A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration

• Published in: Cell genomics Vol. 3; no. 6; p. 100302
• Main Authors: Orozco, Luz D., Owen, Leah A., Hofmann, Jeffrey, Stockwell, Amy D., Tao, Jianhua, Haller, Susan, Mukundan, Vineeth T., Clarke, Christine, Lund, Jessica, Sridhar, Akshayalakshmi, Mayba, Oleg, Barr, Julie L., Zavala, Rylee A., Graves, Elijah C., Zhang, Charles, Husami, Nadine, Finley, Robert, Au, Elizabeth, Lillvis, John H., Farkas, Michael H., Shakoor, Akbar, Sherva, Richard, Kim, Ivana K., Kaminker, Joshua S., Townsend, Michael J., Farrer, Lindsay A., Yaspan, Brian L., Chen, Hsu-Hsin, DeAngelis, Margaret M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 14.06.2023; Elsevier
• Subjects: age-related macular degeneration; AMD; DNA methylation; epigenomics; geographic atrophy; Muller glia; rare variant genetics; Resource; retinal pigment epithelium; RNA-seq; single-cell ATAC-seq; single-cell RNA-seq; Muller glia; single-cell ATAC-seq; geographic atrophy; RNA-seq; AMD; DNA methylation; epigenomics; single-cell RNA-seq; GA; retinal pigment epithelium; age-related macular degeneration; rare variant genetics
• ISSN: 2666-979X; 2666-979X
• DOI: 10.1016/j.xgen.2023.100302

Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease. [Display omitted] •Bulk transcriptome and DNA methylation from RPE/choroid of phenotyped AMD eyes•Single-nucleus RNA-seq and ATAC-seq from retina, RPE, and choroid of control and AMD eyes•Single-nucleus RNA-seq and ATAC-seq prioritized putative causal genes at AMD GWAS loci•Integrative analysis identified WNT pathway regulators FRZB and TLE2 as AMD genes There is limited information on molecular changes in age-related macular degeneration (AMD), a leading cause of blindness. Orozco et al. built expression and epigenetic atlases of control and phenotyped AMD eyes at both bulk-tissue and single-cell levels. Their integrative analysis of these data unveiled genes and pathways driving disease.