Abstract
Glioma CpG-island methylator phenotype (G-CIMP) is associated with IDH mutation and presents better clinical outcomes than for IDH wildtype gliomas. However, a recent stratification of G-CIMP tumors identified a subgroup of patients with distinct epigenetic changes in intergenic regions linked to poor prognosis (G-CIMP-low) compared to G-CIMP-high. Several regulatory elements, such as enhancers and silencers, are located outside gene promoters and DNA methylation changes in these elements could play an important role in regulating the expression of distant genes. In order to identify potential active enhancers by loss of DNA methylation in G-CIMP-low, we investigated 1 G-CIMP-low, 2 G-CIMP-high and 2 non-tumor brain samples profiled by whole-genome bisulfite sequencing (methylome) and RNA-sequencing (transcriptome). Using the GeneHancer database, which includes known enhancers and their potential gene targets assessed by functional studies, we identified 109 downregulated and 856 upregulated genes in G-CIMP-low in relation to G-CIMP-high. These had no DNA methylation differences at their promoters between G-CIMP-low, G-CIMP-high and non-tumor brain samples. However, the associated candidate enhancers for these genes had distinct hyper or hypo-methylation of CpG specific to G-CIMP-low, compared to both G-CIMP-high and non-tumor brain samples. Downregulated genes are associated with negative regulation of both protein phosphorylation and immune response, such as PRKAG2, an AMP-activated protein kinase. G-CIMP-low tumors have expression levels similar to IDH wildtype glioblastomas whereas G-CIMP-high tumors are comparable to non-tumor brain samples. Upregulated genes are enriched for cell cycle and metabolism of RNA, which may relate to observed aggressiveness and proliferation in G-CIMP-low tumors. From this pilot data, we hypothesize that distal elements regulate the expression of genes in G-CIMP-low which leads to a more aggressive phenotype. These findings corroborate the importance of epigenetics in gliomas and propose that intergenic elements might be driving the G-CIMP-low tumorigenesis.