mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities

Molecular Cancer Therapeutics

Volumn 9, Issue 5, 2010, Pages 1080-1091

  Liu, Hongfang ^a   D'Andrade, Petula ^b,c   Fulmer Smentek, Stephanie ^b,c   Lorenzi, Philip ^a,d   Kohn, Kurt W ^a   Weinstein, John N ^a,d   Pommier, Yves ^a   Reinhold, William C ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b AGILENT TECHNOLOGIES   (United States)

^c University of Texas M D Anderson Cancer Center ^*

^d GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMSACRINE; ANCITABINE; APHIDICOLIN; BUSULFAN; CAMPTOTHECIN DERIVATIVE; CARMUSTINE; CHLORMETHINE; CYTARABINE; DAUNORUBICIN; DIANHYDROGALACTITOL; DOXORUBICIN; ETOPOSIDE; GUANAZOLE; HEPSULFAM; HYDROXYUREA; LOMUSTINE; MELPHALAN; MENOGARIL; MESSENGER RNA; MICRORNA; MITOMYCIN C; MITOXANTRONE; OXANTHRAZOLE; PIPERAZINEDIONE; PORFIROMYCIN; SEMUSTINE; TENIPOSIDE; THIOTEPA; UNINDEXED DRUG; ZORUBICIN;

ANTINEOPLASTIC ACTIVITY; ARTICLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REPRODUCIBILITY; RNA ANALYSIS;

ANTINEOPLASTIC AGENTS; CELL LINE, TUMOR; DATABASES, FACTUAL; DRUG INTERACTIONS; DRUG RESISTANCE, NEOPLASM; DRUG SCREENING ASSAYS, ANTITUMOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HCT116 CELLS; HT29 CELLS; HUMANS; MICRORNAS; NATIONAL CANCER INSTITUTE (U.S.); OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; RNA, NEOPLASM; TISSUE BANKS; TREATMENT OUTCOME; UNITED STATES;

EID: 77952202405     PISSN: 15357163     EISSN: None     Source Type: Journal    
DOI: 10.1158/1535-7163.MCT-09-0965     Document Type: Article

References (46)

1. Jay C, Nemunaitis J, Chen P, Fulgham P, Tong AW. mi RNA profiling for diagnosis and prognosis of human cancer. DNA Cell Biol 2007; 26:293-300. (Pubitemid 46799178)
2. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 2009;136:642-655
3. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-297
4. Aravin A, Tuschl T. Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett 2005;579:5830-5840 (Pubitemid 41484129)
5. Barad O, Meiri E, Avniel A, et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 2004;14:2486-2494
6. Friedman JM, Jones PA. MicroRNAs: critical mediators of differentiation, development and disease. Swiss Med Wkly 2009;139:466-472
7. Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005;3:e85.
8. Zhang B, Pan X, Cobb GP, Anderson TA. microRNAs as oncogenes and tumor suppressors. Dev Biol 2007;302:1-12. (Pubitemid 46096921)
9. Hwang HW, Mendell JT. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer 2006;94:776-780
10. Akao Y, Nakagawa Y, Naoe T. let-7 microRNA functions as a potential growth suppressor in human colon cancer cells. Biol Pharm Bull 2006;29:903-906
11. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer 2006;6:857.
12. Calin GA, Croce CM. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res 2006;66:7390.
13. Croce CM, Calin GA. miRNAs, cancer, and stem cell division. Cell 2005;122:6-7. (Pubitemid 40977933)
14. Calin GA, Ferracin M, Cimmino A, et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005;353:1793-1801
15. Lowery AJ, Miller N, McNeill RE, Kerin MJ. MicroRNAs as prognostic indicators and therapeutic targets: potential effect on breast cancer management. Clin Cancer Res 2008;14:360.
16. Saumet A, Vetter G, Cougot N, et al. microRNA-associated therapies. In: Ying S-Y, editor. Current Perspectives in MicroRNAs (miRNA). The Hague, Netherlands; 2008. p. 395-429.
17. Weinstein JN. Spotlight on molecular profiling:" Integromic" analysis of the NCI-60 cancer cell lines. Mol Cancer Ther 2006;5:2601.
18. Shoemaker RH. The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 2006;6:813-823
19. Bussey KJ, Chin K, Lababidi S, et al. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 2006;5:853-867
20. Scherf U, Ross DT, Waltham M, et al. A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000;24:236-244 (Pubitemid 30132190)
21. Weinstein JN. Integromic analysis of the NCI-60 cancer cell lines. Breast Dis 2004;19:11-22. (Pubitemid 39485511)
22. Gaur A, Jewell DA, Liang Y, et al. Characterization of MicroRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 2007;67:2456.
23. Blower PE, Verducci JS, Lin S, et al. MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther 2007;6:1483.
24. Shankavaram UT, Reinhold WC, Nishizuka S, et al. Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther 2007;6:820-832
25. Ikediobi ON, Davies H, Bignell G, et al. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther 2006;5: 2606-2612
26. Lorenzi PL, Reinhold WC, Rudelius M, et al. Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells. Mol Cancer Ther 2006;5:2613-2623
27. Okabe M, Szakacs G, Reimers MA, et al. Profiling SLCO and SLC22 genes in the NCI-60 cancer cell lines to identify drug uptake transporters. Mol Cancer Ther 2008;7:3081-3091
28. Orina JN, Calcagno AM, Wu CP, et al. Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database. Mol Cancer Ther 2009;8:2057-2066
29. Stevens EV, Nishizuka S, Antony S, et al. Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers. Mol Cancer Ther 2008;7:10-18
30. Weinstein JN, Kohn KW, Grever MR, et al. Neural computing in cancer drug development: predicting mechanism of action. Science 1992;258:447-451
31. Weinstein JN, Myers TG, O'Connor PM, et al. An information-intensive approach to the molecular pharmacology of cancer. Science 1997;275:343-349
32. Genomics and Bioinformatics Group. Bethesda, MD: Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, DHHS. Available from: http://discover.nci.nih.gov.
33. NCI-60 DTP Human Tumor Cell Line Screen. Bethesda, MD: NCI. Available from: http://dtp.nci.nih.gov/branches/btb/ivclsp.html.
34. CellMiner. Bethesda, MD: Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI. Available from: http://discover. nci.nih.gov/cellminer.
35. Annereau JP, Szakacs G, Tucker CJ, et al. Analysis of ATP-binding cassette transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance &boxs. Mol Pharmacol 2004;66:1397-1405
36. DTP. DTP Human Tumor Cell Line Screen. [cited 2009 May 21, 2009]; Standard mechanism. Available from: http://dtp.nci.nih.gov/ docs/cancer/ searches/standard-mechanism-list.html.
37. Blower PE, Yang C, Fligner MA, et al. Pharmacogenomic analysis: correlating molecular substructure classes with microarray gene expression data. Pharmacogenomics J 2002;2:259-271 (Pubitemid 35023584)
38. CIMMiner. Bethesda, MD: Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI. Available from: http://discover. nci.nih.gov/cimminer.
39. Ramsköld D, Wang ET, Burge CB, Sandberg R, Jensen LJ, Embl G. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLOS Comput Biol 2009;5:e1000598.
40. Pradervand S, Weber J, Thomas J, et al. Impact of normalization on miRNA microarray expression profiling. RNA 2009;15:493.
41. Ross DT, Scherf U, Eisen MB, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000;24: 227-235
42. Bethesda, MD: Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI. Available from: http://discover.nci.nih.gov.
43. Stinson SF, Alley MC, Kopp WC, et al. Morphological and immunocytochemical characteristics of human tumor cell lines for use in a disease-oriented anticancer drug screen. Anticancer Res 1992;12: 1035-1053
44. Okuda S, Yamada T, Hamajima M, et al. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 2008;36: W423-6.
45. Blower PE, Chung JH, Verducci JS, et al. MicroRNAs modulate the chemosensitivity of tumor cells. Mol Cancer Ther 2008;7:1.
46. Bethesda, MD: Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI. Available from: http://discover.nci.nih.gov/ cellminerdata/NCI60- MCT/index.html.