Neuronal and vascular genome-maintenance states organize opposing multicellular architectures in the aging brain

Abstract

Genome maintenance is predominantly studied as a cell-intrinsic process, although its consequences can extend to tissue aging. Brain aging is characterized by region-specific changes in neuronal, immune, and glial cell abundance, altered expression of multiple molecular pathways, and changes in vascular morphology. These features have largely been reported separately, and the molecular relationships underlying regional cellular alterations remain poorly understood. In particular, whether cell-intrinsic genome maintenance is associated with the composition and spatial organization of neighboring cells is unknown. We investigated whether DNA damage response (DDR) transcriptional states provide a molecular link between age-related cellular changes and the surrounding tissue microenvironment. Using MERFISH, we mapped DDR transcriptional programs across ∼600K single cells in matched brain sections from 2–3- and 22-month-old mice. We found that DDR transcriptional states were associated with distinct multicellular neighborhood organizations. Aging also produced region-specific changes in DNA repair pathway module expression and coordination, accompanied by changes in cell-type abundance. Immune enrichment in fiber tracts and oligodendroglial enrichment in the isocortex corroborated established aging patterns, while deep layer 6b near-projecting cortical glutamatergic neurons showed reduced abundance. We developed two complementary spatial analytical approaches to quantify local cell-type composition and distance-dependent neighborhood organization, revealing distinct novel relationships between neuronal and vascular DDR transcriptional states and their surrounding cell populations. Mostly, immune cells were enriched around DDR-low neuronal and vascular cells, “anchors”, while DDR-low neurons additionally showed greater oligodendroglial representation. In contrast, DDR-high vascular anchors were associated with higher proportion of vascular cells proximally and oligodendroglial populations distally, whereas immune cells were enriched at intermediate distances around DDR-low anchors. Together, we identify DDR transcriptional states as an underlying factor likely reshaping multicellular spatial organization, connecting previously separate observations of regional molecular and cellular changes during brain aging. This relationship raises the possibility that altering neuronal or vascular genome maintenance could influence surrounding immune and oligodendroglial neighborhoods. Thus, we establish a novel spatial framework linking cell-intrinsic genome maintenance to the multicellular architecture of the aging brain and provide a foundation for understanding age-related tissue remodeling. Graphical Abstract