Regional and sub-regional microglial heterogeneity in the steady-state mouse brain and retina

CNS-resident immune cells are uniquely adapted to their microenvironment; however, the extent of their regional specialisation remains unclear. We combined morphometric and transcriptomic profiling of microglia across the healthy adult mouse CNS, including the olfactory bulbs, cortex, hippocampus, cerebellum and retina, to define their regional and sub-regional heterogeneity. Bulk RNA-sequencing revealed region-specific signatures, with retinal microglia showing the most divergent transcriptomes, and genes related to antigen presentation, phagocytosis and chemokine signalling among the top differentially expressed genes. Single-cell RNA sequencing identified predominantly homeostatic microglia across all examined regions, alongside smaller clusters of interferon-responsive, chemokine-enriched, apolipoprotein-enriched and proliferative microglia. Apolipoprotein-enriched microglia were restricted to the olfactory bulbs, whereas interferon-responsive microglia were most abundant in the retina. Single-cell profiling of human retinal microglia confirmed clusters enriched for interferon-stimulated genes. Together, this study reveals previously unrecognised microglial heterogeneity within the healthy brain and eye and provides a comparison of microglia transcriptomes across different neuroanatomical regions of the CNS.