DNA damage response profile distinguishes poor-acting gliomas with shared methylome signatures

Therapies for diffuse glioma induce DNA damage response (DDR), and strategies to exploit DDR defects are active areas of investigation. While global DNA methylation profiling effectively classifies gliomas into subtypes, the epigenetic and gene expression patterns of DDR genes, and their contribution to tumor classification and outcomes, have yet to be fully elucidated. Thus, dissecting the DDR epigenetics, gene expression, and single-cell heterogeneity may reveal key molecular characteristics, refine prognosis, and identify novel treatment strategies and resistance mechanisms.

We characterized DDR epigenetics and gene expression of TCGA glioblastomas (GBM) and low-grade gliomas (LGG). Single-cell protein analysis by imaging mass cytometry (IMC) was performed on a separate cohort of 118 diffuse gliomas.

Analysis of TCGA cohorts revealed two DDR methylation groups that correlated with IDH mutation status and previously reported molecular groups. DDR transcription profiling further classified tumors into four groups. Those with high DDR transcription across pathways were linked to poor survival independent of IDH or MGMT status, and potentially improved prognostication beyond established biomarkers. Single-cell characterization of a separate cohort revealed intratumoral DDR diversity and identified proliferative tumor cells with high DDR protein expression across pathways that are associated with unfavorable grade and survival.

Tumor-level epigenetic and transcriptional DDR signatures alone can distinguish molecular-defined diagnosis and outcomes of gliomas beyond established biomarkers. A higher abundance of glioma cells with high DDR effector expression across pathways is associated with poor survival. Thus, clinical assessment of pan-DDR expression may inform prognosis and identify potential therapeutic targets.