Integrated Analysis of mRNA and microRNA Expression in Corneal Impression Cytology Samples from Patients with PAX6-Related Congenital Aniridia

Abstract

This study aimed to measure mRNA and miRNA expression profile in corneal impression cytology (IC) samples from patients with congenital aniridia (CA) and healthy controls, and to elucidate the key genes and signaling pathways involved in aniridia-associated keratopathy (AAK). Corneal IC samples were collected from 14 patients with CA and 14 healthy controls. RNA sequencing was performed to identify differentially expressed genes (DEGs) and miRNAs. Correlations with age and AAK grade were analyzed, selected miRNAs were validated by RT-qPCR, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to characterize biological functions and pathways. A total of 695 DEGs and 19 differentially expressed miRNAs were identified. KRT24 expression was negatively associated with age, whereas LY6D expression positively correlated with AAK grade. Several miRNAs were linked to disease severity, including positive correlations for miR-224-5p, miR-224-3p, and miR-452-5p, and negative correlations for miR-204-3p, miR-181b-5p, and miR-181a-5p. RT-qPCR confirmed significant downregulation of miR-204-5p and miR-138-5p in aniridia samples. Functional enrichment analyses showed that DEGs were mainly involved in cell adhesion, extracellular matrix remodeling, inflammatory and immune responses, and neural-related processes. Target genes of dysregulated miRNAs were enriched in transcriptional regulation, cell proliferation, apoptosis, and migration, with significant involvement of PI3K-Akt, AGE-RAGE, and EGFR signaling pathways. Corneal epithelial cells from patients with CA exhibit coordinated mRNA and miRNA dysregulation associated with extracellular matrix disruption, inflammation, and altered signaling pathways. These findings improve understanding of AAK pathogenesis and identify potential biomarkers and therapeutic targets.