Integrated Genomic Analysis Prioritizes Causal Genes and Cell Types for Glaucoma

Primary open-angle glaucoma (POAG), characterized by progressive optic neuropathy, is a leading cause of blindness in people over age 55. Elevated intraocular pressure (IOP) is a major risk factor for POAG, but current medications have limited ability to lower IOP. Moreover, about one-third of patients with POAG have normal or near-normal IOP, and conversely, many people with elevated IOP do not develop glaucoma.

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To gain a better understanding of the molecular and cellular causes of POAG, Ayellet V. Segrè, PhD, an assistant scientist in the Ocular Genomics Institute of the Department of Ophthalmology at Mass Eye and Ear, and colleagues, integrated genetic regulation and single cell expression in glaucoma-relevant ocular tissues with summary statistics from genome-wide association studies (GWAS).

In Nature Communications, they report newly identified regulatory mechanisms, genes, pathways, and cell types that may play an important role in POAG etiology, in an IOP-dependent or independent manner.

Methods

The study incorporated multiple datasets:

• Expression quantitative trait loci (eQTLs) and splicing QTLs (sQTLs) from 49 non-ocular tissues in the Genotype-Tissue Expression (GTEx) Project
• eQTLs from retina
• Genome topology (Hi-C) and epigenetic data from retina
• Single-nucleus expression data from a whole-eye cell atlas
• The largest-yet genome-wide association study (GWASs) meta-analyses for POAG and IOP (136 cross-ancestry and/or European loci associated with POAG and 112 loci associated with elevated IOP)

Colocalization, Enrichment, and Mendelian Randomization Analyses

The research team identified known and new causal genes and biological processes for POAG, proposed key ocular cell types that may be pathogenic for glaucoma, and provided evidence for the existence of hundreds of novel genetic associations that may have regulatory effects on glaucoma. Some key results were:

• eQTLs and sQTLs in non-ocular tissues and retina were enriched for hundreds of POAG and IOP associations, suggesting a primary role for transcriptional regulation and alternative splicing in POAG susceptibility
• Putative causal genes were prioritized for 60% of the POAG and IOP loci from GWAS; these genes are enriched in pathways implicated in extracellular matrix organization, cell adhesion, vascular development, and retina or neuronal related processes
• For 80 loci a single gene was proposed, including 10 noncoding genes (lincRNA and antisense), implying transcriptional and post-transcriptional gene regulation contribute to glaucoma susceptibility
• Mendelian randomization prioritized a high confidence set of regulatory mechanisms that may affect POAG risk dependent or independent of IOP
• Chromatin contact map and epigenetic data in retina provided support for causal effects of colocalizing eQTLs and sQTLs on POAG, including for the strongest association with normal tension glaucoma (9p21), CDKN2A/B and CDKN2B-AS1

ECLIPSER: Cell Type Enrichment of Genomic Loci

Part of the research relied on a method the team developed previously, ECLIPSER (Enrichment of Causal Loci and Identification of Pathogenic cells in Single Cell Expression and Regulation data). It tests whether the expression of genes mapped to GWAS loci of complex diseases or traits, based on eQTLs/sQTLs and other functional data, are enriched in specific cell types in one or more tissues.

ECLIPSER, applied to single-nucleus RNA-sequencing of ten anterior and posterior eye tissues, provided support for previously reported relationships between certain cell types and POAG development, as well as providing insight into less well-established or novel pathogenic cell types. For example:

• Gene expression variation was noted not only in trabecular meshwork cells in the conventional outflow pathway, but also in ciliary and iris fibroblasts in the unconventional outflow pathway in the anterior segment; both are possibly important contributors to IOP regulation and POAG risk
• In the peripheral and macular retina there was significant enrichment of POAG colocalizing genes in astrocyte and Müller glia cells, so macroglia may have a role in the initiation and progression of glaucoma
• Genes colocalizing with POAG loci but not IOP loci were enriched in oligodendrocytes and astrocytes in the optic nerve head and optic nerve, suggesting IOP-independent mechanisms
• No significant enrichment of POAG or IOP gene expression was observed in retinal ganglion cells, whose death is the key characteristic of glaucoma, but rather in neuronal support cells, emphasizing the importance of targeting support cells when developing new therapies
• The strongest enrichment for IOP was in vascular endothelial and fibroblast cells, primarily in the choroid but also in the optic nerve head and peripapillary sclera, suggesting vascular structural abnormalities or functional dysregulation of blood to the optic nerve and retina as other important contributors to POAG

Conclusions

These new insights into causal molecular and cellular mechanisms of POAG risk and IOP variation could inform development of neuroprotective therapies or simply more efficacious medications for reducing IOP. Future development by the Segrè lab of detecting eQTLs and sQTLs in additional eye tissues, such as the outflow pathways and optic nerve head, is expected to provide an even more complete picture of the causal mechanisms for glaucoma and other ocular diseases.

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