A genome scale overexpression screen to reveal drug activity in human cells

Genome Medicine

Volumn 6, Issue 4, 2014, Pages

  Arnoldo, Anthony ^a,b   Kittanakom, Saranya ^a,b   Heisler, Lawrence E ^a,b   Mak, Anthony B ^a,b   Shukalyuk, Andrey I ^c   Torti, Dax ^a   Moffat, Jason ^a,b   Giaever, Guri ^a,b,d   Nislow, Corey ^a,b,d  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALVESPIMYCIN; AMINOPTERIN; BLEOMYCIN; CISPLATIN; METHOTREXATE; MITOMYCIN; TETRAHYDROLIPSTATIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR RHOXF2; UNCLASSIFIED DRUG;

ARTICLE; BIOLOGICAL ACTIVITY; CONTROLLED STUDY; CROSS HYBRIDIZATION; DNA DAMAGE; DNA SYNTHESIS; GENE OVEREXPRESSION; HEK293 CELL LINE; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; MAMMAL CELL; MOLECULAR CLONING; MULTIGENE FAMILY; PRIORITY JOURNAL; PROTEIN SYNTHESIS; UPREGULATION; WESTERN BLOTTING;

EID: 84901327956     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm549     Document Type: Article

References (48)

1. Jarosz DF, Taipale M, Lindquist S. Protein homeostasis and the phenotypic manifestation of genetic diversity: principles and mechanisms. Annu Rev Genet 2010, 44:189-216. 10.1146/annurev.genet.40.110405.090412, 21047258.
2. Nobeli I, Favia AD, Thornton JM. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 2009, 27:157-167. 10.1038/nbt1519, 19204698.
3. Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008, 4:682-690. 10.1038/nchembio.118, 18936753.
4. Strebhardt K, Ullrich A. Paul Ehrlich's magic bullet concept: 100 years of progress. Nat Rev Cancer 2008, 8:473-480. 10.1038/nrc2394, 18469827.
5. Agarwal R, Kaye SB. Ovarian cancer: strategies for overcoming resistance to chemotherapy. Nat Rev Cancer 2003, 3:502-516. 10.1038/nrc1123, 12835670.
6. Seruga B, Ocana A, Tannock IF. Drug resistance in metastatic castration-resistant prostate cancer. Nat Rev Clin Oncol 2011, 8:12-23. 10.1038/nrclinonc.2010.136, 20859283.
7. Curt GA, Carney DN, Cowan KH, Jolivet J, Bailey BD, Drake JC, Chien Song KS, Minna JD, Chabner BA. Unstable methotrexate resistance in human small-cell carcinoma associated with double minute chromosomes. N Engl J Med 1983, 308:199-202. 10.1056/NEJM198301273080406, 6294518.
8. Cohen SN, Chang AC, Boyer HW, Helling RB. Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A 1973, 70:3240-3244. 10.1073/pnas.70.11.3240, 427208, 4594039.
9. Chang AC, Nunberg JH, Kaufman RJ, Erlich HA, Schimke RT, Cohen SN. Phenotypic expression in E. coli of a DNA sequence coding for mouse dihydrofolate reductase. Nature 1978, 275:617-624. 10.1038/275617a0, 360074.
10. Rine J, Hansen W, Hardeman E, Davis RW. Targeted selection of recombinant clones through gene dosage effects. Proc Natl Acad Sci U S A 1983, 80:6750-6754. 10.1073/pnas.80.22.6750, 390063, 6316322.
11. Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C, Vandenhaute J, Cusick ME, Albala JS, Hill DE, Vidal M. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 2004, 14:2128-2135. 10.1101/gr.2973604, 528929, 15489335.
12. Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 2007, 89:307-315. 10.1016/j.ygeno.2006.11.012, 17207965.
13. Shin KJ, Wall EA, Zavzavadjian JR, Santat LA, Liu J, Hwang JI, Rebres R, Roach T, Seaman W, Simon MI, Fraser ID. A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc Natl Acad Sci U S A 2006, 103:13759-13764. 10.1073/pnas.0606179103, 1557799, 16945906.
14. Yang X, Boehm JS, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE. A public genome-scale lentiviral expression library of human ORFs. Nat Methods 2011, 8:659-661. 10.1038/nmeth.1638, 3234135, 21706014.
15. ArrayExpress. [http://www.ebi.ac.uk/arrayexpress/].
16. Vichai V, Kirtikara K. Sulforhodamine B colorimetric assay for cytotoxicity screening. Nat Protoc 2006, 1:1112-1116. 10.1038/nprot.2006.179, 17406391.
17. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM. Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006, 7:R100. 10.1186/gb-2006-7-10-r100, 1794559, 17076895.
18. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009, 10:48. 10.1186/1471-2105-10-48, 2644678, 19192299.
19. Abcam Immunohistochemistry Procedure. [http://docs.abcam.com/pdf/protocols/Short_IHC-P_protocol.pdf].
20. Vander Heiden MG. Targeting cancer metabolism: a therapeutic window opens. Nat Rev Drug Discov 2011, 10:671-684. 10.1038/nrd3504, 21878982.
21. Farber S, Diamond LK, Mercer RD, Sylvester RF, Wolff JA. Temporary remissions in acute leukemia in children produced by folic acid antagonist, 4-aminopteroyl-glutamic acid (aminopterin). N Engl J Med 1948, 238:787-793. 10.1056/NEJM194806032382301, 18860765.
22. Shi Y, Burn P. Lipid metabolic enzymes: emerging drug targets for the treatment of obesity. Nat Rev Drug Discov 2004, 3:695-710. 10.1038/nrd1469, 15286736.
23. Hogan S, Fleury A, Hadvary P, Lengsfeld H, Meier MK, Triscari J, Sullivan AC. Studies on the antiobesity activity of tetrahydrolipstatin, a potent and selective inhibitor of pancreatic lipase. Int J Obes 1987, 11:35-42.
24. Rose JL, Reeves KC, Likhotvorik RI, Hoyt DG. Base excision repair proteins are required for integrin-mediated suppression of bleomycin-induced DNA breakage in murine lung endothelial cells. J Pharmacol Exp Ther 2007, 321:318-326. 10.1124/jpet.106.113498, 17202402.
25. Kelland LR. Emerging drugs for ovarian cancer. Expert Opin Emerg Drugs 2005, 10:413-424. 10.1517/14728214.10.2.413, 15934876.
26. Iyer VN, Szybalski W. A molecular mechanism of mitomycin action: linking of complementary DNA strands. Proc Natl Acad Sci U S A 1963, 50:355-362. 10.1073/pnas.50.2.355, 221180, 14060656.
27. Egorin MJ, Lagattuta TF, Hamburger DR, Covey JM, White KD, Musser SM, Eiseman JL. Pharmacokinetics, tissue distribution, and metabolism of 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin (NSC 707545) in CD2F1 mice and Fischer 344 rats. Cancer Chemother Pharmacol 2002, 49:7-19. 10.1007/s00280-001-0380-8, 11855755.
28. Cole PD, Kamen BA, Gorlick R, Banerjee D, Smith AK, Magill E, Bertino JR. Effects of overexpression of gamma-Glutamyl hydrolase on methotrexate metabolism and resistance. Cancer Res 2001, 61:4599-4604.
29. Karlsson M, Reue K, Xia YR, Lusis AJ, Langin D, Tornqvist H, Holm C. Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene. Gene 2001, 272:11-18. 10.1016/S0378-1119(01)00559-5, 11470505.
30. Saario SM, Laitinen JT. Monoglyceride lipase as an enzyme hydrolyzing 2-arachidonoylglycerol. Chem Biodivers 2007, 4:1903-1913. 10.1002/cbdv.200790158, 17712832.
31. Chen J, Stubbe J. Bleomycins: towards better therapeutics. Nat Rev Cancer 2005, 5:102-112. 10.1038/nrc1547, 15685195.
32. Shen CC, Wertelecki W, Driggers WJ, LeDoux SP, Wilson GL. Repair of mitochondrial DNA damage induced by bleomycin in human cells. Mutat Res 1995, 337:19-23. 10.1016/0921-8777(95)00008-8, 7541109.
33. Rossi MN, Carbone M, Mostocotto C, Mancone C, Tripodi M, Maione R, Amati P. Mitochondrial localization of PARP-1 requires interaction with mitofilin and is involved in the maintenance of mitochondrial DNA integrity. J Biol Chem 2009, 284:31616-31624. 10.1074/jbc.M109.025882, 2797232, 19762472.
34. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316:1160-1166. 10.1126/science.1140321, 17525332.
35. Wayne CM, MacLean JA, Cornwall G, Wilkinson MF. Two novel human X-linked homeobox genes, hPEPP1 and hPEPP2, selectively expressed in the testis. Gene 2002, 301:1-11. 10.1016/S0378-1119(02)01087-9, 12490318.
36. Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ, Hide W. Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A 2008, 105:20422-20427. 10.1073/pnas.0810777105, 2603434, 19088187.
37. Korkola JE, Houldsworth J, Chadalavada RS, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti RS. Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res 2006, 66:820-827. 10.1158/0008-5472.CAN-05-2445, 16424014.
38. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009, 10:252-263. 10.1038/nrg2538, 19274049.
39. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 2008, 9:102. 10.1186/1471-2164-9-102, 2292177, 18304323.
40. Yang VW. Eukaryotic transcription factors: identification, characterization and functions. J Nutr 1998, 128:2045-2051.
41. Nishiyama A, Sharov AA, Piao Y, Amano M, Amano T, Hoang HG, Binder BY, Tapnio R, Bassey U, Malinou JN, Correa-Cerro LS, Yu H, Xin L, Meyers E, Zalzman M, Nakatake Y, Stagg C, Sharova L, Qian Y, Dudekula D, Sheer S, Cadet JS, Hirata T, Yang HT, Goldberg I, Evans MK, Longo DL, Schlessinger D, Ko MS. Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells. Sci Rep 2013, 3:1390. 3589720, 23462645.
42. Hoon S, Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, St Onge RP, Nislow C. An integrated platform of genomic assays reveals small-molecule bioactivities. Nat Chem Biol 2008, 4:498-506. 10.1038/nchembio.100, 18622389.
43. Skalamera D, Dahmer M, Purdon AS, Wilson BM, Ranall MV, Blumenthal A, Gabrielli B, Gonda TJ. Generation of a genome scale lentiviral vector library for EF1alpha promoter-driven expression of human ORFs and identification of human genes affecting viral titer. PLoS One 2012, 7:e51733. 10.1371/journal.pone.0051733, 3520899, 23251614.
44. Skalamera D, Ranall MV, Wilson BM, Leo P, Purdon AS, Hyde C, Nourbakhsh E, Grimmond SM, Barry SC, Gabrielli B, Gonda TJ. A high-throughput platform for lentiviral overexpression screening of the human ORFeome. PLoS One 2011, 6:e20057. 10.1371/journal.pone.0020057, 3101218, 21629697.
45. Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJ. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods 2011, 8:1050-1052. 10.1038/nmeth.1764, 3263363, 22037702.
46. Huang Z, Chen K, Zhang J, Li Y, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Liu D, Chen R, Sucgang RS, Pan X. A functional variomics tool for discovering drug-resistance genes and drug targets. Cell Rep 2013, 3:577-585. 10.1016/j.celrep.2013.01.019, 3594652, 23416056.
47. Maclean JA, Chen MA, Wayne CM, Bruce SR, Rao M, Meistrich ML, Macleod C, Wilkinson MF. Rhox: a new homeobox gene cluster. Cell 2005, 120:369-382. 10.1016/j.cell.2004.12.022, 15707895.
48. MacLean JA, Wilkinson MF. The Rhox genes. Reproduction 2010, 140:195-213. 10.1530/REP-10-0100, 20430877.