Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Abstract Background This study aimed to identify potential circular ribonucleic acid (circRNA) signatures involved in the pathogenesis of early-stage lung adenocarcinoma (LAC). Methods The circRNA sequencing dataset of early-stage LAC was downloaded from the Gene Expression Omnibus database. First, the differentially expressed circRNAs (DEcircRNAs) between tumour and non-tumour tissues were screened. Then, the corresponding miRNAs and their target genes were predicted. In addition, prognosis-related genes were identified using survival analysis and further used to build a network of competitive endogenous RNAs (ceRNAs; DEcircRNA–miRNA–mRNA). Finally, the functional analysis and drug–gene interaction analysis of mRNAs in the ceRNA network was performed. Results A total of 35 DEcircRNAs (30 up-regulated and 5 down-regulated circRNAs) were identified. Moreover, 135 DEcircRNA–miRNA and 674 miRNA–mRNA pairs were predicted. The survival analysis of these target mRNAs revealed that 60 genes were significantly associated with survival outcomes in early-stage LAC. Of these, high levels of PSMA 5 and low levels of NAMPT, CPT 2 and TNFSF11 exhibited favourable prognoses. In addition, the DEcircRNA–miRNA–mRNA network was constructed, containing 5 miRNA–circRNA (hsa_circ_0092283/hsa-miR-762/hsa-miR-4685-5p; hsa_circ_0070610/hsa-let-7a-2-3p/hsa-miR-3622a-3p; hsa_circ_0062682/hsa-miR-4268) and 60 miRNA–mRNA pairs. Functional analysis of the genes in the ceRNA network showed that they were primarily enriched in the Wnt signalling pathway. Moreover, PSMA 5, NAMPT, CPT 2 and TNFSF11 had strong correlations with different drugs. Conclusion Three circRNAs (hsa_circ_0062682, hsa_circ_0092283 and hsa_circ_0070610) might be potential novel targets for the diagnosis of early-stage LAC.

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Preliminary screening and functional analysis of circular RNAs associated with hepatic stellate cell activation

Gene ◽

10.1016/j.gene.2018.08.052 ◽

2018 ◽

Vol 677 ◽

pp. 317-323 ◽

Cited By ~ 11

Author(s):

Yuping Zhou ◽

Xueyou Lv ◽

Hui Qu ◽

Kekai Zhao ◽

Liyun Fu ◽

...

Keyword(s):

Functional Analysis ◽

Hepatic Stellate Cell ◽

Cell Activation ◽

Stellate Cell ◽

Circular Rnas ◽

Preliminary Screening ◽

Hepatic Stellate Cell Activation

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Differential expression profiles and functional analysis of circular RNAs in children with fulminant myocarditis

Epigenomics ◽

10.2217/epi-2019-0101 ◽

2019 ◽

Vol 11 (10) ◽

pp. 1129-1141 ◽

Cited By ~ 5

Author(s):

Li Zhang ◽

Bo Han ◽

Jing Wang ◽

Qingqing Liu ◽

Yaru Kong ◽

...

Keyword(s):

Functional Analysis ◽

Healthy Volunteers ◽

Differential Expression ◽

Expression Profiles ◽

Interaction Network ◽

Fulminant Myocarditis ◽

Circular Rnas ◽

Biological Functions ◽

Microarray Experiments ◽

Network Building

Aim: To assess differential expression profiles of circular RNAs (circRNAs) and explore their possible functions in children with fulminant myocarditis. Materials & methods: circRNA microarray experiments were carried out for determining differential expression profiles of circRNAs in three children with fulminant myocarditis and three healthy volunteers. Functional analysis and circRNA–miRNA–mRNA interaction network building were conducted to study biological functions. Results: This work identified 2281 upregulated and 892 downregulated circRNAs. Further assessment confirmed hsa_circ_0071542 upregulation (2.5-fold) in fulminant myocarditis. Functional analysis demonstrated the differentially expressed circRNAs mainly contributed to inflammation and immunity. Conclusion: circRNAs might have substantial roles in pediatric fulminant myocarditis, and hsa_circ_0071542 could serve as a promising biomarker.

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Profiling and functional analysis of differentially expressed circular RNAs in high glucose‐induced human umbilical vein endothelial cells

FEBS Open Bio ◽

10.1002/2211-5463.12709 ◽

2019 ◽

Vol 9 (9) ◽

pp. 1640-1651 ◽

Cited By ~ 6

Author(s):

Guoxi Jin ◽

Qiong Wang ◽

Xiaolei Hu ◽

Xiaoli Li ◽

Xiaoyan Pei ◽

...

Keyword(s):

Functional Analysis ◽

Endothelial Cells ◽

High Glucose ◽

Umbilical Vein ◽

Differentially Expressed ◽

Circular Rnas ◽

Human Umbilical Vein ◽

Umbilical Vein Endothelial Cells

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Microarray Expression Profile and Functional Analysis of Circular RNAs in Osteosarcoma

Cellular Physiology and Biochemistry ◽

10.1159/000481650 ◽

2017 ◽

Vol 43 (3) ◽

pp. 969-985 ◽

Cited By ~ 57

Author(s):

Weihai Liu ◽

Jiajun Zhang ◽

Changye Zou ◽

Xianbiao Xie ◽

Yongqian Wang ◽

...

Keyword(s):

Functional Analysis ◽

Signaling Pathway ◽

Cell Lines ◽

Expression Profile ◽

Differentially Expressed ◽

Circular Rnas ◽

Global Changes ◽

Osteosarcoma Cell ◽

Comprehensive Understanding ◽

Potential Target

Background/Aims: Osteosarcoma (OS) is the most common primary malignant bone tumor in children and adolescents. However, the molecular mechanisms regulating osteosarcoma tumorigenesis and progression are still poorly understood. Circular RNAs (circRNAs) have been identified as microRNA sponges and are involved in many important biological processes. This study aims to investigate the global changes in the expression pattern of circRNAs in osteosarcoma and provide a comprehensive understanding of differentially expressed circRNAs. Methods: Microarray based circRNA expression was determined in osteosarcoma cell lines and compared with hFOB1.19, which was used as the normal control. We confirmed the microarray data by real time-qPCR in both osteosarcoma cell lines and tissues. The circRNA/microRNA/mRNA interaction network was predicted using bioinformatics. Gene Ontology analysis and 4 annotation tools for pathway analysis (KEGG, Biocarta, PANTHER and Reactome) were used to predict the functions of differentially expressed circRNAs. Results: We revealed a number of differentially expressed circRNAs and 12 of them were confirmed, which suggests a potential role of circRNAs in OS. Among these differentially expressed circRNAs, hsa_circRNA_103801 was up-regulated in both osteosarcoma cell lines and tissues, while hsa_circRNA_104980 was down-regulated. The most likely potential target miRNAs for hsa_circRNA_103801 include hsa-miR-370-3p, hsa-miR-338-3p and hsa-miR-877-3p, while the most potential target miRNAs of hsa_circRNA_104980 consist of hsa-miR-1298-3p and hsa-miR-660-3p. Functional analysis found that hsa_circRNA_103801 was involved in pathways in cancer, such as the HIF-1, VEGF and angiogenesis pathway, the Rap1 signaling pathway and the PI3K-Akt signaling pathway, while hsa_circRNA_104980 was related to some pathways such as the tight junction pathway. Conclusions: This study has identified the comprehensive expression profile of circRNAs in osteosarcoma for the first time. And the ceRNA network prediction and bioinformatics functional analysis could provide a comprehensive understanding of hsa_circRNA_103801 and hsa_circRNA_104980, which may be involved in the initiation and progression of osteosarcoma. The present study indicates that circRNAs may play important roles in osteosarcoma and thus serve as biomarkers of osteosarcoma diagnosis and treatment.

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