Decreased PAX6 and DSG1 Protein Expression in Corneal Epithelium of Patients with Epithelial Basal Membrane Dystrophy, Salzmann Nodular Degeneration, and Pterygium

<b>Background/Objectives</b>: Evaluation of stem cell, keratin, retinoic acid metabolism markers and non-coding micro-RNAs (miRNAs) in conjunctival and corneal samples of patients with epithelial basal membrane dystrophy (EBMD), Salzmann nodular degeneration (SND), pterygium and congenital aniridia (CA), to detect similarities and differences in their pathogenesis. <b>Methods</b>: Impression cytology (IC) samples and corneal epithelial samples (CEs) of patients with EBMD, SND, pterygium, congenital aniridia, and healthy control subjects have been analyzed. The IC samples were subjected to qPCR, and the epithelial samples were subjected to qPCR and WB. Limbal epithelial stem cell markers, keratins, retinoic acid metabolism markers, and miRNAs were analyzed. <b>Results</b>: In conjunctival IC samples, PAX6 mRNA expression was significantly lower in EBMD, SND, pterygium, and CA compared to healthy controls (<i>p</i> ≤ 0.02). KRT13 mRNA expression was significantly higher in EBMD, SND, and pterygium (<i>p</i> ≤ 0.018), and FABP5 was increased in pterygium samples (<i>p</i> = 0.007). MiRNA-138-5p was significantly higher in aniridia samples than in normal controls (<i>p</i> = 0.037). In corneal epithelial samples, PAX6 protein, DSG1 mRNA and protein, miRNA-138-5p, and miR-204-5p expression were significantly lower in EBMD, SND, and pterygium samples than in controls (<i>p</i> ≤ 0.02). ALDHA1 mRNA expression was significantly lower (<i>p</i> < 0.0001), and FABP5 mRNA expression was significantly higher (<i>p</i> = 0.014) in pterygium samples than in controls. <b>Conclusions</b>: PAX6, DSG1, miR-138-5p, and miR-204-5p expression is decreased in the corneal epithelium of epithelial basal membrane dystrophy, Salzmann nodular degeneration, and pterygium subjects. In addition, there is a dysregulation of markers of the retinoic acid signaling pathway, such as ADH1A1 and FABP5, in the corneal epithelium of pterygium subjects. These changes may offer therapeutic targets in the treatment of these ocular surface diseases.