Abstract 3910: An integrated genomic and epigenomic approach for identification of novel disease-related regions and genes in bladder cancer progression
Authors: Mariana Brait, Paola Parrella, Paul Cairns, Raffaela Barbano, Prodipto Pal, Leonel Maldonado, Maté Ongenaert, Wim Van Criekinge, David Sidransky, Mohammad O. Hoque
Journal: Cancer Research (2011)

Abstract Different pathways drive bladder cancer distinct presentations, such as superficial papillary (Ta) when compared to carcinoma in situ (Cis) or muscle invasive tumors. Although multiple chromosomal alterations have been identified, the specific genes and loci driving the distinct pathways remain largely unknown. In part this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high-resolution genome-wide method, Affymetrix 250K Nsp1 SNP mapping arrays, to screen for somatic DNA copy number variation (CNV) among 49 bladder tumors [17 (35%) clinical stage 1 (15 Ta and 2 Cis), 11 (23%) stage 2, 15 (31%) stage 3 and 6 to be classified] samples and corresponding normals (lymphocytes from the same patient). GeneChip Genotyping analysis software (GTYPE v4.0), Partek Genomic SuiteTM and Hidden Markov model assuming diploid copy for normal samples were employed to infer the CNV estimates. We utilized a genomic segmentation algorithm (requiring a minimum of 10 probes) to characterize significantly higher or lower intensity ratios into cancer specific CNV regions. A threshold of &amp;gt; 3 (gains, amplifications) and &amp;lt; 1.25 (losses, deletions) was used to categorize altered regions. Genome Wide CNV analysis were determined in different groups of comparison (tumor versus normal, superficial vs muscle-invasive stages, Ta vs Cis). Furthermore, to identify the genes that are inactivated one allele by methylation and the other allele by deletion, we performed genome-wide methylation analysis on a subset of these samples by Illumina Methylation Bead Array containing over 27,000 CpG sites, focused on the promoter regions of 14,495 genes. Significant major alterations were seen on chromosome 6q, 8p, 8q, 9p, 9q, 5p, 12p, 12q, 18p, 18q and 20q. We also identified novel small deletions and amplifications throughout the genome. Amplification of loci 6q21-22 (NKAIN2 and FRK), 9q22 (PHF2) and 11p15 (OR51F2) and deletion of loci 11p15 (MRGPRX1), 16p23 (ADAMTS18), 11q15 (MCT2) and 14q11 (DAD1) were observed in superficial Ta compared to Cis. Interestingly, among the 366 CpG probes classified as significantly methylated in the bladder cancer samples, ADAMTS18 was also present. This gene is a disintegrin and metalloproteinase with thrombospondin motifs and has been reported to be epigenetically inactivated in tumors other than bladder cancer, including nasopharyngeal, esophageal, gastric, colorectal and pancreatic cancers. Genetic alterations have also being described: deletions in breast cancer as well as somatic mutations in melanoma. Our initial findings strengthen ADAMTS18 potential's of being a candidate gene related to bladder tumorigenesis. The integration of genetic and epigenetic alterations may lead to a comprehensive knowledge of the biology of bladder cancer and will open up fertile avenue for further research. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3910. doi:10.1158/1538-7445.AM2011-3910