Abstract 291: Genomewide scale epigenetic profile and prostate cancer recurrence
Authors: Lin Hui-Yi , Berglund Anders , Sellers Thomas , Hakam Ardeshir , Park Hyun , Pow-Sang Julio , Park Jong Y. 
Published: May 2015

Abstract
Development and progression of prostate cancer reflect the accumulation of genetic and epigenetic alterations. Although genetic changes are involved in the inactivation of genes with important anti-cancer functions, DNA methylation in a promoter region is an important epigenetic mechanism for the down-regulation (silencing) of expression of these genes. Therefore, we conducted a genome-wide profile of prostate tumors to identify epigenetically altered regions that distinguish recurrent from non-recurrent cases.
We profiled the epigenetic landscape of 125 prostate tumors using bisulfite treated tumor DNA samples extracted from 65 recurrent and 60 non-recurrent prostate cancer cases. Epigenome-wide methylation analysis was performed at the Molecular Genomic Core Facility of the Moffitt Cancer Center using Illumina Infinium Human Methylation 450K Beadchip, which can quantitatively measure over 485,577 CpG sites with 99% coverage of RefSeq Gene and 96% coverage of CpG islands.
For methylation data analysis, intensities were normalized using Illumina GenomeStudio software. Beta values with assigned detection p-values &gt; 0.01 were treated as missing data. We considered the methylation pattern at a larger region instead of methylation at single sites. Thus, in addition to evaluating methylation at single sites, we were interested in the number of significantly differently methylated probes within a gene as a measure of how significant a gene is. We identified 269 differentially methylated CpG sites between recurrent and non-recurrent tumor tissues, with a false discovery rate (FDR) q-value less than 0.05 and a mean methylation difference greater than 0.1 between the two groups (recurrent /non-recurrent cases).
Eleven genes where more than 25% of the measured positions were differently methylated (p&lt;0.05 and &gt;0.1 between the medians of the two groups) between recurrent and non-recurrent samples.
We further investigated ALEX1 (ARMCX1), which is one of the 11 genes and suggested as a tumor suppressor gene. ALEX1 (Arm protein lost in epithelial cancers, on chromosome X) is involved in a variety of processes such as cell adhesion, embryogenesis and tumorigenesis. Expression of ALEX1 mRNA is significantly reduced in various tumor tissues, including prostate carcinomas and in various cancer cell lines. We investigated expression level of ALEX1 in an additional 392 prostate tumor samples (145 recurrence and 247non-recurrent) using realtime RT-PCR. Based upon average Ct ratios between ALEX1 and β actin, ALEX1 is down regulated 2.67 fold in tumor tissues from recurrent cases as compared with non-recurrent cases (p&lt;0.001). If replicated, these identified biomarkers may be used at the time of diagnosis to predict risk of recurrence and improve clinical treatment decision-making.
Citation Format: Hui-Yi Lin, Anders Berglund, Thomas Sellers, Ardeshir Hakam, Hyun Park, Julio Pow-Sang, Jong Y. Park. Genomewide scale epigenetic profile and prostate cancer recurrence. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 291. doi:10.1158/1538-7445.AM2014-291