DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status

References

• Avritscher EBC, Cooksley CD, Grossman HB, Sabichi AL, Hamblin L, Dinney CP, et al. Clinical model of lifetime cost of treating bladder cancer and associated complications. Urology 2006; 68:549 - 53; http://dx.doi.org/10.1016/j.urology.2006.03.062; PMID: 16979735
   PubMed Web of Science ®Google Scholar
• Sjödahl G, Lauss M, Gudjonsson S, Liedberg F, Halldén C, Chebil G, et al. A systematic study of gene mutations in urothelial carcinoma; inactivating mutations in TSC2 and PIK3R1. PLoS One 2011; 6:e18583; http://dx.doi.org/10.1371/journal.pone.0018583; PMID: 21533174
   PubMed Web of Science ®Google Scholar
• Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, Koppie T, et al. Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res 2005; 11:7012 - 22; http://dx.doi.org/10.1158/1078-0432.CCR-05-0177; PMID: 16203795
   PubMed Web of Science ®Google Scholar
• Blaveri E, Simko JP, Korkola JE, Brewer JL, Baehner F, Mehta K, et al. Bladder cancer outcome and subtype classification by gene expression. Clin Cancer Res 2005; 11:4044 - 55; http://dx.doi.org/10.1158/1078-0432.CCR-04-2409; PMID: 15930339
   PubMed Web of Science ®Google Scholar
• Sanchez-Carbayo M, Socci ND, Lozano J, Saint F, Cordon-Cardo C. Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays. J Clin Oncol 2006; 24:778 - 89; http://dx.doi.org/10.1200/JCO.2005.03.2375; PMID: 16432078
   PubMed Web of Science ®Google Scholar
• Dyrskjøt L, Zieger K, Real FX, Malats N, Carrato A, Hurst C, et al. Gene expression signatures predict outcome in non-muscle-invasive bladder carcinoma: a multicenter validation study. Clin Cancer Res 2007; 13:3545 - 51; http://dx.doi.org/10.1158/1078-0432.CCR-06-2940; PMID: 17575217
   PubMed Web of Science ®Google Scholar
• Lindgren D, Frigyesi A, Gudjonsson S, Sjödahl G, Hallden C, Chebil G, et al. Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome. Cancer Res 2010; 70:3463 - 72; http://dx.doi.org/10.1158/0008-5472.CAN-09-4213; PMID: 20406976
   PubMed Web of Science ®Google Scholar
• Esteller M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 2007; 16:Spec No 1 R50 - 9; http://dx.doi.org/10.1093/hmg/ddm018; PMID: 17613547
   PubMed Web of Science ®Google Scholar
• Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43:768 - 75; http://dx.doi.org/10.1038/ng.865; PMID: 21706001
   PubMed Web of Science ®Google Scholar
• Veerla S, Panagopoulos I, Jin Y, Lindgren D, Höglund M. Promoter analysis of epigenetically controlled genes in bladder cancer. Genes Chromosomes Cancer 2008; 47:368 - 78; http://dx.doi.org/10.1002/gcc.20542; PMID: 18196590
   PubMed Web of Science ®Google Scholar
• Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457 - 66; http://dx.doi.org/10.1038/ng1990; PMID: 17334365
   PubMed Web of Science ®Google Scholar
• Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jönsson G, Olsson H, et al. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 2010; 12:R36; http://dx.doi.org/10.1186/bcr2590; PMID: 20565864
   PubMed Web of Science ®Google Scholar
• Van der Auwera I, Yu W, Suo L, Van Neste L, van Dam P, Van Marck EA, et al. Array-based DNA methylation profiling for breast cancer subtype discrimination. PLoS One 2010; 5:e12616; http://dx.doi.org/10.1371/journal.pone.0012616; PMID: 20830311
   PubMed Web of Science ®Google Scholar
• Fang F, Turcan S, Rimner A, Kaufman A, Giri D, Morris LGT, et al. Breast cancer methylomes establish an epigenomic foundation for metastasis. Sci Transl Med 2011; 3:75ra25; http://dx.doi.org/10.1126/scitranslmed.3001875; PMID: 21430268
   PubMed Web of Science ®Google Scholar
• Hinoue T, Weisenberger DJ, Lange CPE, Shen H, Byun H-M, Van Den Berg D, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 2012; 22:271 - 82; http://dx.doi.org/10.1101/gr.117523.110; PMID: 21659424
   PubMed Web of Science ®Google Scholar
• Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, Alvarez S, et al. A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One 2009; 4:e6986; http://dx.doi.org/10.1371/journal.pone.0006986; PMID: 19750229
   PubMed Web of Science ®Google Scholar
• Stransky N, Vallot C, Reyal F, Bernard-Pierrot I, de Medina SGD, Segraves R, et al. Regional copy number-independent deregulation of transcription in cancer. Nat Genet 2006; 38:1386 - 96; http://dx.doi.org/10.1038/ng1923; PMID: 17099711
   PubMed Web of Science ®Google Scholar
• Vallot C, Stransky N, Bernard-Pierrot I, Hérault A, Zucman-Rossi J, Chapeaublanc E, et al. A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression. J Natl Cancer Inst 2011; 103:47 - 60; http://dx.doi.org/10.1093/jnci/djq470; PMID: 21173382
   PubMed Web of Science ®Google Scholar
• Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund KD, Sugano K, et al. Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res 2010; 70:8169 - 78; http://dx.doi.org/10.1158/0008-5472.CAN-10-1335; PMID: 20841482
   PubMed Web of Science ®Google Scholar
• Wilhelm-Benartzi CS, Koestler DC, Houseman EA, Christensen BC, Wiencke JK, Schned AR, et al. DNA methylation profiles delineate etiologic heterogeneity and clinically important subgroups of bladder cancer. Carcinogenesis 2010; 31:1972 - 6; http://dx.doi.org/10.1093/carcin/bgq178; PMID: 20802236
   PubMed Web of Science ®Google Scholar
• Reinert T, Modin C, Castano FM, Lamy P, Wojdacz TK, Hansen LL, et al. Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin Cancer Res 2011; 17:5582 - 92; http://dx.doi.org/10.1158/1078-0432.CCR-10-2659; PMID: 21788354
   PubMed Web of Science ®Google Scholar
• Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 2007; 39:232 - 6; http://dx.doi.org/10.1038/ng1950; PMID: 17200670
   PubMed Web of Science ®Google Scholar
• Du P, Zhang X, Huang C-C, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 2010; 11:587; http://dx.doi.org/10.1186/1471-2105-11-587; PMID: 21118553
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010; 20:440 - 6; http://dx.doi.org/10.1101/gr.103606.109; PMID: 20219944
   PubMed Web of Science ®Google Scholar
• Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006; 125:301 - 13; http://dx.doi.org/10.1016/j.cell.2006.02.043; PMID: 16630818
   PubMed Web of Science ®Google Scholar
• Heidenblad M, Lindgren D, Jonson T, Liedberg F, Veerla S, Chebil G, et al. Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors. BMC Med Genomics 2008; 1:3; http://dx.doi.org/10.1186/1755-8794-1-3; PMID: 18237450
   PubMed Web of Science ®Google Scholar
• Ball MP, Li JB, Gao Y, Lee J-H, LeProust EM, Park I-H, et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009; 27:361 - 8; http://dx.doi.org/10.1038/nbt.1533; PMID: 19329998
   PubMed Web of Science ®Google Scholar
• James L, Eisenman RN. Myc and Mad bHLHZ domains possess identical DNA-binding specificities but only partially overlapping functions in vivo. Proc Natl Acad Sci U S A 2002; 99:10429 - 34; http://dx.doi.org/10.1073/pnas.162369299; PMID: 12149476
   PubMed Web of Science ®Google Scholar
• Perini G, Diolaiti D, Porro A, Della Valle G. In vivo transcriptional regulation of N-Myc target genes is controlled by E-box methylation. Proc Natl Acad Sci U S A 2005; 102:12117 - 22; http://dx.doi.org/10.1073/pnas.0409097102; PMID: 16093321
   PubMed Web of Science ®Google Scholar
• Fujii G, Nakamura Y, Tsukamoto D, Ito M, Shiba T, Takamatsu N. CpG methylation at the USF-binding site is important for the liver-specific transcription of the chipmunk HP-27 gene. Biochem J 2006; 395:203 - 9; http://dx.doi.org/10.1042/BJ20051802; PMID: 16396632
   PubMed Web of Science ®Google Scholar
• Qiao H, May JM. CpG methylation at the USF-binding site mediates cell-specific transcription of human ascorbate transporter SVCT2 exon 1a. Biochem J 2011; 440:73 - 84; http://dx.doi.org/10.1042/BJ20110392; PMID: 21770893
   PubMed Web of Science ®Google Scholar
• Rishi V, Bhattacharya P, Chatterjee R, Rozenberg J, Zhao J, Glass K, et al. CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. Proc Natl Acad Sci U S A 2010; 107:20311 - 6; http://dx.doi.org/10.1073/pnas.1008688107; PMID: 21059933
   PubMed Web of Science ®Google Scholar
• Rössler J, Stolze I, Frede S, Freitag P, Schweigerer L, Havers W, et al. Hypoxia-induced erythropoietin expression in human neuroblastoma requires a methylation free HIF-1 binding site. J Cell Biochem 2004; 93:153 - 61; http://dx.doi.org/10.1002/jcb.20133; PMID: 15352172
   PubMed Web of Science ®Google Scholar
• Brenner C, Deplus R, Didelot C, Loriot A, Viré E, De Smet C, et al. Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J 2005; 24:336 - 46; http://dx.doi.org/10.1038/sj.emboj.7600509; PMID: 15616584
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41:178 - 86; http://dx.doi.org/10.1038/ng.298; PMID: 19151715
   PubMed Web of Science ®Google Scholar
• Kandimalla R, van Tilborg AAG, Kompier LC, Stumpel DJPM, Stam RW, Bangma CH, et al. Genome-wide Analysis of CpG Island Methylation in Bladder Cancer Identified TBX2, TBX3, GATA2, and ZIC4 as pTa-Specific Prognostic Markers. Eur Urol 2012; 61:1245 - 56; http://dx.doi.org/10.1016/j.eururo.2012.01.011; PMID: 22284968
   PubMed Web of Science ®Google Scholar
• Marsit CJ, Houseman EA, Christensen BC, Gagne L, Wrensch MR, Nelson HH, et al. Identification of methylated genes associated with aggressive bladder cancer. PLoS One 2010; 5:e12334; http://dx.doi.org/10.1371/journal.pone.0012334; PMID: 20808801
   PubMed Web of Science ®Google Scholar
• Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz L-A, Merino VF, et al. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res 2011; 71:6195 - 207; http://dx.doi.org/10.1158/0008-5472.CAN-11-1630; PMID: 21825015
   PubMed Web of Science ®Google Scholar
• Fiegl H, Windbichler G, Mueller-Holzner E, Goebel G, Lechner M, Jacobs IJ, et al. HOXA11 DNA methylation--a novel prognostic biomarker in ovarian cancer. Int J Cancer 2008; 123:725 - 9; http://dx.doi.org/10.1002/ijc.23563; PMID: 18478570
   PubMed Web of Science ®Google Scholar
• Strathdee G, Holyoake TL, Sim A, Parker A, Oscier DG, Melo JV, et al. Inactivation of HOXA genes by hypermethylation in myeloid and lymphoid malignancy is frequent and associated with poor prognosis. Clin Cancer Res 2007; 13:5048 - 55; http://dx.doi.org/10.1158/1078-0432.CCR-07-0919; PMID: 17785556
   PubMed Web of Science ®Google Scholar
• Atkinson SP, Koch CM, Clelland GK, Willcox S, Fowler JC, Stewart R, et al. Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells. Stem Cells 2008; 26:1174 - 85; http://dx.doi.org/10.1634/stemcells.2007-0497; PMID: 18292213
   PubMed Web of Science ®Google Scholar
• Houseman EA, Christensen BC, Karagas MR, Wrensch MR, Nelson HH, Wiemels JL, et al. Copy number variation has little impact on bead-array-based measures of DNA methylation. Bioinformatics 2009; 25:1999 - 2005; http://dx.doi.org/10.1093/bioinformatics/btp364; PMID: 19542153
   PubMed Web of Science ®Google Scholar
• Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, et al. Missing value estimation methods for DNA microarrays. Bioinformatics 2001; 17:520 - 5; http://dx.doi.org/10.1093/bioinformatics/17.6.520; PMID: 11395428
   PubMed Web of Science ®Google Scholar
• Smyth GK Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3:Article3.
   Google Scholar
• Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007; 23:657 - 63; http://dx.doi.org/10.1093/bioinformatics/btl646; PMID: 17234643
   PubMed Web of Science ®Google Scholar
• Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J. Normalization of array-CGH data: influence of copy number imbalances. BMC Genomics 2007; 8:382; http://dx.doi.org/10.1186/1471-2164-8-382; PMID: 17953745
   PubMed Web of Science ®Google Scholar
• Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 2009; 1:177 - 200; http://dx.doi.org/10.2217/epi.09.14; PMID: 22122642
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al, The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25:25 - 9; http://dx.doi.org/10.1038/75556; PMID: 10802651
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009; 37:Web Server issue W202-8; http://dx.doi.org/10.1093/nar/gkp335; PMID: 19458158
   PubMedGoogle Scholar
• Veerla S, Ringnér M, Höglund M. Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs. BMC Genomics 2010; 11:145; http://dx.doi.org/10.1186/1471-2164-11-145; PMID: 20193056
   PubMed Web of Science ®Google Scholar