Integrated transcriptome and proteome analysis identifies keratins as key regulators of corneal scarring in a murine model

To elucidate the mechanism underlying corneal scarring, a murine model of corneal scarring was subjected to transcriptomic and proteomic analyses to explore changes in mRNA and protein levels during scar formation. A surgical model of stromal injury was established, and corneal tissue was harvested 3 weeks post-wounding and subjected to RNA sequencing and tandem mass tag proteomics. A total of 420 differentially expressed genes and 463 differentially expressed proteins were detected, of which 54 were commonly altered. Integrated Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed the predominant involvement of the regulation of actin cytoskeleton organization, cell metabolism, and regulation of inflammatory responses in the scarring process. To further explore the identified gene and protein interactions, we constructed a protein-protein interaction network that highlighted four keratin (Krt) genes (<i>Krt13</i>, <i>Krt14</i>, <i>Krt17</i>, and <i>Krt19</i>) as potential contributors to corneal scarring. The expression levels of these four keratins increased significantly in scarred corneas, which was validated via immunostaining. In vitro experiments revealed the upregulation of fibrosis markers after the overexpression of <i>Krt13</i> in corneal epithelial cells and stromal keratocytes. Altogether, this study provides insights into gene and protein expression profiles that contribute to the development of corneal scarring, which could serve as a basis for developing targeted therapeutics and clarifying its molecular mechanisms.