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

Epigenetics

Volumn 11, Issue 1, 2016, Pages 74-84

  Olsson, Maja ^a   Beck, Stephan ^b   Kogner, Per ^c   Martinsson, Tommy ^d   Carén, Helena ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^d UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

450K; CIMP; DLX5; DNA methylation; epigenetics; neuroblastoma; PCDHGA4; pediatric; TERT

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CFHR4 GENE; DNA METHYLATION; FLUORESCENCE; GENE; GENE EXPRESSION; GENE ONTOLOGY; GENETIC ANALYSIS; HUMAN; HUMAN CELL; MYELOID LEUKEMIA; NEUROBLASTOMA; PHENOTYPE; POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION SITE; ADOLESCENT; ADULT; AGED; CANCER STAGING; CHILD; CLASSIFICATION; CPG ISLAND; FEMALE; GENETIC EPIGENESIS; GENETICS; INFANT; MALE; MIDDLE AGED; PRESCHOOL CHILD; TUMOR GENE; VERY ELDERLY; YOUNG ADULT;

TUMOR MARKER;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; BIOMARKERS, TUMOR; CHILD; CHILD, PRESCHOOL; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENES, NEOPLASM; HUMANS; INFANT; MALE; MIDDLE AGED; NEOPLASM STAGING; NEUROBLASTOMA; YOUNG ADULT;

EID: 84961615355     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.1080/15592294.2016.1138195     Document Type: Article

References (32)

1. H.Carén, J.Erichsen, L.Olsson, C.Enerbäck, R.M.Sjöberg, J.Abrahamsson, P.Kogner, T.Martinsson. 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
2. H.Carén, H.Kryh, M.Nethander, R.M.Sjöberg, C.Träger, S.Nilsson, J.Abrahamsson, P.Kogner, T.Martinsson. 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
3. H.Carén, F.Abel, P.Kogner, T.Martinsson. 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
4. Y.P.Mosse, M.Laudenslager, L.Longo, K.A.Cole, A.Wood, E.F.Attiyeh, M.J.Laquaglia, R.Sennett, J.E.Lynch, P.Perri, et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 2008; 455(7215):930–5; PMID:18724359
5. Y.Chen, J.Takita, Y.L.Choi, M.Kato, M.Ohira, M.Sanada, L.Wang, M.Soda, A.Kikuchi, T.Igarashi, et al. Oncogenic mutations of ALK kinase in neuroblastoma. Nature 2008; 455:971–4; PMID:18923524; http://dx.doi.org/10.1038/nature07399
6. R.E.George, T.Sanda, M.Hanna, S.Frohling, W.Luther, 2nd, J.Zhang, Y.Ahn, W.Zhou, W.B.London, P.McGrady, 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
7. I.Janoueix-Lerosey, D.Lequin, L.Brugieres, A.Ribeiro, L.de Pontual, V.Combaret, V.Raynal, A.Puisieux, G.Schleiermacher, G.Pierron, 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
8. S.L.Cohn, A.D.Pearson, W.B.London, T.Monclair, P.F.Ambros, G.M.Brodeur, A.Faldum, B.Hero, T.Iehara, D.Machin, 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
9. T.Monclair, G.M.Brodeur, P.F.Ambros, H.J.Brisse, G.Cecchetto, K.Holmes, M.Kaneko, W.B.London, K.K.Matthay, J.G.Nuchtern, 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
10. K.Sugito, H.Kawashima, S.Uekusa, S.Yoshizawa, R.Hoshi, T.Furuya, H.Kaneda, T.Hosoda, T.Masuko, K.Ohashi, 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
11. H.Carén, A.Djos, M.Nethander, R.M.Sjöberg, P.Kogner, C.Enström, S.Nilsson, T.Martinsson. 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
12. G.K.Pandey, S.Mitra, S.Subhash, F.Hertwig, M.Kanduri, K.Mishra, S.Fransson, A.Ganeshram, T.Mondal, S.Bandaru, 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
13. M.Alaminos, V.Davalos, N.K.Cheung, W.L.Gerald, M.Esteller. 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
14. M.Abe, M.Ohira, A.Kaneda, Y.Yagi, S.Yamamoto, Y.Kitano, T.Takato, A.Nakagawara, T.Ushijima. CpG island methylator phenotype is a strong determinant of poor prognosis in neuroblastomas. Cancer Res 2005; 65:828–34; PMID:15705880
15. Q.Yang, Y.Tian, K.R.Ostler, A.Chlenski, L.J.Guerrero, H.R.Salwen, L.A.Godley, S.L.Cohn. 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
16. A.Djos, T.Martinsson, P.Kogner, H.Carén. 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
17. T.J.Morris, L.M.Butcher, A.Feber, A.E.Teschendorff, A.R.Chakravarthy, T.K.Wojdacz, S.Beck. ChAMP: 450k Chip Analysis Methylation Pipeline. Bioinformatics 2014; 30:428–30; PMID:24336642; http://dx.doi.org/10.1093/bioinformatics/btt684
18. G.Dennis, Jr., B.T.Sherman, D.A.Hosack, J.Yang, W.Gao, H.C.Lane, R.A.Lempicki. 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
19. S.Gomez, G.Castellano, G.Mayol, M.Sunol, A.Queiros, M.Bibikova, K.L.Nazor, J.F.Loring, I.Lemos, E.Rodriguez, et al. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights. Epigenomics 2015 Oct; 7(7):1137-53; PMID:25687459
20. H.Kocak, S.Ackermann, B.Hero, Y.Kahlert, A.Oberthuer, D.Juraeva, F.Roels, J.Theissen, F.Westermann, H.Deubzer, 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
21. A.Decock, M.Ongenaert, J.Hoebeeck, K.De Preter, G.Van Peer, W.Van Criekinge, R.Ladenstein, J.H.Schulte, R.Noguera, R.L.Stallings, 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
22. D.Dreidax, S.Bannert, K.O.Henrich, C.Schroder, S.Bender, C.C.Oakes, S.Lindner, J.H.Schulte, D.Duffy, T.Schwarzl, 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
23. J.Hoebeeck, E.Michels, F.Pattyn, V.Combaret, J.Vermeulen, N.Yigit, C.Hoyoux, G.Laureys, A.De Paepe, F.Speleman, 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
24. P.G.Buckley, S.Das, K.Bryan, K.M.Watters, L.Alcock, J.Koster, R.Versteeg, R.L.Stallings. 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
25. M.Abe, N.Watanabe, N.McDonell, T.Takato, M.Ohira, A.Nakagawara, T.Ushijima. 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
26. H.Carén, S.Fransson, K.Ejeskär, P.Kogner, T.Martinsson. 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
27. P.Castelo-Branco, S.Choufani, S.Mack, D.Gallagher, C.Zhang, T.Lipman, N.Zhukova, E.J.Walker, D.Martin, D.Merino, 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
28. N.Miyajima, S.Maruyama, K.Nonomura, S.Hatakeyama. 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
29. C.Tocchini, R.Ciosk. TRIM-NHL proteins in development and disease. Semin Cell Dev Biol 2015; 47–48:52–9; PMID:26514622
30. J.El Andaloussi-Lilja, J.Lundqvist, A.Forsby. 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
31. M.Bibikova, B.Barnes, C.Tsan, V.Ho, B.Klotzle, J.M.Le, D.Delano, L.Zhang, G.P.Schroth, K.L.Gunderson, 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
32. W.J.Kent, C.W.Sugnet, T.S.Furey, K.M.Roskin, T.H.Pringle, A.M.Zahler, D.Haussler. The human genome browser at UCSC. Genome Res 2002; 12:996–1006; PMID:12045153; http://dx.doi.org/10.1101/gr.229102