Data integration to prioritize drugs using genomics and curated data

BioData Mining

Volumn 9, Issue 1, 2016, Pages

  Louhimo, Riku ^a   Laakso, Marko ^a   Belitskin, Denis ^a   Klefström, Juha ^a   Lehtonen, Rainer ^a   Hautaniemi, Sampsa ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Breast cancer; Cancer; Data integration; Drug prioritization; Gene ontology

Indexed keywords

ANTINEOPLASTIC AGENT; CYCLIN DEPENDENT KINASE INHIBITOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2 INHIBITOR; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; FIBROBLAST GROWTH FACTOR RECEPTOR 3; FIBROBLAST GROWTH FACTOR RECEPTOR INHIBITOR; RECEPTOR BLOCKING AGENT; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; CHEMOSENSITIVITY; COHORT ANALYSIS; CONCEPTUAL FRAMEWORK; DATA MINING; DATA PROCESSING; DRUG INFORMATION; DRUG TARGETING; ESTROGEN RECEPTOR POSITIVE BREAST CANCER; GENOMICS; GOPREDICT; KNOWLEDGE BASE; MATHEMATICAL COMPUTING; MOLECULAR GENETICS; OVARY CANCER; PRIMARY TUMOR; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

EID: 84971013934     PISSN: None     EISSN: 17560381     Source Type: Journal    
DOI: 10.1186/s13040-016-0097-1     Document Type: Article

References (64)

1. Holohan C, Van Schaeybroeck S, et al. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer. 2013; 13:714-26.
2. Paul SM, Mytelka DS, et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov. 2010; 9:203-14.
3. Li YY, Jones S. Drug repositioning for personalized medicine. Genome Med. 2012; 4:27.
4. Simon R. The use of genomics in clinical trial design. Clin Cancer Res. 2008; 14:5984-993.
5. McDermott U, Downing JR, et al. Genomics and the continuum of cancer care. N Engl J Med. 2011; 364:340-50.
6. Haber DA, Gray NS, et al. The evolving war on cancer. Cell. 2011; 145:19-24.
7. Hood L, Friend SH. Predictive, personalized, preventive, participatory (P4) cancer medicine. Nat Rev Clin Oncol. 2011; 8:184-7.
8. Mirnezami R, Nicholson J, et al. Preparing for precision medicine. N Engl J Med. 2012; 366:489-91.
9. Creixell P, Schoof EM, et al. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol. 2012; 30(9):842-8.
10. Kristensen VN, Lingjærde OC, et al. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer. 2014; 14:299-313.
11. Chen R, Mias G, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012; 148:1293-1307.
12. Louhimo R, Lepikhova T, et al. Comparative analysis of algorithms for integration of copy number and expression data. Nat Methods. 2012; 9:351-5.
13. Dudley JT, Deshpande T, et al. Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform. 2011; 12:303-11.
14. Hurle M, Yang L, et al. Computational drug repositioning: from data to therapeutics. Clin Pharmacol Ther. 2013; 93:335-41.
15. Jin G, Wong ST. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014; 19:637-44.
16. Masica DL, Karchin R. Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Res. 2013; 73:1699-1708.
17. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455:1061-8.
18. The Cancer Genome Atlas Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011; 474:609-15.
19. The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490:61-70.
20. Kolde R, Laur S, et al. Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics. 2012; 28:573-80.
21. Aerts S, Lambrechts D, et al. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006; 24:537-44.
22. Botstein D, Cherry J, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25-9.
23. Chowdhury S, Sarkar RR. Comparison of human cell signaling pathway databases - evolution, drawbacks and challenges. Database. 2015; 2015:bau126.
24. Nguyen N, Lindsey M, et al. Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses. BMC Genom. 2015; 16(Suppl 7):18.
25. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012; 487:330-7.
26. Ovaska K, Laakso M, et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med. 2010; 2:65.
27. Louhimo R, Hautaniemi S. CNAmet: an R package for integration of copy number, expression and methylation data. Bioinformatics. 2011; 27:887-8.
28. Liu C, Louhimo R, et al. Identification of sample-specific regulations using integrative network level analysis. BMC Cancer. 2015; 15(1):319.
29. Beroukhim R, Mermel CH, et al. The landscape of somatic copy-number alteration across human cancers. Nature. 2010; 463:899-905.
30. Futreal PA, Coin L, et al. A census of human cancer genes. Nat Rev Cancer. 2004; 4:177-83.
31. Forbes SA, Bindal N, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011; 39:945.
32. Santarius T, Shipley J, et al. A census of amplified and overexpressed human cancer genes. Nat Rev Cancer. 2010; 10:59-64.
33. Bos PD, Xiang HFZ, et al. Genes that mediate breast cancer metastasis to the brain. Nature. 2009; 459:1005.
34. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001; 29:1165-88.
35. Kanehisa M, Goto S, et al. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010; 38:355-60.
36. Knox C, Law V, et al. Drugbank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011; 39:1035-41.
37. Laakso M, Hautaniemi S. Integrative platform to translate gene sets to networks. Bioinformatics. 2010; 26:1802-3.
38. Brooks JD. Translational genomics: the challenge of developing cancer biomarkers. Genome Res. 2012; 22(2):183-7.
39. Hudis CA. Trastuzumab - mechanism of action and use in clinical practice. N Engl J Med. 2007; 357:39-51.
40. Sørlie T, Perou CM, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA. 2001; 98:10869-74.
41. Subramanian A, Tamayo P, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005; 102:15545-50.
42. Tenhagen M, van Diest PJ, et al. Fibroblast growth factor receptors in breast cancer: expression, downstream effects, and possible drug targets. Endocr Relat Cancer. 2012; 19:115-29.
43. Dienstmann R, Rodon J, et al. Genomic aberrations in the FGFR pathway: opportunities for targeted therapies in solid tumors. Ann Oncol. 2014; 25:552-63.
44. Fabian MA, Biggs WH, et al. A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol. 2005; 23:329-36.
45. Brooks AN, Kilgour E, et al. Molecular pathways: fibroblast growth factor signaling: a new therapeutic opportunity in cancer. Clin Cancer Res. 2012; 18:1855-62.
46. André F, Bachelot T, et al. Targeting FGFR with dovitinib (TKI258): preclinical and clinical data in breast cancer. Clin Cancer Res. 2013; 19:3693-702.
47. Burstein HJ, Temin S, et al. Adjuvant endocrine therapy for women with hormone receptor-positive breast cancer: American society of clinical oncology clinical practice guideline focused update. J Clin Oncol. 2014; 32:2255-269.
48. Tomlinson DC, Knowles MA, et al. Mechanisms of FGFR3 actions in endocrine resistant breast cancer. Int J Cancer. 2012; 130:2857-866.
49. Meijer D, Sieuwerts AM, et al. Fibroblast growth factor receptor 4 predicts failure on tamoxifen therapy in patients with recurrent breast cancer. Endocr Relat Cancer. 2008; 15:101-11.
50. Sikora MJ, Cooper KL, et al. Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Res. 2014; 74:1463-74.
51. Ramaswamy B, Lu Y, et al. Hedgehog signaling is a novel therapeutic target in tamoxifen-resistant breast cancer aberrantly activated by PI3K/AKT pathway. Cancer Res. 2012; 72:5048-059.
52. Gradishar WJ. Emerging approaches for treating HER2-positive metastatic breast cancer beyond trastuzumab. Ann Oncol. 2013; 24:2492-500.
53. Leon LJ, Pasupuleti N, et al. A cell-permeant amiloride derivative induces caspase-independent, AIF-mediated programmed necrotic death of breast cancer cells. PloS ONE. 2013; 8:63038.
54. Rowson-Hodel A, Berg A, et al. Hexamethylene amiloride engages a novel reactive oxygen species- and lysosome-dependent programmed necrotic mechanism to selectively target breast cancer cells. Cancer Lett. 2016. doi: 10.1016/j.canlet.2016.02.042.
55. Lauritzen G, Stock CM, et al. The Na+/H+ exchanger NHE1, but not the Na+, cotransporter NBCn1, regulates motility of MCF7 breast cancer cells expressing constitutively active ErbB2. Cancer Lett. 2012; 317:172-83.
56. Cicenas J, Valius M. The CDK inhibitors in cancer research and therapy. J Cancer Res Clin Oncol. 2011; 137:1409-18.
57. Kusume T, Tsuda H, et al. The p16-Cyclin D1/CDK4-pRb pathway and clinical outcome in Epithelial ovarian cancer. Clin Cancer Res. 1999; 5:4152-157.
58. Guha M. Cyclin-dependent kinase inhibitors move into phase III. Nat Rev Drug Discov. 2012; 11:892-4.
59. Taylor-Harding B, Agadjanian H, et al. Abstract B48: Targeting chemo-resistance in CCNE1-amplified ovarian cancer. Clin Cancer Res. 2013; 19:48.
60. Wiedemeyer WR, Beach JA, et al. Reversing platinum resistance in high-grade serous ovarian carcinoma: targeting BRCA and the homologous recombination system. Front Oncol. 2014;4.
61. Davis AP, Grondin CJ, et al. The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res. 2015; 43(D1):D914-D920.
62. Haitina T, Lindblom J, et al. Fourteen novel human members of mitochondrial solute carrier family 25 (SLC25) widely expressed in the central nervous system. Genomics. 2006; 88:779-90.
63. Hooijberg J, Jansen G, et al. Folates provoke cellular efflux and drug resistance of substrates of the multidrug resistance protein 1 (MRP1). Cancer Chemother Pharmacol. 2014; 73:911-7.
64. Uhlén M, Fagerberg L, et al. Tissue-based map of the human proteome. Science. 2015; 347:1260419.