Recurrent epimutations activate gene body promoters in primary glioblastoma

Abstract

Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MREseq, adjusting for copy number differences, in a small set of non-glioma CpG island methylator phenotype (non-G-CIMP) primary tumors. Recurrent hypomethylated loci were enriched within a region of chromosome 5p15 that is specified as a cancer amplicon and also encompasses TERT, encoding telomerase reverse transcriptase, which plays a critical role in tumorigenesis. Overall, 76 gene body promoters were recurrently hypomethylated, including TERT and the oncogenes GLI3 and TP73. Recurring hypomethylation also affected previously unannotated alternative promoters, and luciferase reporter assays for three of four of these promoters confirmed strong promoter activity in GBM cells. Histone H3 lysine 4 trimethylation (H3K4me3) ChIP-seq on tissue from the GBMs uncovered peaks that coincide precisely with tumor-specific decrease of DNA methylation at 200 loci, 133 of which are in gene bodies. Detailed investigation of TP73 and TERT gene body hypomethylation demonstrated increased expression of corresponding alternate transcripts, which in TP73 encodes a truncated p73 protein with oncogenic function and in TERT encodes a putative reverse transcriptase-null protein. Our findings suggest that recurring gene body promoter hypomethylation events, along with histone H3K4 trimethylation, alter the transcriptional landscape of GBM through the activation of a limited number of normally silenced promoters within gene bodies, in at least one case leading to expression of an oncogenic protein.[Supplemental material is available for this article.]

HIGD1A Regulates Oxygen Consumption, ROS Production, and AMPK Activity during Glucose Deprivation to Modulate Cell Survival and Tumor Growth

“…The gene encoding HIGD1A is located on human chromosome 3p22.1, where many tumor suppressor genes reside, and these are often inactivated via epigenetic mechanisms (Bhat Singh and Amare Kadam, 2013; Buchhagen et al, 1994). From genome-wide analyses of aberrant DNA methylation in glioblastoma multiforme (GBM) (Nagarajan et al, 2014), we identified two candidate regions near the Higd1a promoter that exhibited GBM-specific hypermethylation. As indicated in figure 3B, one of these regions, located upstream of the 5′ CpG island promoter, in a CpG island “shore,” contains consensus core hypoxia response elements (HRE) (blue underlined).…”

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

“…S10). Nucleosome positioning analysis from micrococcal nuclease-digested H3K4me3 ChIP-seq(24) data revealed that both mutation positions lie within a nucleosome free region, with the upstream nucleosomes containing the H3K4me3 modifications (fig. S10).…”

Relation between Established Glioma Risk Variants and DNA Methylation in the Tumor

“…In a previous study, Nagarajan et al found a genomic region, just upstream of the first exon on an alternative TERT transcript, that was hypomethylated in three of five glioblastoma tumors. They also described elevated expression of an alternative TERT transcript in glioblastoma samples compared to normal brain [38]. …”