5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma

Wioletta K Glowacka,Paul Kongkham,Makiko Okura,Harshika Jain,Hamza Farooq,Kenneth Aldape,Romina Nejad,Abulizi Maimaitiming,Yasin Mamatjan,Michael D Taylor

doi:10.1007/s00401-018-1821-3

Abstract

Gliomas demonstrate epigenetic dysregulation exemplified by the Glioma CpG Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. 5-Hydroxymethylcytosine (5hmC) is implicated in glioma pathogenesis; however, its role in IDH1 mutant gliomas is incompletely understood. To characterize 5hmC in IDH1 mutant gliomas further, we examine 5hmC in a cohort of IDH1 mutant and wild-type high-grade gliomas (HGG) using a quantitative locus-specific approach. Regions demonstrating high 5hmC abundance and differentially hydroxymethylated regions (DHMR) enrich for enhancers implicated in glioma pathogenesis. Among these regions, IDH1 mutant tumors possess greater 5hmC compared to wild type. 5hmC contributes to overall methylation status of G-CIMP genes. 5hmC targeting gene body regions correlates significantly with increased gene expression. In particular, a strong correlation between increased 5hmC and increased gene expression is identified for genes highly expressed in the IDH1 mutant cohort. Overall, locus-specific gain of 5hmC targeting regulatory regions and associated with overexpressed genes suggests a significant role for 5hmC in IDH1 mutant HGG.

Highlights

Gliomas are the most common primary human brain tumor, with high-grade gliomas (HGG) of World Health Organization (WHO) grades III and IV being the most aggressive
DNA and mRNA were isolated from 21 fresh frozen human high-grade glioma samples (IDH1 mt n = 12, isocitrate dehydrogenase 1 (IDH1) wt n = 9)
Comparing genes identified as differentially hydroxymethylated between IDH1 mutant (IDH1 mt) and IDH1 wild-type (IDH1 wt) tumors by hydroxymethylation-dependent immunoprecipitation (hMeDIP)-Seq (n = 2379) versus differentially hydroxymethylated regions (DHMR) genes identified by Illumina MethylationEPIC BeadChip using ChAMP (n = 1850), we found 267 common differentially hydroxymethylated targets

Summary

Introduction

Gliomas are the most common primary human brain tumor, with high-grade gliomas (HGG) of World Health Organization (WHO) grades III and IV being the most aggressive. Grade IV tumors (Glioblastoma, GBM) carry the worst prognosis with a median overall survival (OS) of approximately 15 months [61]. GBM may arise de novo or secondarily from lower grade gliomas (LGG). Recent molecular analyses through The Cancer Genome Atlas (TCGA) have identified four molecular GBM subtypes with unique gene expression, DNA copy number, and mutation profiles [70]. Among recurrent events is mutation of isocitrate dehydrogenase 1 (IDH1). IDH1 mutation occurs in 12% of GBMs and with greater frequency among LGGs and secondary GBMs [54, 76]. IDH1 mutation occurs predominantly in the proneural GBM subtype and is associated with the Glioma CpG Island Methylator Phenotype (G-CIMP) [10, 52]

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Conclusion