Epigenomic changes associated with high-grade non-muscle invasive bladder cancer

The development and progression of high-grade non-muscle invasive bladder cancer (NMIBC) results from a complex interplay of environmental and heritable risk factors, including those that impact upon genetic and epigenetic pathways. Recent studies have identified epigenetic changes associated with bladder tumour development, growth patterns and clinical parameters; however, high-grade tumours have not been comprehensively studied for disease and/or subtype specific modifications. To address these shortfalls in our understanding, initial presentation and treatment naïve high-grade NMIBC tumours were analysed for inappropriate DNA methylation, histone modifications and geneexpression, and compared to low-intermediate-grade NMIBC and normal bladder. This thesis reports that genome-wide (LINE-1) methylation is significantly reduced in high-grade tumours relative to their low- and intermediate-grade counterparts and normal bladder, and that concurrent methylation of HOXA9 and ISL1 predicts adverse patient outcomes. Further comprehensive methylation assessment using HumanMethylation450 BeadChip arrays identified 256 differentially methylated genes, many of which have not been described in the context of bladder cancer. Moreover, the frequency and/or mean levels of methylation were significantly higher in the high-grade relative to the low-intermediate-grade tumour cohort for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, HIST1H4F genes. Expression analyses suggested that methylation was significantly associated with reduced transcript expression for the ATP5G2, PON3, STAT5a and ZNF577 genes, signifying a potential role for inappropriate methylation in high-grade tumourigenesis. Further array analyses identified numerous CpG sites that appeared to predict disease behaviour, and are targets for further investigations. The novel studies contained herein, are the first to report genome-wide array analyses in high-grade NMIBC, and demonstrate that methylation is a frequent event in this tumour type, and in some cases, different from other NMIBC tumours. Although inappropriate methylation was infrequently associated with changes in gene expression it did appear to have potential clinical prognostic ability, the assessment and validation of which requires further investigations