Identification of repopulated microglia-associated genes in microglia depleted/repopulated mice after spinal cord injury.

This study aimed to investigate the effects of repopulated microglia on neural repair and functional recovery and identify repopulated microglia-associated repair-promoting genes after spinal cord injury (SCI) in mice following depletion of microglia via the colony-stimulating factor 1 receptor (CSF1R) inhibitor PLX3397. Mice were divided into control, sustained microglial depletion, and microglial depletion/repopulation groups according to being treated standard or PLX3397 diet. Mice in all groups were subjected to a complete spinal cord crush injury. Comprehensive assessments were performed using behavioral scoring, immunofluorescence staining 21 days post-injury, and RNA sequencing 21 days post-injury. Results demonstrated that PLX3397 effectively eliminated approximately 95 % of microglia in the mouse spinal cord. Upon drug withdrawal, microglia rapidly repopulated and exhibited a pro-regenerative phenotype. Repopulated microglia significantly promoted post-injury motor functional recovery, increased neuronal survival, and reduced glial scar formation. Transcriptomic analysis identified genes associated with repopulated microglia, which were enriched in immune response, complement activation, phagocytosis, and cytokine signaling pathways. Protein-protein interaction (PPI) network analysis of these associated genes further pinpointed key genes, includingIl1b,Ccr2, and Il15. This study reveals that repopulated microglia may exert neuroprotective effects by modulating the immune microenvironment. The 336 repopulated microglia-associated genes identified in this study, and the identified key genes that are preferentially upregulated in repopulated microglia may represent novel therapeutic targets for SCI.