Abstract
Purpose: :
RNR (Retina–specific Nuclear Receptor, Nr2e3) is a photoreceptor–specific nuclear receptor identified at Merck in 1999 in an effort to identify nuclear receptors important in retinal disease. Data from Rnr mutant mice [mice with a targeted deletion of Rnr as well as rd7 mice with a sporadic hypomorphic/null mutation of RNR] and human patients with mutations in the RNR gene provide evidence for RNR’s having a role in both photoreceptor differentiation and maintenance. We have performed expression profiling in order to elucidate RNR’s role in the developing and adult retina and to identify its direct targets.
Methods: :
RNA was isolated from retinas of postnatal day (p)2, p6, p10, p14, p30, and p180 Rnr KO, rd7, and wild–type C57BL/6 mice. Expression profiling of six individual samples for each group relative to a pool of wild–type samples of the same age was performed utilizing a 2–color method. Following amplification and labeling, samples were hybridized to 60–mer oligonucleotide microarrays (Agilent). Genes differentially expressed between wild–type and Rnr mutant mice were identified based on ANOVA models. The genes were used for principal component analysis to study changes in expression profiles over time.
Results: :
We used molecular profiling of Rnr KO and rd7 retinas to identify putative RNR–dependent genes. Principal component analysis identified two distinct temporal phases of gene expression during retinal degeneration caused by the lack of RNR function. The phases are defined by a group of genes which develop transient differences in expression between wild–type and Rnr mutant retinas. These differences develop until approximately P10, after which they gradually decrease and disappear. The presence of two phases may indicate two distinct roles for RNR in photoreceptor development and maintenance. We utilized Ingenuity Pathways Analysis to identify the pathways and functional categories associated with these genes in regard to either the development or maintenance of photoreceptors.
Conclusions: :
The presence of two phases of RNR–dependent gene expression revealed by principal component analysis is consistent with RNR’s having a dual role in photoreceptor development as well as photoreceptor maintenance in the adult retina. Identification of downstream target genes will shed light on the pathways activated by RNR and will be useful in the determination of potential new targets for retinal degeneration.
Keywords: gene microarray • photoreceptors • transgenics/knock-outs