A Versatile Assay for Detection of Aberrant DNA Methylation in Bladder Cancer
Urothelial carcinoma of the bladder is one of the most common malignancies in the industrialized world, mainly caused by smoking and occupational exposure to chemicals. The favorable prognosis of early stage bladder cancer underscores the importance of early detection for the treatment of this disease. The high recurrence rate of this malignancy also highlights the need for close post-diagnosis monitoring of bladder cancer patients. As for other malignancies, aberrant DNA methylation has been shown to play a crucial role in the initiation and progression of bladder cancer, and thus holds great promise as a diagnostic and prognostic biological marker. Here, we describe a protocol for a versatile DNA methylation enrichment method, the Methylated CpG Island Recovery Assay (MIRA), which enables analysis of the DNA methylation status in individual genes or across the entire genome. MIRA is based on the ability of the methyl-binding domain (MBD) proteins, the MBD2B/MBD3L1 complex, to specifically bind methylated CpG dinucleotides. This easy-to-perform method can be used to analyze the methylome of bladder cancer or urothelial cells shed in the urine to elucidate the evolution of bladder carcinogenesis and/or identify epigenetic signatures of chemicals known to cause this malignancy.
Key wordsAromatic amines Biomarkers Epigenetics Methyl-binding domain (MBD) proteins Tobacco smoke Urine
ST and AB declare no conflicts of interest.
Work of the authors is funded by grants from the National Institute of Dental and Craniofacial Research of the National Institutes of Health (1R01DE026043-01) to AB and from the University of California Tobacco-Related Disease Research Program (TRDRP-25IP-0001) to ST.
- 1.Stewart BW, Wild CP (eds) (2014) World Cancer Report 2014. International Agency for Research on Cancer (IARC), Lyon, FranceGoogle Scholar
- 13.U.S. Department of Health and Human Services (2014) The health consequences of smoking – 50 years of progress. A report of the Surgeon General. U.S. Department of Health and Human Services. Public Health Service. Office of the Surgeon General. Rockville, MDGoogle Scholar
- 15.Internationa Agency for Research on Cancer (IARC) (2010) Some aromatic amines, organic dyes, and related exposures. In: IARC monographs on the evaluation of carcinogenic risk to humans, vol 99. Lyon, FranceGoogle Scholar
- 17.Stern MC, Lin J, Figueroa JD, Kelsey KT, Kiltie AE, Yuan JM, Matullo G, Fletcher T, Benhamou S, Taylor JA, Placidi D, Zhang ZF, Steineck G, Rothman N, Kogevinas M, Silverman D, Malats N, Chanock S, Wu X, Karagas MR, Andrew AS, Nelson HH, Bishop DT, Sak SC, Choudhury A, Barrett JH, Elliot F, Corral R, Joshi AD, Gago-Dominguez M, Cortessis VK, Xiang YB, Gao YT, Vineis P, Sacerdote C, Guarrera S, Polidoro S, Allione A, Gurzau E, Koppova K, Kumar R, Rudnai P, Porru S, Carta A, Campagna M, Arici C, Park SS, Garcia-Closas M, International Consortium of Bladder C (2009) Polymorphisms in DNA repair genes, smoking, and bladder cancer risk: findings from the international consortium of bladder cancer. Cancer Res 69(17):6857–6864CrossRefPubMedPubMedCentralGoogle Scholar
- 35.Chung W, Bondaruk J, Jelinek J, Lotan Y, Liang S, Czerniak B, Issa JP (2011) Detection of bladder cancer using novel DNA methylation biomarkers in urine sediments. Cancer Epidemiol Biomarkers Prev 20(7):1483–1491Google Scholar
- 43.Choi JH, Li Y, Guo J, Pei L, Rauch TA, Kramer RS, Macmil SL, Wiley GB, Bennett LB, Schnabel JL, Taylor KH, Kim S, Xu D, Sreekumar A, Pfeifer GP, Roe BA, Caldwell CW, Bhalla KN, Shi H (2010) Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One 5(9):e13020CrossRefPubMedPubMedCentralGoogle Scholar
- 50.Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NYGoogle Scholar