Integrative Prioritization of IOP-associated Genes Using High Throughput Genomic Data

Abstract

Purpose : Intraocular pressure (IOP) is the only modifiable major risk factor for glaucoma. Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with elevated IOP and primary open-angle glaucoma (POAG). This study aims to prioritize the genes related to these variants for functional studies.

Methods : Two recent GWAS have identified ~157 IOP-associated genomic regions. Prioritization of genes located in these regions is crucial to promote focused research. Since trabecular meshwork (TM) and Schlemm’s canal (SC) are responsible for IOP regulation, we used a comprehensive approach to prioritize these genes: (1) differential expression in POAG-affected human TM tissue (n=27, array), (2) differential expression in primary POAG-affected SC endothelial cells (n=8, array), (3) high expression in primary human TM and SC cells (n=6, RNA-Seq), (4) high expression in human ocular tissue expression database (pooled samples, array), (5) variants located in regions with histone modifications in GTEx Portal database, (6) differential expression correlation analysis with all differentially expressed genes and IOP-associated genes in glaucoma vs. normal human TM tissue (n=27, array), and (7) responsive to cyclic mechanical stretch (24 hours) in human TM cells (n=5, RNA-Seq).

Results : 29 genes were found to have a |fold change| ≥ 1.5 based on TM or SC microarray data. 18 of these had high expression in primary TM/SC cells. 16 leading IOP-associated variants near these 18 genes are in enhancer or promoter regions. Our differential expression correlation analysis identified 68 correlation pairs (containing 70 distinct genes) with significant differential correlation in POAG samples (FDR ≤ 0.05). Ingenuity Pathway analysis of these 70 genes revealed gene networks centered on PPARG (peroxisome proliferator-activated receptor gamma) and ESR1 (estrogen receptor 1) with TNXB, CAV2, FBXO32, HHEX, and VEGFC. Our integrative analysis further emphasizes the role of the estrogen-driven pathway in glaucoma. Many of them, such as ANKH, FBXO32, LTBP2, and HGF, are responsive to mechanical stretch in primary human TM cells.

Conclusions : Overall, we have established a comprehensive pipeline to prioritize a large number of genes located in IOP-associated regions for further functional studies centered around PPARG and ESR1-related gene networks.

This is a 2020 ARVO Annual Meeting abstract.