Monocytes can efficiently replace all brain macrophages and instruct different microglial identities depending on their origin
Microglia and border-associated macrophages (BAMs) are critical for brain health and their dysfunction is closely linked to disease. Replacing brain macrophages holds significant therapeutic promise, but remains challenging. Here, we demonstrate that monocytes can efficienty replace all brain macrophages. Monocytes readily replaced embryonal BAMs upon their depletion and engrafted as monocyte-derived microglia (Mo-Microglia) upon more sustained niche availability. Mo-Microglia expanded comparably to their embryonic counterparts and showed similar longevity. However, monocytes were unable to replicate the unique identity of embryonically-derived BAMs and microglia. Using humanized models, we found that human monocytes exhibited similar behavior, enabling us to identify putative Mo-Microglia in Alzheimer's disease patients. In mice and humans, the ontogeny of monocytes shaped their identity as brain macrophages. Importantly, mouse fetal liver monocytes exhibited a distinct epigenetic landscape and could develop a bonafide microglial identity. Our results illuminate brain macrophage development and highlight the potential of monocytes as an abundant progenitor source for brain macrophage replacement therapies. Overall design: CITE-seq and scRNA-seq.: CD45+ CD11b+ CX3CR1mid CLEC12- high brain or leptomeningeal cells from Flt3-Cre R26-YFP mice, which received control chow or 2 weeks PLX3397 chow followed by 7 weeks of repopulation on control chow; CD45+ brain cells from adult and neonate C57BL/6 mice, following an adoptive transfer of Cx3cr1 GFP/+ bone marrow derived monocytes; CD45+ CD11b+ brain cells from  Cx3cr1CreER:Csf1rfl/fl neonate mice,  intracerebrally injected with Cx3cr1 GFP/+  E14 fetal liver monocytes; CD45+ CD11b+ GFP+  brain cells from Cx3cr1CreER:Csf1rfl/fl mice, intracerebrally injected with CD319+ (MDP-Mo) or CD177+ (GMP-Mo) bone marrow monocytes from Cx3cr1Cre-GFP/+ mice; C57BL/6 E14 fetal liver monocytes and adult bone marrow monocytes; CD45+ cells from brains of naive hCSF1:Rag2-/-:?c-/-  mouse neonates, intracerebrally injected at PD4 with either human cord or adult blood-derived MACS-sorted monocytes. SnATACseq:  C57BL/6 E14 fetal liver monocytes and adult bone marrow monocytes. For the raw sequencing reads of the scRNA-seq samples from human monocytes injected in mouse brains, sensitive genetic information was eliminated by masking the donor-specific single nucleotide variants using BAMboozle v0.5.0