Integrating the NCI-60 data with "omics" for drug discovery

Drug Development Research

Volumn 73, Issue 7, 2012, Pages 420-429

  Burkard, Mark E ^a  

^a UNIVERSITY OF WISCONSIN   (United States)

Author keywords

gene expression; methotrexate; NCI 60; variance

Indexed keywords

BLEOMYCIN; BORTEZOMIB; CARBOPLATIN; CISPLATIN; CYCLOPHOSPHAMIDE; CYTARABINE; DOXORUBICIN; EPIDERMAL GROWTH FACTOR RECEPTOR; FLOXURIDINE; FLUOROURACIL; GEMCITABINE; HALICHONDRIN B; IFOSFAMIDE; MELPHALAN; METHOTREXATE; MITOXANTRONE; PACLITAXEL; PROCARBAZINE; RAPAMYCIN; TAMOXIFEN; TOPOTECAN; VINCRISTINE;

CANCER CELL CULTURE; CANCER INHIBITION; CELL PROLIFERATION; DRUG SCREENING; DRUG SENSITIVITY; DRUG TARGETING; GENE EXPRESSION; GENOMICS; HUMAN; NATIONAL HEALTH ORGANIZATION; NONHUMAN; PROTEIN EXPRESSION; REVIEW;

EID: 84870057798     PISSN: 02724391     EISSN: 10982299     Source Type: Journal    
DOI: 10.1002/ddr.21033     Document Type: Review

References (35)

1. Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, et al. 2008. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res 68: 415-424.
2. Baggerly KA, Coombes KR,. 2009. Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology. Ann Appl Stat 3: 1309-1334.
3. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, et al. 2012. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483: 603-607.
4. Blower PE, Verducci JS, Lin S, Zhou J, Chung JH, Dai Z, Liu CG, Reinhold W, Lorenzi PL, Kaldjian EP, et al. 2007. MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther 6: 1483-1491.
5. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay, Kouros-Mehr H, Fridlyand J, et al. 2006. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 5: 853-867.
6. Chabner BA,. 1990. In defense of cell-line screening. J Natl Cancer Inst 82: 1083-1085.
7. Chang JT, Carvalho C, Mori S, Bild AH, Gatza ML, Wang Q, Lucas JE, Potti A, Febbo PG, West M, et al. 2009. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell 34: 104-114.
8. Dhar S, Nygren P, Csoka K, Botling J, Nilsson K, Larsson R,. 1996. Anti-cancer drug characterisation using a human cell line panel representing defined types of drug resistance. Br J Cancer 74: 888-896.
9. Einhorn LH, Donohue J,. 1977. Cis-diamminedichloroplatinum, vinblastine, and bleomycin combination chemotherapy in disseminated testicular cancer. Ann Intern Med 87: 293-298.
10. Einhorn LH, Williams SD,. 1979. The role of cis-platinum in solid-tumor therapy. N Engl J Med 300: 289-291.
11. Farmer H, McCabe N, Lord CJ, Tutt AN, Johnson DA, Richardson TB, Santarosa M, Dillon KJ, Hickson I, Knights C, et al. 2005. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434: 917-921.
12. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, et al. 2012. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483: 570-575.
13. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, Israel MA,. 2007. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67: 2456-2468.
14. Gmeiner WH, Reinhold WC, Pommier Y,. 2010. Genome-wide mRNA and microRNA profiling of the NCI 60 cell-line screen and comparison of FdUMP[10] with fluorouracil, floxuridine, and topoisomerase 1 poisons. Mol Cancer Ther 9: 3105-3114.
15. Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S, Santarius T, Avis T, Barthorpe S, Brackenbury L, et al. 2006. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther 5: 2606-2612.
16. Izquierdo MA, Shoemaker RH, Flens MJ, Scheffer GL, Wu L, Prather TR, Scheper RJ,. 1996. Overlapping phenotypes of multidrug resistance among panels of human cancer-cell lines. Int J Cancer 65: 230-237.
17. Jain M, Nilsson R, Sharma S, Madhusudhan N, Kitami T, Souza AL, Kafri R, Kirschner MW, Clish CB, Mootha VK,. 2012. Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science 336: 1040-1044.
18. Liu H, D'Andrade P, Fulmer-Smentek S, Lorenzi P, Kohn KW, Weinstein JN, Pommier Y, Reinhold WC,. 2010. mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Mol Cancer Ther 9: 1080-1091.
19. Monks A, Scudiero D, Skehan P, Shoemaker R, Paull K, Vistica D, Hose C, Langley J, Cronise P, Vaigro-Wolff A, et al. 1991. Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. J Natl Cancer Inst 83: 757-766.
20. Monks A, Scudiero DA, Johnson GS, Paull KD, Sausville EA,. 1997. The NCI anti-cancer drug screen: a smart screen to identify effectors of novel targets. Anticancer Drug Des 12: 533-541.
21. Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, et al. 2003. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A 100: 14229-14234.
22. Omenn GS, (Chair). 2012. Evolution of translational omics: lessons learned and the path forward. Washington, DC: National Academies Press.
23. Park ES, Rabinovsky R, Carey M, Hennessy BT, Agarwal R, Liu W, Ju Z, Deng W, Lu Y, Woo HG, et al. 2010. Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set. Mol Cancer Ther 9: 257-267.
24. Paull KD, Lin CM, Malspeis L, Hamel E,. 1992. Identification of novel antimitotic agents acting at the tubulin level by computer-assisted evaluation of differential cytotoxicity data. Cancer Res 52: 3892-3900.
25. Paull KD, Shoemaker RH, Hodes L, Monks A, Scudiero DA, Rubinstein L, Plowman J, Boyd MR,. 1989. Display and analysis of patterns of differential activity of drugs against human tumor cell lines: development of mean graph and COMPARE algorithm. J Natl Cancer Inst 81: 1088-1092.
26. Roschke AV, Tonon G, Gehlhaus KS, McTyre N, Bussey KJ, Lababidi S, Scudiero DA, Weinstein JN, Kirsch IR,. 2003. Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res 63: 8634-8647.
27. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, et al. 2000. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24: 227-235.
28. Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, et al. 2007. Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther 6: 820-832.
29. Shen L, Kondo Y, Ahmed S, Boumber Y, Konishi K, Guo Y, Chen X, Vilaythong JN, Issa JP,. 2007. Drug sensitivity prediction by CpG island methylation profile in the NCI-60 cancer cell line panel. Cancer Res 67: 11335-11343.
30. Shoemaker RH,. 2006. The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 6: 813-823.
31. Sokilde R, Kaczkowski B, Podolska A, Cirera S, Gorodkin J, Moller S, Litman T,. 2011. Global microRNA analysis of the NCI-60 cancer cell panel. Mol Cancer Ther 10: 375-384.
32. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, et al. 2001. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 98: 10787-10792.
33. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
34. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, et al. 2007. The genomic landscapes of human breast and colorectal cancers. Science 318: 1108-1113.
35. Wu L, Smythe AM, Stinson SF, Mullendore LA, Monks A, Scudiero DA, Paull KD, Koutsoukos AD, Rubinstein LV, Boyd MR, et al. 1992. Multidrug-resistant phenotype of disease-oriented panels of human tumor cell lines used for anticancer drug screening. Cancer Res 52: 3029-3034.