Microglial clonal dynamics and the impact of clonal hematopoiesis in autologously transplanted rhesus macaques

Microglia are central nervous system (CNS)-resident macrophages, with key roles in immune surveillance, phagocytosis, and synaptic pruning. Yolk sac-derived microglia show minimal turnover from hematopoietic stem/progenitor cells (HSPCs) under steady-state conditions in mice. However, clinical benefits observed in patients receiving HSPC gene therapies for CNS disorders suggest functional integration of HSPC-derived cells. To investigate microglia replacement and the impact of clonal hematopoiesis (CH) on microglia, we analyzed microglia in rhesus macaques receiving barcoded or CRISPR-edited (TET2-mutant) HSPC transplants. We found that <2% microglia were derived from HSPCs many years following transplant, with no evidence of enhanced replacement in CH. The rare HSPC-derived tissue-resident cells exhibited a macrophage-like gene expression profile. Our results demonstrate limited long-term microglia replacement from adult HSPCs, even with CH, contrasting prior human studies. This work provides insights into microglia ontogeny and informs strategies for CNS-targeted HSPC gene therapies and interpretation of CH-related neuroprotection.