Data from Beyond the Promoter: Total <i>MGMT</i> Gene Methylation Modulates Response to DNA-Alkylating Agents in Glioma

<div>Abstract<p>Patients with malignant gliomas with methylated <i>MGMT</i> promoters are generally more sensitive to alkylating chemotherapy as this modification impedes DNA repair. However, inconsistencies in the predictive accuracy of <i>MGMT</i> promoter methylation have been observed. We hypothesize that these variations may be partially explained by a counteracting influence of <i>MGMT</i> gene body methylation. Data from The Cancer Genome Atlas were analyzed to assess correlations between <i>MGMT</i> 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 <i>MGMT</i> protein levels and carmustine response. Correlations and linear regression analyses were conducted to investigate association of carmustine sensitivity with different levels of <i>MGMT</i> expression. <i>MGMT</i> 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 <i>IDH1/2</i> wild-type glioma subcohort but not correlated in the <i>IDH1/2</i>-mutated subcohort. Most glioma cell lines did not express <i>MGMT</i> 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 <i>MGMT</i> 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.</p></div>