RNA-Seq Analysis Unraveling Novel Genes and Pathways Influencing Corneal Wound Healing.

Abstract

Purpose: Transdifferentiation of corneal fibroblasts to myofibroblasts in the stroma is a central mechanistic event in corneal wound healing. This study sought to characterize genes and pathways influencing transdifferentiation of human corneal fibroblasts (hCSFs) to human corneal myofibroblasts (hCMFs) using RNA sequencing (RNA-seq) to develop comprehensive mechanistic information and identify newer targets for corneal fibrosis management.

Methods: Primary hCSFs were derived from donor human corneas. hCMFs were generated by treating primary hCSFs with transforming growth factor β1 (TGFβ1; 5 ng/mL) for 72 hours under serum-free conditions. RNA was extracted using the RNeasy Plus Mini Kit and subjected to RNA-seq analysis after quality control testing. Differential gene expression, pathway enrichment, and protein-protein network analyses were performed using DESeq2, GSEA/PANTHER/Reactome, and Cytoscape/cytoHubba, respectively.

Results: RNA-seq analysis of hCMFs and hCSFs identified 3843 differentially expressed genes and transcripts (adjusted P < 0.05). The log(fold change) ≥ ±1.5 filter showed 816 upregulated and 739 downregulated genes between two cell types. Pathway enrichment analysis showed the highest normalized enrichment score for epithelial-to-mesenchymal transition (5.569), followed by mTORC1 signaling (2.949), angiogenesis (2.176), and TGFβ signaling (2.008). Protein-protein interaction network analysis identified the top 20 nodes influencing corneal myofibroblast development. The expression of a novel MXRA5 in corneal stroma and its association with corneal fibrosis was verified by real-time quantitative reverse transcription PCR and immunofluorescence. RNA-seq and gene count files were submitted to the NCBI Gene Expression Omnibus (GSE260476).

Conclusions: This study identified several novel genes involved in myofibroblast development, offering potential targets for developing newer therapeutic strategies for corneal fibrosis.