Integrating gene regulation and single cell expression with genetic associations identifies genes and cell types contributing to primary open angle glaucoma risk and intraocular pressure

Abstract

Purpose : There is no cure for primary open-angle glaucoma (POAG), characterized by progressive optic nerve damage and vision loss, due to limited understanding of the molecular and cellular causes. Here we aimed to identify genes and cell types that may affect POAG risk by integrating known POAG and intraocular pressure (IOP) genetic loci with genetic regulation of gene expression (eQTLs) and splicing (sQTLs), and single cell expression in ocular tissues.

Methods : We developed a method called ECLIPSER, that tests whether expression of genes mapped to genome-wide association study (GWAS) loci of a complex trait, based on e/sQTLs, is enriched in specific cell types. For each trait, tissue, and cell type, a GWAS locus is scored based on the fraction of cell type-specific genes (fold-change>1.3, FDR<0.1). Cell type enrichment of a GWAS loci set is assessed against a null distribution of loci of unrelated traits taken from Open Target Genetics, using a Bayesian Fisher’s exact test. We mapped genes to 127 POAG loci and 133 IOP loci found in large GWAS meta-analyses, by applying colocalization methods, eCAVIAR and enloc, to the GWAS loci and overlapping e/sQTLs from 49 GTEx tissues and retina eQTLs (EyeGEx). GeneEnrich was used for gene set enrichment in biological processes.

Results : ≥1 e/sQTL colocalized with 61% (202 loci) of POAG and IOP GWAS loci (Posterior Prob>0.01), with an average of 3-4 genes per locus. POAG genes were enriched in elastic fiber formation and extracellular matrix organization (P<6E-05, FDR<0.01), and IOP genes in vasculature development (P=5E-05, FDR=0.13). Applying ECLIPSER to the mapped genes and single-nucleus RNA-seq of the anterior segment (AS), optic nerve head (ONH) and retina from healthy eyes, identified significant enrichment (P=0.01-4E-04, FDR=0.008-0.16) for POAG in astrocyte and Müller glia in ONH and retina, and ciliary and iris fibroblasts in the aqueous outflow pathway in AS. The IOP genes were enriched in smooth muscle, astrocyte, pericyte, and vascular endothelium in ONH, astrocyte in retina, and trabecular meshwork and ciliary fibroblasts in AS (P=0.001-0.009, FDR=0.02-0.15).

Conclusions : This work suggests hundreds of regulatory mechanisms and genes that may contribute to POAG risk in specific cell types in the front and back of the eye, which could help guide novel therapies.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.