New insights into the genetics of primary open-angle glaucoma based on meta-analyses of intraocular pressure and optic disc characteristics

Abstract

Primary open-angle glaucoma (POAG), the most common optic neuropathy, is a heritable disease. Siblings of POAG cases have a ten-fold increased risk of developing the disease. Intraocular pressure (IOP) and optic nerve head characteristics are used clinically to predict POAG risk. We conducted a genome-wide association meta-analysis of IOP and optic disc parameters and validated our findings in multiple sets of POAG cases and controls. Using imputation to the 1000 genomes (1000G) reference set, we identified 9 new genomic regions associated with vertical cup-disc ratio (VCDR) and 1 new region associated with IOP. Additionally, we found 5 novel loci for optic nerve cup area and 6 for disc area. Previously it was assumed that genetic variation influenced POAG either through IOP or via changes to the optic nerve head; here we present evidence that some genomic regions affect both IOP and the disc parameters. We characterized the effect of the novel loci through pathway analysis and found that pathways involved are not entirely distinct as assumed so far. Further, we identified a novel association between CDKN1A and POAG. Using a zebrafish model we show that six6b (associated with POAG and optic nerve head variation) alters the expression of cdkn1a. In summary, we have identified several novel genes influencing the major clinical risk predictors of POAG and showed that genetic variation in CDKN1A is important in POAG risk.

Figure 1.

Overlap between the genes associated with one or more endophenotypes. Genes with a genome-wide significant association for at least one trait are shown. These genes are counted as overlapping genes if they are Bonferroni significantly associated with the other trait(s). Chr 11p11.2 (see intraocular pressure circle) means a region on chromosome 11p11.2 that is associated with IOP and has many genes in it; the likely causative gene in this region is not identified yet. Genes in bold are genes associated with primary open-angle glaucoma (POAG) in our meta-analysis of four case-control studies.*Genes associated with familial forms of POAG (e.g. MYOC and OPTN) or found in case-control association studies which did not show an association with the endophenotypes explored in this study.

Figure 2.

Pathways significantly enriched for: (A) Loci associated with the vertical cup-disc ratio, cup area and intraocular pressure (P-value <7.0 × 10-6 in the GWAS). In total 11 meta-pathways were identified after clustering the 57 pathways identified by DEPICT. B) Loci associated with vertical cup-disc ratio, cup area and disc area (P-value <1.0 × 10-5). In total 17 meta-pathways were identified after clustering the 100 pathways identified by DEPICT. In both figures, meta-pathways are represented by nodes coloured according to statistical significance, and edges are scaled according to the correlation between meta-pathways. *The pathway “Abnormal eye morphology” clustered with the meta-pathway “Chordate embryonic development”. ELL2 = Elongation Factor, RNA Polymerase II, DVL3= Dishevelled Segment Polarity Protein 3, THBS1 = Thrombospondin 1, RFX2= Regulatory Factor X, 2. MDFI = MyoD Family Inhibitor.

Figure 3.

cdkn1a mRNA expression change Overexpression of cdkn1a and cdkn2a/cdkn2b in response to six6b depletion is shown. All samples expression were normalized to the control gene sdha. Relative expression was calculated by setting the wild-type expression level at 1. Values represent mean ± standard error of the mean. *P < 0.05; **P < 0.005.