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S. Scott Whitmore, Terry A. Braun, Todd E. Scheetz, Aditi Khanna, Louisa M. Affatigato, Edwin M. Stone, Robert F. Mullins; ARMS2 A69S Associated Alternative Splicing and Differential Gene Expression in Human RPE/Choroid. Invest. Ophthalmol. Vis. Sci. 2012;53(14):6501.
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© ARVO (1962-2015); The Authors (2016-present)
Age-related macular degeneration (AMD) is the leading cause of irreversible blindness among elderly populations in industrial countries. Variations in numerous genes have been associated with AMD, including a locus on chromosome 10 that includes ARMS2. The molecular consequences of these variants in human eyes are poorly understood. In this study, we investigated the impact of the ARMS2 A69S risk allele on alternative splicing and differential gene expression in the human RPE/choroid.
Human donor eyes were obtained and ARMS2 genotype was determined using a Taqman assay. RNA was extracted from the RPE/choroid layer of eyes with different genotypes. Exon expression levels were assessed using Affymetrix GeneChip Human Exon 1.0 ST Arrays. Data processing was performed using Affymetrix Power Tools, Partek Genomics Suite, and DAVID (http://david.abcc.ncifcrf.gov). Alternative splicing and differential gene expression were evaluated for AA (n=3) and AS/SS (n=6) genotypes by ANOVA.
We identified 44 genes upregulated and 9 genes downregulated when groups were segregated based on the A69S allele (20% up or down, p < 0.001). Upregulated genes included CD59 (30% up, p = 0.00035), TLR3 (44% up, p = 0.00053), FBLN5 (27% up, p = 0.00054), PDGFA (33% up, p = 0.00071), and ITGA9 (27% up, p = 0.00095). Eighty six genes showed evidence of alternative splicing with p < 1.0e-10. This group included PECAM1 (p = 2.29E-19), COL1A2 (p = 4.35E-18), HLA-E (p = 1.09E-16), CFH (p = 2.58E-16), COL12A1 (p = 3.18E-15), ITGBL1 (p = 7.60E-15), CD59 (p = 1.71E-12), LRP1 (1.97E-11), and IGF2R (2.96E-11). DAVID revealed gene clusters associated with cell adhesion, conserved EGF-like regions, and extracellular matrix.
Several genes previously associated with AMD are impacted by the presence of the ARMS2 A69S risk allele. Notably, genes involved in cell adhesion and extracellular matrix show alternative splicing or differential regulation. These results suggest novel potential roles for how the 10q locus affects risk of AMD.
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