Acute Inflammation Drives Corneal Pathological Regeneration.

PURPOSE: This study aimed to characterize transcriptional and epigenetic remodeling in the cornea induced by acute inflammation. METHODS: Limbal-corneal tissues were collected on days 5 and 10 after intrastromal administration of lipopolysaccharide or PBS. ScRNA-seq and scATAC-seq were used to delineate the transcriptomic and epigenomic atlas of the inflamed cornea, following the Seurat and Signac pipelines. Immunofluorescence was performed to assess changes in corneal epithelial markers and immune cell infiltration. RESULTS: We identified 16 cell clusters, including ten epithelial cell subpopulations, keratocytes, fibroblasts, corneal endothelial cells, blood vessel cells, lymphatic vessel cells, and immune cells. Lipopolysaccharide induced the infiltration of five major immune cell types: neutrophils, MHC-II⁻ macrophages, MHC-II⁺ macrophages, T cells, and natural killer cells. We characterized gene expression and chromatin accessibility dynamics across all cell types during the inflammatory response, revealing cell-type-specific gene regulatory elements and cis-regulatory chromatin interactions. Regulon activity and motif accessibility analyses identified critical transcription factors that drive distinct inflammatory response programs. Inflammation was found to inhibit limbal stem/progenitor cell differentiation. CellChat analysis revealed a set of secreted intercellular crosstalk signals among all cell types. CONCLUSIONS: Our work provides a comprehensive, time-resolved single-cell transcriptomic and epigenomic atlas of the inflamed cornea, defining cellular functional heterogeneity, cis-regulatory networks, and intercellular communication during corneal pathological regeneration. These findings offer valuable insights into corneal pathology.