ABSTRACT: Alkali burns cause rapid corneal remodeling, which is characterized by fibrosis, neovascularization, and immune infiltration; however, the cellular dynamics driving these responses remain poorly understood. Here, we present the first single-cell transcriptomic atlas of the rabbit cornea on day 14 postalkali injury, capturing the cellular and molecular architecture of stromal fibrosis. Single-cell RNA sequencing of naïve and injured corneas identified 14 transcriptionally distinct populations, including keratocytes, EMT-like epithelial cells, immune infiltrates, and heterogeneous fibroblast subtypes. Injury induced the expansion of ECM-remodeling fibroblasts and immune cells, accompanied by widespread transcriptional reprogramming. Stromal subclustering revealed four fibroblast states—quiescent, activated, proliferative, and progenitor-like—each with distinct gene signatures and functions. Pseudotime analysis revealed a trajectory from proliferative fibroblasts to ECM-secreting myofibroblasts, marked by stage-specific activation of mitotic, matrix, and contractile programs. Ligand–receptor inference via CellChat identified coordinated signaling through the TGFβ, PDGF, VEGF, and FGF pathways, alongside lesser-known axes such as NAMPT and NECTIN, implicating stromal–vascular crosstalk and metabolic stress in fibrotic progression. This study provides a comprehensive cellular framework for alkali-induced corneal fibrosis and identifies actionable targets for antifibrotic and antiangiogenic intervention in ocular surface disease.
