EPIG-16MOST DIFFERENTIAL DNA METHYLATION CHANGES OCCUR AT CANDIDATE ENHANCER ELEMENTS FOR RECURRENT LOWER GRADE GLIOMA AND GLIOBLASTOMA

Clinical behavior of lower grade glioma (LGG) and glioblastoma (GBM) is characterized by recurrence and progression, yet with highly variable patterns and intervals. Our current study aims to establish a DNA methylation profile associated with the recurrence of LGG (n = 28) and GBM (n = 24) by comparing primary and recurrent matched samples. Illumina Methylation 450k data were used from The Cancer Genome Atlas (TCGA) project. Genome-wide DNA methylation remained almost unchanged at CpG islands and shores. Unsupervised DNA methylation consensus clustering of 2,000 CpG with highest standard deviation (sd > 0.25) demonstrated that recurrent LGG and GBM clustered next to their primary counterparts. Strikingly, 78.6% of recurrent LGG showed depletion of DNA methylation at recurrence and 50% of recurrent GBM showed enrichment of DNA methylation at recurrence. Enrichment analysis of CpG sites with most DNA methylation changes between primary and recurrent samples revealed that 14.3% of LGG and 33.3% of GBM samples showed enrichment of opensea located probes (fold > 1.3). A random permutation of 10,000 probes and confidence intervals (99%) demonstrated that these results do not occur by chance. More than 50% of CpG sites enriched at openseas map to candidate TSS distal and hypomethylated enhancers, and are related to adhesion, apoptotic, developmental, immune system, and metabolic processes. Compared to 10 paired non-glioma tumor (lung, colon, liver, sarcoma), the signature of glioma relapse appears distinctive. Our results provide evidence that DNA methylation may represent a stable signature of glioma recurrence and that the crosstalk between DNA hypomethylation at openseas and chromosomal instability is involved in glioma recurrence. We plan to integrate our findings with whole-genome & RNA sequencing and perform DNA motif analyses to identify networks disrupted and associated with such pronounced epigenetic signature.