Abstract
BACKGROUND: DNA methyltransferase (DNMT) inhibitors are emerging as a promising class of agents for personalized and targeted cancer therapy, particularly in malignancies with limited therapeutic options such as glioblastoma (GB). In GB, the MGMT/DGKI methylation profile serves as a biomarker for stratifying patients by treatment response. Specifically, the MGMT(methylated)/DGKI(unmethylated) profile is associated with favorable outcomes, whereas the MGMT(methylated)/DGKI(methylated) profile correlates with poor outcome. These findings suggest that selective demethylation of DGKI without altering MGMT or inducing widespread genomic hypomethylation, which may promote tumorigenesis, could represent a novel and more effective therapeutic strategy. RESULTS: Current DNMT inhibitors lack specificity for glioblastoma relevant methylation profiles, thereby limiting their therapeutic efficacy. To address this challenge, AlphaFold-based protein-protein interaction predictions were integrated with sequential chromatin immunoprecipitation assays and established DNMT1 interactome data. This integrative approach led to the identification of a DNMT1/ELK1 complex as a critical regulator of DGKI methylation. A peptide mimicking the DNMT1/ELK1 interface, designated EXD(DNMT1/ELK1), was designed and shown to induce selective DGKI demethylation without altering MGMT or inducing global DNA hypomethylation. Notably, EXD(DNMT1/ELK1) did note promote cellular proliferation or invasion, and successfully restored sensitivity to standard glioblastoma therapy in both cellular and in vivo models. These findings also support the use of MGMT and DGKI methylation levels in cell-free DNA as potential biomarkers to identify patients likely to benefit from EXD(DNMT1/ELK1) treatment. CONCLUSION: This study identifies a clinically actionable biomarker (MGMT(Methylated)/DGKI(Methylated)), detectable in both solid and liquid biopsies, enabling patient stratification. Furthermore, it establishes EXD(DNMT1/ELK1) as a highly selective epigenetic therapeutic agent to treat GB patients.