Transcriptional and DNA Methylation Changes in the Hippocampus and Prefrontal Cortex after Fractionated Cranial Radiation in Mice

Fractionated whole-brain irradiation is essential for treating brain tumors, but many long-term survivors develop cognitive decline whose molecular basis is poorly understood. We asked which cell types and gene programs change late after irradiation, how the hippocampus and prefrontal cortex compare, and whether DNA methylation changes affect the same genes or programs. Male and female mice received whole-brain irradiation (5 x 4 Gy) or anesthesia alone. Irradiated mice showed persistent deficits in executive function and spatial memory. Eleven weeks after irradiation, single-nucleus RNA sequencing and whole-genome bisulfite sequencing of pooled hippocampal (CA1-3) and prefrontal tissue showed cell-type-specific transcriptional changes in neurons of both regions. Both regions showed reduced ribosomal-protein gene expression and changes in adhesion genes, with reduced respiratory-chain genes in prefrontal neurons and bidirectional synaptic gene changes in hippocampus. Differentially methylated regions were enriched at promoters, with hypermethylation predominating in three of the four sex-by-region contrasts. Methylation and gene expression changes pointed to overlapping synaptic and signaling programs, largely through different genes.