Genome-Wide Methylation Analyses in Glioblastoma Multiforme

Abstract

Few studies had investigated genome-wide methylation in glioblastoma multiforme (GBM). Our goals were to study differential methylation across the genome in gene promoters using an array-based method, as well as repetitive elements using surrogate global methylation markers. The discovery sample set for this study consisted of 54 GBM from Columbia University and Case Western Reserve University, and 24 brain controls from the New York Brain Bank. We assembled a validation dataset using methylation data of 162 TCGA GBM and 140 brain controls from dbGAP. HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in both the discovery and validation datasets. Global methylation levels were assessed by analysis of L1 retrotransposon (LINE1), 5 methyl-deoxycytidine (5m-dC) and 5 hydroxylmethyl-deoxycytidine (5hm-dC) in the discovery dataset. We validated a total of 1548 CpG sites (1307 genes) that were differentially methylated in GBM compared to controls. There were more than twice as many hypomethylated genes as hypermethylated ones. Both the discovery and validation datasets found 5 tumor methylation classes. Pathway analyses showed that the top ten pathways in hypomethylated genes were all related to functions of innate and acquired immunities. Among hypermethylated pathways, transcriptional regulatory network in embryonic stem cells was the most significant. In the study of global methylation markers, 5m-dC level was the best discriminant among methylation classes, whereas in survival analyses, high level of LINE1 methylation was an independent, favorable prognostic factor in the discovery dataset. Based on a pathway approach, hypermethylation in genes that control stem cell differentiation were significant, poor prognostic factors of overall survival in both the discovery and validation datasets. Approaches that targeted these methylated genes may be a future therapeutic goal.

Global hypomethylation is an independent prognostic factor in diffuse large B cell lymphoma

“…Global hypomethylation is linked to increased metastatic potential and poorer survival in melanoma, and to disease recurrence in proximal colon cancers . Also, supporting this evidence, LINE1 hypermethylation is described as a positive prognostic factor in glioblastoma multiforme …”

Acute exposure to methamphetamine alters TLR9-mediated cytokine expression in human macrophage

“…Yet, levels of methylation of both CpG islands are not affected by addition of Meth or CpG ODN, indicating that Meth does not regulate the methylation status of CCL7. Not all of the transcriptional regulatory mechanisms of CCL7 are known, but one report to date found the DNA of CCL7 differentially methylated in glioblastoma multiforme (Lai, Chen et al 2014). …”

Assessment of Changes in Global DNA Methylation Levels by Pyrosequencing® of Repetitive Elements

“…Pyrosequencing assays for the analysis of TE (LINE or Alu ) DNA methylation interrogate several thousand copies of elements across the genome, as opposed to one unique locus. CpG sites are particularly enriched at TEs, accounting for >65 % of those found throughout the human genome [ 7 ], and therefore the methylation of these elements has been suggested as an indicator of global DNA methylation [ 8 -10 ]. However, several investigations have reported poor correlations in normal tissues between the DNA methylation of TEs and global genomic DNA methylation, as determined by the "gold standard" of high performance liquid chromatography (HPLC) [ 11 , 12 ].…”