Dataset Information

Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).

ABSTRACT: BACKGROUND The aim of this study was to analyze the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in human retinal tissues following detachment with proliferative vitreoretinopathy (PVR). MATERIAL AND METHODS Expression data of 19 human detached retinas with PVR and 19 normal retinas from postmortem donors were downloaded from Gene Expression Omnibust (GEO) database (GSE28133). The R package "limma" was utilized to discriminate the dysregulated lncRNA and mRNA profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed mRNAs were performed using R packages "Clusterprofiler." The ceRNA network of dysregulated genes was constructed by using mircode, miRDB, miRTarBase and TargetScan databases, and was visualized by Cytoscape v3.6.1. RESULTS A total of 23 lncRNAs and 994 mRNAs were identified significantly expressed between the human detached retinas with PVR and the normal retina tissues, with thresholds of |log?FoldChange| >1.0 and adjusted P-value <0.05. The constructed ceRNA network (lncRNA-miRNA-mRNA regulatory axis) included 9 PVR-specific lncRNAs, as well as 27 miRNAs and 73 mRNAs. CONCLUSIONS We demonstrated the di?erential lncRNA expression profile and constructed a lncRNA-associated ceRNA network in human detached retinas with PVR. This may ferret out an unknown ceRNA regulatory network in human retinal detachment with PVR.

SUBMITTER: Yao K

PROVIDER: S-EPMC7061588 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).

Yao Ke K Yu Yixian Y Zhang Hong H

Medical science monitor : international medical journal of experimental and clinical research 20200227

BACKGROUND The aim of this study was to analyze the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network in human retinal tissues following detachment with proliferative vitreoretinopathy (PVR). MATERIAL AND METHODS Expression data of 19 human detached retinas with PVR and 19 normal retinas from postmortem donors were downloaded from Gene Expression Omnibust (GEO) database (GSE28133). The R package "limma" was utilized to discriminate the dysregulated lncRNA and mRNA ...[more]

PMID: 32103829

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Project description:PurposeTo compare baseline levels of exploratory biomarkers in the vitreous fluid of patients with primary retinal detachment who subsequently develop proliferative vitreoretinopathy (PVR) versus those who do not.MethodsIn this exploratory case-control study, we evaluated the baseline protein biomarker levels from a biobank containing the vitreous fluid of patients who had undergone primary pars plana vitrectomy (PPV) for rhegmatogenous retinal detachment. Undiluted samples were collected at the time of PPV and stored at -80°C. Samples from 13 patients who developed PVR within 6 months (PVR group) and 13 age- and gender-matched controls who did not develop PVR (control group) were included. Protein abundance levels were evaluated using a proximity extension assay, and a confirmatory enzyme-linked immunosorbent assay (ELISA) was used to measure the concentration of vimentin.ResultsBaseline vimentin (Normalized Protein eXpression [NPX], 8.6 vs. 6.4, P < 0.0001) and heme oxygenase 1 (NPX 8.9 vs. 7.0, P < 0.001) levels were found to be elevated in vitreous fluid of patients who subsequently developed PVR compared to those who did not. Confirmatory analysis using ELISA demonstrated mean vimentin concentrations of 7254 vs. 2727 ng/mL in the PVR versus control groups (P = 0.0152). The odds ratio for developing PVR was 14 (confidence interval, 1.4-168; P = 0.03), assuming a baseline vimentin threshold of 7500 ng/mL.ConclusionsVimentin is an intermediate filament protein expressed by retinal glial cells, and our data combined with prior evidence suggest that it may serve as an early vitreous biomarker for subsequent PVR formation and reactive gliosis. Furthermore, we found, for the first time, elevated baseline levels of heme oxygenase 1, a measurable indicator of oxidative stress.Translational relevanceOur positive findings could impact clinical care for retinal detachment patients by facilitating risk stratification for targeted interventions or closer monitoring in those at the highest risk of developing PVR.

Project description:Background: Precise classification has been reported as a central challenge in the clinical research on diagnosis and prediction of treatment efficacy in asthma. In this study, the aim was to investigate the underlying competing endogenous RNA network mechanism of asthma, especially T2 asthma, as well as to find more diagnostic biomarkers and effective therapeutic targets. Methods: Multiple sets of T2 asthma airway biopsy transcription profiles were collected, which involved long non-coding RNA (lncRNA), mRNA, and microRNA (miRNA). DIANA-LncBase, targetscan, mirwalk, and miRDB databases were employed to predict interactions between lncRNAs, miRNAs and target mRNAs. To identify mRNAs correlated with T2 asthma, differential expression and network analyses were conducted through weighted gene co-expression network analysis (WGCNA). Subsequently, the expressions of potential biomarkers were examined through qRT-PCR analysis in the T2 asthma coreinteracting cellular factor (IL-13/IL-33) induced experimental model. Lastly, the ceRNA network was confirmed by plasmid transfection and RNAi experiments in a 16HBE cell line. Results: 30 lncRNAs, 22 miRNAs and 202 mRNAs were differentially expressed in airway biopsies from T2 asthma patients. As indicated by the ROC analysis, the lncRNA, PCAT19, had high diagnostic accuracy (AUC >0.9) in distinguishing T2 asthma patients from non-T2 asthma patients and healthy controls. Furthermore, a competing ceRNA network was established, consisting of 13 lncRNAs, 12 miRNAs, as well as eight mRNAs. The reliability of this network was verified by testing several representative interactions in the network. Conclusion: To the best of our knowledge, this study has been the first to establish an lncRNA-mediated ceRNA regulatory network for studying T2 asthma. The findings of this study may elucidate the pathogenesis and help find potential therapeutic targets for T2 asthma. In T2 asthma, PCAT19-dominated ceRNA regulation networks may play a critical role, and PCAT19 may serve as a potential immune-related biomarker for asthma and other respiratory diseases correlated with eosinophilic inflammation.

Project description:Background:Recurrent retinal detachment (RD) is still a widespread event despite the therapeutic options available. Proliferative vitreoretinopoathy (PVR) is one of the main causes of redetachment. Little is known about the use of endoscopy-assisted vitrectomy (E-PPV) in complex recurrent RD with PVR. The purpose of this study was to identify the potential advantages of E-PPV in complex RD with PVR compared with pars plana vitrectomy (PPV) alone. Methods:Single-center, retrospective, observational, descriptive study. The medical records of 293 patients were reviewed. Patients who underwent PPV for complex rhegmatogenous RD and associated PVR between 2009 and 2017 were included. Patients with diabetic tractional RD, trauma, uveitis or detachment postendophthalmitis were excluded. After 2013, an endoscopic visualization system was used in a nonrandomized fashion at the surgeon's discretion. Outcome measures (reattachment rate, number of surgeries, lens status, PVR stage, intraocular pressure, phthisis rate) were compared between the E-PPV and PPV-only groups with independent samples t-tests (continuous variables) and Fisher's exact test (categorical variables), as well as time-adjusted analyses. Postoperative time to retinal redetachment was assessed with Kaplan-Meier survival analysis. Results:One hundred one eyes from 100 patients met the inclusion criteria. The mean participant age was 63.3 years old (95% CI 60.4-66.1 years), without a significant difference between groups. E-PPV was performed in 36.6% (n?=?37) of eyes, and 63.4% (n?=?64) underwent PPV only. The mean follow-up was significantly longer in the PPV-only group (31.9 vs. 21.1 months; p?=?0.021). Upon adjustment for follow-up duration, the mean number of surgeries was significantly lower in the PPV-only group (2.6 vs. 4.3 number of surgeries; p?<?0.001) than in the E-PPV group. A significantly higher risk for redetachment was observed in the PPV-only group (HR [95% CI] 4.1 [1.4-11.8]) than in the E-PPV group (p?=?0.037). The evolution to phthisis was 7% (n?=?4) in the PPV-only group and 2.7% (n?=?1) in the E-PPV group (p?>?0.05). Conclusions:Compared to PPV alone, endoscopy-assisted vitrectomy seems to be advantageous in achieving better reattachment rates in complex RD with advanced PVR. Endoscopic visualization allows a thorough examination and extensive anterior PVR and vitreous base dissection.

Dataset Information

Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).

Publications

Construction for Long Non-Coding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network in Human Retinal Detachment (RD) with Proliferative Vitreoretinopathy (PVR).

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