RNA sequencing data of leptomeningeal/perivascular CAMs and MG following LPS stimulation 8 weeks after repopulation

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: Three WT or three Ccr2-/- mice per group either were left untreated or were treated with Vehicle (CTL) or with BLZ945 and 8 weeks later, all treated mice were injected with LPS. 12h later, mice were perfused and CAMs as well as MG were sorted for the generation of bulk transcriptomics data. In addition, three Ccr2CreERT2 R26tdT mice per group were treated with BLZ945 and 8 weeks later injected with either PBS or LPS. 12h later, mice were perfused and CAMs (tdTpos and tdTneg) as well as MG were sorted for the generation of bulk transcriptomics data. RNA expression levels between the different groups were compared. For details reagrding the analysis see methods section of the publication.