Epigenetic pathways and glioblastoma treatment

References

• Lacroix M, Abi-Said D, Fourney DR, Gokaslan ZL, Shi W, DeMonte F, et al. A multivariate analysis of 416 patients with glioblastoma multiforme: prognosis, extent of resection, and survival. J Neurosurg 2001; 95:190 - 8; http://dx.doi.org/10.3171/jns.2001.95.2.0190; PMID: 11780887
   PubMed Web of Science ®Google Scholar
• Chen J, McKay RM, Parada LF. Malignant glioma: lessons from genomics, mouse models, and stem cells. Cell 2012; 149:36 - 47; http://dx.doi.org/10.1016/j.cell.2012.03.009; PMID: 22464322
   PubMed Web of Science ®Google Scholar
• Liu C, Sage JC, Miller MR, Verhaak RG, Hippenmeyer S, Vogel H, et al. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell 2011; 146:209 - 21; http://dx.doi.org/10.1016/j.cell.2011.06.014; PMID: 21737130
   PubMed Web of Science ®Google Scholar
• Koso H, Takeda H, Yew CC, Ward JM, Nariai N, Ueno K, et al. Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells. Proc Natl Acad Sci U S A 2012; 109:E2998 - 3007; http://dx.doi.org/10.1073/pnas.1215899109; PMID: 23045694
   PubMed Web of Science ®Google Scholar
• Friedmann-Morvinski D, Bushong EA, Ke E, Soda Y, Marumoto T, Singer O, et al. Dedifferentiation of neurons and astrocytes by oncogenes can induce gliomas in mice. Science 2012; 338:1080 - 4; http://dx.doi.org/10.1126/science.1226929; PMID: 23087000
   PubMed Web of Science ®Google Scholar
• Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F. The probable cell of origin of NF1- and PDGF-driven glioblastomas. PLoS One 2011; 6:e24454; http://dx.doi.org/10.1371/journal.pone.0024454; PMID: 21931722
   PubMedGoogle Scholar
• Chen J, Li Y, Yu TS, McKay RM, Burns DK, Kernie SG, et al. A restricted cell population propagates glioblastoma growth after chemotherapy. Nature 2012; 488:522 - 6; http://dx.doi.org/10.1038/nature11287; PMID: 22854781
   PubMed Web of Science ®Google Scholar
• Driessens G, Beck B, Caauwe A, Simons BD, Blanpain C. Defining the mode of tumour growth by clonal analysis. Nature 2012; 488:527 - 30; http://dx.doi.org/10.1038/nature11344; PMID: 22854777
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455:1061 - 8; http://dx.doi.org/10.1038/nature07385; PMID: 18772890
   PubMed Web of Science ®Google Scholar
• Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, et al. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science 2012; 337:1231 - 5; http://dx.doi.org/10.1126/science.1220834; PMID: 22837387
   PubMed Web of Science ®Google Scholar
• Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008; 321:1807 - 12; http://dx.doi.org/10.1126/science.1164382; PMID: 18772396
   PubMed Web of Science ®Google Scholar
• Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W, et al. IDH1 and IDH2 mutations in gliomas. N Engl J Med 2009; 360:765 - 73; http://dx.doi.org/10.1056/NEJMoa0808710; PMID: 19228619
   PubMed Web of Science ®Google Scholar
• Pe’er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell 2011; 144:864 - 73; http://dx.doi.org/10.1016/j.cell.2011.03.001; PMID: 21414479
   PubMed Web of Science ®Google Scholar
• Kalari S, Pfeifer GP. Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv Genet 2010; 70:277 - 308; http://dx.doi.org/10.1016/B978-0-12-380866-0.60010-1; PMID: 20920752
   PubMed Web of Science ®Google Scholar
• Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012; 482:226 - 31; http://dx.doi.org/10.1038/nature10833; PMID: 22286061
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646 - 74; http://dx.doi.org/10.1016/j.cell.2011.02.013; PMID: 21376230
   PubMed Web of Science ®Google Scholar
• Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, et al, Cancer Genome Atlas Research Network. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010; 17:98 - 110; http://dx.doi.org/10.1016/j.ccr.2009.12.020; PMID: 20129251
   PubMed Web of Science ®Google Scholar
• Riddick G, Fine HA. Integration and analysis of genome-scale data from gliomas. Nat Rev Neurol 2011; 7:439 - 50; http://dx.doi.org/10.1038/nrneurol.2011.100; PMID: 21727940
   PubMed Web of Science ®Google Scholar
• Natsume A, Kondo Y, Ito M, Motomura K, Wakabayashi T, Yoshida J. Epigenetic aberrations and therapeutic implications in gliomas. Cancer Sci 2010; 101:1331 - 6; http://dx.doi.org/10.1111/j.1349-7006.2010.01545.x; PMID: 20384628
   PubMed Web of Science ®Google Scholar
• Kreth S, Thon N, Kreth FW. Epigenetics in human gliomas. Cancer Lett 2012; In press; http://dx.doi.org/10.1016/j.canlet.2012.04.008; PMID: 22531315
   PubMed Web of Science ®Google Scholar
• Dawson MA, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell 2012; 150:12 - 27; http://dx.doi.org/10.1016/j.cell.2012.06.013; PMID: 22770212
   PubMed Web of Science ®Google Scholar
• Sturm D, Witt H, Hovestadt V, Khuong-Quang DA, Jones DT, Konermann C, et al. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 2012; 22:425 - 37; http://dx.doi.org/10.1016/j.ccr.2012.08.024; PMID: 23079654
   PubMed Web of Science ®Google Scholar
• Chan JA, Krichevsky AM, Kosik KS. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 2005; 65:6029 - 33; http://dx.doi.org/10.1158/0008-5472.CAN-05-0137; PMID: 16024602
   PubMed Web of Science ®Google Scholar
• Ciafrè SA, Galardi S, Mangiola A, Ferracin M, Liu CG, Sabatino G, et al. Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 2005; 334:1351 - 8; http://dx.doi.org/10.1016/j.bbrc.2005.07.030; PMID: 16039986
   PubMed Web of Science ®Google Scholar
• Gabriely G, Yi M, Narayan RS, Niers JM, Wurdinger T, Imitola J, et al. Human glioma growth is controlled by microRNA-10b. Cancer Res 2011; 71:3563 - 72; http://dx.doi.org/10.1158/0008-5472.CAN-10-3568; PMID: 21471404
   PubMed Web of Science ®Google Scholar
• Guessous F, Alvarado-Velez M, Marcinkiewicz L, Zhang Y, Kim J, Heister S, et al. Oncogenic effects of miR-10b in glioblastoma stem cells. J Neurooncol 2013; 112:153 - 63; http://dx.doi.org/10.1007/s11060-013-1047-0; PMID: 23307328
   PubMed Web of Science ®Google Scholar
• Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011; 147:344 - 57; http://dx.doi.org/10.1016/j.cell.2011.09.029; PMID: 22000013
   PubMed Web of Science ®Google Scholar
• Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011; 147:370 - 81; http://dx.doi.org/10.1016/j.cell.2011.09.041; PMID: 22000015
   PubMed Web of Science ®Google Scholar
• Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, et al. In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 2011; 147:382 - 95; http://dx.doi.org/10.1016/j.cell.2011.09.032; PMID: 22000016
   PubMed Web of Science ®Google Scholar
• Fang L, Du WW, Yang X, Chen K, Ghanekar A, Levy G, et al. Versican 3′-untranslated region (3′-UTR) functions as a ceRNA in inducing the development of hepatocellular carcinoma by regulating miRNA activity. FASEB J 2013; 27:907 - 19; http://dx.doi.org/10.1096/fj.12-220905; PMID: 23180826
   PubMed Web of Science ®Google Scholar
• Sarver AL, Subramanian S. Competing endogenous RNA database. Bioinformation 2012; 8:731 - 3; http://dx.doi.org/10.6026/97320630008731; PMID: 23055620
   PubMedGoogle Scholar
• Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409 - 19; http://dx.doi.org/10.1016/j.cell.2010.06.040; PMID: 20673990
   PubMed Web of Science ®Google Scholar
• Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 2011; 145:622 - 34; http://dx.doi.org/10.1016/j.cell.2011.03.042; PMID: 21549415
   PubMed Web of Science ®Google Scholar
• Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011; 29:742 - 9; http://dx.doi.org/10.1038/nbt.1914; PMID: 21804560
   PubMed Web of Science ®Google Scholar
• Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 2011; 43:621 - 9; http://dx.doi.org/10.1038/ng.848; PMID: 21642992
   PubMed Web of Science ®Google Scholar
• Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, et al. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 2008; 14:723 - 30; http://dx.doi.org/10.1038/nm1784; PMID: 18587408
   PubMed Web of Science ®Google Scholar
• Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10:155 - 9; http://dx.doi.org/10.1038/nrg2521; PMID: 19188922
   PubMed Web of Science ®Google Scholar
• Wang P, Ren Z, Sun P. Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation. J Cell Biochem 2012; 113:1868 - 74; http://dx.doi.org/10.1002/jcb.24055; PMID: 22234798
   PubMed Web of Science ®Google Scholar
• Han L, Zhang K, Shi Z, Zhang J, Zhu J, Zhu S, et al. LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int J Oncol 2012; 40:2004 - 12; PMID: 22446686
   PubMed Web of Science ®Google Scholar
• Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One 2013; 8:e53823; http://dx.doi.org/10.1371/journal.pone.0053823; PMID: 23405074
   PubMed Web of Science ®Google Scholar
• Katsushima K, Shinjo K, Natsume A, Ohka F, Fujii M, Osada H, et al. Contribution of microRNA-1275 to Claudin11 protein suppression via a polycomb-mediated silencing mechanism in human glioma stem-like cells. J Biol Chem 2012; 287:27396 - 406; http://dx.doi.org/10.1074/jbc.M112.359109; PMID: 22736761
   PubMed Web of Science ®Google Scholar
• Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 2010; 38:662 - 74; http://dx.doi.org/10.1016/j.molcel.2010.03.021; PMID: 20541999
   PubMed Web of Science ®Google Scholar
• Suvà ML, Riggi N, Janiszewska M, Radovanovic I, Provero P, Stehle JC, et al. EZH2 is essential for glioblastoma cancer stem cell maintenance. Cancer Res 2009; 69:9211 - 8; http://dx.doi.org/10.1158/0008-5472.CAN-09-1622; PMID: 19934320
   PubMed Web of Science ®Google Scholar
• Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, et al. Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells. Neuropathol Appl Neurobiol 2011; 37:381 - 94; http://dx.doi.org/10.1111/j.1365-2990.2010.01132.x; PMID: 20946108
   PubMed Web of Science ®Google Scholar
• Shih AH, Abdel-Wahab O, Patel JP, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer 2012; 12:599 - 612; http://dx.doi.org/10.1038/nrc3343; PMID: 22898539
   PubMed Web of Science ®Google Scholar
• Lee JM, Lee JS, Kim H, Kim K, Park H, Kim JY, et al. EZH2 generates a methyl degron that is recognized by the DCAF1/DDB1/CUL4 E3 ubiquitin ligase complex. Mol Cell 2012; 48:572 - 86; http://dx.doi.org/10.1016/j.molcel.2012.09.004; PMID: 23063525
   PubMed Web of Science ®Google Scholar
• Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329:689 - 93; http://dx.doi.org/10.1126/science.1192002; PMID: 20616235
   PubMed Web of Science ®Google Scholar
• Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, et al. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 2010; 24:2615 - 20; http://dx.doi.org/10.1101/gad.1983810; PMID: 21123648
   PubMed Web of Science ®Google Scholar
• Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, et al. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 2011; 71:6320 - 6; http://dx.doi.org/10.1158/0008-5472.CAN-11-1021; PMID: 21862635
   PubMed Web of Science ®Google Scholar
• Yang F, Zhang L, Huo XS, Yuan JH, Xu D, Yuan SX, et al. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology 2011; 54:1679 - 89; http://dx.doi.org/10.1002/hep.24563; PMID: 21769904
   PubMed Web of Science ®Google Scholar
• McCabe MT, Ott HM, Ganji G, Korenchuk S, Thompson C, Van Aller GS, et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 2012; 492:108 - 12; http://dx.doi.org/10.1038/nature11606; PMID: 23051747
   PubMed Web of Science ®Google Scholar
• Knutson SK, Wigle TJ, Warholic NM, Sneeringer CJ, Allain CJ, Klaus CR, et al. A selective inhibitor of EZH2 blocks H3K27 methylation and kills mutant lymphoma cells. Nat Chem Biol 2012; 8:890 - 6; PMID: 23023262
   PubMed Web of Science ®Google Scholar
• Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, et al. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science 2008; 322:1695 - 9; http://dx.doi.org/10.1126/science.1165395; PMID: 19008416
   PubMed Web of Science ®Google Scholar
• Smits M, Nilsson J, Mir SE, van der Stoop PM, Hulleman E, Niers JM, et al. miR-101 is down-regulated in glioblastoma resulting in EZH2-induced proliferation, migration, and angiogenesis. Oncotarget 2010; 1:710 - 20; PMID: 21321380
   PubMed Web of Science ®Google Scholar
• Carén H, Pollard SM, Beck S. The good, the bad and the ugly: Epigenetic mechanisms in glioblastoma. Mol Aspects Med 2013; 34:849 - 62; http://dx.doi.org/10.1016/j.mam.2012.06.007; PMID: 22771539
   PubMed Web of Science ®Google Scholar
• Linnet K, Ejsing TB. A review on the impact of P-glycoprotein on the penetration of drugs into the brain. Focus on psychotropic drugs. Eur Neuropsychopharmacol 2008; 18:157 - 69; http://dx.doi.org/10.1016/j.euroneuro.2007.06.003; PMID: 17683917
   PubMed Web of Science ®Google Scholar
• Fronza R, Tramonti M, Atchley WR, Nardini C. Brain cancer prognosis: independent validation of a clinical bioinformatics approach. J Clin Bioinforma 2012; 2:2; http://dx.doi.org/10.1186/2043-9113-2-2; PMID: 22297051
   PubMedGoogle Scholar
• Wuchty S, Arjona D, Li A, Kotliarov Y, Walling J, Ahn S, et al. Prediction of Associations between microRNAs and Gene Expression in Glioma Biology. PLoS One 2011; 6:e14681; http://dx.doi.org/10.1371/journal.pone.0014681; PMID: 21358821
   PubMed Web of Science ®Google Scholar
• Kunkle B, Yoo C, Roy D. Discovering gene-environment interactions in Glioblastoma through a comprehensive data integration bioinformatics method. Neurotoxicology 2013; 35:1 - 14; http://dx.doi.org/10.1016/j.neuro.2012.11.001; PMID: 23261424
   PubMed Web of Science ®Google Scholar
• Jobe EM, McQuate AL, Zhao X. Crosstalk among Epigenetic Pathways Regulates Neurogenesis. Front Neurosci 2012; 6:59; http://dx.doi.org/10.3389/fnins.2012.00059; PMID: 22586361
   PubMedGoogle Scholar
• Sima C, Hua J, Jung S. Inference of gene regulatory networks using time-series data: a survey. Curr Genomics 2009; 10:416 - 29; http://dx.doi.org/10.2174/138920209789177610; PMID: 20190956
   PubMed Web of Science ®Google Scholar
• Allen L. An Introduction to Stochastic Processes with Applications to Biology. 2nd Ed CRC Press/Chapman & Hall, Boca Raton, Fl 2010.
   Google Scholar
• Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics 2005; 21:Suppl 1 i159 - 68; http://dx.doi.org/10.1093/bioinformatics/bti1022; PMID: 15961453
   PubMed Web of Science ®Google Scholar
• Genolini C, Falissard B. KmL: a package to cluster longitudinal data. Comput Methods Programs Biomed 2011; 104:e112 - 21; http://dx.doi.org/10.1016/j.cmpb.2011.05.008; PMID: 21708413
   PubMed Web of Science ®Google Scholar
• Friedman N, Linial M, Nachman I, Pe’er D. Using Bayesian networks to analyze expression data. J Comput Biol 2000; 7:601 - 20; http://dx.doi.org/10.1089/106652700750050961; PMID: 11108481
   PubMed Web of Science ®Google Scholar
• Bilmes J. Dynamic Graphic Models. IEEE Signal Process Mag 2010; 34:29 - 42
   Google Scholar
• Dobra A, Hans C, Jones B, Nevins JR, Yao G, West M. Sparse graphical models for exploring gene expression data. J Multivariate Anal 2004; 90:196 - 212; http://dx.doi.org/10.1016/j.jmva.2004.02.009
   Web of Science ®Google Scholar
• J. M. Bernardo JOB. A. P. Dawid and A. F. M. Smith (eds). Bayesian Statistics Oxford: Oxford University Press 1999; 6.
   Google Scholar
• Futschik ME, Herzel H. Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics 2008; 24:1063 - 9; http://dx.doi.org/10.1093/bioinformatics/btn072; PMID: 18310054
   PubMed Web of Science ®Google Scholar
• West PA. Time Series: Modeling, Computation, and Inference Chapman & Hall/CRC Texts in Statistical Science) 2010.
   Google Scholar
• Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell 2013; 49:202 - 12; http://dx.doi.org/10.1016/j.molcel.2012.12.020; PMID: 23352241
   PubMed Web of Science ®Google Scholar
• Ioannidis JP. Why most published research findings are false. PLoS Med 2005; 2:e124; http://dx.doi.org/10.1371/journal.pmed.0020124; PMID: 16060722
   PubMed Web of Science ®Google Scholar
• Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, et al. Repeatability of published microarray gene expression analyses. Nat Genet 2009; 41:149 - 55; http://dx.doi.org/10.1038/ng.295; PMID: 19174838
   PubMed Web of Science ®Google Scholar