Spatial transcriptomic analysis reveals inflammatory foci defined by senescent cells in the white matter, hippocampi and cortical grey matter in the aged mouse brain

There is strong evidence that aging is associated with an increased presence of senescent cells in the brain. The finding that treatment with senolytic drugs improves cognitive performance of aged laboratory mice suggests that increased cellular senescence is causally linked to age-related cognitive decline. The relationship between senescent cells and their relative locations within the brain is critical to understanding the pathology of age-related cognitive decline and dementia. To assess spatial distribution of cellular senescence in the aged mouse brain, spatially resolved whole transcriptome mRNA expression was analyzed in sections of brains derived from young (3 months old) and aged (28 months old) C57BL/6 mice while capturing histological information in the same tissue section. Using this spatial transcriptomics (ST)-based method, microdomains containing senescent cells were identified on the basis of their senescence-related gene expression profiles (i.e., expression of the senescence marker cyclin-dependent kinase inhibitor p16INK4A encoded by the Cdkn2a gene) and were mapped to different anatomical brain regions. We confirmed that brain aging is associated with increased cellular senescence in the white matter, the hippocampi and the cortical grey matter. Transcriptional analysis of the senescent cell-containing ST spots shows that presence of senescent cells is associated with a gene expression signature suggestive of neuroinflammation. GO enrichment analysis of differentially expressed genes in the outer region of senescent cell-containing ST spots ("neighboring ST spots") also identified functions related to microglia activation and neuroinflammation. In conclusion, senescent cells accumulate with age in the white matter, the hippocampi and cortical grey matter and likely contribute to the genesis of inflammatory foci in a paracrine manner.