Whole genome sequencing for rare variants and imaging analyses in model organisms identify SLC16A8 as a significant contributor for AMD risk

Abstract

Purpose : Polygenic predisposition to advanced age-related macular degeneration (AMD) enables strategies to define the complex pathogenesis of this disease. We combined human genetics and in vivo functional studies in Drosophila melanogaster to identify novel pathways implicated in AMD pathogenesis.

Methods : Whole genome sequencing (WGS) and subsequent rare variant (RV) burden test analyses were performed for 6055 advanced AMD cases and 8294 non-AMD diseased controls. We extracted rare exonic SNPs (minor allele frequency <1%) predicted to alter amino acids or affect functionality of the protein. Since comparison cohorts were comprised of non-AMD clinical trial patients, a reverse regression with a Bayesian spike and slab prior was used to remove non-AMD specific associations. For functional characterization of candidate genes at association signals, we performed RNAi screens using Drosophila models. The impact of whole eye knockdowns of orthologous genes of interest on photoreceptor survival was assessed using deep pseudopupil (DPP) and optic neutralization of cornea imaging approaches that follow ommatidial morphology.

Results : WGS for RV burden tests pinpointed multiple genes, including the top hits CFI (P=3.13E-14; OR=4.57), CFH (P=2.14E-06; OR=2.05), and SLC16A8 (P=1.50E-05; OR=1.78), all from loci previously associated with AMD (Table 1). We focused functional analysis on the proton-coupled monocarboxylate transporter SLC16A8 (solute carrier family 16 member 8) which is expressed only in the retinal pigment epithelia of humans and also rodents. Knockdown of the Drosophila ortholog sln (silnoon) led to progressive loss of retinal homeostasis in the adult fly, as visualized by changes in photoreceptor EGFP expression patterns at day 14 (95% mean loss of DPP), but not by day 1, 7, or in comparison to negative controls (n=10 for each line and timepoint; reproduced in two separate assays).

Conclusions : An unbiased, genome-wide analysis of rare coding variants provided additional support of a causal role for SLC16A8 in protection against AMD when functional. We demonstrate that deletion of the Drosophila ortholog sln disrupts retinal homeostasis, and highlight a potential therapeutic opportunity for the treatment of AMD.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.

 

Table 1. Human genes associated with AMD (P < 5.0E-04) by RV burden tests.