Abstract 3823: Identification of critical DNA methylation events in medulloblastoma using functional epigenomics

Most studies of cancer DNA methylation have focused on defining aberrant gene promoter and, in particular, CpG island-associated events and their contribution to tumour development. A number of genes have been found to be epigenetically silenced by promoter hypermethylation in medulloblastoma (MB), however, the genome-wide role of DNA methylation in this disease has not been widely investigated. Using a functional epigenomics analysis of methylation-dependent gene expression alterations, combined with a genome-wide analysis of DNA methylation, we sought to undertake a comprehensive characterisation of methylation events that are associated with expression alterations and that may play a role in MB development. We treated a panel of 10 MB cell lines with the DNA methylation inhibitor 5-aza-2′-deoxycytidine (5azaCdR) and assessed methylation-dependent changes in gene expression using the Illumina HT12v4.0 array. In total, 283 genes showed methylation-dependent expression in 2 or more cell lines. Using the Illumina 450K Methylation array, a relationship between methylation-dependent expression and methylation at specific CpG residues was found for 63 genes (encompassing 184 CpG sites), suggesting a direct role for their methylation in transcription regulation and tumour development. Thirty-seven of the 63 genes identified (59%) had events occurring at multiple CpG residues, while the remaining 26 showed a relationship between expression and methylation at a single CpG residue only. Detailed characterisation of the distribution of the 184 CpG sites identified found them harboured mainly within gene promoter regions and associated with CpG islands and shores. However, for 33 genes (52% of total), events were also found at one or more sites located within the gene body. Ten of these genes contained one or more gene body events that were isolated sites, not in an island or shore, and for 3 of these, an isolated non-CpG island/shore gene body event was the only event found. We have identified a series of methylation events that show a strong relationship to gene expression and may contribute to MB tumourigenesis. In addition to extensive CpG island/gene promoter events, isolated CpG gene body events may play a significant role in regulating gene transcription in tumour development. Further work will now be undertaken to validate the methylation events identified and to establish their role in primary tumours, as well as their functional significance in tumour deve