Beyond the Promoter: Total MGMT Gene Methylation Modulates Response to DNA-Alkylating Agents in Glioma

Abstract Patients with malignant gliomas with methylated MGMT promoters are generally more sensitive to alkylating chemotherapy as this modification impedes DNA repair. However, inconsistencies in the predictive accuracy of MGMT promoter methylation have been observed. We hypothesize that these variations may be partially explained by a counteracting influence of MGMT gene body methylation. Data from The Cancer Genome Atlas were analyzed to assess correlations between MGMT promoter and body methylation with transcript production across cancer types and within glioma subcohorts. Thirty-six human glioma cell lines underwent molecular profiling via Illumina 850k Methylation Arrays and RNA sequencing. A subset was further tested for MGMT protein levels and carmustine response. Correlations and linear regression analyses were conducted to investigate association of carmustine sensitivity with different levels of MGMT expression. MGMT mRNA expression was positively correlated with body methylation and negatively correlated with promoter methylation across cancers from The Cancer Genome Atlas. Body and promoter methylation were anticorrelated in the non-glioma cohort and IDH1/2 wild-type glioma subcohort but not correlated in the IDH1/2-mutated subcohort. Most glioma cell lines did not express MGMT mRNA. In the cell lines tested for carmustine response, sensitivity was negatively correlated with body methylation and mRNA expression and positively correlated with promoter methylation. Our findings further expound the relationship between MGMT methylation patterns and alkylating agent response, with body methylation playing a significant role. The identified role of gene body methylation underscores the need to integrate the interplay between promoter and body methylation in clinical testing and predicting treatment outcomes.