Abstract
Purpose :
Many animal studies of retinitis pigmentosa (RP) focus on pathologies during retinal degeneration. However, in the rd1 mouse model, mutant gene Pde6b was expressed at embryonic day 12(E12), well in advance of the onset of degeneration. This suggests other disease mechanisms might exist during retinal developmental stage. Using RNA-seq technology in combination with robust downstream analysis software, we conducted a transcriptome analysis of gene expression in postnatal day 4 (P4) rd1 mouse retina, aiming to discover novel pathogenesis during early retinal development.
Methods :
Using RNA seq data from retinal samples harvested from wild type (wt) and rd1 retinas at P4, Kallisto and Sleuth pipeline was applied to perform transcript level quantification and differential expression analysis. Reactome and KEGG were used to conduct enrichment analysis on significant gene sets. Quantitative real time PCR (qRT-PCR) was used for verification of gene expression.
Results :
Sample heatmap generated by Sleuth shows low divergence between replicate groups. Over-representation analysis by Reactome shows gene enrichment in a diverse range of biological processes such as metabolism, signal transduction, cell cycle, DNA repair and neuronal system. More specifically, KEGG pathway mapper results show enrichment in cancer and multiple neurodegeneration pathways, which bring multiple signaling, metabolic and cell cycle processes together. qRT-PCR was used to validate the candidate genes in these pathways.
Conclusions :
Our results show gene dysregulation in various biological processes during early postnatal development of the rd1 retina. KEGG mapper provides possible cause and effect relationships to these different events. Together they may shed light on the cascade of events that ultimately leads to retinal degeneration in RP.
This is a 2020 ARVO Annual Meeting abstract.