Integrative Genomic Analysis Identifies Multi-layer Regulatory Mechanisms Underlying Retinal Ganglion and Nerve Fiber Layer Thickness

ABSTRACT

Background: Ganglion cell inner plexiform layer thickness (GCIPLT) and Retinal nerve fiber layer thickness (RNFLT), as measured by optical coherence tomography, are quantitative traits reflective of retinal integrity and are increasingly recognized as non-invasive biomarkers for neurodegenerative diseases. While genome-wide association studies (GWAS) have identified loci associated with these traits, the underlying regulatory mechanisms remain poorly understood. Objective: To identify putative causal genes and elucidate the genetic and epigenetic regulatory architecture of GCIPLT and RNFLT using an integrative genomics framework. Methods: We performed summary-data-based Mendelian randomization (SMR) and HEIDI colocalization analyses to integrate GWAS summary statistics for GCIPLT and RNFLT (N = 31,434, UK Biobank) with brain-derived eQTL, mQTL, and sQTL datasets. We prioritized genes with statistically significant and LD-independent associations and investigated the roles of DNA methylation and alternative splicing in gene regulation. Results: We identified 40 and 31 genes significantly associated with GCIPLT and RNFLT, respectively, with 26 and 15 passing the HEIDI filter (p > 0.01), indicating likely causal relationships. Among these, several genes showed negative associations suggestive of detrimental effects on retinal integrity. Epigenetic analyses revealed that 13 GCIPLT related and 12 RNFLT-related genes were regulated by DNA methylation, while 12 and 13 genes, respectively, were regulated by alternative splicing. Seven genes (DYNC1I2, ARL17B, HERC2, KANSL1, LRRC37A2, MRPL12, OCA2) were implicated in both phenotypes, with OCA2 and MRPL12 acting as multi-layer regulatory hubs. These genes have known links to neurodevelopmental and neurodegenerative disorders. Conclusions: Our study provides a comprehensive genetic and epigenetic map of retinal structural traits, highlighting convergent regulatory mechanisms involving gene expression, DNA methylation, and alternative splicing. These 186 findings deepen our understanding of retinal biology and suggest shared molecular pathways linking retinal structure to neurodegenerative disease risk. an integrative genomics framework combining GWAS