mRNA Sequencing of Limbal Epithelial Cells and mRNA/miRNA Profiling of Limbal Stromal Cells in PAX6-Related Congenital Aniridia

The dysfunction of limbal epithelial cells (LECs) and limbal stromal cells (LSCs) in congenital aniridia remains incompletely understood. We aimed to analyze mRNA expression profiles of primary human LECs and LSCs, as well as microRNA (miRNA) expression in LSCs, from patients with congenital aniridia (AN-LECs and AN-LSCs). mRNA sequencing of primary human LECs and mRNA and miRNA sequencing of LSCs were performed from patients with aniridia and healthy controls. Gene ontology and pathway analyses were used to evaluate biological processes, cellular components, and molecular functions. Selected deregulated mRNAs and miRNAs were validated by quantitative real-time PCR (RT-qPCR). A total of 188 differentially expressed genes (DEGs) were identified in AN-LECs, and 3001 DEGs in AN-LSCs. In AN-LECs, the top hub genes were associated with inflammatory and interferon-related responses. In contrast, AN-LSCs showed predominant deregulation of mitochondrial and metabolic genes. Pathway analysis revealed involvement of inflammation-related pathways in AN-LECs and metabolic pathways in AN-LSCs. Additionally, 48 deregulated miRNAs were identified in AN-LSCs. This study provides comprehensive mRNA profiles of LECs and LSCs and miRNA profiles of LSCs in congenital aniridia. The findings emphasize the importance of LSC influence and offer insights into molecular mechanisms underlying aniridia-associated keratopathy (AAK), supporting future research and potential therapeutic target identification.