Single-cell multiome and enhancer mapping of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of vision loss, with genetic variants contributing to disease susceptibility. To identify functional regulatory variants, we performed allelic-specific STARR-seq under both normal conditions and complement-stimulated environments, mimicking inflammatory stress relevant to AMD pathogenesis. Using a high-throughput screening approach, we systematically assessed the impact of AMD-associated single nucleotide polymorphisms (SNPs) on enhancer activity. Our analysis revealed a subset of SNPs exhibiting differential regulatory effects between normal and stimulated conditions, highlighting context-dependent enhancer modulation. These findings provide insights into the genetic regulation of AMD and potential targets for therapeutic intervention. Overall design: Age-related macular degeneration (AMD) is a leading cause of vision loss worldwide. Genome-wide association studies (GWAS) of AMD have identified dozens of risk loci that may house disease targets. However, variants in these loci are largely noncoding, making it difficult to assess their function and whether they are causal. Here, we present a single-cell gene expression and chromatin accessibility atlas of human retinal pigment epithelium (RPE) and choroid to systematically analyze both coding and noncoding variants implicated in AMD. We employ HiChIP and Activity-by-Contact modeling to map enhancers in these tissues and predict cell and gene targets for risk variants. We further perform allele-specific self-transcribing active regulatory region sequencing (STARR-seq) to functionally test variant activity in RPE cells, including in the context of complement activation. Our work nominates new pathogenic variants and mechanisms in AMD and offers a rich and accessible resource for studying diseases of the RPE and choroid.