Chromatin and transcriptional adaptation accompany monocyte engraftment in the injured retina

Distinguishing resident microglia from engrafted peripheral myeloid cells is important for interpreting CNS inflammation. P2RY12, TMEM119, and FCRLS are widely used to identify microglia, but their ability to distinguish cellular origin after prolonged engraftment remains context dependent. Using bone marrow chimeras, single-cell and bulk RNA sequencing, ATAC-seq, flow cytometry, and immunostaining, we examined myeloid adaptation after retinal injury. Donor-derived cells acquired P2RY12, TMEM119, and FCRLS expression with different kinetics and degrees of heterogeneity, while subsets downregulated CCR2, Ly6C, and CD45. These phenotypic changes were accompanied by altered chromatin accessibility at microglia-associated loci and changes in transcription factor motif enrichment. At one year after injury, engrafted cells and injured host microglia share inflammatory transcriptional features while retaining population-associated differences with significantly lower expression of Sall1 in engrafted cells compared to naive microglia. Donor-derived cells infiltrating the brain and spinal cord without additional CNS injury also acquired microglial markers. These observations establish phenotypic overlap and persistent molecular differences in engrafted retinal monocytes and support combining marker expression with cellular-origin information to identify CNS myeloid populations after long-term engraftment.