Proteomic analysis of corneal astigmatism identifies reduced apolipoprotein A-IV as a candidate biomarker

Introduction: Astigmatism is a common refractive error associated with myopia, yet its molecular mechanisms remain poorly understood. This study aimed to identify and validate differentially expressed proteins (DEPs) in corneal astigmatism through a label-free quantitative proteomic approach, followed by biomarker validation using parallel reaction monitoring (PRM). Methods: This two-phase, retrospective case-control study aimed to identify and verify differentially expressed proteins (DEPs) associated with corneal astigmatism. Phase I (discovery) employed label-free quantitative (LFQ) proteomics to compare stromal samples from 9 patients (10 eyes) with compound myopic astigmatism (Group A) and 8 patients (10 eyes) with simple myopia (Group B). Phase II (verification) involved targeted parallel reaction monitoring (PRM) in an independent cohort comprising 13 patients (15 eyes) in Group A and 14 patients (15 eyes) in Group B, quantifying discovery-prioritized proteins. Bioinformatic analyses including COG, GO, KEGG, and protein-protein interaction mapping were performed to characterize enriched pathways and guide PRM target selection. Results: A total of 127 DEPs were identified, with 31 upregulated and 96 downregulated in Group A. Bioinformatic analysis of the discovery dataset showed enrichment of proteins associated with wound healing, blood coagulation, and lipid metabolism; these enrichments were exploratory and were used only to prioritize candidates for targeted verification. Targeted PRM verified a significant reduction in APOA4 in astigmatism; other candidates showed concordant trends without statistical significance. Conclusion: After targeted verification, APOA4 was the only protein that remained significantly reduced in corneal astigmatism, supporting reduced APOA4 as a candidate biomarker that warrants further study. The discovery-phase associations with coagulation, lipid metabolism, and wound-healing pathways were not confirmed at the protein level and should be regarded as hypothesis-generating, requiring confirmation in larger, adequately powered cohorts.