a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.
b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy.
Cell Cycle. 2019 Jan;18(1):84-104. doi: 10.1080/15384101.2018.1558873. Epub 2018 Dec 28.
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 Proton 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.
色素性视网膜炎（RP）是一种非常异质性的遗传性眼病，其特征是进行性视网膜破坏。视网膜色素上皮（RPE）退化是由于氧化应激导致对光感受器的代谢支持停止，这是 RP 的主要原因之一。在这里，通过对用 100μg/ml oxLDL 处理和未处理的人 RPE 细胞在不同时间点进行的全转录组比较分析，研究了氧化应激在 RP 发病和进展中的作用。该实验重复了三次，在 Ion Proton 测序系统上进行。数据分析包括低质量读数修剪和基因表达定量，使用 CLC Genomics Workbench 软件实现。整个分析突出了 14 个聚类的“宏途径”和许多亚途径，这些途径是通过选择表达变化最大的 5271 个基因来分类的。其中，23 个基因已被确认为 RP 致病基因（15 个过表达，8 个下调），其富集和交集分析突出了 77 个新的候选相关基因（49 个过表达，28 个下调）。然后进行了最终的过滤分析，突出了 29 个候选基因。这些数据表明，许多尚未与 RP 相关的新基因可能会影响其发病机制。
