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This study aimed to evaluate FOXC1-mediated regulatory mechanisms on gene and protein expression profiles in primary human limbal epithelial cells (pLECs), via siRNA knockdown; under basal and lipopolysaccharide (LPS) and interleukin-1β (IL-1β) induced inflammatory conditions. Gene expression was analysed for markers related to inflammation (CCL2, IL-6, IL-8, TNF-α, TGF-β), epithelial differentiation (KRT3, KRT12, KRT13, PAX6, FOXC1), cell proliferation and remodelling (FOSL2, MKi67, MMP2, VEGFA) and retinoic acid metabolism (ALDH3A1, CRABP2, CYP1B1, FABP5, RDH10, RBP1, STRA6). FOXC1 siRNA silencing in human pLECs significantly altered mRNA expression across multiple functional pathways, including inflammatory signaling (CCL2, IL-6, IL-8, IL-1α, VEGFA; p≤0.030), epithelial differentiation (KRT12, KRT13, PAX6; p≤0.045), cell proliferation and stress response (FOSL2, MKi67, VEGFA; p≤0.048) and retinoic acid metabolism (ALDH3A1, CRABP2, CYP1B1, FABP5, RDH10, STRA6; p≤0.037). Corresponding protein levels, evaluated by Western blotting and ELISA, were significantly modulated for the FABP5–CRABP2 axis, IL-6, IL-8, IL-1α, KRT12, KRT13, TGF-β, and RDH10 under different treatment conditions; (p≤0.045). FOXC1 maintains an anti-inflammatory, immune-quiescent state and coordinates TGF-β–mediated signaling, keratin expression, and retinoic acid metabolism to preserve corneal epithelial identity and homeostasis. Disruption of FOXC1 expression perturbs these pathways, potentially predisposing the ocular surface to fibrosis, lineage instability, and impaired regenerative capacity.