Determining Genetic Cause of Posterior Staphylomas in Eyes with Pathologic Myopia by Whole Exome Sequencing

Purpose To identify genetic variants in posterior staphylomas in eyes with pathologic myopia (PM) using whole exome sequencing (WES), and to determine possible molecular mechanisms contributing to the pathogenesis. Design Observational, case-control study. Participants 264 unrelated Japanese patients with myopia (≤ -0.50 diopters) and posterior staphyloma, which was diagnosed by ultra-widefield optical coherence tomography (UWF-OCT), three-dimensional magnetic resonance imaging (3D-MRI), and Optos imaging. Methods WES was performed on genomic DNA from peripheral blood. After variant filtering, the allelic frequencies were compared to control data obtained from East Asian subsets of the 1000 Genomes Project Phase 3 (1000GP3), the Exome Aggregation Consortium (ExAC), and the Japanese Multi-Omics Reference Panel (jMorp) using Fisher's exact test. A gene panel was constructed based on 13 staphyloma-associated disorders. Variants showing significant frequency differences ( P ≤0.05) and an overlap of the gene panel were analyzed using gene set enrichment analysis (GSEA) with the DAVID Knowledgebase (v2023q4). Protein-protein interaction (PPI) analysis was performed to assess functional associations. Main Outcome Measures The statistically associated variants and genes, GSEA results, PPI networks, involvement of basement membrane structures including the inner limiting membrane (ILM) and Bruch's membrane were studied. Results WES identified 16,656 missense variants in 8,628 genes. Comparative allele frequency analyses with public databases revealed 3,925 variants that had significantly higher allelic frequencies in the subjects. Of these, 81 genes overlapped with a curated staphyloma-related gene panel and were subjected to GSEA. The findings showed enrichment in basement membrane, extracellular matrix, and collagen-related pathways. The COL4A5, COL18A1, COL2A1 , and COL9A3 genes are concurrently enriched across these pathways. A missense variant in COL4A5 was identified in 27 patients, and 96.3% of whom were females. PPI analysis demonstrated functional connections among these four genes. Conclusions Variants in the COL4A5, COL18A1, COL2A1, and COL9A3 genes probably contribute to the pathogenesis of a posterior staphyloma through the disruption of collagen synthesis and basement membrane integrity. This was especially effective for the ILM and Bruch's membrane. The COL4A5 variant may cause an ocular-predominant phenotype in heterozygous female carriers, independent of the classical features of Alport syndrome.