Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis

Forkhead box C1 (FOXC1) is required for neural crest and ocular development, and mutations in FOXC1 lead to inherited Axenfeld–Rieger syndrome. Here, we find that FOXC1 and paired box 6 (PAX6) are co-expressed in the human limbus and central corneal epithelium. Deficiency of FOXC1 and alternation in epithelial features occur in patients with corneal ulcers. FOXC1 governs the fate of the corneal epithelium by directly binding to lineage-specific open promoters or enhancers marked by H3K4me2. FOXC1 depletion not only activates the keratinization pathway and reprograms corneal epithelial cells into skin-like epithelial cells but also disrupts the collagen metabolic process and interferon signaling pathways. Loss of interferon regulatory factor 1 (IRF1) and PAX6 induced by FOXC1 dysfunction is linked to the corneal ulcer. Collectively, our results reveal a FOXC1-mediated regulatory network responsible for corneal epithelial homeostasis and provide a potential therapeutic target for corneal ulcer. Overall design: ATAC-seq and ChIP-seq for H3K4me2 and FOXC1 in wildtype limbal stem cells (LSCs). RNA-seq for wildtype LSCs and 3D-differentiated corneal epithelial cells (dCECs). RNA-seq for scrambled shRNA- and shFOXC1-treated LSCs. RNA-seq for scrambled shRNA- and shFOXC1-treated dCESs.