Rat retinal transcriptome: effects of aging and AMD-like retinopathy

Abstract

Pathogenesis of age-related macular degeneration (AMD), the leading cause of vision loss in the elderly, remains poorly understood due to the paucity of animal models that fully replicate the human disease. Recently, we showed that senescence-accelerated OXYS rats develop a retinopathy similar to human AMD. To identify alterations in response to normal aging and progression of AMD-like retinopathy, we compared gene expression profiles of retina from 3- and 18-mo-old OXYS and control Wistar rats by means of high-throughput RNA sequencing (RNA-Seq). We identified 160 and 146 age-regulated genes in Wistar and OXYS retinas, respectively. The majority of them are related to the immune system and extracellular matrix turnover. Only 24 age-regulated genes were common for the two strains, suggestive of different rates and mechanisms of aging. Over 600 genes showed significant differences in expression between the two strains. These genes are involved in disease-associated pathways such as immune response, inflammation, apoptosis, Ca ( 2+) homeostasis and oxidative stress. The altered expression for selected genes was confirmed by qRT-PCR analysis. To our knowledge, this study represents the first analysis of retinal transcriptome from young and old rats with biologic replicates generated by RNA-Seq technology. We can conclude that the development of AMD-like retinopathy in OXYS rats is associated with an imbalance in immune and inflammatory responses. Aging alters the expression profile of numerous genes in the retina, and the genetic background of OXYS rats has a profound impact on the development of AMD-like retinopathy.

Keywords: OXYS rats; RNA-Seq; age-related macular degeneration; aging; retinal transcriptome.

Figure 1. Principal component analysis (PCA) of RNA-Seq samples without prior statistical filtering. PC1 and PC2 scores for 5,000 most variably expressed genes were visualized. Different experimental groups tend to cluster together upon PCA, reflecting strain (PC1) and age (PC2) differences.

Figure 2. qRT-PCR validation of RNA-Seq results. Comparison of fold change (log2 scale) in differential expression values determined by RNA-Seq (white) and qPCR (black) for DEGs.

Figure 3. The most representative enriched gene ontology categories for differentially expressed genes in retinas: (A) between 3-mo-old OXYS and Wistar rats; (B) between 18-mo-old OXYS and Wistar rats; (C) between 3-mo and 18-mo-old Wistar rats; D. between 3-mo and 18-mo-old OXYS rats.