Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression

Genome Medicine

Volumn 3, Issue 11, 2011, Pages

  Ben Hamo, Rotem ^a   Efroni, Sol ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CELECOXIB; HSA MICRORNA 9; ISOTRETINOIN; LOMUSTINE; MICRORNA; MITOGEN ACTIVATED PROTEIN KINASE P38; RETINOIC ACID; SORAFENIB; TAMOXIFEN; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CANCER CHEMOTHERAPY; CANCER GROWTH; CANCER PROGNOSIS; DRUG CONTROL; DRUG RESPONSE; FEMALE; GENE DOSAGE; GENE EXPRESSION; GENETIC ALGORITHM; GLIOBLASTOMA; HUMAN; MAJOR CLINICAL STUDY; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL;

EID: 82155202989     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm293     Document Type: Article

References (35)

1. Krex D, Klink B, Hartmann C, von Deimling A, Pietsch T, Simon M, Sabel M, Steinbach JP, Heese O, Reifenberger G, Weller M, Schackert G, . German Glioma Network Long-term survival with glioblastoma multiforme. Brain 2007, 130:2596-2606. 10.1093/brain/awm204, 17785346, German Glioma Network.
2. Prados M, Cloughesy T, Samant M, Fang L, Wen PY, Mikkelsen T, Schiff D, Abrey LE, Yung WK, Paleologos N, Nicholas MK, Jensen R, Vredenburgh J, Das A, Friedman HS. Response as a predictor of survival in patients with recurrent glioblastoma treated with bevacizumab. Neuro Oncol 2011, 13:143-151. 10.1093/neuonc/noq151, 3018914, 21084434.
3. Yasrebi H, Sperisen P, Praz V, Bucher P. Can survival prediction be improved by merging gene expression data sets?. PLoS One 2009, 4:e7431. 10.1371/journal.pone.0007431, 2761544, 19851466.
4. Xu JZ, Wong CW. Hunting for robust gene signature from cancer profiling data: sources of variability, different interpretations, and recent methodological developments. Cancer Lett 2010, 296:9-16. 10.1016/j.canlet.2010.05.008, 20579805.
5. Kim SY. Effects of sample size on robustness and prediction accuracy of a prognostic gene signature. BMC Bioinformatics 2009, 10:147. 10.1186/1471-2105-10-147, 2689196, 19445687.
6. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210. 10.1093/nar/30.1.207, 99122, 11752295.
7. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF. Gene expression profiling of gliomas strongly predicts survival. Cancer Res 2004, 64:6503-6510. 10.1158/0008-5472.CAN-04-0452, 15374961.
8. Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, Hamou MF, de Tribolet N, Regli L, Wick W, Kouwenhoven MC, Hainfellner JA, Heppner FL, Dietrich PY, Zimmer Y, Cairncross JG, Janzer RC, Domany E, Delorenzi M, Stupp R, Hegi ME. Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol 2008, 26:3015-3024. 10.1200/JCO.2007.15.7164, 18565887.
9. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, Misra A, Nigro JM, Colman H, Soroceanu L, Williams PM, Modrusan Z, Feuerstein BG, Aldape K. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 2006, 9:157-173. 10.1016/j.ccr.2006.02.019, 16530701.
10. Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, Farooqi HK, Liau LM, Horvath S, Mischel PS, Nelson SF. Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics 2008, 1:52. 10.1186/1755-8794-1-52, 2596165, 18940004.
11. The Cancer Genome Atlas. , http://cancergenome.nih.gov/
12. Efroni S, Schaefer CF, Buetow KH. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS ONE 2007, 2:e425. 10.1371/journal.pone.0000425, 1855990, 17487280.
13. Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res 2009, 37:D674-679. 10.1093/nar/gkn653, 2686461, 18832364.
14. Pinkel D, Seagraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20:207-211. 10.1038/2524, 9771718.
15. Li M, Li J, Ding X, He M, Cheng SY. microRNA and cancer. AAPS J 2010, 12:309-317. 10.1208/s12248-010-9194-0, 2895440, 20422339.
16. Coe BP, Ylstra B, Carvalho B, Meijer GA, MacAulay C, Lam WL. Resolving the resolution of array CGH. Genomics 2007, 89:647-653. 10.1016/j.ygeno.2006.12.012, 17276656.
17. Gorringe KL, George J, Anglesio MS, Ramakrishna M, Etemadmoghadam D, Cowin P, Sridhar A, Williams LH, Boyle SE, Yanaihara N, Okamoto A, Urashima M, Smyth GK, Campbell IG, Bowtell DD, . Australian Ovarian Cancer Study Copy number analysis identifies novel interactions between genomic loci in ovarian cancer. PLoS One 2010, 5:e11408. 10.1371/journal.pone.0011408, 2937017, 20844748, Australian Ovarian Cancer Study.
18. Haverty PM, Hon LS, Kaminker JS, Chant J, Zhang Z. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Med Genomics 2009, 2:21. 10.1186/1755-8794-2-21, 2694826, 19419571.
19. Gorringe KL, Jacobs S, Thompson ER, Sridhar A, Qiu W, Choong DY, Campbell IG. High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications. Clin Cancer Res 2007, 13:4731-4739. 10.1158/1078-0432.CCR-07-0502, 17699850.
20. Costa BM, Smith JS, Chen Y, Chen J, Phillips HS, Aldape KD, Zardo G, Nigro J, James CD, Fridlyand J, Reis RM, Costello JF. Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res 2010, 70:453-462. 10.1158/0008-5472.CAN-09-2189, 2849935, 20068170.
21. Efroni S, Carmel L, Schaefer CG, Buetow KH. Superposition of transcriptional behaviors determines gene state. PLoS ONE 2008, 3:e2901. 10.1371/journal.pone.0002901, 2488367, 18682855.
22. Nomura N, Nomura M, Sugiyama K, Hamada J. Phorbol 12-myristate 13-acetate (PMA)-induced migration of glioblastoma cells is mediated via p38MAPK/Hsp27 pathway. Biochem Pharmacol 2007, 74:690-701. 10.1016/j.bcp.2007.06.018, 17640620.
23. Agami R. microRNAs, RNA binding proteins and cancer. Eur J Clin Invest 2010, 40:370-374. 10.1111/j.1365-2362.2010.02279.x, 20486997.
24. Ohlsson Teague EM, Van der Hoek KH, Van der Hoek MB, Perry N, Wagaarachchi P, Robertson SA, Print CG, Hull LM. MicroRNA-regulated pathways associated with endometriosis. Mol Endocrinol 2009, 23:265-275.
25. Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, Chin L, Brown D, Slack FJ. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 2007, 67:7713-7722. 10.1158/0008-5472.CAN-07-1083, 17699775.
26. Papagiannakopoulos T, Shapiro A, Kosik KS. MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells. Cancer Res 2008, 68:8164-8172. 10.1158/0008-5472.CAN-08-1305, 18829576.
27. Visvanathan J, Lee S, Lee B, Lee JW, Lee SK. The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 2007, 21:744-749. 10.1101/gad.1519107, 1838526, 17403776.
28. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284. 10.1038/ng2135, 17893677.
29. Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006, 34:D668-672. 10.1093/nar/gkj067, 1347430, 16381955.
30. Auffray C, Chen Z, Hood L. Systems medicine: the future of medical genomics and healthcare. Genome Med 2009, 1:2. 10.1186/gm2, 2651587, 19348689.
31. van't Veer LJ, Bernards R. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature 2008, 452:564-570. 10.1038/nature06915, 18385730.
32. Weller M, Felsberg J, Hartmann C, Berger H, Steinbach JP, Schramm J, Westphal M, Schackert G, Simon M, Tonn JC, Heese O, Krex D, Nikkhah G, Pietsch T, Wiestler O, Reifenberger G, von Deimling A, Loeffler M. Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J Clin Oncol 2009, 27:5743-5750. 10.1200/JCO.2009.23.0805, 19805672.
33. Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis 2010, 31:2-8. 10.1093/carcin/bgp261, 2802670, 19861649.
34. Emmert-Streib F, Glazko GV. Network biology: a direct approach to study biological function. Wiley Interdiscip Rev Syst Biol Med 2011, 3:379-391. 10.1002/wsbm.134, 21197659.
35. Rask-Andersen M, Almen MS, Schioth HB. Trends in the exploitation of novel drug targets. Nat Rev Drug Discov 2011, 10:579-590. 10.1038/nrd3478, 21804595.