Disease mechanisms elucidated by genetic regulation of human RPE gene expression

Abstract

Purpose : To identify potential common modifier alleles of monogenic ocular diseases and uncover mechanisms for risk variants associated with complex eye phenotypes

Methods : We performed a detailed characterization of the transcriptome of 23 differentiated low passage primary human fetal RPE (fRPE) lines across two culture conditions (glucose or galactose). We identified genes and pathways modulated by metabolic perturbation using GSEA and GO enrichment. We compared the fRPE gene expression profile to that of 53 GTEx tissues. We performed high-density genotyping and imputation, followed by RASQUAL, LeafCutter and FastQTL analysis to discover shared and condition-specific expression and splicing quantitative trait loci (e/sQTL). We used eCAVIAR to assess co-localization between e/sQTL signals and GWAS data for myopia and AMD. We treated differentiated RPE cells with cycloheximide to assess a role for nonsense-mediated decay (NMD) in the origin of a particular e/sQTL.

Results : We identified 100 protein coding and 30 long non-coding fRPE-selective genes (expression > 4 S.D. from GTEx mean). fRPE-selective genes are enriched for genes related to monogenic ocular diseases. Variants near fRPE-selective genes explain a larger fraction of risk for both AMD and myopia than variants near genes enriched in GTEx tissues. Increased mitochondrial oxidation (galactose condition) promoted fRPE expression of lipid synthesis genes implicated in AMD. We found 726 shared, 272 glucose-specific, and 191 galactose-specific eQTL (FDR < 0.05), including two not previously described in any tissue. We discovered 210 and 193 sQTL for the glucose and galactose conditions, respectively. Variant rs3138141 in an intron of RDH5 is associated with an sQTL and an eQTL in the RDH5 transcript. The minor allele correlates with increased skipping of the adjacent coding exon, NMD of the aberrant transcript, and three-fold lower minor allele-specific expression. The e/sQTL marked by this common variant colocalizes with high statistical significance with GWAS loci for both AMD and myopia, but with opposing directions of effect.

Conclusions : Our study highlights the unique transcriptomic characteristics of fRPE, lays the foundation for connecting e/sQTL in a critical ocular cell type to monogenic and complex eye disorders, and describes a molecular mechanism by which the same common variant of RDH5 contributes to both increased AMD risk and decreased myopia risk.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.