Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus

This study aimed to elucidate the genetic determinants of keratoconus (KC) using a multi-omics approach, with a focus on identifying key causal genes to address gaps in understanding the disease’s pathological mechanisms. An integrated multi-omics study combining bioinformatics analysis of transcriptome data with clinical validation. This approach does not include a traditional control group but utilizes public databases and patient samples to assess genetic associations. Five KC patients from the First Affiliated Hospital of Xi’an Jiaotong University provided corneal tissues and blood samples. The control group consisted of five age-matched donors who provided excess corneal tissue from transplantation surgeries. The study involved analyzing two KC transcriptome datasets from GEO to identify differentially expressed genes (DEGs). This was followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, summary-data Mendelian randomization (SMR), two-sample Mendelian randomization (TSMR), Bayesian colocalization, and clinical validation through immunohistochemical staining and PCR assays. Primary measures included gene expression levels, causal association statistics (e.g., posterior probability PP4, SMR p-value, OR), and RNA and protein expression of key genes (HLA-DRB5, ODAPH, MMP-9) assessed through molecular assays. The analysis identified 2,884 DEGs enriched in cell adhesion, immune response, and the TNF and IL-17 signaling pathways. Twenty-four genes demonstrated strong causal associations with KC (PP4 > 0.8), with HLA-DRB5 (PP4 = 0.844, SMR p = 0.001, OR = 1.768) and ODAPH (PP4 = 1.0, SMR p = 0.013, OR = 202.851) showing the highest confidence. Clinical validation confirmed significantly elevated expression of HLA-DRB5, ODAPH, and MMP-9 in the KC cornea and whole blood. HLA-DRB5 and ODAPH were identified as key causal risk genes for KC, bridging critical gaps in genetic knowledge and providing a foundation for early diagnostic biomarkers and etiology-targeted therapies, such as Meplazumab, an HLA-DRB5 inhibitor.