Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

DNA methylation-based biomarkers in bladder cancer

Abstract

Urinary bladder cancer is the fifth most common cancer in the Western world. Increasing evidence has shown that DNA methylation in bladder cancer is expansive and is implicated in pathogenesis. Furthermore, distinct methylation patterns have been identified between non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), as well as between FGFR3-mutant and wild-type tumours. Given these distinctions in expression, methylated genes have been proposed as diagnostic and prognostic biomarkers for patients with bladder cancer. Indeed, several studies have revealed that methylated genes—including CDH1, FHIT, LAMC2, RASSF1A, TIMP3, SFRP1, SOX9, PMF1 and RUNX3—are associated with poor survival in patients with MIBC. Further validation of these markers for prognostication as well as surveillance (of patients with NMIBC) is required. Validated markers for progression, diagnosis, survival and BCG response will contribute to clinical decision-making and individualized treatment.

Key Points

  • DNA methylation in bladder tumours might be an early event in cancer pathogenesis

  • Distinct methylation patterns have been identified between non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), as well as between FGFR3-mutant and wild-type tumours

  • The methylation of several genes involved in processes—such as cell cycle arrest, transcription, cell–cell adhesion, apoptosis and cellular differentiation—have been associated with progression in NMIBC

  • Methylation of the CDH1, FHIT, LAMC2, RASSF1A, TIMP3, SFRP1, SOX9, PMF1 and RUNX3 genes is associated with poor survival in patients with MIBC

  • Methylation of SYNPO2 is associated with resistance to BCG treatment in different cohorts of patients with T1G3 bladder cancer

  • DNA methylation might represent a potential target for future therapies in the bladder cancer setting

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: DNA methylation in normal and cancer cells.
Figure 2: Methylated genes implicated in predicting bladder tumour disease course.

Similar content being viewed by others

References

  1. Jemal, A. et al. Global cancer statistics. CA Cancer J. Clin. 61, 69–90 (2011).

    Article  PubMed  Google Scholar 

  2. Babjuk, M. et al. EAU guidelines on non-muscle-invasive urothelial carcinoma of the bladder. Eur. Urol. 54, 303–314 (2008).

    Article  PubMed  Google Scholar 

  3. Allard, P., Bernard, P., Fradet, Y. & Têtu, B. The early clinical course of primary Ta and T1 bladder cancer: a proposed prognostic index. Br. J. Urol. 81, 692–698 (1998).

    Article  CAS  PubMed  Google Scholar 

  4. Kurth, K. H. et al. Factors affecting recurrence and progression in superficial bladder tumours. Eur. J. Cancer 31A, 1840–1846 (1995).

    Article  CAS  PubMed  Google Scholar 

  5. Habuchi, T. et al. Prognostic markers for bladder cancer: International Consensus Panel on bladder tumor markers. Urology 66 (Suppl. 1), 64–74 (2005).

    Article  PubMed  Google Scholar 

  6. Sobin, L. H., Gospodarowicz, M. K. & Wittekind, C. (Eds) TNM Classification of Malignant Tumors (UICC International Union Against Cancer) (Wiley-Blackwell, New York, NY, 2009).

    Google Scholar 

  7. Kompier, L. C. et al. The development of multiple bladder tumour recurrences in relation to the FGFR3 mutation status of the primary tumour. J. Pathol. 218, 104–112 (2009).

    Article  CAS  PubMed  Google Scholar 

  8. Stenzl, A. et al. Treatment of muscle-invasive and metastatic bladder cancer: update of the EAU guidelines. Eur. Urol. 59, 1009–1018 (2011).

    Article  CAS  PubMed  Google Scholar 

  9. Sylvester, R. J. et al. 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, 466–467 (2006).

    Article  PubMed  Google Scholar 

  10. Rouprêt, M. et al. European guidelines for the diagnosis and management of upper urinary tract urothelial cell carcinomas: 2011 update. Eur. Urol. 59, 584–594 (2011).

    Article  PubMed  Google Scholar 

  11. van Rhijn, B. W. et al. Molecular grading of urothelial cell carcinoma with fibroblast growth factor receptor 3 and MIB-1 is superior to pathologic grade for the prediction of clinical outcome. J. Clin. Oncol. 21, 1912–1921 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Bakkar, A. A. et al. FGFR3 and TP53 gene mutations define two distinct pathways in urothelial cell carcinoma of the bladder. Cancer Res. 63, 8108–8112 (2003).

    CAS  PubMed  Google Scholar 

  13. van Rhijn, B. W. et al. The fibroblast growth factor receptor 3 (FGFR3) mutation is a strong indicator of superficial bladder cancer with low recurrence rate. Cancer Res. 61, 1265–1268 (2001).

    CAS  PubMed  Google Scholar 

  14. Knowles, M. A. Bladder cancer subtypes defined by genomic alterations. Scand. J. Urol. Nephrol. Suppl. 218, 116–130 (2008).

    Article  Google Scholar 

  15. Esteller, M. Epigenetics in cancer. N. Engl. J. Med. 358, 1148–1159 (2008).

    Article  CAS  PubMed  Google Scholar 

  16. Sanchez-Carbayo, M. Hypermethylation in bladder cancer: biological pathways and translational applications. Tumour Biol. 33, 347–361 (2012).

    Article  CAS  PubMed  Google Scholar 

  17. Laird, P. W. The power and the promise of DNA methylation markers. Nat. Rev. Cancer 3, 253–266 (2003).

    Article  CAS  PubMed  Google Scholar 

  18. Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 8, 286–298 (2007).

    Article  CAS  PubMed  Google Scholar 

  19. Esteller, M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum. Mol. Genet. 16 (Spec. No. 1), R50–R59 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Jones, P. A. & Baylin, S. B. The epigenomics of cancer. Cell 128, 683–692 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Nishiyama, N. et al. Genome-wide DNA methylation profiles in urothelial carcinomas and urothelia at the precancerous stage. Cancer Sci. 101, 231–240 (2010).

    Article  CAS  PubMed  Google Scholar 

  22. Wolff, E. M. et al. Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res. 70, 8169–8178 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kandimalla, R. 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. 61, 1245–1256 (2012).

    Article  CAS  PubMed  Google Scholar 

  24. Viré, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).

    Article  PubMed  Google Scholar 

  25. Chung, W. et al. Detection of bladder cancer using novel DNA methylation biomarkers in urine sediments. Cancer Epidemiol. Biomarkers Prev. 20, 1483–1491 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Fernandez, A. F. et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 22, 407–419 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Reinert, T. 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. 17, 5582–5592 (2011).

    Article  CAS  PubMed  Google Scholar 

  28. van Rhijn, B. W. et al. The FGFR3 mutation is related to favorable pT1 bladder cancer. J. Urol. 187, 310–314 (2012).

    Article  CAS  PubMed  Google Scholar 

  29. Hurst, C. D., Platt, F. M., Taylor, C. F. & Knowles, M. A. Novel tumor subgroups of urothelial carcinoma of the bladder defined by integrated genomic analysis. Clin. Cancer Res. 18, 5865–5877 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Vallot, C. et al. A novel epigenetic phenotype associated with the most aggressive pathway of bladder tumor progression. J. Natl Cancer Inst. 103, 47–60 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Costa, V. L. et al. Three epigenetic biomarkers, GDF15, TMEFF2, and VIM, accurately predict bladder cancer from DNA-based analyses of urine samples. Clin. Cancer Res. 16, 5842–5851 (2010).

    Article  CAS  PubMed  Google Scholar 

  32. Lin, H. H. et al. Increase sensitivity in detecting superficial, low grade bladder cancer by combination analysis of hypermethylation of E-cadherin, p16, p14, RASSF1A genes in urine. Urol. Oncol. 28, 597–602 (2010).

    Article  CAS  PubMed  Google Scholar 

  33. Serizawa, R. R. et al. Integrated genetic and epigenetic analysis of bladder cancer reveals an additive diagnostic value of FGFR3 mutations and hypermethylation events. Int. J. Cancer 129, 78–87 (2011).

    Article  CAS  PubMed  Google Scholar 

  34. Marsit, C. J. et al. Carcinogen exposure and gene promoter hypermethylation in bladder cancer. Carcinogenesis 27, 112–116 (2006).

    Article  CAS  PubMed  Google Scholar 

  35. Owen, H. C. et al. Low frequency of epigenetic events in urothelial tumors in young patients. J. Urol. 184, 459–463 (2010).

    Article  CAS  PubMed  Google Scholar 

  36. Sobti, R. C. et al. Hypermethylation-mediated partial transcriptional silencing of DAP-kinase gene in bladder cancer. Biomarkers 15, 167–174 (2010).

    Article  CAS  PubMed  Google Scholar 

  37. Wolff, E. M. et al. RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking. Cancer Res. 68, 6208–6214 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Maruyama, R. et al. Aberrant promoter methylation profile of bladder cancer and its relationship to clinicopathological features. Cancer Res. 61, 8659–8663 (2001).

    CAS  PubMed  Google Scholar 

  39. Sathyanarayana, U. G. et al. Molecular detection of noninvasive and invasive bladder tumor tissues and exfoliated cells by aberrant promoter methylation of laminin-5 encoding genes. Cancer Res. 64, 1425–1430 (2004).

    Article  CAS  PubMed  Google Scholar 

  40. Catto, J. W. et al. Promoter hypermethylation is associated with tumor location, stage, and subsequent progression in transitional cell carcinoma. J. Clin. Oncol. 23, 2903–2910 (2005).

    Article  CAS  PubMed  Google Scholar 

  41. Marsit, C. J. et al. Epigenetic inactivation of SFRP genes and TP53 alteration act jointly as markers of invasive bladder cancer. Cancer Res. 65, 7081–7085 (2005).

    Article  CAS  PubMed  Google Scholar 

  42. Kim, W. J. et al. RUNX3 inactivation by point mutations and aberrant DNA methylation in bladder tumors. Cancer Res. 65, 9347–9354 (2005).

    Article  CAS  PubMed  Google Scholar 

  43. Friedrich, M. G. et al. Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma. Eur. J. Cancer 41, 2769–2778 (2005).

    Article  CAS  PubMed  Google Scholar 

  44. Yates, D. R. et al. Promoter hypermethylation identifies progression risk in bladder cancer. Clin. Cancer Res. 13, 2046–2053 (2007).

    Article  CAS  PubMed  Google Scholar 

  45. Aleman, A. et al. Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays. Br. J. Cancer 98, 466–473 (2008).

    Article  CAS  PubMed  Google Scholar 

  46. Hoque, M. O. et al. Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. J. Natl Cancer Inst. 98, 996–1004 (2006).

    Article  CAS  PubMed  Google Scholar 

  47. Cebrian, V. et al. Discovery of myopodin methylation in bladder cancer. J. Pathol. 216, 111–119 (2008).

    Article  CAS  PubMed  Google Scholar 

  48. Aleman, A. et al. Identification of PMF1 methylation in association with bladder cancer progression. Clin. Cancer Res. 14, 8236–8243 (2008).

    Article  CAS  PubMed  Google Scholar 

  49. Marsit, C. J. et al. Identification of methylated genes associated with aggressive bladder cancer. PLoS ONE 5, e12334 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Alvarez-Mugica, M. et al. Myopodin methylation is associated with clinical outcome in patients with T1G3 bladder cancer. J. Urol. 184, 1507–1513 (2010).

    Article  CAS  PubMed  Google Scholar 

  51. Yan, C. et al. RUNX3 methylation as a predictor for disease progression in patients with non-muscle-invasive bladder cancer. J. Surg. Oncol. 105, 425–430 (2012).

    Article  CAS  PubMed  Google Scholar 

  52. Kim, J. S. et al. Ras association domain family 1A: a promising prognostic marker in recurrent nonmuscle invasive bladder cancer. Clin. Genitourin. Cancer 10, 114–120 (2012).

    Article  PubMed  Google Scholar 

  53. Agundez, M. et al. Evaluation of the methylation status of tumour suppressor genes for predicting bacillus Calmette-Guérin response in patients with T1G3 high-risk bladder tumours. Eur. Urol. 60, 131–140 (2011).

    Article  CAS  PubMed  Google Scholar 

  54. Alvarez-Mugica, M. et al. Polyamine-modulated factor-1 methylation predicts Bacillus Calmette-Guérin response in patients with high-grade non-muscle-invasive bladder carcinoma. Eur. Urol. 63, 364–370 (2012).

    Article  PubMed  Google Scholar 

  55. Zuiverloon, T. C. et al. A methylation assay for the detection of non-muscle-invasive bladder cancer (NMIBC) recurrences in voided urine. BJU Int. 109, 941–948 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. van Rhijn, B. W., van der Poel, H. G. & van der Kwast, T. H. Urine markers for bladder cancer surveillance: a systematic review. Eur. Urol. 47, 736–748 (2005).

    Article  CAS  PubMed  Google Scholar 

  57. Yu, J. et al. A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer. Clin. Cancer Res. 13, 7296–7304 (2007).

    Article  CAS  PubMed  Google Scholar 

  58. Renard, I. et al. 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, 96–104 (2010).

    Article  CAS  PubMed  Google Scholar 

  59. Dulaimi, E., Uzzo, R. G., Greenberg, R. E., Al-Saleem, T. & Cairns, P. Detection of bladder cancer in urine by a tumor suppressor gene hypermethylation panel. Clin. Cancer Res. 10, 1887–1893 (2004).

    Article  CAS  PubMed  Google Scholar 

  60. Eissa, S. et al. Urinary retinoic acid receptor-β2 gene promoter methylation and hyaluronidase activity as noninvasive tests for diagnosis of bladder cancer. Clin. Biochem. 45, 402–407 (2012).

    Article  CAS  PubMed  Google Scholar 

  61. Zhao, Y. et al. Methylcap-seq reveals novel DNA methylation markers for the diagnosis and recurrence prediction of bladder cancer in a Chinese population. PLoS ONE 7, e35175 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Rouprêt, M. et al. A comparison of the performance of microsatellite and methylation urine analysis for predicting the recurrence of urothelial cell carcinoma, and definition of a set of markers by Bayesian network analysis. BJU Int. 101, 1448–1453 (2008).

    Article  PubMed  Google Scholar 

  63. Vinci, S. et al. Quantitative methylation analysis of BCL2, hTERT, and DAPK promoters in urine sediment for the detection of non-muscle-invasive urothelial carcinoma of the bladder: a prospective, two-center validation study. Urol. Oncol. 29, 150–156 (2011).

    Article  CAS  PubMed  Google Scholar 

  64. Grossman, H. B. et al. A phase III, multicenter comparison of hexaminolevulinate fluorescence cystoscopy and white light cystoscopy for the detection of superficial papillary lesions in patients with bladder cancer. J. Urol. 178, 62–67 (2007).

    Article  PubMed  Google Scholar 

  65. Jocham, D. et al. Improved detection and treatment of bladder cancer using hexaminolevulinate imaging: a prospective, phase III multicenter study. J. Urol. 174, 862–866 (2005).

    Article  PubMed  Google Scholar 

  66. Ellinger, J. et al. Hypermethylation of cell-free serum DNA indicates worse outcome in patients with bladder cancer. J. Urol. 179, 346–352 (2008).

    Article  CAS  PubMed  Google Scholar 

  67. Valenzuela, M. T. et al. Assessing the use of p16(INK4a) promoter gene methylation in serum for detection of bladder cancer. Eur. Urol. 42, 622–630 (2002).

    Article  CAS  PubMed  Google Scholar 

  68. Shariat, S. F. et al. Statistical consideration for clinical biomarker research in bladder cancer. Urol. Oncol. 28, 389–400 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  69. Baker, S. G. et al. Evaluating markers for the early detection of cancer: overview of study designs and methods. Clin. Trials 3, 43–56 (2006).

    Article  PubMed  Google Scholar 

  70. Bossuyt, P. M. et al. Toward complete and accurate reporting of studies of diagnostic accuracy. The STARD initiative. Am. J. Clin. Pathol. 119, 18–22 (2003).

    Article  PubMed  Google Scholar 

  71. McShane, L. M. et al. REporting recommendations for tumor MARKer prognostic studies (REMARK). Nat. Clin. Pract. Urol. 2, 416–422 (2005).

    CAS  PubMed  Google Scholar 

  72. Cabello, M. J. et al. Multiplexed methylation profiles of tumor suppressor genes in bladder cancer. J. Mol. Diagn. 13, 29–40 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Duarte-Pereira, S. et al. Prognostic value of opioid binding protein/cell adhesion molecule-like promoter methylation in bladder carcinoma. Eur. J. Cancer 47, 1106–1114 (2011).

    Article  CAS  PubMed  Google Scholar 

  74. Xuan, Y., Kim, S. & Lin, Z. Protein expression and gene promoter hypermethylation of CD99 in transitional cell carcinoma of urinary bladder. J. Cancer Res. Clin. Oncol. 137, 49–54 (2011).

    Article  CAS  PubMed  Google Scholar 

  75. Lin, Y. L., Liu, X. Q., Li, W. P., Sun, G. & Zhang, C. T. Promoter methylation of H-cadherin is a potential biomarker in patients with bladder transitional cell carcinoma. Int. Urol. Nephrol. 44, 111–117 (2012).

    Article  CAS  PubMed  Google Scholar 

  76. Chan, M. W. et al. Hypermethylation of multiple genes in tumor tissues and voided urine in urinary bladder cancer patients. Clin. Cancer Res. 8, 464–470 (2002).

    CAS  PubMed  Google Scholar 

  77. Friedrich, M. G. et al. Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients. Clin. Cancer Res. 10, 7457–7465 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Urakami, S. et al. Combination analysis of hypermethylated Wnt-antagonist family genes as a novel epigenetic biomarker panel for bladder cancer detection. Clin. Cancer Res. 12, 2109–2116 (2006).

    Article  CAS  PubMed  Google Scholar 

  79. Yates, D. R. et al. Methylational urinalysis: a prospective study of bladder cancer patients and age stratified benign controls. Oncogene 25, 1984–1988 (2006).

    Article  CAS  PubMed  Google Scholar 

  80. Dudziec, E., Goepel, J. R. & Catto, J. W. Global epigenetic profiling in bladder cancer. Epigenomics 3, 35–45 (2011).

    Article  CAS  PubMed  Google Scholar 

  81. Chen, P.-C. et al. Distinct DNA methylation epigenotypes in bladder cancer from different Chinese sub-populations and its implication in cancer detection using voided urine. BMC Med. Genomics 4, 45 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are supported by a research grant from Erasmus MC (Mrace) and a grant from the Dutch Cancer Society (EMCR 2007-3863).

Author information

Authors and Affiliations

Authors

Contributions

R. Kandimalla researched the data for the article. All authors discussed the article's content, wrote the manuscript and edited it before submission.

Corresponding author

Correspondence to Ellen C. Zwarthoff.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Overview of all DNA methylation markers in bladder cancer (reported up to April 2012). (DOC 465 kb)

Supplementary Table 2

Urine methylation markers in bladder cancer (DOC 212 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kandimalla, R., van Tilborg, A. & Zwarthoff, E. DNA methylation-based biomarkers in bladder cancer. Nat Rev Urol 10, 327–335 (2013). https://doi.org/10.1038/nrurol.2013.89

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrurol.2013.89

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing