Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis

Cell Systems

Volumn 3, Issue 2, 2016, Pages 172-186

  Plaisier, Christopher L ^a   O'Brien, Sofie ^a   Bernard, Brady ^a   Reynolds, Sheila ^a   Simon, Zac ^a   Reiss, David J ^a   Baliga, Nitin S ^a   Toledo, Chad M ^b,c   Ding, Yu ^b   Paddison, Patrick J ^b,c  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

gene regulation; glioblastoma multiforme; glioma; network; systems biology; systems genetics

Indexed keywords

CASPASE 9; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MICRORNA; MICRORNA 486 3P; ROMIDEPSIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ETV6; UNCLASSIFIED DRUG;

ANTIPROLIFERATIVE ACTIVITY; ARTICLE; CANCER PROGNOSIS; CANCER SURVIVAL; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; GENE CONTROL; GENE MUTATION; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ANALYSIS; GLIOBLASTOMA; HUMAN; HUMAN TISSUE; LYMPHOCYTIC INFILTRATION; MAJOR CLINICAL STUDY; PHENOTYPE; PRIORITY JOURNAL; SYSTEMS GENETICS NETWORK ANALYSIS; GENE EXPRESSION REGULATION; ONCOGENE;

GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GLIOBLASTOMA; HUMANS; MICRORNAS; ONCOGENES;

EID: 84978811202     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2016.06.006     Document Type: Article

References (48)

1. Alexander, B.M., Lee, E.Q., Reardon, D.A., Wen, P.Y., Current and future directions for Phase II trials in high-grade glioma. Expert Rev. Neurother. 13 (2013), 369–387.
2. Aten, J.E., Fuller, T.F., Lusis, A.J., Horvath, S., Using genetic markers to orient the edges in quantitative trait networks: the NEO software. BMC Syst. Biol., 2, 2008, 34.
3. Baek, D., Villén, J., Shin, C., Camargo, F.D., Gygi, S.P., Bartel, D.P., The impact of microRNAs on protein output. Nature 455 (2008), 64–71.
4. Bansal, M., Yang, J., Karan, C., Menden, M.P., Costello, J.C., Tang, H., Xiao, G., Li, Y., Allen, J., Zhong, R., et al. NCI-DREAM Community, NCI-DREAM Community. A community computational challenge to predict the activity of pairs of compounds. Nat. Biotechnol. 32 (2014), 1213–1222.
5. Bliss, C.I., The toxicity of poisons applied jointly. Ann. Appl. Biol. 26 (1939), 585–615.
6. Bouchie, A., First microRNA mimic enters clinic. Nat. Biotechnol., 31, 2013, 577.
7. Brennan, C.W., Verhaak, R.G.W., McKenna, A., Campos, B., Noushmehr, H., Salama, S.R., Zheng, S., Chakravarty, D., Sanborn, J.Z., Berman, S.H., et al., TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell 155 (2013), 462–477.
8. Brooks, A.N., Reiss, D.J., Allard, A., Wu, W.-J., Salvanha, D.M., Plaisier, C.L., Chandrasekaran, S., Pan, M., Kaur, A., Baliga, N.S., A system-level model for the microbial regulatory genome. Mol. Syst. Biol., 10, 2014, 740.
9. Cai, W., Hu, L., Foulkes, J.G., Transcription-modulating drugs: mechanism and selectivity. Curr. Opin. Biotechnol. 7 (1996), 608–615.
10. Carro, M.S., Lim, W.K., Alvarez, M.J., Bollo, R.J., Zhao, X., Snyder, E.Y., Sulman, E.P., Anne, S.L., Doetsch, F., Colman, H., et al. The transcriptional network for mesenchymal transformation of brain tumours. Nature 463 (2010), 318–325.
11. Chen, J.C., Alvarez, M.J., Talos, F., Dhruv, H., Rieckhof, G.E., Iyer, A., Diefes, K.L., Aldape, K., Berens, M., Shen, M.M., Califano, A., Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell 159 (2014), 402–414.
12. Choi, C.H., Park, Y.-A., Choi, J.-J., Song, T., Song, S.Y., Lee, Y.-Y., Lee, J.-W., Kim, T.-J., Kim, B.-G., Bae, D.-S., Angiotensin II type I receptor and miR-155 in endometrial cancers: synergistic antiproliferative effects of anti-miR-155 and losartan on endometrial cancer cells. Gynecol. Oncol. 126 (2012), 124–131.
13. Friedman, R.C., Farh, K.K.-H., Burge, C.B., Bartel, D.P., Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19 (2009), 92–105.
14. Gonzalez-Perez, A., Perez-Llamas, C., Deu-Pons, J., Tamborero, D., Schroeder, M.P., Jene-Sanz, A., Santos, A., Lopez-Bigas, N., IntOGen-mutations identifies cancer drivers across tumor types. Nat. Methods 10 (2013), 1081–1082.
15. Goodarzi, H., Elemento, O., Tavazoie, S., Revealing global regulatory perturbations across human cancers. Mol. Cell 36 (2009), 900–911.
16. Gravendeel, L.A.M., Kouwenhoven, M.C.M., Gevaert, O., de Rooi, J.J., Stubbs, A.P., Duijm, J.E., Daemen, A., Bleeker, F.E., Bralten, L.B.C., Kloosterhof, N.K., et al. Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res. 69 (2009), 9065–9072.
17. Heneghan, H.M., Miller, N., Kerin, M.J., MiRNAs as biomarkers and therapeutic targets in cancer. Curr Opin Pharmacol. 10 (2010), 543–550.
18. Iwamoto, F.M., Lamborn, K.R., Kuhn, J.G., Wen, P.Y., Yung, W.K.A., Gilbert, M.R., Chang, S.M., Lieberman, F.S., Prados, M.D., Fine, H.A., A phase I/II trial of the histone deacetylase inhibitor romidepsin for adults with recurrent malignant glioma: North American Brain Tumor Consortium Study 03-03. Neuro-oncol. 13 (2011), 509–516.
19. Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G., Liu, Y., miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 37 (2009), D98–D104.
20. Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K.R., Rastas, P., Morgunova, E., Enge, M., Taipale, M., Wei, G., et al. DNA-binding specificities of human transcription factors. Cell 152 (2013), 327–339.
21. Jörnsten, R., Abenius, T., Kling, T., Schmidt, L., Johansson, E., Nordling, T.E.M., Nordlander, B., Sander, C., Gennemark, P., Funa, K., et al. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol. Syst. Biol., 7, 2011, 486.
22. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E., The role of site accessibility in microRNA target recognition. Nat. Genet. 39 (2007), 1278–1284.
23. Lehár, J., Krueger, A.S., Avery, W., Heilbut, A.M., Johansen, L.M., Price, E.R., Rickles, R.J., Short, G.F. 3rd, Staunton, J.E., Jin, X., et al. Synergistic drug combinations tend to improve therapeutically relevant selectivity. Nat. Biotechnol. 27 (2009), 659–666.
24. Liu, Q., Zheng, J.-M., Chen, J.-K., Yan, X.-L., Chen, H.-M., Nong, W.-X., Huang, H.-Q., Histone deacetylase 5 promotes the proliferation of glioma cells by upregulation of Notch 1. Mol. Med. Rep. 10 (2014), 2045–2050.
25. Lu, M., Zhang, Q., Deng, M., Miao, J., Guo, Y., Gao, W., Cui, Q., An analysis of human microRNA and disease associations. PLoS ONE, 3, 2008, e3420.
26. Madhavan, S., Zenklusen, J.-C., Kotliarov, Y., Sahni, H., Fine, H.A., Buetow, K., Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol. Cancer Res. 7 (2009), 157–167.
27. Mathelier, A., Zhao, X., Zhang, A.W., Parcy, F., Worsley-Hunt, R., Arenillas, D.J., Buchman, S., Chen, C.Y., Chou, A., Ienasescu, H., et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42 (2014), D142–D147.
28. Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34 (2006), D108–D110.
29. Murat, A., Migliavacca, E., Gorlia, T., Lambiv, W.L., Shay, T., Hamou, M.-F., de Tribolet, N., Regli, L., Wick, W., Kouwenhoven, M.C.M., et al. Stem cell-related “self-renewal” signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J. Clin. Oncol. 26 (2008), 3015–3024.
30. Neph, S., Vierstra, J., Stergachis, A.B., Reynolds, A.P., Haugen, E., Vernot, B., Thurman, R.E., John, S., Sandstrom, R., Johnson, A.K., et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489 (2012), 83–90.
31. Newburger, D.E., Bulyk, M.L., UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 37 (2009), D77–D82.
32. Ohka, F., Natsume, A., Wakabayashi, T., Current trends in targeted therapies for glioblastoma multiforme. Neurol. Res. Int., 2012, 2012, 878425.
33. Patil, S.A., Hosni-Ahmed, A., Jones, T.S., Patil, R., Pfeffer, L.M., Miller, D.D., Novel approaches to glioma drug design and drug screening. Expert Opin. Drug Discov. 8 (2013), 1135–1151.
34. Piñero, J., Queralt-Rosinach, N., Bravo, À., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz, F., Furlong, L.I., DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database, 2015, 2015, bav028.
35. Plaisier, C.L., Horvath, S., Huertas-Vazquez, A., Cruz-Bautista, I., Herrera, M.F., Tusie-Luna, T., Aguilar-Salinas, C., Pajukanta, P., A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet., 5, 2009, e1000642.
36. Plaisier, C.L., Pan, M., Baliga, N.S., A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. 22 (2012), 2302–2314.
37. Reiss, D.J., Plaisier, C.L., Wu, W.-J., Baliga, N.S., cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res., 43, 2015, e87.
38. Rutledge, W.C., Kong, J., Gao, J., Gutman, D.A., Cooper, L.A.D., Appin, C., Park, Y., Scarpace, L., Mikkelsen, T., Cohen, M.L., et al. Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class. Clin. Cancer Res. 19 (2013), 4951–4960.
39. Sathornsumetee, S., Reardon, D.A., Desjardins, A., Quinn, J.A., Vredenburgh, J.J., Rich, J.N., Molecularly targeted therapy for malignant glioma. Cancer 110 (2007), 13–24.
40. Sawa, H., Murakami, H., Kumagai, M., Nakasato, M., Yamauchi, S., Matsuyama, N., Tamura, Y., Satone, A., Ide, W., Hashimoto, I., Kamada, H., Histone deacetylase inhibitor, FK228, induces apoptosis and suppresses cell proliferation of human glioblastoma cells in vitro and in vivo. Acta Neuropathol. 107 (2004), 523–531.
41. Smith, C., Santi, M., Rajan, B., Rushing, E.J., Choi, M.R., Rood, B.R., Cornelison, R., MacDonald, T.J., Vukmanovic, S., A novel role of HLA class I in the pathology of medulloblastoma. J. Transl. Med., 7, 2009, 59.
42. Sumazin, P., Yang, X., Chiu, H.-S., Chung, W.-J., Iyer, A., Llobet-Navas, D., Rajbhandari, P., Bansal, M., Guarnieri, P., Silva, J., Califano, A., An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147 (2011), 370–381.
43. Sun, P., Xia, S., Lal, B., Eberhart, C.G., Quinones-Hinojosa, A., Maciaczyk, J., Matsui, W., Dimeco, F., Piccirillo, S.M., Vescovi, A.L., Laterra, J., DNER, an epigenetically modulated gene, regulates glioblastoma-derived neurosphere cell differentiation and tumor propagation. Stem Cells 27 (2009), 1473–1486.
44. Toledo, C.M., Ding, Y., Hoellerbauer, P., Davis, R.J., Basom, R., Girard, E.J., Lee, E., Corrin, P., Hart, T., Bolouri, H., et al. Genome-wide CRISPR-Cas9 screens reveal loss of redundancy between PKMYT1 and WEE1 in glioblastoma stem-like cells. Cell Rep. 13 (2015), 2425–2439.
45. Wang, J., Zhuang, J., Iyer, S., Lin, X., Whitfield, T.W., Greven, M.C., Pierce, B.G., Dong, X., Kundaje, A., Cheng, Y., et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 22 (2012), 1798–1812.
46. Wen, P.Y., Kesari, S., Drappatz, J., Malignant gliomas: strategies to increase the effectiveness of targeted molecular treatment. Expert Rev. Anticancer Ther. 6 (2006), 733–754.
47. Wingender, E., Schoeps, T., Dönitz, J., TFClass: an expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41 (2013), D165–D170.
48. Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., Kellis, M., Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434 (2005), 338–345.