Abstract
Purpose :
Changes in gene expression with age in retinal pigment epithelium (RPE) may drive the development of age-related macular degeneration (AMD). One possible mechanism to explain gene expression changes and corresponding RPE dysfunction relates to post-transcriptional modifications of messenger RNA (mRNA) in the RPE. RNA editing (adenosine-to-inosine [A-to-I] conversion) by ADAR family enzymes can both modify protein sequences, and limit the immunogenicity of double-stranded RNAs. This study characterised age-related changes in A-to-I RNA editing in the murine RPE-choroidal transcriptome.
Methods :
RNA was extracted from RPE-choroidal tissues of C57BL/6J mice (N=6 per group) at 3 and 22 months old of age. RNA-seq was performed using the Illumina NovaSeq 6000 System. A-to-I editing candidate sites were identified using JACUSA software and the REDIportal database. Differential gene expression and Gene Ontology overrepresentation analyses were performed using EdgeR and clusterProfiler R packages respectively.
Results :
We identified 593 unique A-to-I RNA editing sites present in at least four RPE-choroidal samples. Approximately 93% of the edited sites (N=551) resided within protein-coding transcripts, with most (N=413) located within the 3’ untranslated region. Differential RNA editing analysis between the young and aged RPE-choroidal transcriptome, identified 18 protein-coding sites with significant changes in RNA editing activity during ageing. Of those, 15 showed significantly enriched A-to-I editing in the aged RPE-choroidal samples (Welch’s t-test, P<0.05). This age-dependent increase in A-to-I editing was accompanied by increased expression of genes that encode mRNA modifying enzymes, such as Adarb1 which is important for A-to-I editing (false discovery rate, FDR<0.05). Nine of the significantly edited sites were detected in eight genes, which showed significant expression changes in the aged RPE-choroid (FDR<0.05). These significantly edited and dysregulated genes included three AMD-associated genes: Rdh5 and Rgr visual cycle genes; and Gpnmb, a regulator of inflammation.
Conclusions :
An age-related increase in A-to-I RNA editing was found in RPE-choroidal genes. The enriched A-to-I editing in the inflammatory Gpnmb gene and the vision-related Rdh5 and Rgr genes may result in RPE-choroidal gene dysregulation during ageing, ultimately contributing to RPE dysfunction in AMD.
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.