Variant-to-gene mapping in ocular cell types identifies candidate effector genes for primary open-angle glaucoma

Abstract

Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness worldwide, has a strong genetic basis. The Primary Open-Angle African Ancestry Glaucoma Genetics study previously identified 46 risk loci associated with this disease. To pinpoint causal variants and their corresponding effector genes, we analyzed gene expression, chromatin accessibility, and conformation in two ocular cell types: trabecular meshwork cells (hTMCs) and retinal ganglion cells derived from induced pluripotent stem cells (hiPSC-RGCs). We identified 24 candidate genes in hTMCs and 56 in hiPSC-RGCs. Several prioritized genes showed altered mRNA expression, implicating pathways involved in oxidative stress, tissue homeostasis, neuronal maintenance, and retinal degeneration. Among these genes, ARHGEF12 was selected for further validation because local and distal promoter interactions nominated it in both cell types, and prior evidence reproducibly links it to POAG. While its role in hTMCs is established, its function in RGCs is unclear. hiPSC-RGCs generated from a POAG donor homozygous for the risk allele exhibited reduced ARHGEF12 expression, altered morphology, and disrupted neuronal activity. By linking POAG risk loci to candidate effector genes in ocular cell types, this study provides a framework for functional evaluation of additional POAG risk variants.