Transcriptional landscape of aniridia-associated keratopathy through single-cell RNA sequencing

Aniridia-associated keratopathy (AAK) is a progressive condition characterized by conjunctivalization of the cornea, yet its molecular mechanisms remain largely unknown. This study aims to elucidate the transcriptional landscape of AAK by characterizing the gene expression profiles of corneal epithelial cells in a patient with congenital aniridia.

Single-cell RNA sequencing (scRNA-seq) was performed on epithelial tissues collected from the clear central corneal region and limbus of a 48-year-old female patient with congenital aniridia. The transcriptomic profiles were compared with those of healthy control samples.

scRNA-seq analysis revealed that a subpopulation of cells from the clear central corneal region expressed the cornea-specific keratins KRT3 and KRT12 despite a significant reduction in PAX6 expression. These cells exhibited corneal, conjunctival, or mixed gene signatures. Genes associated with wound healing and apoptosis were upregulated in the cornea-like cells from the aniridic cornea, indicating a chronic wound healing state. Elevated KLF4 expression and regulon activity were observed in these cornea-like cells. Most limbal epithelial cells exhibited conjunctiva-like characteristics, reflecting a loss of limbal cell identity.

While acknowledging the limitations of a single case study, this study provides deeper insights into the transcriptional signatures associated with AAK using scRNA-seq. We identified transcriptional alterations reflecting AAK progression and highlighted potential transcription factors that may contribute to corneal identity maintenance despite PAX6 deficiency. These findings enhance our understanding of AAK and suggest potential therapeutic strategies to slow its progression.