Lysosomal Glycosaminoglycan Catabolism Regulates Microglial Cell State in the Developing CNS

Remodeling of the extracellular matrix (ECM), a complex structural and signaling network of the nervous system, is essential for CNS development, plasticity, and injury responses, yet how individual neural cell types contribute to this process remains poorly understood. Here, we show that phagocytic clearance of glycosaminoglycans (GAGs), major components of the ECM, is an intrinsic function of microglia in the developing CNS. Our studies reveal an unexpected finding that impaired GAG clearance shifts microglia toward a non-homeostatic cell state seen in immature and disease-associated microglia (DAM), supporting a reciprocal relationship between the ECM and microglia. Using mouse models of Mucopolysaccharidosis VII, we examined the consequences of deleting β-glucuronidase (GUSB), a lysosomal enzyme required for GAG degradation. Loss of GUSB causes early accumulation of undegraded chondroitin sulfate within microglial lysosomes, as confirmed by LC-MS analysis of intracellular GAGs isolated from cortical microglia. Single-cell RNA sequencing identified Gusb -null microglia as a distinct transcriptional population enriched for a core transcriptome shared by immature and disease-associated microglia. Together, these findings establish lysosomal GAG catabolism as a pathway that links ECM remodeling to the acquisition of adult homeostatic microglial identity during CNS development.