Spatial profiling of chromatin accessibility reveals alteration of glial cells in Alzheimer's disease mouse brain

Abnormal epigenetic modifications, including altered chromatin accessibility, have been implicated in the development and progression of Alzheimer's disease (AD). In this study, we applied spatially resolved chromatin accessibility profiling using spatial assay for transposase-accessible chromatin using sequencing (ATAC-seq) to analyze brain tissues from 5xFAD AD model and C57BL/6J control mice. Our analysis identified seven major cell types across 11 brain regions and further characterized glial subtypes such as microglia and astrocytes, revealing subtype-specific chromatin accessibility changes in 5xFAD mice relative to controls. These alterations were associated with AD-related pathways, including neuroinflammation and immune dysregulation, as well as synaptic dysfunction and neuronal signaling in microglia, and lysosomal and proteasomal activity, lipoprotein metabolism, and mitochondrial dysfunction in astrocytes. We also characterized cell-type-specific enrichments of motifs and transcription factors, including enrichment of Bcl11a in microglia. Furthermore, we linked chromatin accessibility changes in 5xFAD mice to human AD risk genes, highlighting altered epigenetic signatures in genes such as Trem2. Supporting these findings, flow cytometry confirmed a selective increase in VISTA (encoded by Vsir) protein expression in 5xFAD microglia, indicating a shift toward a pro-inflammatory, disease-associated microglial (DAM-like) phenotype. These results underscore the utility of spatial chromatin accessibility profiling for uncovering brain-region-specific cell identities and epigenetic mechanisms underlying AD pathogenesis.