Integrated analysis of transcriptome and proteome of the human cornea and aqueous humor reveal novel biomarkers for corneal endothelial cell dysfunction

Previous studies have reported that elevated protein levels in the aqueous humor (AH) are associated with corneal endothelial cell dysfunction (CECD), but the detailed underlying mechanism as well as specific biomarkers for CECD remain elusive. In the present study, we aimed to identify protein markers in AH directly associated with changes in Corneal endothelial cells (CECs), as AH can be easily obtained for analysis. We carried out an in-depth proteomic analysis of patient-derived AH as well as transcriptomic analysis of CECs from the same patients with bullous keratopathy (BK) resulting from CECD. We first determined differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) from CECs and AH in CECD, respectively. By combining transcriptomic and proteomic analyses, 13 shared upregulated markers were observed between DEGs and DEPs. Through data integration with individual analysis via data-independent acquisition, three upregulated transcripts and proteins were identified, namely metallopeptidase inhibitor 1 (TIMP1), Fc fragment of IgG binding protein (FCGBP), and angiopoietin-related protein 7 (ANGPTL7). Furthermore, we confirmed AH biomarkers for CECD using individual proteome verification and immunoassay validation. Conclusively, our findings may provide valuable insights into the disease process and identify biofluid markers for the assessment of CEC function during BK development. Overall design: human corneal endothelium mRNA profiles of Normal and CECD were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.