RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis

Abstract

The discovery of thousands of non-coding RNAs has revolutionized molecular biology, being implicated in several biological processes and diseases. To clarify oxidative stress role on Retinitis pigmentosa, a very heterogeneous and inherited ocular disorder group characterized by progressive retinal degeneration, we realized a comparative transcriptome analysis of human retinal pigment epithelium cells, comparing two groups, one treated with oxLDL and one untreated, in four time points (1 h, 2 h, 4 h, 6 h). Data analysis foresaw a complex pipeline, starting from CLC Genomics Workbench, STAR and TopHat2/TopHat-Fusion alignment comparisons, followed by transcriptomes assembly and expression quantification. We then filtered out non-coding RNAs and continued the computational analysis roadmap with specific tools and databases for long non-coding RNAs (FEELnc), circular RNAs (CIRCexplorer, UROBORUS, CIRI, KNIFE, CircInteractome) and piwi-interacting RNAs (piRNABank, piRNA Cluster, piRBase, PILFER). Finally, all detected non-coding RNAs underwent pathway analysis by Cytoscape software. Eight-hundred and fifty-four non-coding RNAs, between long non-coding RNAs and PIWI-interacting, were differentially expressed throughout all considered time points, in treated and untreated samples. These non-coding RNAs target host genes involved in several biochemical pathways are related to compromised response to oxidative stress, visual functions, synaptic impairment of retinal neurotransmission, impairment of the interphotoreceptor matrix and blood – retina barrier, all leading to retinal cell death. These data suggest that non-coding RNAs could play a relevant role in Retinitis pigmentosa etiopathogenesis.

Effects of A2E-Induced Oxidative Stress on Retinal Epithelial Cells: New Insights on Differential Gene Response and Retinal Dystrophies

“…If oxidized, they may impair transduction pathways and gene expression [19]. Although fatty acid oxidation was already confirmed to cause macular degeneration, oxidative stress mechanism in RP development requires further clarifications [20]. Therefore, to better understand how high ROS levels may lead to retinal dystrophies onset and progression, we performed a comparison of transcriptomes' profiles among human RPE cells exposed to the oxidant agent N-retinylidene-N-retinylethanolamine (A2E).…”

Retinoprotective Effect of 2-Ethyl-3-hydroxy-6-methylpyridine Nicotinate

“…miRNA expression evaluation of oxidative stress-induced retinal pigment epithelium cells has shown a regulative role of miRNA in retinitis pigmentosa that should lead to the discovery of new ways to influence the etiopathogenesis of this disease [14]. Moreover, a decrease in the activity of detected piRNAs could be explained by the inhibition of silencing activity of miRNA regulation of the DNA damage response and transporter activity of retinal pigment epithelium cells in oxidative stress [15].…”

Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus

“…FEELnc, an alignment-free program that accurately annotates lncRNAs based on a random forest model trained with general features, and BLASTX (McGinnis and Madden, 2004) were used to identify and classify lncRNAs in this study. FEELnc (Wucher et al, 2017) has been shown to achieve similar or better classification performance on GENCODE (Harrow et al, 2012) and NONCODE (Bu et al, 2011) data sets when compared with five programs [PhyloCSF (Lin et al, 2011), CPC (Kong et al, 2007), CPAT (Wang et al, 2013), PLEK (Li et al, 2014), and CNCI (Sun et al, 2013)], and has previously been used to identify lncRNAs (Che et al, 2018; Donato et al, 2018; Wang et al, 2018). In this study, 2,623 novel lncRNAs were identified, of which 1,484 were classified.…”