Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

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 <i>frequencies</i> in high-grade tumors relative to low-intermediate-grade tumors for the <i>ATP5G2, IRX1</i> and <i>VAX2</i> genes (<i>P</i>&lt;0.05), and similarly significant increases in <i>mean levels</i> of methylation in high-grade tumors for the <i>ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1</i>, and <i>HIST1H4F</i> genes (<i>P</i>&lt;0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the <i>ARHGEF4, PON3, STAT5a</i>, and <i>VAX2</i> gene transcripts (<i>P</i>&lt;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.