Applications of RNA interference highthroughput screening technology in cancer biology and virology

Abstract

RNA interference (RNAi) is an ancient intra-cellular mechanism that regulates gene expression and cell function. Large-scale gene silencing using RNAi high-throughput screening (HTS) has opened an exciting frontier to systematically study gene function in mammalian cells. This approach enables researchers to identify gene function in a given biological context and will provide considerable novel insight. Here, we review RNAi HTS strategies and applications using case studies in cancer biology and virology.

Keywords

RNA interference (RNAi) / short interfering RNA (siRNA) / short hairpin RNA (shRNA) / high-throughput screening / cancer / virology

References

[1] Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF (2000) The genome sequence of Drosophila melanogaster. Science 287: 2185-2195

[2] Almeida R, Allshire RC (2005) RNA silencing and genome regulation. Trends Cell Biol15: 251-258

[3] Ashworth A, Lord CJ, Reis-Filho JS (2011) Genetic interactions in cancer progression and treatment. Cell145: 30-38

[4] Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou LH (2012) Sequence analysis of mutations and translocations across breast cancer subtypes. Nature486: 405-409

[5] Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P, Meylan E, Scholl C (2009) Systematic RNA interference reveals that oncogenic KRASdriven cancers require TBK1. Nature462: 108-112

[6] Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N (2012) Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet44: U107-U685

[7] Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C (2011) The genomic complexity of primary human prostate cancer. Nature470: 214-220

[8] Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409: 363-366

[9] Beronja S, Janki P, Heller E, Lien WH, Keyes BE, Oshimori N, Fuchs E (2013) RNAi screens in mice identify physiological regulators of oncogenic growth. Nature501(7466): 185-190

[10] Boutros M, Ahringer J (2008) The art and design of genetic screens: RNA interference. Nat Rev Genet9: 554-566

[11] Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ (2008) Identification of host proteins required for HIV infection through a functional genomic screen. Science319: 921-926

[12] Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E (2009) The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell139: 1243-1254

[13] Cherry S, Doukas T, Armknecht S, Whelan S, Wang H, Sarnow P, Perrimon N (2005) Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev19: 445-452

[14] Cipriano R, Graham J, Miskimen KL, Bryson BL, Bruntz RC, Scott SA, Brown HA, Stark GR, Jackson MW (2012) FAM83B mediates EGFR- and RAS-driven oncogenic transformation. J Clin Invest122: 3197-3210

[15] Corcoran RB, Cheng KA, Hata AN, Faber AC, Ebi H, Coffee EM, Greninger P, Brown RD, Godfrey JT, Cohoon TJ (2013) Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models. Cancer Cell23: 121-128

[16] Echeverri CJ, Perrimon N (2006) High-throughput RNAi screening in cultured cells: a user’s guide. Nat Rev Genet7: 373-384

[17] Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature411: 494-498

[18] Fellmann C, Lowe SW (2014) Stable RNA interference rules for silencing. Nat Cell Biol16: 10-18

[19] Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by doublestranded RNA in Caenorhabditis elegans. Nature391: 806-811

[20] Friedel CC, Haas J (2011) Virus-host interactomes and global models of virus-infected cells. Trends Microbiol19: 501-508

[21] Gao S, Giansanti MG, Buttrick GJ, Ramasubramanyan S, Auton A, Gatti M, Wakefield JG (2008) Australin: a chromosomal passenger protein required specifically for Drosophila melanogaster male meiosis. J Cell Biol180: 521-535

[22] Geisbert TW, Lee AC, Robbins M, Geisbert JB, Honko AN, Sood V, Johnson JC, de Jong S, Tavakoli I, Judge A (2010) Postexposure protection of non-human primates against a lethal Ebola virus challenge with RNA interference: a proof-of-concept study. Lancet375: 1896-1905

[23] Girard MP, Cherian T, Pervikov Y, Kieny MP (2005) A review of vaccine research and development: human acute respiratory infections. Vaccine23: 5708-5724

[24] Guo X, Wang XF (2012) A mediator lost in the war on cancer. Cell151: 927-929

[25] Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell144: 646-674

[26] Hannon GJ (2002) RNA interference. Nature418: 244-251

[27] Hao L, Sakurai A, Watanabe T, Sorensen E, Nidom CA, Newton MA, Ahlquist P, Kawaoka Y (2008) Drosophila RNAiscreen identifies host genes important for influenza virus replication. Nature454: 890-893

[28] He L, Guo L, Vathipadiekal V, Sergent PA, Growdon WB, Engler DA, Rueda BR, Birrer MJ, Orsulic S, Mohapatra G (2013) Identification of LMX1B as a novel oncogene in human ovarian cancer. Oncogene1-10.

[29] Hock J, Meister G (2008) The Argonaute protein family. Genome Biol9: 210

[30] Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci USA103: 17402-17407

[31] Huang S, Holzel M, Knijnenburg T, Schlicker A, Roepman P, McDermott U, Garnett M, Grernrum W, Sun C, Prahallad A (2012) MED12 controls the response tomultiple cancer drugs through regulation of TGF-beta receptor signaling. Cell151: 937-950

[32] Huang L, Jin J, Deighan P, Kiner E, McReynolds L, Lieberman J (2013) Efficient and specific gene knockdown by small interfering RNAs produced in bacteria. Nat Biotechnol31: 350-356

[33] Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol23: 995-1001

[34] Hussain M, Asgari S (2014) MicroRNA-like viral small RNA from dengue virus 2 autoregulates its replication in mosquito cells. Proc Natl Acad Sci USA111: 2746-2751

[35] Iorns E, Lord CJ, Turner N, Ashworth A (2007) Utilizing RNA interference to enhance cancer drug discovery. Nat Rev Drug Discov6: 556-568

[36] Jiang L, Siu MK, Wong OG, Tam KF, Lu X, Lam EW, Ngan HY, Le XF, Wong ES, Monteiro LJ (2011) iASPP and chemoresistance in ovarian cancers: effects on paclitaxel-mediated mitotic catastrophe. Clin Cancer Res17: 6924-6933

[37] Karlas A, Machuy N, Shin Y, Pleissner KP, Artarini A, Heuer D, Becker D, Khalil H, Ogilvie LA, Hess S (2010) Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature463: 818-822

[38] Kim DH, Rossi JJ (2007) Strategies for silencing human disease using RNA interference. Nat Rev Genet8: 173-184

[39] Kittler R, Putz G, Pelletier L, Poser I, Heninger AK, Drechsel D, Fischer S, Konstantinova I, Habermann B, Grabner H (2004) An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature432: 1036-1040

[40] Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, Tu BP, De Jesus PD, Lilley CE (2008) Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell135: 49-60

[41] Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y (2010) Human host factors required for influenza virus replication. Nature463: 813-817

[42] Krausz E (2007) High-content siRNA screening. Mol Biosyst3: 232-240

[43] Kumar MS, Hancock DC, Molina-Arcas M, Steckel M, East P, Diefenbacher M, Armenteros-Monterroso E, Lassailly F, Matthews N, Nye E (2012) The GATA2 transcriptional network is requisite for RAS oncogene-driven non-small cell lung cancer. Cell149: 642-655

[44] Lambert LC, Fauci AS (2010) Influenza vaccines for the future. N Engl J Med363: 2036-2044

[45] Lander ES, Consortium IHGS, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M (2001) Initial sequencing and analysis of the human genome. Nature409: 860-921

[46] Lawson ND, Wolfe SA (2011) Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish. Dev Cell 21: 48-64

[47] Liu YP, Vink MA, Westerink JT, Ramirez de Arellano E, Konstantinova P, Ter Brake O, Berkhout B (2010) Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies. RNA16: 1328-1339

[48] Luo J, Emanuele MJ, Li D, Creighton CJ, Schlabach MR, Westbrook TF, Wong KK, Elledge SJ (2009) A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell137: 835-848

[49] Madan V, Paul D, Lohmann V, Bartenschlager R (2014) Inhibition of HCV replication by cyclophilin antagonists is linked to replication fitness and occurs by inhibition of membranous web formation. Gastroenterology146(5): 1361-72.e1-1361-72.e9

[50] Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell110: 563-574

[51] Mbeunkui F, Johann DJ (2009) Cancer and the tumor microenvironment: a review of an essential relationship. Cancer Chemother Pharmacol 63: 571-582

[52] Mercer J, Snijder B, Sacher R, Burkard C, Bleck CK, Stahlberg H, Pelkmans L, Helenius A (2012) RNAi screening reveals proteasome- and Cullin3-dependent stages in vaccinia virus infection. Cell Rep2: 1036-1047

[53] Moffat J, Sabatini DM (2006) Building mammalian signalling pathways with RNAi screens. Nat Rev Mol Cell Biol7: 177-187

[54] Ng TI, Mo H, Pilot-Matias T, He Y, Koev G, Krishnan P, Mondal R, Pithawalla R, He W, Dekhtyar T (2007) Identification of host genes involved in hepatitis C virus replication by small interfering RNA technology. Hepatology: 1413-1421

[55] Osterholm MT, Kelley NS, Sommer A, Belongia EA (2012) Efficacy and effectiveness of influenza vaccines: a systematic review and meta-analysis. Lancet Infect Dis12: 36-44

[56] Pattle SB, Farrell PJ (2006) The role of Epstein-Barr virus in cancer. Expert Opin Biol Ther6: 1193-1205

[57] Petrocca F, Altschuler G, Tan SM, Mendillo ML, Yan HH, Jerry DJ, Kung AL, Hide W, Ince TA, Lieberman J (2013) A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basallike triple-negative breast cancer cells. Cancer Cell24: 182-196

[58] Reynolds A, Anderson EM, Vermeulen A, Fedorov Y, Robinson K, Leake D, Karpilow J, Marshall WS, Khvorova A (2006) Induction of the interferon response by siRNA is cell type- and duplex length-dependent. RNA12: 988-993

[59] Rositch AF, Soeters HM, Offutt-Powell TN, Wheeler BS, Taylor SM, Smith JS (2014) The incidence of human papillomavirus infection following treatment for cervical neoplasia: a systematic review. Gynecol Oncol132(3): 767-779

[60] Sharma S, Rao A (2009) RNAi screening: tips and techniques. Nat Immunol10: 799-804

[61] Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K (2008) Profiling essential genes in human mammary cells by multiplex RNAi screening. Science319: 617-620

[62] Sims D, Mendes-Pereira AM, Frankum J, Burgess D, Cerone MA, Lombardelli C, Mitsopoulos C, Hakas J, Murugaesu N, Isacke CM (2011) High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing. Genome Biol12(10): 104

[63] Singh A, Sweeney MF, Yu M, Burger A, Greninger P, Benes C, Haber DA, Settleman J (2012) TAK1 inhibition promotes apoptosis in KRAS-dependent colon cancers. Cell148: 639-650

[64] Siu MK, Chan HY, Kong DS, Wong ES, Wong OG, Ngan HY, Tam KF, Zhang H, Li Z, Chan QK (2010) p21-activated kinase 4 regulates ovarian cancer cell proliferation, migration, and invasion and contributes to poor prognosis in patients. Proc Natl Acad Sci USA107: 18622-18627

[65] Siu MK, Wong ES, Kong DS, Chan HY, Jiang L, Wong OG, Lam EW, Chan KK, Ngan HY, Le XF (2013) Stem cell transcription factor NANOG controls cell migration and invasion via dysregulation of E-cadherin and FoxJ1 and contributes to adverse clinical outcome in ovarian cancers. Oncogene32: 3500-3509

[66] Sivan G, Martin SE, Myers TG, Buehler E, Szymczyk KH, Ormanoglu P, Moss B (2013) Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Proc Natl Acad Sci USA110: 3519-3524

[67] Turner NC, Lord CJ, Iorns E, Brough R, Swift S, Elliott R, Rayter S, Tutt AN, Ashworth A (2008) A synthetic lethal siRNA screen identifying genes mediating sensitivity to a PARP inhibitor. EMBO J27: 1368-1377

[68] Wang S, Huang X, Li Y, Lao H, Zhang Y, Dong H, Xu W, Li JL, Li M (2011) RN181 suppresses hepatocellular carcinoma growth by inhibition of the ERK/MAPK pathway. Hepatology53: 1932-1942

[69] Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P (2002) Initial sequencing and comparative analysis of the mouse genome. Nature420: 520-562

[70] Yang D, Buchholz F, Huang ZD, Goga A, Chen CY, Brodsky FM, Bishop JM (2002) Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA99: 9942-9947

[71] Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science296: 79-92

[72] Zhou H, Xu M, Huang Q, Gates AT, Zhang XD, Castle JC, Stec E, Ferrer M, Strulovici B, Hazuda DJ (2008) Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe4: 495-504

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