Integrated functional, gene expression and genomic analysis for the identification of cancer targets

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Iorns, Elizabeth ^a   Lord, Christopher J ^a   Grigoriadis, Anita ^a   McDonald, Sarah ^a   Fenwick, Kerry ^a   MacKay, Alan ^a   Mein, Charles A ^b   Natrajan, Rachael ^a   Savage, Kay ^a   Tamber, Narinder ^a   Reis Filho, Jorge S ^a   Turner, Nicholas C ^a   Ashworth, Alan ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^b ROYAL LONDON HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NEW DRUG; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHOTRANSFERASE; CELL CYCLE PROTEIN; NUCLEAR PROTEIN; PIK3CA PROTEIN, HUMAN; PROTEIN TYROSINE KINASE; SMALL INTERFERING RNA; TUMOR PROTEIN; WEE1 PROTEIN, HUMAN;

ARTICLE; BREAST TUMOR; CANCER CELL; CANCER CELL CULTURE; CELL STRAIN MCF 7; CELL SURVIVAL; CELL VIABILITY; CONTROLLED STUDY; DRUG APPROVAL; DRUG TARGETING; GENE EXPRESSION; GENE IDENTIFICATION; GENE MUTATION; GENE SILENCING; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; ONCOGENE; RNA INTERFERENCE; DNA MICROARRAY; DRUG SCREENING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; MOLECULAR GENETICS; NEOPLASM; TUMOR CELL LINE;

1-PHOSPHATIDYLINOSITOL 3-KINASE; CELL CYCLE PROTEINS; CELL LINE, TUMOR; DRUG SCREENING ASSAYS, ANTITUMOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; NEOPLASM PROTEINS; NEOPLASMS; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN-TYROSINE KINASES; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 65249161106     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005120     Document Type: Article

References (37)

1. Collins I, Workman P (2006) New approaches to molecular cancer therapeutics. Nat Chem Biol 2: 689-700.
2. Iorns E, Lord CJ, Turner N, Ashworth A (2007) Utilizing RNA interference to enhance cancer drug discovery. Nat Rev Drug Discov 6: 556-568.
3. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349.
4. Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, et al. (2003) Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 12: 627-637.
5. Mukherji M, Bell R, Supekova L, Wang Y, Orth AP, et al. (2006) Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A 103: 14819-14824.
6. Iorns E, Turner NC, Elliott R, Syed N, Garrone O, et al. (2008) Identification of CDK10 as an Important Determinant of Resistance to Endocrine Therapy for Breast Cancer. Cancer Cell 13: 91-104.
7. MacKeigan JP, Murphy LO, Blenis J (2005) Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemo-resistance. Nat Cell Biol 7: 591-600.
8. Abdi H (2007) Z-Scores. In: Salkind N, ed. Encyclopedia of Measurement and Statistics. Thousand Oaks (CA): Sage. pp 1-4.
9. Karakas B, Bachman KE, Park BH (2006) Mutation of the PIK3CA oncogene in human cancers. Br J Cancer 94: 455-459.
10. Wu G, Xing M, Mambo E, Huang X, Liu J, et al. (2005) Somatic mutation and gain of copy number of PIK3CA in human breast cancer. Breast Cancer Res 7: R609-616.
11. Shayesteh L, Lu Y, Kuo WL, Baldocchi R, Godfrey T, et al. (1999) PIK3CA is implicated as an oncogene in ovarian cancer. Nat Genet 21: 99-102.
12. Ma YY, Wei SJ, Lin YC, Lung JC, Chang TC, et al. (2000) PIK3CA as an oncogene in cervical cancer. Oncogene 19: 2739-2744.
13. Jonkers J, Berns A (2004) Oncogene addiction: sometimes a temporary slavery. Cancer Cell 6: 535-538.
14. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, et al. (2001) Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia. N Engl J Med 344: 1031-1037.
15. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, et al. (2004) A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res 14: 2347-2356.
16. Takeuchi O, Kawai T, Sanjo H, Copeland NG, Gilbert DJ, et al. (1999) TLR6: A novel member of an expanding toll-like receptor family. Gene 231: 59-65.
17. Naugler WE, Sakurai T, Kim S, Maeda S, Kim K, et al. (2007) Gender disparity in liver cancer due to sex differences in MyD88-dependent IL-6 production. Science 317: 121-124.
18. Heald R, McLoughlin M, McKeon F (1993) Human wee1 maintains mitotic timing by protecting the nucleus from cytoplasmically activated Cdc2 kinase. Cell 74: 463-474.
19. Watanabe N, Arai H, Iwasaki J, Shiina M, Ogata K, et al. (2005) Cyclin-dependent kinase (CDK) phosphorylation destabilizes somatic Wee1 via multiple pathways. Proc Natl Acad Sci U S A 102: 11663-11668.
20. Kawabe T (2004) G2 checkpoint abrogators as anticancer drugs. Mol Cancer Ther 3: 513-519.
21. Palmer BD, Thompson AM, Booth RJ, Dobrusin EM, Kraker AJ, et al. (2006) 4-Phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione inhibitors of the checkpoint kinase Wee1. Structure-activity relationships for chromophore modification and phenyl ring substitution. J Med Chem 49: 4896-4911.
22. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-527.
23. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, et al. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10: 529-541.
24. Arriola E, Rodriguez-Pinilla SM, Lambros MB, Jones RL, James M, et al. (2007) Topoisomerase II alpha amplification may predict benefit from adjuvant anthracyclines in HER2 positive early breast cancer. Breast Cancer Res Treat.
25. Savage K, Lambros MB, Robertson D, Jones RL, Jones C, et al. (2007) Caveolin 1 is overexpressed and amplified in a subset of basal-like and metaplastic breast carcinomas: a morphologic, ultrastructural, immunohistochemical, and in situ hybridization analysis. Clin Cancer Res 13: 90-101.
26. Nielsen TO, Hsu FD, Jensen K, Cheang M, Karaca G, et al. (2004) Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 10: 5367-5374.
27. Shaffer AL, Emre NC, Lamy L, Ngo VN, Wright G, et al. (2008) IRF4 addiction in multiple myeloma. Nature 454: 226-231.
28. Silva JM, Marran K, Parker JS, Silva J, Golding M, et al. (2008) Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319: 617-620.
29. Schlabach MR, Luo J, Solimini NL, Hu G, Xu Q, et al. (2008) Cancer proliferation gene discovery through functional genomics. Science 319: 620-624.
30. Boutros M, Bras LP, Huber W (2006) Analysis of cell-based RNAi screens. Genome Biol 7: R66.
31. Du P, Kibbe WA, Lin SM (2007) nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. Biol Direct 2: 16.
32. Lin SM, Du P, Huber W, Kibbe WA (2008) Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36: e11.
33. Reis-Filho JS, Simpson PT, Jones C, Steele D, Mackay A, et al. (2005) Pleomorphic lobular carcinoma of the breast: role of comprehensive molecular pathology in characterization of an entity. J Pathol 207: 1-13.
34. Arriola E, Marchio C, Tan DS, Drury SC, Lambros MB, et al. (2008) Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. Lab Invest.
35. Arriola E, Lambros MB, Jones C, Dexter T, Mackay A, et al. (2007) Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation. Lab Invest 87: 75-83.
36. Harvey JM, Clark GM, Osborne CK, Allred DC (1999) Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer. J Clin Oncol 17: 1474-1481.
37. Rodriguez-Pinilla SM, Jones RL, Lambros MB, Arriola E, Savage K, et al. (2007) MYC amplification in breast cancer: a chromogenic in situ hybridisation study. J Clin Pathol 60: 1017-1023.