Altered expression of miRNAs and its implication for Pseudomonas aeruginosa keratitis

Pseudomonas aeruginosa (PA) keratitis is a major ocular infection that can lead to vision loss without appropriate medical care. Although antibiotics are effective in infection management, poor outcomes often occur due to rapid ulceration driven by the inflammation-induced tissue damage. In this study, we profiled the microRNAs (miRNAs) expressed during corneal ulceration in PA keratitis patients and predicted the signalling pathways influencing ulcer pathogenesis.

Small RNA sequencing was performed on ulcerated corneal buttons obtained from PA keratitis patients undergoing therapeutic penetrating keratoplasty, with healthy post-mortem donor corneas serving as controls. miRNA identification and differential expression (DE) analysis were conducted using standard bioinformatics pipelines, and the altered expression of selected DE miRNAs was subsequently confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) in an independent set of samples.

Expression profiling revealed 122 DE miRNAs, among which 54 were upregulated and 68 were downregulated. Based on pathway enrichment, network analysis, and literature evidence, five among the DE miRNAs were selected for further studies. The RT-qPCR results demonstrated the altered expression of three selected miRNAs, namely, miR-184, miR-21-5p, and miR-22-3p, with statistical significance. The DE miRNAs were predicted to contribute to corneal ulceration in PA keratitis mainly by targeting genes within the Neurotrophin, Autophagy, and MAPK signaling pathways.

This study comprehensively profiled human corneal miRNAs from PA keratitis patients using small-RNAseq and validated the DE of three selected miRNAs using RT-PCR. Bioinformatic target prediction showed functional relevance in keratitis and warrants further experimental studies.