Genetic regulation of splicing in human retina highlights the visual cycle as an emerging pathway in age-related macular degeneration (AMD)

Abstract

Purpose : Molecular mechanisms and cellular pathways underlying AMD, a leading cause of central vision loss in the elderly, are still poorly understood. We asked if genetic variants that alter splicing in the retina underlie causal mechanisms at known AMD genome-wide association study (GWAS) loci and contribute to the missing heritability of AMD and broadly in retinal diseases.

Methods : We analyzed RNA-seq of 403 peripheral retina (peri) and 185 macula (mac) samples from postmortem healthy and AMD eyes and imputed the donor’s genotype data to GTEx v8 whole genome sequencing variant calls. LeafCutter was used to quantify alternative splicing (AS) events (intron excision ratios) based on exon-exon splice junction reads. Using FastQTL, we tested for association of common variants in cis (±1Mb) with splicing events (splicing quantitative trait loci, sQTLs) in all genes, adjusting for sex, age, AMD grade, top 10 genotype PCs and inferred covariates (PEERs). We applied colocalization (eCAVIAR) and summary data-based Mendelian randomization (SMR) analyses to identify retina sQTLs that may be causal to 34 AMD loci. We further tested whether retina sQTLs were enriched for new AMD associations beyond genome-wide significance (QTLEnrich).

Results : Significant sQTLs (FDR<0.05) were identified for 1,390 and 2,850 genes (sGenes) in mac and peri respectively, 24% of which were retina-specific when compared to 49 GTEx tissues. Target genes of the mac and peri sQTLs were enriched in phototransduction, retina homeostasis and immune processes (FDR<0.05). We detected significant colocalization of retina sQTLs with 4 AMD loci, including a mac sQTL acting on BLOC1S1-RDH5, supported by SMR. SMR proposed additional 9 sQTLs acting on 7 genes for 6 AMD loci (Bonferroni P<0.05), including PDE6G and DXO sQTLs that are mac-specific. Notably the mac and peri sQTLs were enriched for known and subthreshold AMD associations (QTLenrich,P<1E-05), proposing ~80 new AMD associations, whose sQTL target genes were enriched in sensory perception of light stimulus and complement cascade processes (FDR<0.07), and 13 inherited retinal degeneration genes (P=2E-04) clustering in visual perception.

Conclusions : Our study suggests that regulation of splicing may play an important role in AMD susceptibility and proposes a link between AS of Mendelian disease genes and AMD affecting the visual cycle in retina.

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.