Integrative analysis of an lncRNA‑associated competing endogenous RNA network in human trabecular meshwork cells under oxidative stress

RNA-sequencing analysis reveals the long noncoding RNA profile in the mouse myopic retina

Aim: Myopia is a prevalent public health problem. The long noncoding RNA (lncRNA) mechanisms for dysregulated retinal signaling in the myopic eye have remained elusive. The aim of this study was to analyze the expression profiles and possible pathogenic roles of lncRNAs in mouse form-deprived myopia (FDM) retinas. Methods: A mouse FDM model was induced and retinas from the FDM right eyes and the contralateral eyes were collected for RNA sequencing. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and lncRNA-mRNA coexpression network analyses were conducted to explore the biological functions of the differentially expressed lncRNAs. In addition, the levels of differentially expressed lncRNAs in the myopic retinas were validated by quantitative real-time PCR (qRT-PCR). Fluorescence in situ hybridization (FISH) was used to detect the localization of lncRNAs in mouse retinas. Results: FDM eyes exhibited reduced refraction and increased ocular axial length compared to control fellow eyes. RNA sequencing revealed that there were 655 differentially expressed lncRNAs between the FDM and control retinas. Functional enrichment analysis indicated that the differentially expressed RNAs were mostly enriched in cellular processes, cytokine-cytokine receptor interactions, retinol metabolism, and rhythmic processes. Differentially expressed lncRNAs were validated by qRT-PCR. Additionally, RNA FISH showed that XR_384718.4 (Gm35369) localized in the ganglion cell (GCL) and inner nuclear layers (INL). Conclusion: This study identified the differential expression profiles of lncRNAs in myopic mouse retinas. Our results provide scientific evidence for investigations of myopia and the development of putative interventions in the future.

Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Antioxidant Potential of Dietary Lutein in Chickens

Lutein can increase the body's skin color and has antioxidant potential. However, how it affects lipid metabolism and oxidative stress in chickens remains unknown. In this study, 74-day-old male chickens raised on feed supplemented with lutein had higher hip, back, breast, leg, shin and abdominal fat yellowness than the control group, and the livers of chickens in the lutein group had higher superoxide dismutase and glutathione peroxidase and lower malondialdehyde activities. To clarify the potential regulatory network regulated by lutein, we used RNA-seq and nontargeted metabolomics to detect changes in the male chicken liver and plasma, respectively. A total of 243 differentially expressed genes were significantly enriched in cytokine–cytokine receptor interaction signaling pathways, among others. A total of 237 significantly different metabolites were enriched in lysine biosynthesis and degradation and glycerophospholipid metabolism signaling pathways, among others. Finally, we comprehensively analyzed metabolome and transcriptome data and found that many differentially expressed genes and significantly different metabolites play crucial roles in lipid metabolism and oxidative stress. In summary, dietary lutein can improve male chicken skin yellowness and antioxidant indices and affect liver gene expression and plasma metabolites and may help improve the health of chickens.

Identification of Immune Infiltration-Related ceRNAs as Novel Biomarkers for Prognosis of Patients With Primary Open-Angle Glaucoma

Glaucoma is the leading cause of irreversible blindness globally; hence, relevant clinical biomarkers are necessary to enable diagnosis, early detection, and development of novel therapies. The differentially expressed genes were annotated and visualized using Gene Ontology and Kyoto Encyclopedia. In addition, a competitive endogenous ribonucleic acids network was constructed using Cytoscape, which explained the regulation of gene expression in glaucoma. The CIBERSORT algorithm was employed to analyze the immune microenvironment. We validated that the core genes could predict glaucoma occurrence and development and identified potential molecular mechanism pathways, which were associated with immune infiltration and participated in endogenous regulation networks. Our data may partially explain the pathogenesis of glaucoma and they provide potential theoretical support for targeted therapy.

Crosstalk between MicroRNA and Oxidative Stress in Primary Open-Angle Glaucoma

Reactive oxygen species (ROS) plays a key role in the pathogenesis of primary open-angle glaucoma (POAG), a chronic neurodegenerative disease that damages the trabecular meshwork (TM) cells, inducing apoptosis of the retinal ganglion cells (RGC), deteriorating the optic nerve head, and leading to blindness. Aqueous humor (AH) outflow resistance and intraocular pressure (IOP) elevation contribute to disease progression. Nevertheless, despite the existence of pharmacological and surgical treatments, there is room for the development of additional treatment approaches. The following review is aimed at investigating the role of different microRNAs (miRNAs) in the expression of genes and proteins involved in the regulation of inflammatory and degenerative processes, focusing on the delicate balance of synthesis and deposition of extracellular matrix (ECM) regulated by chronic oxidative stress in POAG related tissues. The neutralizing activity of a couple of miRNAs was described, suggesting effective downregulation of pro-inflammatory and pro-fibrotic signaling pathways, including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB), transforming growth factor-beta 2 (TGF-β2), Wnt/β-Catenin, and PI3K/AKT. In addition, with regards to the elevated IOP in many POAG patients due to increased outflow resistance, Collagen type I degradation was stimulated by some miRNAs and prevented ECM deposition in TM cells. Mitochondrial dysfunction as a consequence of oxidative stress was suppressed following exposure to different miRNAs. In contrast, increased oxidative damage by inhibiting the mTOR signaling pathway was described as part of the action of selected miRNAs. Summarizing, specific miRNAs may be promising therapeutic targets for lowering or preventing oxidative stress injury in POAG patients.