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Charles Zhang, Leah A Owen, John Lillvis, Brian Madow, Akbar Shakoor, Albert T Vitale, Tamim Shaikh, Neena B Haider, Michael Farkas, Lindsay Farrer, Ivana K Kim, Margaret M DeAngelis; Patterns of gene expression vary among macular tissues and clinical stages of Age-related Macular Degeneration. Invest. Ophthalmol. Vis. Sci. 2022;63(7):0004.
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© ARVO (1962-2015); The Authors (2016-present)
Gene expression varies among individuals and between tissues in the same person. Gene expression analyses in disease-affected tissues can help ascribe function to previously associated disease susceptibility variants in complex disorders such as age-related macular degeneration (AMD). We aimed to uncover patterns of differential gene expression between different disease stages to uncover the pathogenesis of AMD.
Utilizing well-characterized fresh human donor tissue from rapidly autopsied eyes, phenotyped and dissected according to a standardized protocol; the macula of the neural retina and separately the macula of the RPE/choroid. Analysis was performed on 27 donors (12 normals, 10 intermediate AMD and 5 neovascular AMD) that underwent poly A tail RNA-sequencing to identify differentially expressed genes (DEG) between the AMD subtypes.
Following principal component analysis, DESeq2 pipeline analysis and correction with Benjamini -Hochberg, significant DEG within the macular RPE/choroid tissues was observed for 40 genes between intermediate AMD and normal eyes, 1,204 genes between neovascular AMD and normal eyes, and 1,194 genes between intermediate and neovascular AMD. Within the macular neural retina, 30, 41, and 50 genes were differentially expressed when comparing the same respective groups. Among genes associated with AMD from prior GWAS and candidate gene studies, expression was significantly higher for ABCA4, ABCA7, RORA and VTN in neovascular AMD versus normal macular RPE/choroid tissue; significantly lower for ABCA4, ABCA7, SPEF2 and significantly higher for TNFRSF10B and TRPM1 in intermediate versus neovascular AMD macular RPE/choroid. There was no overlap between significant DEG and tissue type. 16 pathways in the GSEA Hallmark collection were significantly enriched; 14 unique to the comparison of intermediate with normal eyes and 10 of those specific to the RPE/choroid tissue.
Our analysis demonstrates differential patterns of gene expression between AMD phenotypes in macula retina and RPE/choroid tissue with the later demonstrating greater variability underscoring the importance of assessing expression in a cell-type specific manner. Several genes and pathways were differentially expressed between phenotypes suggesting that clinical AMD may represent a spectrum of molecular pathophysiology.
This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.
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