RNA sequencing data of whole tissue or CAMs isolated from WT mice after ischemic stroke

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 for seven consecutive days either with Vehicle or BLZ945 (200 mg/KG BW). Eight weeks the treatment, mice were subjected to a thromboembolic MCAo model of ischemic stroke. At 1d after stroke induction, whole tissue sections of contralateral and ipsilateral hemispheres were isolated for bulk RNAseq. In addition, leptomeningeal/perivascular CNS-associated macrophages (CAMs) were sorted from contralateral and ipsilateral hemisphere for bulk RNAseq.