Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors

References

• Carén H, Erichsen J, Olsson L, Enerbäck C, Sjöberg RM, Abrahamsson J, Kogner P, Martinsson T. High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: Four cases of homozygous deletions of the CDKN2A gene. BMC Genomics 2008; 9:353; http://dx.doi.org/10.1186/1471-2164-9-353
   PubMed Web of Science ®Google Scholar
• Carén H, Kryh H, Nethander M, Sjöberg RM, Träger C, Nilsson S, Abrahamsson J, Kogner P, Martinsson T. High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc Natl Acad Sci U S A 2010; 107:4323–8; http://dx.doi.org/10.1073/pnas.0910684107
   PubMed Web of Science ®Google Scholar
• Carén H, Abel F, Kogner P, Martinsson T. High incidence of DNA mutations and gene amplifications of the ALK gene in advanced sporadic neuroblastoma tumours. Biochem J 2008; 416:153–9; http://dx.doi.org/10.1042/BJ20081834
   PubMed Web of Science ®Google Scholar
• Mosse YP, Laudenslager M, Longo L, Cole KA, Wood A, Attiyeh EF, Laquaglia MJ, Sennett R, Lynch JE, Perri P, et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 2008; 455(7215):930–5; PMID:18724359
   PubMed Web of Science ®Google Scholar
• Chen Y, Takita J, Choi YL, Kato M, Ohira M, Sanada M, Wang L, Soda M, Kikuchi A, Igarashi T, et al. Oncogenic mutations of ALK kinase in neuroblastoma. Nature 2008; 455:971–4; PMID:18923524; http://dx.doi.org/10.1038/nature07399
   PubMed Web of Science ®Google Scholar
• George RE, Sanda T, Hanna M, Frohling S, Luther W, 2nd, Zhang J, Ahn Y, Zhou W, London WB, McGrady P, et al. Activating mutations in ALK provide a therapeutic target in neuroblastoma. Nature 2008; 455:975–8; PMID:18923525; http://dx.doi.org/10.1038/nature07397
   PubMed Web of Science ®Google Scholar
• Janoueix-Lerosey I, Lequin D, Brugieres L, Ribeiro A, de Pontual L, Combaret V, Raynal V, Puisieux A, Schleiermacher G, Pierron G, et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 2008; 455:967–70; PMID:18923523; http://dx.doi.org/10.1038/nature07398
   PubMed Web of Science ®Google Scholar
• Cohn SL, Pearson AD, London WB, Monclair T, Ambros PF, Brodeur GM, Faldum A, Hero B, Iehara T, Machin D, et al. The International Neuroblastoma Risk Group (INRG) classification system: an INRG Task Force report. J Clin Oncol 2009; 27:289–97; PMID:19047291; http://dx.doi.org/10.1200/JCO.2008.16.6785
   PubMed Web of Science ®Google Scholar
• Monclair T, Brodeur GM, Ambros PF, Brisse HJ, Cecchetto G, Holmes K, Kaneko M, London WB, Matthay KK, Nuchtern JG, et al. The International Neuroblastoma Risk Group (INRG) staging system: an INRG Task Force report. J Clin Oncol 2009; 27:298–303; PMID:19047290; http://dx.doi.org/10.1200/JCO.2008.16.6876
   PubMed Web of Science ®Google Scholar
• Sugito K, Kawashima H, Uekusa S, Yoshizawa S, Hoshi R, Furuya T, Kaneda H, Hosoda T, Masuko T, Ohashi K, et al. Identification of aberrant methylation regions in neuroblastoma by screening of tissue-specific differentially methylated regions. Pediatr Blood Cancer 2013; 60:383–9; PMID:22911660; http://dx.doi.org/10.1002/pbc.24282
   PubMed Web of Science ®Google Scholar
• Carén H, Djos A, Nethander M, Sjöberg RM, Kogner P, Enström C, Nilsson S, Martinsson T. Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma. BMC Cancer 2011; 11:66; http://dx.doi.org/10.1186/1471-2407-11-66
   PubMed Web of Science ®Google Scholar
• Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, Fransson S, Ganeshram A, Mondal T, Bandaru S, et al. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell 2014; 26:722–37; PMID:25517750; http://dx.doi.org/10.1016/j.ccell.2014.09.014
   PubMed Web of Science ®Google Scholar
• Alaminos M, Davalos V, Cheung NK, Gerald WL, Esteller M. Clustering of gene hypermethylation associated with clinical risk groups in neuroblastoma. J Natl Cancer Inst 2004; 96:1208–19; PMID:15316056; http://dx.doi.org/10.1093/jnci/djh224
   PubMed Web of Science ®Google Scholar
• Abe M, Ohira M, Kaneda A, Yagi Y, Yamamoto S, Kitano Y, Takato T, Nakagawara A, Ushijima T. CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. Cancer Res 2005; 65:828–34; PMID:15705880
   PubMed Web of Science ®Google Scholar
• Yang Q, Tian Y, Ostler KR, Chlenski A, Guerrero LJ, Salwen HR, Godley LA, Cohn SL. Epigenetic alterations differ in phenotypically distinct human neuroblastoma cell lines. BMC Cancer 2010; 10:286; PMID:20546602; http://dx.doi.org/10.1186/1471-2407-10-286
   PubMed Web of Science ®Google Scholar
• Djos A, Martinsson T, Kogner P, Carén H. The RASSF gene family members RASSF5, RASSF6 and RASSF7 show frequent DNA methylation in neuroblastoma. Mol Cancer 2012; 11:40; PMID:22695170; http://dx.doi.org/10.1186/1476-4598-11-40
   PubMed Web of Science ®Google Scholar
• Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S. ChAMP: 450k Chip Analysis Methylation Pipeline. Bioinformatics 2014; 30:428–30; PMID:24336642; http://dx.doi.org/10.1093/bioinformatics/btt684
   PubMed Web of Science ®Google Scholar
• Dennis G, Jr., Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003; 4:P3; PMID:12734009; http://dx.doi.org/10.1186/gb-2003-4-5-p3
   PubMed Web of Science ®Google Scholar
• Gomez S, Castellano G, Mayol G, Sunol M, Queiros A, Bibikova M, Nazor KL, Loring JF, Lemos I, Rodriguez E, et al. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights. Epigenomics 2015 Oct; 7(7):1137-53; PMID:25687459
   PubMed Web of Science ®Google Scholar
• Kocak H, Ackermann S, Hero B, Kahlert Y, Oberthuer A, Juraeva D, Roels F, Theissen J, Westermann F, Deubzer H, et al. Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma. Cell Death Dis 2013; 4:e586; PMID:23579273; http://dx.doi.org/10.1038/cddis.2013.84
   PubMedGoogle Scholar
• Decock A, Ongenaert M, Hoebeeck J, De Preter K, Van Peer G, Van Criekinge W, Ladenstein R, Schulte JH, Noguera R, Stallings RL, et al. Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers. Genome Biol 2012; 13:R95; PMID:23034519; http://dx.doi.org/10.1186/gb-2012-13-10-r95
   PubMedGoogle Scholar
• Dreidax D, Bannert S, Henrich KO, Schroder C, Bender S, Oakes CC, Lindner S, Schulte JH, Duffy D, Schwarzl T, et al. p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas. Hum Mol Genet 2014; 23:6826–37; PMID:25104850; http://dx.doi.org/10.1093/hmg/ddu406
   PubMed Web of Science ®Google Scholar
• Hoebeeck J, Michels E, Pattyn F, Combaret V, Vermeulen J, Yigit N, Hoyoux C, Laureys G, De Paepe A, Speleman F, et al. Aberrant methylation of candidate tumor suppressor genes in neuroblastoma. Cancer Lett 2009; 273:336–46; PMID:18819746; http://dx.doi.org/10.1016/j.canlet.2008.08.019
   PubMed Web of Science ®Google Scholar
• Buckley PG, Das S, Bryan K, Watters KM, Alcock L, Koster J, Versteeg R, Stallings RL. Genome-wide DNA methylation analysis of neuroblastic tumors reveals clinically relevant epigenetic events and large-scale epigenomic alterations localized to telomeric regions. Int J Cancer 2011; 128:2296–305; PMID:20669225; http://dx.doi.org/10.1002/ijc.25584
   PubMed Web of Science ®Google Scholar
• Abe M, Watanabe N, McDonell N, Takato T, Ohira M, Nakagawara A, Ushijima T. Identification of genes targeted by CpG island methylator phenotype in neuroblastomas, and their possible integrative involvement in poor prognosis. Oncology 2008; 74:50–60; PMID:18544995; http://dx.doi.org/10.1159/000139124
   PubMed Web of Science ®Google Scholar
• Carén H, Fransson S, Ejeskär K, Kogner P, Martinsson T. Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours. Br J Cancer 2007; 97:1416–24; http://dx.doi.org/10.1038/sj.bjc.6604032
   PubMed Web of Science ®Google Scholar
• Castelo-Branco P, Choufani S, Mack S, Gallagher D, Zhang C, Lipman T, Zhukova N, Walker EJ, Martin D, Merino D, et al. Methylation of the TERT promoter and risk stratification of childhood brain tumours: an integrative genomic and molecular study. Lancet Oncol 2013; 14:534–42; PMID:23598174; http://dx.doi.org/10.1016/S1470-2045(13)70110-4
   PubMed Web of Science ®Google Scholar
• Miyajima N, Maruyama S, Nonomura K, Hatakeyama S. TRIM36 interacts with the kinetochore protein CENP-H and delays cell cycle progression. Biochem Biophys Res Commun 2009; 381:383–7; PMID:19232519; http://dx.doi.org/10.1016/j.bbrc.2009.02.059
   PubMed Web of Science ®Google Scholar
• Tocchini C, Ciosk R. TRIM-NHL proteins in development and disease. Semin Cell Dev Biol 2015; 47–48:52–9; PMID:26514622
   PubMed Web of Science ®Google Scholar
• El Andaloussi-Lilja J, Lundqvist J, Forsby A. TRPV1 expression and activity during retinoic acid-induced neuronal differentiation. Neurochem Int 2009; 55:768–74; PMID:19651168; http://dx.doi.org/10.1016/j.neuint.2009.07.011
   PubMed Web of Science ®Google Scholar
• Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98:288–95; PMID:21839163; http://dx.doi.org/10.1016/j.ygeno.2011.07.007
   PubMed Web of Science ®Google Scholar
• Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002; 12:996–1006; PMID:12045153; http://dx.doi.org/10.1101/gr.229102
   PubMed Web of Science ®Google Scholar