Differentially expressed circular RNAs and the competing endogenous RNA network associated with preeclampsia

Placenta ◽  
2021 ◽  
Vol 103 ◽  
pp. 232-241
Author(s):  
Bo Ma ◽  
Huanqiang Zhao ◽  
Lili Gong ◽  
Xirong Xiao ◽  
Qiongjie Zhou ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Circular Rnas ◽  
Competing Endogenous Rna ◽  
Competing Endogenous Rna Network

scholarly journals Identification of Non-coding RNA Biomarkers in Stress-induced Depression via Comprehensive Analysis of Competing Endogenous RNA Network

2020 ◽  
Author(s):  
xuanjun liu ◽  
Lan Yan ◽  
Chun Lin ◽  
Yiliang Zhang ◽  
Haofei Miao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Psychiatric Disease ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Competing Endogenous Rna ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Promising Perspective

Abstract BackgroundDepression is one of the most common psychiatric disease worldwide. Although the research about the pathogenesis of depression have achieved progress, the detailed effect of non-coding RNAs (ncRNAs) in depression are still not clearly elucidated. This study was aimed to identify non-coding RNA biomarkers in stress-induced depression via comprehensive analysis of competing endogenous RNA networkMethodsIn this present study, we acquired RNA expression from RNA seq expression profile in three mice with depressive-like behaviors using chronic restraint stress paradigm and three C57BL/6J wild-type mice as control mice. ResultsA total of 41 differentially expressed circular RNAs (circRNAs) and 181 differentially expressed messenger RNAs (mRNAs) were up-regulated, and 65 differentially expressed circRNAs and 289 differentially expressed mRNAs were down-regulated, which were selected by a threshold of fold change ≥2 and a p-value < 0.05. Gene Ontology was performed to analyze the biological functions, and we predicted potential signaling pathways based on Kyoto Encyclopedia of Genes and Genomes pathway database. In addition, we constructed a circRNA-microRNA (miRNA)-mRNA regulatory network to further identify non-coding RNAs biomarkers. ConclusionsOur findings provide a promising perspective for further research into molecular mechanisms of depression, and targeting circRNA -mediated competing endogenous RNA (ceRNA) network is a useful strategy to early recognize the depression.

scholarly journals Identification of lncRNA and mRNA Biomarkers in Osteoarthritic Degenerative Meniscus by Weighted Gene Coexpression Network and Competing Endogenous RNA Network Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Jun Zhao ◽  
Yu Su ◽  
Jianfei Jiao ◽  
Zhengchun Wang ◽  
Xiangchun Fang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Roc Curve ◽  
Diagnostic Value ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Coexpression Network ◽  
Competing Endogenous Rna ◽  
Roc Curve Analysis ◽  
Competing Endogenous Rna Network ◽  
Meniscus Degeneration

Background. Long noncoding RNAs (lncRNAs) play a crucial role in varieties of biological processes. This study is aimed at investigating meniscal degeneration-specific lncRNAs and mRNAs and their related networks in knee osteoarthritis (KOA). Methods. The dataset GSE98918, which included 24 meniscus samples and related clinical data, was downloaded from the Gene Expression Omnibus database. The differentially expressed lncRNAs and mRNAs in the meniscus between KOA and control groups were identified. Based on the enriched differentially expressed lncRNAs and mRNAs, we constructed the coexpression network using WGCNA (weighted correlation network analysis) and identified the critical module related to KOA. For mRNAs in the key module, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were carried out using the DAVID database. A competing endogenous RNA network (ceRNA) based on the screened mRNAs, lncRNAs, and related miRNAs was constructed to reveal presumptive biomarkers further. Finally, the hub lncRNAs and mRNAs were screened, and the diagnostic value was evaluated using a receiver operating characteristic (ROC) curve. Hub mRNAs were validated using the dataset GSE113825. Results. We screened 208 significantly differentially expressed lncRNAs and mRNAs in menisci between the KOA and non-KOA samples, which were enriched in sixteen modules using WGCNA, especially the green module. Coexpression network based on the enriched differentially expressed lncRNAs and mRNAs in the green module uncovered 5 lncRNAs and 56 mRNAs. The lncRNA-miRNA-mRNA ceRNA network revealed that lnc-HLA-DQA1-5, lnc-RP11-127H5.1.1-1, lnc-RTN2-1, IGFBP4 (insulin-like growth factor binding protein 4), and KLF2 (Kruppel-like factor 2) were significantly correlated with the meniscus degeneration of KOA. ROC curve analysis revealed that these hub lncRNAs and mRNAs showed excellent diagnostic value for KOA. Conclusions. These hub lncRNAs and mRNAs were potential prognostic biomarkers for the meniscus degeneration of KOA. Further studies are required to validate these new biomarkers and better understand the pathological process of the meniscus degeneration of KOA.

scholarly journals Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yifang Liao ◽  
Ping Li ◽  
Yanxia Wang ◽  
Hong Chen ◽  
Shangwei Ning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Repositioning ◽  
New Drugs ◽  
Differentially Expressed ◽  
Interaction Data ◽  
Competing Endogenous Rna ◽  
Non Coding Rna ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

Abstract Background Asthma is a heterogeneous disease characterized by chronic airway inflammation. Long non-coding RNA can act as competing endogenous RNA to mRNA, and play significant role in many diseases. However, there is little known about the profiles of long non-coding RNA and the long non-coding RNA related competing endogenous RNA network in asthma. In current study, we aimed to explore the long non-coding RNA-microRNA-mRNA competing endogenous RNA network in asthma and their potential implications for therapy and prognosis. Methods Asthma-related gene expression profiles were downloaded from the Gene Expression Omnibus database, re-annotated with these genes and identified for asthma-associated differentially expressed mRNAs and long non-coding RNAs. The long non-coding RNA-miRNA interaction data and mRNA-miRNA interaction data were downloaded using the starBase database to construct a long non-coding RNA-miRNA-mRNA global competing endogenous RNA network and extract asthma-related differentially expressed competing endogenous RNA network. Finally, functional enrichment analysis and drug repositioning of asthma-associated differentially expressed competing endogenous RNA networks were performed to further identify key long non-coding RNAs and potential therapeutics associated with asthma. Results This study constructed an asthma-associated competing endogenous RNA network, determined 5 key long non-coding RNAs (MALAT1, MIR17HG, CASC2, MAGI2-AS3, DAPK1-IT1) and identified 8 potential new drugs (Tamoxifen, Ruxolitinib, Tretinoin, Quercetin, Dasatinib, Levocarnitine, Niflumic Acid, Glyburide). Conclusions The results suggested that long non-coding RNA played an important role in asthma, and these novel long non-coding RNAs could be potential therapeutic target and prognostic biomarkers. At the same time, potential new drugs for asthma treatment have been discovered through drug repositioning techniques, providing a new direction for the treatment of asthma.

scholarly journals Genome-wide characterization of coding and non-coding RNAs in the ovary of honeybee workers and queens

Apidologie ◽  
2020 ◽  
Vol 51 (5) ◽  
pp. 777-792
Author(s):  
Xiao Chen ◽  
Wei Shi
Keyword(s):  
Egg Laying ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Competing Endogenous Rna ◽  
Genome Wide ◽  
Competing Endogenous Rna Network ◽  
Non Coding Rnas ◽  
Virgin Queens ◽  
Potential Interactions

Abstract Adult honeybee queens and workers drastically differ in ovary state and ovary size. However, this reproductive bias is only partially understood from the view of a single RNA type. In this study, we predicted 10,271 mRNAs, 7235 lncRNAs, 11,794 circRNAs, and 164 miRNAs in the ovary of honeybee workers through bioinformatics. Combining RNA sequencing data of honeybee virgin queens, 4385 mRNAs, 2390 lncRNAs, 5602 circRNAs, and 75 miRNAs were differentially expressed in workers compared with virgins. Compared with egg-laying queens, 6536 mRNAs, 3130 lncRNAs, 5751 circRNAs, and 81 miRNAs were differentially expressed in workers. Further, functional annotation revealed that neural regulation was closely related to ovary state. Moreover, the potential interactions among circRNAs, miRNAs, lncRNAs, and mRNAs revealed that vitellogenin, ecdysone-induced protein 74, ame_circ_0001176, and ame_circ_0001243 might play critical roles in the competing endogenous RNA network. These findings suggest that the integrative RNA networks have potential effects in ovarian phenotype differences in honeybees.

scholarly journals Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells

2020 ◽  
Vol 10 ◽  
Author(s):  
Liang Gao ◽  
Kunwei Shen ◽  
Ni Yin ◽  
Min Jiang
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Endocrine Therapy ◽  
Breast Cancer Cells ◽  
Regulatory Networks ◽  
Endocrine Resistance ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Competing Endogenous Rna ◽  
Non Coding Rnas

BackgroundTamoxifen and fulvestrant, both approved for endocrine therapy, have remarkably increased the prognosis of hormone receptor-positive breast cancer patients. However, acquired resistance to endocrine therapy greatly reduces its clinical efficacy. Accumulating evidence suggests a pivotal role of non-coding RNAs (ncRNAs) in breast cancer endocrine resistance, but the specific functions of ncRNAs in tamoxifen and fulvestrant resistance remain largely unknown.MethodsMicroarray analysis was performed for endocrine therapy sensitive (MCF-7), tamoxifen-resistant (LCC2), and dual tamoxifen and fulvestrant-resistant (LCC9) breast cancer cells. Gene ontology and pathway analysis were conducted for functional prediction of the unannotated differentially expressed ncRNAs. Competing endogenous RNA regulatory networks were constructed.ResultsWe discovered a total of 3,129 long non-coding RNAs (lncRNAs), 13,556 circular RNAs (circRNAs), 132 microRNAs, and 3358 mRNAs that were significantly differentially expressed. We constructed co-expression networks for lncRNA-mRNA, circRNA-mRNA, and microRNA-mRNA. In addition, we established lncRNA-microRNA-mRNA and circRNA-microRNA-mRNA regulatory networks to depict ncRNA crosstalk and transcriptomic regulation of endocrine resistance.ConclusionsOur study delineates a comprehensive profiling of ncRNAs in tamoxifen and fulvestrant resistant breast cancer cells, which enriches our understanding of endocrine resistance and sheds new light on identifying novel endocrine resistance biomarkers and potential therapeutic targets to overcome endocrine resistance.

scholarly journals Building a Competing Endogenous RNA Network to Find Potential Long Non-Coding RNA Biomarkers for Pheochromocytoma

2018 ◽  
Vol 51 (6) ◽  
pp. 2916-2924 ◽  
Author(s):  
Ying-Chun Liang ◽  
Yu-Peng Wu ◽  
Dong-Ning Chen ◽  
Shao-Hao Chen ◽  
Xiao-Dong Li ◽  
...  
Keyword(s):  
Digital Gene Expression ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Competing Endogenous Rna ◽  
Cerna Network ◽  
Competing Endogenous Rna Network ◽  
Patient Prognosis

Background/Aims: Accumulating evidence has shown that long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks play crucial roles in tumor survival and patient prognosis; however, studies investigating ceRNA networks in pheochromocytoma (PCC) are lacking. In this study, we investigated the pathogenesis of PCC and whether lncRNAs acting through ceRNAs networks were associated with prognosis. Methods: A total of 183 PCC samples and 3 control samples from The Cancer Genome Atlas database were analyzed. The Empirical Analysis of Digital Gene Expression Data package in R (edgeR) was used to analyze differentially expressed RNAs. Biological processes and pathways functional enrichment analysis were performed based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. LncRNA/mRNA/miRNA ceRNA network was constructed by Cytoscape v3.0 software based on the differentially expressed RNAs Survival package in R was used to perform survival analysis. Results: In total, 554 differentially expressed lncRNAs, 1775 mRNAs and 40 miRNAs were selected for further analysis. Subsequently, 23 lncRNAs, 22 mRNAs, and 6 miRNAs were included in the constructed ceRNA network. Meanwhile, two of the 23 lncRNAs (C9orf147 and BSN-AS2) were identified as independent predictors of overall survival in PCC patients (P< 0.05). Conclusion: This study improves the understanding of lncRNA-related ceRNA networks in PCC and suggests that the lncRNAs C9orf147 and BSN-AS2 could be independent prognostic biomarkers and potential therapeutic targets for PCC.

Identification and Comparison of Novel Circular RNAs With Associated Co-expression and Competing Endogenous Rna Networks in Postmenopausal Osteoporosis

2020 ◽  
Author(s):  
Weiyi Diao ◽  
Yongguang Wang ◽  
Jun Zhang ◽  
Haiyu Shao ◽  
Yazeng Huang ◽  
...  
Keyword(s):  
Postmenopausal Osteoporosis ◽  
Regulatory Networks ◽  
Mononuclear Cells ◽  
Regulatory Mechanism ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Competing Endogenous Rna ◽  
Peripheral Blood Mononuclear ◽  
Go Annotation ◽  
Regulatory Actions

Abstract Background: circular RNAs (circRNAs) are emerging as crucial regulators in many human diseases. So far, the expression profile and regulatory mechanism of circRNAs in postmenopausal osteoporosis (PMOP) are less studied, and needed to be deciphered urgently. Herein, we aimed to reveal key circRNAs affecting PMOP, and clarify their compounding regulatory actions.Methods: To reveal key circRNAs affecting PMOP, and clarify their compounding regulatory actions. Whole transcriptome sequencing and bioinformatics analysis were performed to identify the differentially expressed circRNAs (DECs). The expression pattern and regulatory networks of DECs in peripheral blood mononuclear cells (PBMCs) were unearthed.Results: 373 DECs comprising 123 intronic, 100 antisense, 70 exonic, 55 intergenic and 25 sense-overlapping circRNAs were identified. Among these, 73 circRNAs were upregulated and 300 circRNAs were downregulated. These DECs exerted pivotal functions in the pathogenesis of PMOP as demonstrated by Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The circRNA-miRNA-mRNA co-expression network comprising 28 DECs, 145 miRNAs and 175 differentially expressed mRNAs predicted the possible mechanism of the pathogenesis and progression of PMOP.Conclusion: The results of present study provided a further comprehension of circRNA‑associated competing endogenous RNA regulatory mechanism in PMOP. These steadily expressed and disease-specific DECs may serve as promising diagnostic and prognostic biomarkers for PMOP.

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