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.

Key words： 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.

PMID

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