Integrative Single-Cell RNA and ATAC Sequencing Uncovers Dosage-Sensitive, Cluster-Specific Regulatory Dynamics in Glioblastoma

Glioblastoma (GBM) is an aggressive brain tumor that inevitably recurs after radiation therapy, resulting in poor patient outcomes. Given GBM’s cellular heterogeneity, we hypothesized that radiation induces sub-population specific alterations to survive and adapt to radiation stress. We performed integrated single-cell RNA-seq and ATAC-seq analyses across multiple GBM models exposed to clinically relevant radiation doses. Radiation reshaped the cellular landscape, altering both cell type composition and GBM subtype distribution. Cluster-specific and shared transcriptional programs were induced in a dose-dependent manner, with differentially expressed genes enriching distinct biological pathways. Chromatin accessibility analyses revealed parallel cluster-specific remodeling, with both opening and closing of regulatory elements linked to functional pathway shifts. Notably, 2 Gy and 6 Gy exposures elicited conserved transcriptional profiles in RNA clusters across independent GBM lines. Together, these results highlight radiation-induced transcriptional and chromatin remodeling programs in GBM at single-cell resolution and identify conserved cluster-specific adaptations that may underlie therapeutic resistance.