Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [Cut-n-Tag]

Microglia arise from yolk sac progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain unsettled. Here, we combine lineage tracing, pharmacological microglia depletion, and multi-omics profiling to define the ontogeny, identity, and function of brain parenchymal macrophages. Despite sharing the parenchymal milieu, MDM display transcriptional and epigenetic landscapes distinct from YSM. Fate-mapping reveals that brain-engrafted MDM transiently express CD206, echoing a developmental stage of microglial precursors. MDM engraftment and polarization are modulated by IL-34 and CCR2. Furthermore, parabiosis and skull‑flap transplantation reveal that both blood and skull marrow supply the niche, yielding origin‑biased MDM states. Functionally, MDM engraftment enhanced cuprizone-mediated demyelination. Together, our study defines the origins, molecular features, and context-dependent roles of brain parenchymal macrophages across homeostasis, turnover, and CNS pathology.