Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data

Nucleic Acids Research

Volumn 43, Issue 4, 2015, Pages 1997-2007

  Ping, Yanyan ^a   Deng, Yulan ^a   Wang, Li ^a   Zhang, Hongyi ^a   Zhang, Yong ^a   Xu, Chaohan ^a   Zhao, Hongying ^a   Fan, Huihui ^a   Yu, Fulong ^a   Xiao, Yun ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GENOMICS; GLIOBLASTOMA; HUMAN; MORTALITY; PROCEDURES; PROTEIN ANALYSIS; SURVIVAL; TUMOR GENE;

GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GENES, NEOPLASM; GENOMICS; GLIOBLASTOMA; HUMANS; PROTEIN INTERACTION MAPPING; SURVIVAL ANALYSIS;

EID: 84941044659     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv074     Document Type: Article

References (67)

1. Ricke, R.M., van Deursen, J.M. (2013) Aneuploidy in health, disease, and aging. J. Cell Biol., 201, 11-21.
2. Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A. Jr and Kinzler, K.W. (2013) Cancer genome landscapes. Science, 339, 1546-1558.
3. Jonsson, P.F., Bates, P.A. (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics, 22, 2291-2297.
4. Qiu, Y.Q., Zhang, S., Zhang, X.S., Chen, L. (2010) Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics, 11, 26.
5. Youn, A., Simon, R. (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics, 27, 175-181.
6. Beroukhim, R., Getz, G., Nghiemphu, L., Barretina, J., Hsueh, T., Linhart, D., Vivanco, I., Lee, J.C., Huang, J.H., Alexander, S. et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. U.S.A., 104, 20007-20012.
7. Mermel, C.H., Schumacher, S.E., Hill, B., Meyerson, M.L., Beroukhim, R., Getz, G. (2011) GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol., 12, R41.
8. Cancer Genome Atlas Research Network. (2011) Integrated genomic analyses of ovarian carcinoma. Nature, 474, 609-615.
9. Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
10. Vandin, F., Upfal, E., Raphael, B.J. (2012) De novo discovery of mutated driver pathways in cancer. Genome Res., 22, 375-385.
11. Leiserson, M.D., Blokh, D., Sharan, R., Raphael, B.J. (2013) Simultaneous identification of multiple driver pathways in cancer. PLoS Comput. Biol., 9, e1003054.
12. Ciriello, G., Cerami, E., Sander, C., Schultz, N. (2012) Mutual exclusivity analysis identifies oncogenic network modules. Genome Res., 22, 398-406.
13. Ping, Y., Zhang, H., Deng, Y., Wang, L., Zhao, H., Pang, L., Fan, H., Xu, C., Li, F., Zhang, Y. et al. (2014) IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals. Mol. Biosyst., 10, 2031-2042.
14. Bredel, M., Scholtens, D.M., Harsh, G.R., Bredel, C., Chandler, J.P., Renfrow, J.J., Yadav, A.K., Vogel, H., Scheck, A.C., Tibshirani, R. et al. (2009) A network model of a cooperative genetic landscape in brain tumors. JAMA, 302, 261-275.
15. Klijn, C., Bot, J., Adams, D.J., Reinders, M., Wessels, L., Jonkers, J. (2010) Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach. PLoS Comput. Biol., 6, e1000631.
16. Akavia, U.D., Litvin, O., Kim, J., Sanchez-Garcia, F., Kotliar, D., Causton, H.C., Pochanard, P., Mozes, E., Garraway, L.A., Pe'er, D. (2010) An integrated approach to uncover drivers of cancer. Cell, 143, 1005-1017.
17. Kim, Y.A., Wuchty, S., Przytycka, T.M. (2011) Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput. Biol., 7, e1001095.
18. Masica, D.L., Karchin, R. (2011) Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res., 71, 4550-4561.
19. Bashashati, A., Haffari, G., Ding, J., Ha, G., Lui, K., Rosner, J., Huntsman, D.G., Caldas, C., Aparicio, S.A., Shah, S.P. (2012) DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol., 13, R124.
20. Mehnert, J.M., Kluger, H.M. (2012) Driver mutations in melanoma: lessons learned from bench-to-bedside studies. Curr. Oncol. Rep., 14, 449-457.
21. Kalari, S., Pfeifer, G.P. (2010) Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv. Genet., 70, 277-308.
22. Cancer Genome Atlas Network. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
23. Cancer Genome Atlas Research Network, Kandoth, C., Schultz, N., Cherniack, A.D., Akbani, R., Liu, Y., Shen, H., Robertson, A.G., Pashtan, I., Shen, R. et al. (2013) Integrated genomic characterization of endometrial carcinoma. Nature, 497, 67-73.
24. Cancer Genome Atlas Research Network. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061-1068.
25. Weller, M., Stupp, R., Reifenberger, G., Brandes, A.A., van den Bent, M.J., Wick, W., Hegi, M.E. (2010) MGMT promoter methylation in malignant gliomas: ready for personalized medicine? Nat. Rev. Neurol., 6, 39-51.
26. Walz, S., Lorenzin, F., Morton, J., Wiese, K.E., von Eyss, B., Herold, S., Rycak, L., Dumay-Odelot, H., Karim, S., Bartkuhn, M. et al. (2014) Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature, 511, 483-487.
27. Guo, H., Ingolia, N.T., Weissman, J.S., Bartel, D.P. (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466, 835-840.
28. Li, W., Zhang, S., Liu, C.C., Zhou, X.J. (2012) Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics, 28, 2458-2466.
29. Xiao, Y., Ping, Y., Fan, H., Xu, C., Guan, J., Zhao, H., Li, Y., Lv, Y., Jin, Y., Wang, L. et al. (2013) Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro-oncology, 15, 818-828.
30. Xiao, Y., Guan, J., Ping, Y., Xu, C., Huang, T., Zhao, H., Fan, H., Li, Y., Lv, Y., Zhao, T. et al. (2012) Prioritizing cancer-related key miRNA-target interactions by integrative genomics. Nucleic Acids Res., 40, 7653-7665.
31. Kristensen, V.N., Lingjaerde, O.C., Russnes, H.G., Vollan, H.K., Frigessi, A., Borresen-Dale, A.L. (2014) Principles and methods of integrative genomic analyses in cancer. Nat. Rev. Cancer, 14, 299-313.
32. de la Fuente, A. (2010) From 'differential expression' to 'differential networking'-identification of dysfunctional regulatory networks in diseases. Trends Genet., 26, 326-333.
33. Garnis, C., Buys, T.P., Lam, W.L. (2004) Genetic alteration and gene expression modulation during cancer progression. Mol. Cancer, 3, 9.
34. You, J.S., Jones, P.A. (2012) Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell, 22, 9-20.
35. Jornsten, R., Abenius, T., Kling, T., Schmidt, L., Johansson, E., Nordling, T.E., Nordlander, B., Sander, C., Gennemark, P., Funa, K. et al. (2011) Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol. Syst. Biol., 7, 486.
36. Setty, M., Helmy, K., Khan, A.A., Silber, J., Arvey, A., Neezen, F., Agius, P., Huse, J.T., Holland, E.C., Leslie, C.S. (2012) Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma. Mol. Syst. Biol., 8, 605.
37. Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., Li, T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105-D110.
38. Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I., Schacherer, F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
39. Keshava Prasad, T.S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
40. Bjornstad, A., Westad, F., Martens, H. (2004) Analysis of genetic marker-phenotype relationships by jack-knifed partial least squares regression (PLSR). Hereditas, 141, 149-165.
41. Verhaak, R.G., Hoadley, K.A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M.D., Miller, C.R., Ding, L., Golub, T., Mesirov, J.P. et al. (2010) Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell, 17, 98-110.
42. Huse, J.T., Holland, E., DeAngelis, L.M. (2013) Glioblastoma: molecular analysis and clinical implications. Annu. Rev. Med., 64, 59-70.
43. Ding, H., Shannon, P., Lau, N., Wu, X., Roncari, L., Baldwin, R.L., Takebayashi, H., Nagy, A., Gutmann, D.H., Guha, A. (2003) Oligodendrogliomas result from the expression of an activated mutant epidermal growth factor receptor in a RAS transgenic mouse astrocytoma model. Cancer Res., 63, 1106-1113.
44. Di Fiore, R., D'Anneo, A., Tesoriere, G., Vento, R. (2013) RB1 in cancer: different mechanisms of RB1 inactivation and alterations of pRb pathway in tumorigenesis. J. Cell. Physiol., 228, 1676-1687.
45. Goldhoff, P., Clarke, J., Smirnov, I., Berger, M.S., Prados, M.D., James, C.D., Perry, A., Phillips, J.J. (2012) Clinical stratification of glioblastoma based on alterations in retinoblastoma tumor suppressor protein (RB1) and association with the proneural subtype. J. Neuropathol. Exp. Neurol., 71, 83-89.
46. Molenaar, J.J., Ebus, M.E., Koster, J., van Sluis, P., van Noesel, C.J., Versteeg, R., Caron, H.N. (2008) Cyclin D1 and CDK4 activity contribute to the undifferentiated phenotype in neuroblastoma. Cancer Res., 68, 2599-2609.
47. Wang, L., Hurley, D.G., Watkins, W., Araki, H., Tamada, Y., Muthukaruppan, A., Ranjard, L., Derkac, E., Imoto, S., Miyano, S. et al. (2012) Cell cycle gene networks are associated with melanoma prognosis. PLoS One, 7, e34247.
48. Hamosh, A., Scott, A.F., Amberger, J., Valle, D., McKusick, V.A. (2000) OnlineMendelian Inheritance inMan (OMIM). Hum. Mutat., 15, 57-61.
49. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., Stratton, M.R. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
50. Becker, K.G., Barnes, K.C., Bright, T.J., Wang, S.A. (2004) The genetic association database. Nat. Genet., 36, 431-432.
51. Thrane, S., Lykkesfeldt, A.E., Larsen, M.S., Sorensen, B.S., Yde, C.W. (2013) Estrogen receptor alpha is the major driving factor for growth in tamoxifen-resistant breast cancer and supported by HER/ERK signaling. Breast Cancer Res. Treat., 139, 71-80.
52. Rahman, M.T., Nakayama, K., Rahman, M., Ishikawa, M., Katagiri, H., Katagiri, A., Ishibashi, T., Sato, E., Iida, K., Ishikawa, N. et al. (2013) ESR1 gene amplification in endometrial carcinomas: a clinicopathological analysis. Anticancer Res., 33, 3775-3781.
53. Uhlmann, K., Rohde, K., Zeller, C., Szymas, J., Vogel, S., Marczinek, K., Thiel, G., Nurnberg, P., Laird, P.W. (2003) Distinct methylation profiles of glioma subtypes. Int. J. Cancer, 106, 52-59.
54. Han, W., Carpenter, R.L., Cao, X., Lo, H.W. (2013) STAT1 gene expression is enhanced by nuclear EGFR and HER2 via cooperation With STAT3. Mol. Carcinog., 52, 959-969.
55. Camicia, R., Bachmann, S.B., Winkler, H.C., Beer, M., Tinguely, M., Haralambieva, E., Hassa, P.O. (2013) BAL1/ARTD9 represses the anti-proliferative and pro-apoptotic IFNgamma-STAT1-IRF1-p53 axis in diffuse large B-cell lymphoma. J. Cell Sci., 126, 1969-1980.
56. Li, J., Bennett, K., Stukalov, A., Fang, B., Zhang, G., Yoshida, T., Okamoto, I., Kim, J.Y., Song, L., Bai, Y. et al. (2013) Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol. Syst. Biol., 9, 705.
57. Jiang, X., Xing, H., Kim, T.M., Jung, Y., Huang, W., Yang, H.W., Song, S., Park, P.J., Carroll, R.S., Johnson, M.D. (2012) Numb regulates glioma stem cell fate and growth by altering epidermal growth factor receptor and Skp1-Cullin-F-box ubiquitin ligase activity. Stem Cells, 30, 1313-1326.
58. Feng, H., Hu, B., Vuori, K., Sarkaria, J.N., Furnari, F.B., Cavenee, W.K., Cheng, S.Y. (2013) EGFRvIII stimulates glioma growth and invasion through PKA-dependent serine phosphorylation of Dock180. Oncogene, 33, 2504-2512.
59. Lockwood, W.W., Chari, R., Coe, B.P., Girard, L., Macaulay, C., Lam, S., Gazdar, A.F., Minna, J.D., Lam, W.L. (2008) DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene, 27, 4615-4624.
60. Olson, J.M., Hallahan, A.R. (2004) p38 MAP kinase: a convergence point in cancer therapy. Trends Mol. Med., 10, 125-129.
61. Carduner, L., Picot, C.R., Leroy-Dudal, J., Blay, L., Kellouche, S., Carreiras, F. (2013) Cell cycle arrest or survival signaling through alphav integrins, activation of PKC and ERK1/2 lead to anoikis resistance of ovarian cancer spheroids. Exp. Cell Res, 320, 329-342.
62. Leelahavanichkul, K., Amornphimoltham, P., Molinolo, A.A., Basile, J.R., Koontongkaew, S., Gutkind, J.S. (2013) A role for p38 MAPK in head and neck cancer cell growth and tumor-induced angiogenesis and lymphangiogenesis. Mol. Oncol, 8, 105-108.
63. Donnelly, S.M., Paplomata, E., Peake, B.M., Sanabria, E., Chen, Z., Nahta, R. (2013) P38 MAPK Contributes to Resistance and Invasiveness of HER2-Overexpressing Breast Cancer. Curr. Med. Chem, 21, 501-510.
64. de la Cruz-Morcillo, M.A., Garcia-Cano, J., Arias-Gonzalez, L., Garcia-Gil, E., Artacho-Cordon, F., Rios-Arrabal, S., Valero, M.L., Cimas, F.J., Serrano-Oviedo, L., Villas, M.V. et al. (2013) Abrogation of the p38 MAPK alpha signaling pathway does not promote radioresistance but its activity is required for 5-Fluorouracil-associated radiosensitivity. Cancer Lett., 335, 66-74.
65. Hirose, Y., Katayama, M., Stokoe, D., Haas-Kogan, D.A., Berger, M.S., Pieper, R.O. (2003) The p38 mitogen-activated protein kinase pathway links the DNA mismatch repair system to the G2 checkpoint and to resistance to chemotherapeutic DNA-methylating agents. Mol. Cell. Biol., 23, 8306-8315.
66. Ghosh, S., Kumar, A., Tripathi, R.P., Chandna, S. (2013) Connexin-43 regulates p38-mediated cell migration and invasion induced selectively in tumour cells by low doses of gamma-radiation in an ERK-1/2-independent manner. Carcinogenesis, 35, 383-395.
67. Ohgaki, H., Kleihues, P. (2007) Genetic pathways to primary and secondary glioblastoma. Am. J. Pathol., 170, 1445-1453.