scRNA sequencing data of cells from leptomeninges, cortex and dura mater from CTL, 5d and 8 weeks after macrophage deletion
Perivascular and leptomeningeal macrophages are non-parenchymal macrophages summarized as central nervous system (CNS)-associated macrophages (CAMs) that mediate immune responses at brain boundaries. Both, CAMs and juxtaneuronal microglia are derived from prenatal yolk sac (YS) precursors, long-living and maintain their populations by homeostatic self-renewal without input from the periphery. Whereas microglia have been shown to be repopulated by CNS endogenous remnants of the same lineage following depletion, the renewal biology of CAMs is still poorly understood. Here, by combining multilineage myeloid fate mapping, bulk and single-cell profiling and high resolution confocal imaging, we show that the repopulation is strikingly different between CAMs and microglia. In contrast to microglia, CAMs do not renew exclusively cell-autonomously, but transiently utilize CCR2+Ly-6C+ monocytes after niche induction in an integrin-dependent manner. Remarkably and unlike repopulated microglia, replenished monocyte-derived CAMs remain transcriptionally and functionally distinct from their YS-derived counterparts. Finally, we established a protocol that allows to selectively exchange CAMs modulating disease response without functionally affecting parenchymal microglia. These new insights into the biology of the CNS immune system offer completely new therapeutic avenues for diverse neuroinflammatory and neurodegenerative diseases. Overall design: WT mice were treated with BLZ945 or Vehicle (CTL) and cells were isolated from cerebral cortex, dura mater and leptomeninges 8 weeks, 5 days post 7 days BLZ945-mediated macrophage depletion or CTL. After isolating whole brain and removing choroid plexuses under a stereomicroscope in ice cold PBS, cortex and leptomeningeal and dural immune and niche cells were sorted by gating DAPI- cells and then for CD11b+CD45+ (immune), CD31+ (endothelial), PDPN+ (fibroblasts) and marker negative (other cell types) cells as described in the flow cytometry section and as seen in the gating strategies (Supplementary Fig. 1).