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.

Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy

“…DAVID revealed significant enrichment in Gene Ontology We compared the data on transcriptomic analysis of the retina in 20-dayold animals with the results on 3-and 18-month-old OXYS and Wistar rats described earlier. 16 Retinal expression of 64 genes was significantly different between OXYS and Wistar rats at both 20 d and 3 months of age. These genes participate in the processes regulating DNA repair (Lig4, Mdc1, RTEL1, and Hmg1l1) and metabolic processes related to DNA (Prim1, Lig4, Mdc1, and RTEL1), cell cycle (Cks2, Kif2c, Mdc1, Haus1, and Mapk12), and metabolic processes (n D 24) and catabolic processes associated with lipids (Acadsb, Pla2g2c, and Lipa).…”

“…Therefore, our RNA-Seq results must be reliable. 16 In this study, in addition to gene expression profiles of 20-day-old animals, we used previously obtained RNA-Seq data on differences in gene expression between OXYS and Wistar retinas at ages of 3 and 18 months. According to DAVID, at the age of 20 days, 32 DE genes were found to be associated with apoptosis; of these, 26 were downregulated, and 6 were upregulated.…”

“…Earlier to validate the RNA-Seq data, we performed quantitative RT-PCR for selected genes. 16 Independent agematched groups of animals were used for qPCR validation. RT-PCR confirmed that the chosen genes were significantly down/ upregulated in the OXYS strain.…”

“…[11][12][13][14][15][16] OXYS rats develop retinopathy similar to the dry form of human AMD according to the clinical signs, morphological features, and some molecular changes. In these rats, the clinical signs of retinopathy appear by the age of 3 months during a reduction in the transverse area of the RPE and impairment of choroidal microcirculation.…”

“…Most of them are linked to immune responses, inflammation, the response to oxidative stress, Ca 2C homeostasis, and apoptosis. 16 The main aim of this study was to identify the pathways of retinal cell death involved in the retinopathy initiation and progression. Further research on the gene expression changes involved in the regulation of apoptosis and identification of novel modes of cell death at different stages of the development of retinopathy in OXYS rats (particularly at the early preclinical stage) are expected to advance the understanding of the relevant pathogenesis.…”