA-33 and the SREBP host genes cooperate to control cholesterol homeostasis. Science328 (5985), 1566–1569 (2010).
   PubMed Web of Science ®Google Scholar
• Rayner KJ , SheedyFJ, EsauCCet al. Antagonism of miR-33 in mice promotes reverse cholesterol transport and regression of atherosclerosis. J. Clin. Invest.121 (7), 2921–2931 (2011).
   PubMed Web of Science ®Google Scholar
• Rayner KJ , SuarezY, DavalosAet al. MiR-33 contributes to the regulation of cholesterol homeostasis. Science328 (5985), 1570–1573 (2010).
   PubMed Web of Science ®Google Scholar
• Rayner KJ , EsauCC, HussainFNet al. Inhibition of miR-33a/b in non-human primates raises plasma HDL and lowers VLDL triglycerides. Nature478 (7369), 404–407 (2011).
   PubMed Web of Science ®Google Scholar
• Mi S , LuJ, SunMet al. MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc. Natl Acad. Sci. USA104 (50), 19971–19976 (2007).
   PubMed Web of Science ®Google Scholar
• Yu F , YaoH, ZhuPet al. let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell131 (6), 1109–1123 (2007).
   PubMed Web of Science ®Google Scholar
• Esquela-Kerscher A , TrangP, WigginsJFet al. The let-7 microRNA reduces tumor growth in mouse models of lung cancer. Cell Cycle7 (6), 759–764 (2008).
   PubMed Web of Science ®Google Scholar
• Kumar MS , ErkelandSJ, PesterREet al. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc. Natl Acad. Sci. USA105 (10), 3903–3908 (2008).
   PubMed Web of Science ®Google Scholar
• Chorn G , Klein-McdowellM, ZhaoLet al. Single-stranded microRNA mimics. RNA18 (10), 1796–1804 (2012).
   PubMed Web of Science ®Google Scholar
• Ebert MS , SharpPA. Emerging roles for natural microRNA sponges. Curr. Biol.20 (19), R858–R861 (2010).
   PubMed Web of Science ®Google Scholar
• Choi WY , GiraldezAJ, SchierAF. Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science318 (5848), 271–274 (2007).
   PubMed Web of Science ®Google Scholar
• Broderick JA , ZamorePD. MicroRNA therapeutics. Gene Ther.18 (12), 1104–1110 (2011).
   PubMed Web of Science ®Google Scholar
• Robertson B , DalbyAB, KarpilowJ, KhvorovaA, LeakeD, VermeulenA. Specificity and functionality of microRNA inhibitors. Silence1 (1), 10 (2010).
   PubMedGoogle Scholar
• Obad S , Dos SantosCO, PetriAet al. Silencing of microRNA families by seed-targeting tiny LNAs. Nat. Genet.43 (4), 371–378 (2011).
   PubMed Web of Science ®Google Scholar
• Chiu YL , RanaTM. siRNA function in RNAi: a chemical modification analysis. RNA9 (9), 1034–1048 (2003).
   PubMed Web of Science ®Google Scholar
• Meister G , LandthalerM, DorsettY, TuschlT. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA10 (3), 544–550 (2004).
   PubMed Web of Science ®Google Scholar
• Chiu YL , RanaTM. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol. Cell10 (3), 549–561 (2002).
   PubMed Web of Science ®Google Scholar
• Davis S , ProppS, FreierSMet al. Potent inhibition of microRNA in vivo without degradation. Nucleic Acids Res.37 (1), 70–77 (2009).
   PubMed Web of Science ®Google Scholar
• Esau CC . Inhibition of microRNA with antisense oligonucleotides. Methods44 (1), 55–60 (2008).
   PubMed Web of Science ®Google Scholar
• Braasch DA , CoreyDR. Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem. Biol.8 (1), 1–7 (2001).
   PubMed Web of Science ®Google Scholar
• Kloosterman WP , LagendijkAK, KettingRF, MoultonJD, PlasterkRH. Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development. PLoS Biol.5 (8), e203 (2007).
   PubMed Web of Science ®Google Scholar
• Torres AG , FabaniMM, VigoritoEet al. Chemical structure requirements and cellular targeting of microRNA-122 by peptide nucleic acids anti-miRs. Nucleic Acids Res.40 (5), 2152–2167 (2012).
   PubMed Web of Science ®Google Scholar
• Lennox KA , BehlkeMA. A direct comparison of anti-microRNA oligonucleotide potency. Pharm. Res.27 (9), 1788–1799 (2010).
   PubMed Web of Science ®Google Scholar
• Lennox KA , BehlkeMA. Chemical modification and design of anti-miRNA oligonucleotides. Gene Ther.18 (12), 1111–1120 (2011).
   PubMed Web of Science ®Google Scholar
• Torres AG , FabaniMM, VigoritoE, GaitMJ. MicroRNA fate upon targeting with anti-miRNA oligonucleotides as revealed by an improved Northern-blot-based method for miRNA detection. RNA17 (5), 933–943 (2011).
   PubMed Web of Science ®Google Scholar
• Lu Y , XiaoJ, LinHet al. A single anti-microRNA antisense oligodeoxyribonucleotide (AMO) targeting multiple microRNAs offers an improved approach for microRNA interference. Nucleic Acids Res.37 (3), e24 (2009).
   PubMed Web of Science ®Google Scholar
• Horwich MD , ZamorePD. Design and delivery of antisense oligonucleotides to block microRNA function in cultured Drosophila and human cells. Nat. Protoc.3 (10), 1537–1549 (2008).
   PubMed Web of Science ®Google Scholar
• Takahashi M , YamadaN, HatakeyamaHet al. In vitro optimization of 2′-OMe-4′-thioribonucleoside-modified anti-microRNA oligonucleotides and its targeting delivery to mouse liver using a liposomal nanoparticle. Nucleic Acids Res.41 (22), 10659–10667 (2013).
   PubMed Web of Science ®Google Scholar
• Muthiah M , ParkIK, ChoCS. Nanoparticle-mediated delivery of therapeutic genes: focus on miRNA therapeutics. Expert Opin. Drug Deliv.10 (9), 1259–1273 (2013).
   PubMed Web of Science ®Google Scholar
• Muthiah M , IslamMA, ChoCS, HwangJE, ChungIJ, ParkIK. Substrate-mediated delivery of microRNA-145 through a polysorbitol-based osmotically active transporter suppresses smooth muscle cell proliferation: implications for restenosis treatment. J. Biomed. Nanotechnol.10 (4), 571–579 (2014).
   PubMed Web of Science ®Google Scholar
• Anand S , MajetiBK, AcevedoLMet al. MicroRNA-132-mediated loss of p120RasGAP activates the endothelium to facilitate pathological angiogenesis. Nat. Med.16 (8), 909–914 (2010).
   PubMed Web of Science ®Google Scholar
• Cheng CJ , SaltzmanWM. Polymer nanoparticle-mediated delivery of microRNA inhibition and alternative splicing. Mol. Pharm.9 (5), 1481–1488 (2012).
   PubMed Web of Science ®Google Scholar
• Thomas M , Lange-GrunwellerK, DayyoubEet al. PEI-complexed LNA antiseeds as miRNA inhibitors. RNA Biol.9 (8), 1088–1098 (2012).
   PubMed Web of Science ®Google Scholar
• Shi SJ , ZhongZR, LiuJ, ZhangZR, SunX, GongT. Solid lipid nanoparticles loaded with anti-microRNA oligonucleotides (AMOs) for suppression of microRNA-21 functions in human lung cancer cells. Pharm. Res.29 (1), 97–109 (2012).
   PubMed Web of Science ®Google Scholar
• Zhang M , ZhouX, WangBet al. Lactosylated gramicidin-based lipid nanoparticles (Lac-GLN) for targeted delivery of anti-miR-155 to hepatocellular carcinoma. J. Control. Release168 (3), 251–261 (2013).
   PubMed Web of Science ®Google Scholar
• Hatakeyama H , MurataM, SatoYet al. The systemic administration of an anti-miRNA oligonucleotide encapsulated pH-sensitive liposome results in reduced level of hepatic microRNA-122 in mice. J. Control. Release173, 43–50 (2014).
   PubMed Web of Science ®Google Scholar
• Baigude H , McCarrollJ, YangCS, SwainPM, RanaTM. Design and creation of new nanomaterials for therapeutic RNAi. ACS Chem. Biol.2 (4), 237–241 (2007).
   PubMed Web of Science ®Google Scholar
• Baigude H , SuJ, McCarrollJ, RanaTM. In vivo delivery of RNAi by reducible interfering nanoparticles (iNOPs). ACS Med. Chem. Lett.4, 720–723 (2013).
   PubMed Web of Science ®Google Scholar
• Su J , BaigudeH, McCarrollJ, RanaTM. Silencing microRNA by interfering nanoparticles in mice. Nucleic Acids Res.39 (6), e38 (2011).
   PubMed Web of Science ®Google Scholar