High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts.
The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
Epigenetics. 2016 Mar 01 [Epub ahead of print]
Mark O Kitchen, Richard T Bryan, Richard D Emes, John R Glossop, Christopher Luscombe, Kk Cheng, Maurice P Zeegers, Nicholas D James, Adam J Devall, Charles A Mein, Lyndon Gommersall, Anthony A Fryer, William E Farrell
a Institute for Science and Technology in Medicine, Keele University , UK., c Institute of Cancer and Genomic Sciences, University of Birmingham , UK., d Advanced Data Analysis Centre, University of Nottingham , UK., a Institute for Science and Technology in Medicine, Keele University , UK., b Urology Department , University Hospitals of North Midlands NHS Trust , UK., c Institute of Cancer and Genomic Sciences, University of Birmingham , UK., c Institute of Cancer and Genomic Sciences, University of Birmingham , UK., h Cancer Research Unit, University of Warwick , UK., c Institute of Cancer and Genomic Sciences, University of Birmingham , UK., i The Genome Centre, Barts and the London School of Medicine and Dentistry , London , UK., b Urology Department , University Hospitals of North Midlands NHS Trust , UK., a Institute for Science and Technology in Medicine, Keele University , UK., a Institute for Science and Technology in Medicine, Keele University , UK.