Gene expression microarray analysis of early oxygen-induced retinopathy in the rat

Abstract

Different inbred strains of rat differ in their susceptibility to oxygen-induced retinopathy (OIR), an animal model of human retinopathy of prematurity. We examined gene expression in Sprague-Dawley (susceptible) and Fischer 344 (resistant) neonatal rats after 3 days exposure to cyclic hyperoxia or room air, using Affymetrix rat Genearrays. False discovery rate analysis was used to identify differentially regulated genes. Such genes were then ranked by fold change and submitted to the online database, DAVID. The Sprague-Dawley list returned the term "response to hypoxia," absent from the Fischer 344 output. Manual analysis indicated that many genes known to be upregulated by hypoxia-inducible factor-1alpha were downregulated by cyclic hyperoxia. Quantitative real-time RT-PCR analysis of Egln3, Bnip3, Slc16a3, and Hk2 confirmed the microarray results. We conclude that combined methodologies are required for adequate dissection of the pathophysiology of strain susceptibility to OIR in the rat. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12177-009-9041-7) contains supplementary material, which is available to authorized users.

Fig. 1

Montages of representative sectors of retinae of room air-exposed and cyclic hyperoxia-exposed rats collected at post-natal day 3 and stained with fluorochrome-conjugated GS-IB4 to highlight the vasculature. a F344 rat raised in room air; b F344 rat exposed to cyclic hyperoxia from birth; c SD rat raised in room air; d SD rat exposed to cyclic hyperoxia from birth

Fig. 2

RT-PCR quantification of retinal gene expression in cyclic hyperoxia-treated and untreated F344 and SD rats at post-natal day 3. a Egln3; b Bnip3; c Slc16a3; d Hk2. Quantification was performed on RNA pools identical to those used in the microarray analysis. Expression levels were normalized to the reference genes Arbp and Hprt. Numbers above the bars are fold inhibition by hyperoxia. Error bars ± standard deviation. *p < 0.05