Abstract
Many differentially methylated genes have been identified in prostate cancer (PCa), primarily using candidate gene-based assays. Recently, several global DNA methylation profiles have been reported in PCa, however, each of these has weaknesses in terms of ability to observe global DNA methylation alterations in PCa. We hypothesize that there remains unidentified aberrant DNA methylation in PCa, which may be identified using higher resolution assay methods. We used the newly developed Illumina HumanMethylation450 BeadChip in PCa (n = 19) and adjacent normal tissues (n = 4) and combined these with gene expression data for identifying new DNA methylation that may have functional consequences in PCa development and progression. We also confirmed our methylation results in an independent data set. Two aberrant DNA methylation genes were validated among an additional 56 PCa samples and 55 adjacent normal tissues. A total 28,735 CpG sites showed significant differences in DNA methylation (FDR adjusted P<0.05), defined as a mean methylation difference of at least 20% between PCa and normal samples. Furthermore, a total of 122 genes had more than one differentially methylated CpG site in their promoter region and a gene expression pattern that was inverse to the direction of change in DNA methylation (e.g. decreased expression with increased methylation, and vice-versa). Aberrant DNA methylation of two genes, AOX1 and SPON2, were confirmed via bisulfate sequencing, with most of the respective CpG sites showing significant differences between tumor samples and normal tissues. The AOX1 promoter region showed hypermethylation in 92.6% of 54 tested PCa samples in contrast to only three out of 53 tested normal tissues. This study used a new BeadChip combined with gene expression data in PCa to identify novel differentially methylated CpG sites located within genes. The newly identified differentially methylated genes may be used as biomarkers for PCa diagnosis.
Highlights
DNA methylation is a covalent addition of a methyl group at the 5 position carbon of a cytosine base and this epigenetic change is almost exclusively found in cytosine guanine dinucleotides (CpG) in differentiated human cells [1]
We evaluated four paired tumor samples and adjacent normal tissues, plus 15 additional unpaired tumor samples that were originally collected from Swedish subjects (Table S2A)
To identify aberrant differentially methylated CpG sites (DMCs) in prostate cancer, we performed statistical analysis and narrowed down the selection of CpG sites based on DNA methylation differences (Figure 1)
Summary
DNA methylation is a covalent addition of a methyl group at the 5 position carbon of a cytosine base and this epigenetic change is almost exclusively found in cytosine guanine dinucleotides (CpG) in differentiated human cells [1]. Multiple studies have reported aberrant patterns of genome-wide DNA methylation in PCa tissue samples, using Agilent CpG island microarrays, Illumina HumanMethylation (HM27) BeadChips or next-generation sequencing methods [15,16,17,18,19,20]. Mahapatra et al identified and confirmed many aberrantly methylated genes that can be used as diagnostic or prognostic biomarkers [20] This HM27 BeadChip method provides DNA methylation data at single-nucleotide resolution in more than 27,000 CpG sites. This HM27 platform covers only 0.1% of all CpG sites in the human genome and all test CpG sites are located in promoter regions
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
