Data from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers

Abstract

<div>Abstract<p><b>Purpose:</b> Epigenetic alterations are common and can now be addressed in a parallel fashion. We investigated the methylation in bladder cancer with respect to location in genome, consistency, variation in metachronous tumors, impact on transcripts, chromosomal location, and usefulness as urinary markers.</p><p><b>Experimental Design:</b> A microarray assay was utilized to analyze methylation in 56 samples. Independent validation was conducted in 63 samples by a PCR-based method and bisulfite sequencing. The methylation levels in 174 urine specimens were quantified. Transcript levels were analyzed using expression microarrays and pathways were analyzed using dedicated software.</p><p><b>Results:</b> Global methylation patterns were established within and outside CpG islands. We validated methylation of the eight tumor markers genes <i>ZNF154</i> (<i>P</i> < 0.0001), <i>HOXA9</i> (<i>P</i> < 0.0001), <i>POU4F2</i> (<i>P</i> < 0.0001), <i>EOMES</i> (<i>P</i> = 0.0005), <i>ACOT11</i> (<i>P</i> = 0.0001), <i>PCDHGA12</i> (<i>P</i> = 0.0001), <i>CA3</i> (<i>P</i> = 0.0002), and <i>PTGDR</i> (<i>P</i> = 0.0110), the candidate marker of disease progression <i>TBX4</i> (<i>P</i> < 0.04), and other genes with stage-specific methylation. The methylation of metachronous tumors was stable and targeted to certain pathways. The correlation to expression was not stringent. Chromosome 21 showed most differential methylation (<i>P</i> < 0.0001) and specifically hypomethylation of keratins, which together with keratin-like proteins were epigenetically regulated. In DNA from voided urine, we detected differential methylation of ZNF154 (<i>P</i> < 0.0001), POU4F2 (<i>P</i> < 0.0001), HOXA9 (<i>P</i> < 0.0001), and EOMES (<i>P</i> < 0.0001), achieving 84% sensitivity and 96% specificity.</p><p><b>Conclusions:</b> We initiated a detailed mapping of the methylome in metachronous bladder cancer. Novel genes with tumor, chromosome, as well as pathway-specific differential methylation in bladder cancer were identified. The methylated genes were promising cancer markers for early detection of bladder cancer. <i>Clin Cancer Res; 17(17); 5582–92. ©2011 AACR</i>.</p></div>