Simultaneous spatial transcriptomics and morphology profiling as tools to explore how microglia change with age

Cellular morphology is tightly linked to function, but how subcellular transcript localization contributes remains unclear. Using microglia, the brain's resident macrophages, as a model, we combined multiplexed error-robust fluorescence in situ hybridization with immunohistochemistry to map how morphology and subcellular mRNA localization interact with function in young and aged mouse brains. We show that mRNA spatial organization varies across microglial states and defines distinct localization patterns within their processes, revealing morphological heterogeneity within transcriptomically defined populations. Notably, we found a subpopulation of disease-associated-like microglia with a ramified morphology (that is, displaying numerous processes), challenging the conventional assumption between morphology and microglial states. Finally, we found that aging may reshape mRNA distributions and their co-localization networks, shifting microglial programs from intracellular signaling and regulation of phagocytosis toward migration and catabolic regulation. Our findings highlight the role of subcellular transcript organization in shaping microglial morphology and function, offering new avenues for studying and modulating microglial states in health, disease and aging.