Single-cell transcriptomic analysis reveals the cellular landscape and aberrant vascular endothelial growth factor signaling in corneal alkali burns

Corneal alkali burns constitute one of the most severe forms of ocular trauma and are frequently associated with intense inflammation, defective re-epithelialization, stromal scarring, and irreversible visual impairment. Limbal stem cells (LSCs) are indispensable for maintaining corneal epithelial homeostasis and regeneration; however, the cell-type-specific transcriptional responses and intercellular communication networks that underlie the pathological sequelae of alkali burns remain incompletely characterized. Single-cell RNA sequencing (scRNA-seq) was performed to systematically profile the cellular composition and transcriptional landscape of corneal and limbal tissues from a murine alkali burn (AK) model and corresponding wild-type (WT) controls. Comprehensive bioinformatic analyses were conducted, including cell clustering, differential gene expression, functional enrichment, and inference of cell–cell communication networks. Unsupervised clustering delineated the major corneal cell populations, including LSCs, transient amplifying cells (TACs), keratinocytes, epithelial cells, stromal cells, and immune cells, all of which exhibited marked shifts in relative abundance following injury. LSCs displayed profound transcriptional reprogramming, characterized by suppression of stemness- and pluripotency-associated pathways. TACs demonstrated pronounced upregulation of pro-apoptotic genes, such as Casp3 and Bax , alongside increased expression of pro-angiogenic mediators, including Vegfa. Distinct keratocyte subsets showed activation of inflammatory signaling cascades, notably NF-κB and TNF pathways. Immune cell populations, particularly monocyte–macrophages and neutrophils, exhibited robust induction of immune effector programs, cytokine signaling, and metabolic reprogramming. Vascular endothelial cells were enriched for pathways associated with angiogenesis and PI3K–Akt signaling. Importantly, cell–cell communication analysis predicted a substantial amplification of VEGF signaling in AK corneas, with keratocytes, TACs, and notably injury-responsive LSCs and monocyte–macrophages acting as key signal senders to endothelial cells, thereby potentially driving pathological neovascularization. This study presents a comprehensive single-cell transcriptomic atlas of corneal alkali burns, revealing coordinated dysregulation of stem cell function, apoptosis, inflammation, and angiogenesis. We further reconstruct a profoundly altered intercellular communication network centered on VEGF signaling. Together, these findings advance the mechanistic understanding of corneal chemical injury and identify candidate cellular targets and signaling pathways for therapeutic intervention aimed at preventing vision loss.