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.