Single-cell RNA sequencing reveals microglial proliferative bias and neuroinflammatory communication reprogramming following traumatic brain injury

Traumatic brain injury (TBI) remains a major global health challenge, with complex and incompletely understood pathophysiological mechanisms. In this study, single-cell RNA sequencing was employed to systematically characterize the transcriptional landscape of cortical cells in the mice model of moderate controlled cortical impact. Analysis of three TBI samples and three sham samples identified 14 different cell groups. In particular, seven microglial subclusters were identified, revealing significant phenotype remodeling of microglial. After TBI, the homeostatic microglial subclusters (C0 and C2) were reduced, whereas disease-association subclusters (C1, C4, and C5) and a proliferation subgroup (MC Cycle) were markedly increased. Pseudotime trajectory analysis further confirmed the transition of microglial subclusters from a homeostatic state to a pro-inflammatory state, characterized by the downregulation of Tmem119 and the upregulation of Tnf, Spp1, Il1a, Il1b, and Cxcl2. Moreover, proliferating microglial in the TBI group predominantly exhibited an M1-like phenotype. Intercellular communication analysis revealed a substantial reconstruction of a cellular interaction network. Notably, microglia enhanced signal transmission through specific pathways, thereby promoting M1 polarization, contributing to barrier dysfunction and mediating neuroinflammation responses. Overall, our findings provide a high-resolution map of cellular dynamics of TBI posterior cortical cells, highlighting the preferential shift of the regeneration of microglial toward a pro-inflammatory phenotype, and revealing a complex multicellular communication network centered on M1-like microglia.