DNA methylation variations of DNA damage response in glioblastoma: NSUN5 modulates tumor-intrinsic cytosolic DNA-sensing and microglial behavior.

BACKGROUND: Variations in DNA methylation within the DNA damage response (DDR) mechanism could have significant implications for glioma prognosis and immune responses. This study aimed to explore the global DNA methylation landscape of DDR genes in gliomas and identify key epigenetically regulated genes influencing glioma biology and immunity. METHODS: This study incorporated a range of public and local glioma datasets. Multiple clinical, bioinformatic, and in vitro experimental analyses were conducted to explore clinical and biological aspects. RESULTS: Global DNA methylation variations in DDR genes correlated with distinct glioma prognoses, with five CpGs identified as potent predictors. Hierarchical clustering and a risk-score model based on these CpGs unveiled immune-related prognostic subgroups in glioblastomas (GBMs) and lower-grade gliomas (LGGs). NSUN5, epigenetically regulated by one of these CpGs, highlighted the biological significance of the DDR CpG panel. In vitro, NSUN5 displayed tumor-suppressor-like activities in GBM cells, but clinically, it was an unfavorable prognostic marker. Depletion of NSUN5 shifted cytosolic DNA sensing from a STING-dependent (cGAS-STING) pathway to a STING-independent (DNA-PK-HSPA8) pathway, leading to a delayed but more robust type I interferon (IFN) response in GBM cells and enhancing microglial M1 polarization and chemotaxis. This may partially account for the functional discrepancy of NSUN5 observed between experimental and clinical contexts. CONCLUSION: This study highlights the complex interplay between DNA methylation, the DDR mechanism, cytosolic DNA sensing, and glioma immunity. These findings may inspire novel strategies for DNA sensing-based immunotherapy.