Single-Cell RNA Sequencing of the Primary Visual Cortex in Mice With Optic Nerve Injury.

Purpose: Glial cells play a critical role in primary visual cortex (V1 region) damage caused by optic nerve injury, but the mechanisms driving progression of V1 region injury and glial cell heterogeneity remain poorly understood. This study aimed to investigate the damage changes in the V1 region of mice after optic nerve crush (ONC) by single-cell RNA sequencing (scRNA-seq). Methods: Hematoxylin and eosin (H&E) and immunofluorescence staining were used to evaluate the changes of retinal thickness, astrocytes, and microglia in the V1 region after ONC in mice. Single cell suspensions in the V1 region of mice were prepared and analyzed by scRNA-seq with Seurat, cellchat, CytoTRACE in R software. The expression of PTGDS and CRYAB was measured by qPCR, Western blot, and immunofluorescence. Results: After unilateral ONC, retinal thinning in both eyes and activation of astrocytes and microglia in contralateral V1 region were observed. Genes related to neuroinflammation and apoptosis in the bilateral V1 region were upregulated, and the related pathways included MAPK, TNF, and apoptosis signaling pathways. Notably, the V1 region contralateral to the ONC eye exhibited more pronounced differential gene expression, and the protein expression of neuroinflammation-related genes Ptgds and Cryab increased. We further investigated the heterogeneity and pseudotime trajectories of astrocytes and microglia, demonstrating the key branches that dominate neuroinflammation. Conclusions: This study generates an atlas of the V1 region of the mouse brain, highlighting the role of astrocytes and microglia in the damage changes in the V1 region after ONC, and suggesting Ptgds and Cryab as potential targets to reduce neuroinflammation.