Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis.
Luigi DonatoConcetta ScimoneGiacomo NicociaRosalia D'AngeloAntonina SidotiPublished in: Cell cycle (Georgetown, Tex.) (2018)
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
Keyphrases
- oxidative stress
- rna seq
- single cell
- data analysis
- gene expression
- induced apoptosis
- genome wide
- multiple sclerosis
- dna damage
- dna methylation
- ischemia reperfusion injury
- poor prognosis
- diabetic rats
- optical coherence tomography
- deep learning
- quality improvement
- long non coding rna
- binding protein
- cardiac arrest
- endoplasmic reticulum stress
- bioinformatics analysis
- artificial intelligence
- newly diagnosed