Combined Analysis of Metabolomics and Proteomics in Immune-Related Dry Eye Disease

Dry eye disease (DED) is a chronic ocular surface disorder with immune factors significantly contributing to its pathogenesis. Traditional research methods, often focused on single-dimensional approaches, have limited the understanding of the complex mechanisms involved in DED. The advent of multi-omics technologies, however, offers a comprehensive framework to explore molecular mechanisms across multiple levels, presenting new possibilities for diagnosing and treating DED. This study specifically aimed to compare the proteomics and metabolomics profiles of individuals with Sjögren’s Syndrome (SS), a condition often associated with DED, to healthy controls, and to identify potential biomarkers and pathways that play a role in its development. Serum proteins and metabolites were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS), followed by multivariate and univariate statistical analysis to pinpoint differentially expressed proteins (DEPs) and metabolites (DEMs). Functional annotations and pathway enrichment analyses were conducted using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases to identify key molecular pathways. Bioinformatics tools were then applied to integrate the proteomics and metabolomics data, highlighting crucial differential proteins, metabolites, and biomarkers. The study identified 112 DEPs in individuals with SS, including 94 upregulated and 18 downregulated proteins. The most significantly enriched pathways in KEGG analysis included amino acid biosynthesis, glycolysis/gluconeogenesis, the Rap1 signaling pathway, carbon metabolism, focal adhesion, platelet activation, the pentose phosphate pathway, and actin cytoskeleton regulation. Key proteins identified as potentially related to SS development included GAPDH, CFL1, ENO1, VCL, MYH9, FLNA, TPI1, ITGA2B, TLN1, and TXN. In the metabolomics analysis, 372 DEMs were identified, with 268 upregulated and 104 downregulated metabolites, primarily enriched in glycine, serine, threonine metabolism, as well as taurine and hypotaurine metabolism. The integration of proteomics and metabolomics data underscored the significance of the Rap1 signaling pathway, suggesting its potential involvement in the development of DED. Overall, this study revealed several key differential proteins, metabolites, and potential biomarkers, providing valuable insights into the molecular mechanisms underlying DED and offering new avenues for further research into its pathogenesis.