Genome-wide analysis of CpG Island methylation in bladder cancer identified TBX2, TBX3, GATA2, and ZIC4 as pTa-specific prognostic markers

European Urology

Volumn 61, Issue 6, 2012, Pages 1245-1256

  Kandimalla, Raju ^a   Van Tilborg, Angela A G ^a   Kompier, Lucie C ^a   Stumpel, Dominique J P M ^a   Stam, Ronald W ^a   Bangma, Chris H ^a   Zwarthoff, Ellen C ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Biomarkers; Bladder cancer; DNA methylation; Epigenetics; Prognostic markers; Progression

Indexed keywords

T BOX TRANSCRIPTION FACTOR; T BOX TRANSCRIPTION FACTOR 2; T BOX TRANSCRIPTION FACTOR 3; TRANSCRIPTION FACTOR GATA 2; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; BLADDER CANCER; CANCER GROWTH; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; GENE; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; MALE; MICROARRAY ANALYSIS; MICTURITION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROGRESSION FREE SURVIVAL; SENSITIVITY AND SPECIFICITY; ZIC FAMILY MEMBER 4 GENE;

AGED; CPG ISLANDS; DISEASE PROGRESSION; DISEASE-FREE SURVIVAL; DNA METHYLATION; FEMALE; GATA2 TRANSCRIPTION FACTOR; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; KAPLAN-MEIER ESTIMATE; MALE; MIDDLE AGED; MULTIVARIATE ANALYSIS; NEOPLASM STAGING; NERVE TISSUE PROTEINS; NETHERLANDS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PREDICTIVE VALUE OF TESTS; PROPORTIONAL HAZARDS MODELS; REPRODUCIBILITY OF RESULTS; RETROSPECTIVE STUDIES; RISK ASSESSMENT; RISK FACTORS; SENSITIVITY AND SPECIFICITY; T-BOX DOMAIN PROTEINS; TIME FACTORS; TRANSCRIPTION FACTORS; TUMOR MARKERS, BIOLOGICAL; URINARY BLADDER NEOPLASMS;

EID: 84860282565     PISSN: 03022838     EISSN: 18737560     Source Type: Journal    
DOI: 10.1016/j.eururo.2012.01.011     Document Type: Article

References (42)

1. D.M. Parkin, F. Bray, J. Ferlay, and P. Pisani Global cancer statistics, 2002 CA Cancer J Clin 55 2005 74 108 (Pubitemid 40372904)
2. A.A Bakkar, H. Wallerand, and F. Radvanyi FGFR3 and TP53 gene mutations define two distinct pathways in urothelial cell carcinoma of the bladder Cancer Res 63 2003 8108 8112 (Pubitemid 37549454)
3. B.W. van Rhijn, I. Lurkin, F. Radvanyi, W.J. Kirkels, T.H. van der Kwast, and E.C. Zwarthoff The fibroblast growth factor receptor 3 (FGFR3) mutation is a strong indicator of superficial bladder cancer with low recurrence rate Cancer Res 61 2001 1265 1268 (Pubitemid 34292538)
4. M.A. Knowles Bladder cancer subtypes defined by genomic alterations Scand J Urol Nephrol Suppl 2008 116 130
5. B.W.G. van Rhijn, T.C.M. Zuiverloon, and A.N. Vis Molecular grade (FGFR3/MIB-1) and EORTC risk scores are predictive in primary non-muscle-invasive bladder cancer Eur Urol 58 2010 433 441
6. L.C. Kompier, I. Lurkin, M.N. van der Aa, B.W. van Rhijn, T.H. van der Kwast, and E.C. Zwarthoff FGFR3, HRAS, KRAS, NRAS and PIK3CA mutations in bladder cancer and their potential as biomarkers for surveillance and therapy PLoS One 5 2010 e13821
7. R.J. Sylvester, A.P.M. van der Meijden, and W. Oosterlinck Predicting recurrence and progression in individual patients with stage Ta T1 bladder cancer using EORTC risk tables: a combined analysis of 2596 patients from seven EORTC trials Eur Urol 49 2006 466 477 discussion 475-7
8. L.C. Kompier, A.A. van Tilborg, and E.C. Zwarthoff Bladder cancer: novel molecular characteristics, diagnostic, and therapeutic implications Urol Oncol 28 2010 91 96
9. J.M. van Oers, I. Lurkin, and A.J. van Exsel A simple and fast method for the simultaneous detection of nine fibroblast growth factor receptor 3 mutations in bladder cancer and voided urine Clin Cancer Res 11 2005 7743 7748 (Pubitemid 41611617)
10. B.W. van Rhijn, I. Lurkin, and D.K. Chopin Combined microsatellite and FGFR3 mutation analysis enables a highly sensitive detection of urothelial cell carcinoma in voided urine Clin Cancer Res 9 2003 257 263 (Pubitemid 36109742)
11. M.E. Hegi, A.C. Diserens, and T. Gorlia MGMT gene silencing and benefit from temozolomide in glioblastoma N Engl J Med 352 2005 997 1003 (Pubitemid 40349502)
12. M. Babjuk, W. Oosterlinck, and R. Sylvester EAU guidelines on non-muscle-invasive urothelial carcinoma of the bladder Eur Urol 54 2008 303 314
13. L.M. McShane, D.G. Altman, and W. Sauerbrei Reporting recommendations for tumor marker prognostic studies J Clin Oncol 23 2005 9067 9072
14. P.S. Yan, S.H. Wei, and T.H. Huang Differential methylation hybridization using CpG island arrays Methods Mol Biol 200 2002 87 100
15. D.J. Stumpel, P. Schneider, and E.H. van Roon Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options Blood 114 2009 5490 5498
16. A. Brazma Minimum Information About a Microarray Experiment (MIAME) - successes, failures, challenges ScientificWorldJournal 9 2009 420 423
17. Y. Benjamini, D. Drai, G. Elmer, N. Kafkafi, and I. Golani Controlling the false discovery rate in behavior genetics research Behav Brain Res 125 2001 279 284 (Pubitemid 33000466)
18. J.E. Ohm, K.M. McGarvey, and X. Yu A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing Nat Genet 39 2007 237 242 (Pubitemid 46184356)
19. Y. Schlesinger, R. Straussman, and I. Keshet Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer Nat Genet 39 2007 232 236 (Pubitemid 46184355)
20. A.P. Feinberg, R. Ohlsson, and S. Henikoff The epigenetic progenitor origin of human cancer Nat Rev Genet 7 2006 21 33 (Pubitemid 41828945)
21. Y.G. Crawford, M.L. Gauthier, and A. Joubel Histologically normal human mammary epithelia with silenced p16(INK4a) overexpress COX-2, promoting a premalignant program Cancer Cell 5 2004 263 273 (Pubitemid 38402118)
22. A.P. Feinberg, and B. Vogelstein Hypomethylation distinguishes genes of some human cancers from their normal counterparts Nature 301 1983 89 92 (Pubitemid 13154475)
23. C.R. Holst, G.J. Nuovo, and M. Esteller Methylation of p16(INK4a) promoters occurs in vivo in histologically normal human mammary epithelia Cancer Res 63 2003 1596 1601 (Pubitemid 36373649)
24. J. Smith T-box genes: what they do and how they do it Trends Genet 15 1999 154 158 (Pubitemid 29155438)
25. M. Sanchez-Carbayo, N.D. Socci, J. Lozano, F. Saint, and C. Cordon-Cardo Defining molecular profiles of poor outcome in patients with invasive bladder cancer using oligonucleotide microarrays J Clin Oncol 24 2006 778 789 (Pubitemid 46622045)
26. J. Lu, X.P. Li, Q. Dong, H.F. Kung, and M.L. He TBX2 and TBX3: the special value for anticancer drug targets Biochim Biophys Acta 1806 2010 268 274
27. C.N. Hahn, C.E. Chong, and C.L. Carmichael Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia Nat Genet 43 2011 1012 1017
28. D.R. Yates, I. Rehman, and M.F. Abbod Promoter hypermethylation identifies progression risk in bladder cancer Clin Cancer Res 13 2007 2046 2053 (Pubitemid 46649871)
29. M.G. Friedrich, S. Chandrasoma, and K.D. Siegmund Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma Eur J Cancer 41 2005 2769 2778 (Pubitemid 41607571)
30. T. Reinert, C. Modin, and F. Mansilla Castano 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 17 2011 5582 5592
31. Y.K. Kim, and W.J. Kim Epigenetic markers as promising prognosticators for bladder cancer Int J Urol 16 2009 17 22
32. V.L. Costa, R. Henrique, and S.A. Danielsen Three epigenetic biomarkers, GDF15, TMEFF2, and VIM, accurately predict bladder cancer from DNA-based analyses of urine samples Clin Cancer Res 16 2010 5842 5851
33. I. Renard, S. Joniau, and B. van Cleynenbreugel Identification and validation of the methylated TWIST1 and NID2 genes through real-time methylation-specific polymerase chain reaction assays for the noninvasive detection of primary bladder cancer in urine samples Eur Urol 58 2010 96 104
34. W. Chung, J. Bondaruk, and J. Jelinek Detection of bladder cancer using novel DNA methylation biomarkers in urine sediments Cancer Epidemiol Biomarkers Prev 20 2011 1483 1491
35. R.R. Serizawa, U. Ralfkiaer, and K. Steven Integrated genetic and epigenetic analysis of bladder cancer reveals an additive diagnostic value of FGFR3 mutations and hypermethylation events Int J Cancer 129 2011 78 87
36. M. Toyota, N. Ahuja, M. Ohe-Toyota, J.G. Herman, S.B. Baylin, and J.P. Issa CpG island methylator phenotype in colorectal cancer Proc Natl Acad Sci U S A 96 1999 8681 8686 (Pubitemid 29354851)
37. S. Ogino, T. Kawasaki, G.J. Kirkner, P. Kraft, M. Loda, and C.S. Fuchs Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample J Mol Diagn 9 2007 305 314 (Pubitemid 47305066)
38. H. Noushmehr, D.J. Weisenberger, and K. Diefes Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma Cancer Cell 17 2010 510 522
39. T. Hinoue, D.J. Weisenberger, and C.P. Lange Genome-scale analysis of aberrant DNA methylation in colorectal cancer Genome Res 22 2012 271 282
40. R.A. Irizarry, C. Ladd-Acosta, and B. Wen The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores Nat Genet 41 2009 178 186
41. A.P. Bracken, and K. Helin Polycomb group proteins: navigators of lineage pathways led astray in cancer Nat Rev Cancer 9 2009 773 784
42. E.M. Wolff, Y. Chihara, and F. Pan Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue Cancer Res 70 2010 8169 8178