DNA demethylation is associated with malignant progression of lower-grade gliomas

Masashi Nomura,Nobuhito Saito,Hiroki Ueda,Takahide Nejo,Fumi Higuchi,Genta Nagae,Shota Tanaka,Shunsaku Takayanagi,Satoshi Takahashi,Yoshihiro Muragakı ,Yosuke Kitagawa,Ryohei Otani,Motoo Nagane,Shiro Fukuda,Tomohiro Umeda ,Hiroyuki Aburatani,Ryo Nishikawa,Taishi Nakamura,Mayu Omata,Keisuke Ueki,Kenji Tatsuno,Taijun Hana,Kuniaki Saito,Shozo Yamamoto ,Koki Aihara,Yoshitaka Narita,Akitake Mukasa

doi:10.1038/s41598-019-38510-0

Abstract

To elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively. This cohort included 24 matched pairs of initial lower-grade gliomas and recurrent tumors, most of which showed malignant progression. Nearly half of IDH-mutant glioblastomas that had progressed from lower-grade gliomas exhibited characteristic partial DNA demethylation in previously methylated genomic regions of their corresponding initial tumors, which had the glioma CpG island methylator phenotype (G-CIMP). In these glioblastomas, cell cycle-related genes, RB and PI3K-AKT pathway genes were frequently altered. Notably, late-replicating domain was significantly enriched in the demethylated regions that were mostly located in non-regulatory regions, suggesting that the loss of DNA methylation during malignant transformation may involve mainly passive demethylation due to a delay in maintenance of methylation during accelerated cell division. Nonetheless, a limited number of genes including IGF2BP3, which potentially drives cell proliferation, were presumed to be upregulated due to demethylation of their promoter. Our data indicated that demethylation of the G-CIMP profile found in a subset of recurrent gliomas reflects accelerated cell divisions accompanied by malignant transformation. Oncogenic genes activated by such epigenetic change represent potential therapeutic targets.

Highlights

To elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively
Genome-wide methylation analyses showed that the glioma CpG island methylator phenotype (G-CIMP), which is named after the well-known CIMP status observed in colorectal cancers, is frequent in lower-grade gliomas and secondary GBMs and is tightly associated with the presence of IDH mutations[8,9]
Our molecular profile analysis focusing on the differences between initial lower-grade gliomas and recurrent progressed tumors demonstrated that changes observed during malignant transformation are not uniform

Summary

Introduction

To elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively. Half of IDH-mutant glioblastomas that had progressed from lower-grade gliomas exhibited characteristic partial DNA demethylation in previously methylated genomic regions of their corresponding initial tumors, which had the glioma CpG island methylator phenotype (G-CIMP). In these glioblastomas, cell cycle-related genes, RB and PI3K-AKT pathway genes were frequently altered. Recent analysis using next-generation sequencing (NGS) and microarray technology has revealed dramatic changes including complicated subclonal somatic mutations and branched evolution of the glioma genome, as well as loss of DNA hypermethylation in G-CIMP tumors coincident with upregulation of cell cycle-related genes during malignant progression of lower-grade gliomas[13,14,15]. Despite accelerated research in this field, the mechanisms associated with lower-grade gliomas have not been clarified, partly because of difficulties in obtaining paired initial tumor tissue and recurrent tissue samples

Methods

Results

Conclusion