A high-throughput siRNA screening platform to identify MYC-synthetic lethal genes as candidate therapeutic targets

Methods in Molecular Biology

Volumn 1012, Issue , 2013, Pages 187-200

  Grandori, Carla ^a  

^a USA   (United States)

Author keywords

Cancer; High throughput screening; MYC; Oncogenes; RNA interference; siRNA screens; Synthetic lethal genes; Therapeutic targets

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; ESSENTIAL GENE; GENE IDENTIFICATION; GENE TARGETING; HIGH THROUGHPUT SCREENING; HUMAN; LETHAL GENE; ONCOGENE MYC; PRIORITY JOURNAL; SENESCENCE;

GENE EXPRESSION; GENES, LETHAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR TARGETED THERAPY; NEOPLASMS; PROTO-ONCOGENE PROTEINS C-MYC; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 84934441310     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-429-6_12     Document Type: Article

References (39)

1. Soucek L, Whitfield J, Martins CP, Finch AJ, Murphy DJ, Sodir NM, Karnezis AN, Swigart LB, Nasi S, Evan GI (2008) Modelling Myc inhibition as a cancer therapy. Nature 455: 679-683
2. Felsher DW, Bishop JM (1999) Reversible tumorigenesis by MYC in hematopoietic lineages. Mol Cell 4: 199-207
3. Jain M, Arvanitis C, Chu K, Dewey W, Leonhardt E, Trinh M, Sundberg CD, Bishop JM, Felsher DW (2002) Sustained loss of a neoplastic phenotype by brief inactivation of MYC. Science 297: 102-104
4. Evan GI, Wyllie AH, Gilbert CS, Littlewood TD, Land H, Brooks M, Waters CM, Penn LZ, Hancock DC (1992) Induction of apoptosis in fibroblasts by c-myc protein. Cell 69: 119-128
5. Juin P, Hueber AO, Littlewood T, Evan G (1999) c-Myc-induced sensitization to apoptosis is mediated through cytochrome c release. Genes Dev 13: 1367-1381
6. Morrish F, Isern N, Sadilek M, Jeffrey M, Hockenbery DM (2009) c-Myc activates multiple metabolic networks to generate substrates for cell-cycle entry. Oncogene 28: 2485-2491
7. Dang CV (2011) Therapeutic targeting of Myc-reprogrammed cancer cell metabolism. Cold Spring Harb Symp Quant Biol 76: 369-374
8. Barna M, Pusic A, Zollo O, Costa M, Kondrashov N, Rego E, Rao PH, Ruggero D (2008) Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency. Nature 456: 971-975
9. Mai S, Fluri M, Siwarski D, Huppi K (1996) Genomic instability in MycER-activated Rat1A-MycER cells. Chromosome Res 4: 365-371
10. Felsher DW, Zetterberg A, Zhu J, Tlsty T, Bishop JM (2000) Overexpression of MYC causes p53-dependent G2 arrest of normal fibroblasts. Proc Natl Acad Sci USA 97: 10544-10548
11. Wade M, Wahl GM (2006) c-Myc, genome instability, and tumorigenesis: the devil is in the details. Curr Top Microbiol Immunol 302: 169-203
12. Goga A, Yang D, Tward AD, Morgan DO, Bishop JM (2007) Inhibition of CDK1 as a potential therapy for tumors over-expressing MYC. Nat Med 13: 820-827
13. Dominguez-Sola D, Ying CY, Grandori C, Ruggiero L, Chen B, Li M, Galloway DA, Gu W, Gautier J, Dalla-Favera R (2007) Nontranscriptional control of DNA replication by c-Myc. Nature 448: 445-451
14. Robinson K, Asawachaicharn N, Galloway DA, Grandori C (2009) c-Myc accelerates S-phase and requires WRN to avoid replication stress. PLoS One 4:e5951
15. Yang D, Liu H, Goga A, Kim S, Yuneva M, Bishop JM (2010) Therapeutic potential of a synthetic lethal interaction between the MYC proto-oncogene and inhibition of aurora-B kinase. Proc Natl Acad Sci USA 107: 13836-13841
16. Moser R, Toyoshima M, Robinson K, Gurley KE, Howie HL, Davison J, Morgan M, Kemp CJ, Grandori C (2012) MYC-driven tumorigenesis is inhibited by WRN syndrome gene deficiency. Mol Cancer Res 10: 535-545
17. Hartwell LH, Szankasi P, Roberts CJ, Murray AW, Friend SH (1997) Integrating genetic approaches into the discovery of anticancer drugs. Science 278: 1064-1068
18. Kaelin WG Jr (2005) The concept of synthetic lethality in the context of anticancer therapy. Nat Rev Cancer 5: 689-698
19. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428: 427-431
20. Hu G, Kim J, Xu Q, Leng Y, Orkin SH, Elledge SJ (2009) A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 23: 837-848
21. Blakely K, Ketela T, Moffat J (2011) Pooled lentiviral shRNA screening for functional genomics in mammalian cells. Methods Mol Biol 781: 161-182
22. Toyoshima M, Howie HL, Imakura M, Walsh RM, Annis JE, Chang AN, Frazier J, Chau BN, Loboda A, Linsley PS, Cleary MA, Park JR, Grandori C (2012) Functional genomics identifies therapeutic targets for MYC-driven cancer. Proc Natl Acad Sci USA 109: 9545-9550
23. Kessler JD, Kahle KT, Sun T, Meerbrey KL, Schlabach MR, Schmitt EM, Skinner SO, Xu Q, Li MZ, Hartman ZC, Rao M, Yu P, Dominguez-Vidana R, Liang AC, Solimini NL, Bernardi RJ, Yu B, Hsu T, Golding I, Luo J, Osborne CK, Creighton CJ, Hilsenbeck SG, Schiff R, Shaw CA, Elledge SJ, Westbrook TF (2012) A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science 335: 348-353
24. Liu L, Ulbrich J, Muller J, Wustefeld T, Aeberhard L, Kress TR, Muthalagu N, Rycak L, Rudalska R, Moll R, Kempa S, Zender L, Eilers M, Murphy DJ (2012) Deregulated MYC expression induces dependence upon AMPK-related kinase 5. Nature 483: 608-612
25. Benanti JA, Galloway DA (2004) Normal human fibroblasts are resistant to RASinduced senescence. Mol Cell Biol 24: 2842-2852
26. Benanti JA, Wang ML, Myers HE, Robinson KL, Grandori C, Galloway DA (2007) Epigenetic down-regulation of ARF expression is a selection step in immortalization of human fibroblasts by c-Myc. Mol Cancer Res 5: 1181-1189
27. Wang ML, Walsh R, Robinson KL, Burchard J, Bartz SR, Cleary M, Galloway DA, Grandori C (2011) Gene expression signature of c-MYC-immortalized human fibroblasts reveals loss of growth inhibitory response to TGFbeta. Cell Cycle 10: 2540-2548
28. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C (2011) Pathway commons, a web resource for biological pathway data. Nucleic Acids Res 39:D685-690
29. Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4: 67-73
30. Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE (2009) Statistical methods for analysis of highthroughput RNA interference screens. Nat Methods 6: 569-575
31. Chung N, Zhang XD, Kreamer A, Locco L, Kuan PF, Bartz S, Linsley PS, Ferrer M, Strulovici B (2008) Median absolute deviation to improve hit selection for genome-scale RNAi screens. J Biomol Screen 13: 149-158
32. Jackson AL, Linsley PS (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 9: 57-67
33. Chau BN, Diaz RL, Saunders MA, Cheng C, Chang AN, Warrener P, Bradshaw J, Linsley PS, Cleary MA (2009) Identification of SULF2 as a novel transcriptional target of p53 by use of integrated genomic analyses. Cancer Res 69: 1368-1374
34. Meerbrey KL, Hu G, Kessler JD, Roarty K, Li MZ, Fang JE, Herschkowitz JI, Burrows AE, Ciccia A, Sun T, Schmitt EM, Bernardi RJ, Fu X, Bland CS, Cooper TA, Schiff R, Rosen JM, Westbrook TF, Elledge SJ (2011) The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo. Proc Natl Acad Sci USA 108: 3665-3670
35. Zuber J, McJunkin K, Fellmann C, Dow LE, Taylor MJ, Hannon GJ, Lowe SW (2010) Toolkit for evaluating genes required for proliferation and survival using tetracyclineregulated RNAi. Nat Biotechnol 29: 79-83
36. Scuoppo C, Miething C, Lindqvist L, Reyes J, Ruse C, Appelmann I, Yoon S, Krasnitz A, Teruya-Feldstein J, Pappin D, Pelletier J, Lowe SW (2012) A tumour suppressor network relying on the polyamine-hypusine axis. Nature 487: 244-248
37. Schuhmacher M, Staege MS, Pajic A, Polack A, Weidle UH, Bornkamm GW, Eick D, Kohlhuber F (1999) Control of cell growth by c-Myc in the absence of cell division. Curr Biol 9: 1255-1258
38. Lutz W, Stohr M, Schurmann J, Wenzel A, Lohr A, Schwab M (1996) Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. Oncogene 13: 803-812
39. Mateyak MK, Obaya AJ, Adachi S, Sedivy JM (1997) Phenotypes of c-Myc-deficient rat fibroblasts isolated by targeted homologous recombination. Cell Growth Differ 8:1039-1048