Gene Expression Profiling of Normal and Degenerated Mouse Retina Using a Custom Retina cDNA Microarray

Abstract

Abstract: : Purpose: To better understand the mechanisms of retinal degeneration by comparing the gene expression profiles of normal and degenerating rd1/rd1 retina. Methods: RNA was extracted from rd1 and wild-type retinas at post-natal day 14, 35 and 50, then reverse transcribed, labeled with cy3 or cy5 dyes, and hybridized to custom mouse retina 5,376 gene cDNA microarrays. Each gene was spotted twice on the array and the hybridizations included a dye-swap. Comparisons were made to age-matched wild-type retinas using a common reference sample. Statistical analyses were performed using SAM (Significance Analysis of Microarrays) and Genesight software, and expression changes of selected genes were confirmed by real-time PCR. Results: The arrays include mouse genes with roles in normal retinal function, development and degeneration, and genes implicated in retinal disease. Array analysis of p14 retinas (peak of rod degeneration), p35 (post-rod and early cone degeneration) and p50 (during cone degeneration) demonstrated that approximately 3% of genes on the array were differentially expressed at least two-fold at each time-point. These included genes known to be involved in cell death as well as many genes not previously implicated in degeneration. We identified a large group of genes that were changed at all three degenerative stages, and others that were unique to each stage. Genes expressed in rods, such as opsin and phosducin, were significantly decreased at all time-points. As expected, later time-points had greater decreases in these genes. However, there was less overlap in the genes that were upregulated at each stage of degeneration, suggesting the involvement of distinct molecular pathways. ESTs and genes of unknown function were also identified as differentially expressed, representing interesting candidates for further study. Conclusions: We have compared the expression of over 5,300 genes using a custom retina microarray, and have identified patterns of gene expression changes in the degenerating and normal mouse retina. These results provide clues to underlying molecular processes occurring during photoreceptor degeneration, and provide direction for future in vivo studies.

Keywords: retinal degenerations: cell biology • animal model • gene microarray