Association of IMGMT/I Promoter and Enhancer Methylation with Genetic Variants, Clinical Parameters, and Demographic Characteristics in Glioblastoma

Glioblastoma is the most common and most aggressive brain tumor in adults. The chemotherapeutic substance temozolomide plays an important role in glioblastoma therapy. However, the response of glioblastoma patients to temozolomide depends on the expression level of the repair protein O6-methylguanine-DNA methyltransferase (MGMT) in the tumor. Since the DNA methylation status of the MGMT promoter has an impact on MGMT expression, it serves as biomarker for predicting the response to temozolomide and prognosis of glioblastoma. We investigated if the DNA methylation status of enhancers, other important regulatory elements, is also associated with MGMT expression. We found the methylation status of several regions of enhancers to be associated with MGMT expression. In addition, we found associations with common genetic variants and clinical parameters, including overall survival. The response of glioblastoma (GBM) patients to the alkylating agent temozolomide (TMZ) vitally depends on the expression level of the repair protein O6-methylguanine-DNA methyltransferase (MGMT). Since MGMT is strongly regulated by promoter methylation, the methylation status of the MGMT promoter has emerged as a prognostic and predictive biomarker for GBM patients. By determining the methylation levels of the four enhancers located within or close to the MGMT gene, we recently found that enhancer methylation contributes to MGMT regulation. In this study, we investigated if methylation of the four enhancers is associated with SNP rs16906252, TERT promoter mutations C228T and C250T, TERT SNP rs2853669, proliferation index Ki-67, overall survival (OS), age, and sex of the patients. In general, associations with genetic variants, clinical parameters, and demographic characteristics were caused by a complex interplay of multiple CpGs in the MGMT promoter and of multiple CpGs in enhancer regions. The observed associations for intragenic enhancer 4, located in intron 2 of MGMT, differed from associations observed for the three intergenic enhancers. Some findings were restricted to subgroups of samples with either methylated or unmethylated MGMT promoters, underpinning the relevance of the MGMT promoter status in GBMs.