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J.C. Morrison, E.C. Johnson, L. Jia, W.O. Cepurna, S.L. Barber; Statistical Analysis of Retinal Gene Expression Following Chronic IOP Elevation Using cDNA Microarrays . Invest. Ophthalmol. Vis. Sci. 2005;46(13):1250.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: Understanding specific cellular responses to elevated IOP provides potential opportunities for neuroprotection in glaucoma. This study uses statistical analysis to determine significant changes in gene expression in individual rat retinas exposed to chronically elevated IOP using cDNA microarrays. These results are compared with previously published findings (Ahmed et al IOVS, 2004 45:1247) in this same model using Affymetrix microarrays and pooled samples. Methods: cDNA arrays representing the entire NIA mouse library were used, totaling over 15,000 genes (approximately half the genome). RNA was separately isolated from normal retinas and retinas with advanced optic nerve degeneration produced by 5 weeks of elevated IOP (n=6/group). Each array consisted of an individual RNA sample independently compared to a pooled reference standard, allowing statistical analysis of results. Array data were normalized using intensity–based local regression (BioConductor). Significant differences between groups were determined using Significance Analysis of Microarrays (SAM). Gene ontology websites DAVID and GenMapp were used to identify affected biologic processes. Results: SAM uncovered 476 upregulated and 373 downregulated genes (2% FDR, 1.3–fold change and q<0.02). Limiting results to a 2–fold change yielded 102 up and 24 down genes. Cellular processes with the most significantly regulated genes were transport (39 up and 21 down), DNA–dependent regulation of transcription (24 up and 17 down) and cell adhesion (19 up). Of the 81 genes previously identified as differentially regulated by elevated IOP (Ahmed et al), 33 were present on our cDNA arrays and 27 of these (87%) had statistically significant changes in expression. These included Igfbp3, lipocalin–2 and alpha–2–macroglobulin, the 3 genes with the greatest increase on our cDNA arrays. Among the 99 newly identified genes were two with 5–fold upregulation: Suppressor of cytokine signaling–3 and ADAMTS–1(a metalloproteinase associated with synaptic reorganization) and two with 3–fold downregulation: gamma synuclein (neurofilament network integrity) and Kv4.2 potassium channel (action potential membrane repolarization). Conclusions: These results statistically confirm changes in retinal genes previously reported to be altered by elevated IOP, and identify many more similarly affected new genes. Specific identification of altered cellular processes suggests intriguing possibilities for therapeutic intervention in the retinal responses triggered by chronically elevated IOP.
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