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Comprehensive analysis of long noncoding RNA-associated competing endogenous RNA network in cholangiocarcinoma.
Biochem Biophys Res Commun. 2018 12 02; 506(4):1004-1012.BB

Abstract

BACKGROUND

Long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which can largely influence on tumorigenesis and tumor progression. However, the role of lncRNA-mediated ceRNAs in cholangiocarcinoma (CCA) remains unknown. This study aimed to develop novel lncRNAs as well as their action mechanisms in CCA.

METHODS

The expression profiles of lncRNAs, miRNAs, and mRNAs of 36 CCA tissues and 9 non-tumor bile duct tissues were obtained from The Cancer Genome Atlas (TCGA) database. The differentially expressed RNAs werre identified using the DESeq package in R. The ceRNA network was constructed in CCA based on bioinformatics generated from miRcode, miRTarBase, miRDB, and TargetScan. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using "DAVID 6.8" and R packages "Clusterprofile". Survival analysis was performed based on Kaplan-Meier curve analysis.

RESULTS

We identified a total of 1411 differentially expressed lncRNAs, 3494 mRNAs, and 64 miRNAs between CCA and matched normal tissues. By combining the data predicted by databases with intersection RNAs, a lncRNA-miRNA-mRNA ceRNA network consisting of 116 lncRNAs, 14 miRNAs and 59 mRNAs was established. According to the survival analysis, we detected 11 DElncRNA to have a significant impact on the overall survival in patients with CCA (P < 0.05).

CONCLUSIONS

Our study identified novel lncRNAs associated with CCA progression and prognosis and provided data to further understand lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of CCA.

Authors+Show Affiliations

Department of Intervention and Vascular Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou Cancer Medical Center, Suzhou, Jiangsu, 215001, China. Electronic address: szmhsw@163.com.Department of Intervention and Vascular Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou Cancer Medical Center, Suzhou, Jiangsu, 215001, China.Department of Intervention and Vascular Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou Cancer Medical Center, Suzhou, Jiangsu, 215001, China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30404735

Citation

Song, Wei, et al. "Comprehensive Analysis of Long Noncoding RNA-associated Competing Endogenous RNA Network in Cholangiocarcinoma." Biochemical and Biophysical Research Communications, vol. 506, no. 4, 2018, pp. 1004-1012.
Song W, Miao DL, Chen L. Comprehensive analysis of long noncoding RNA-associated competing endogenous RNA network in cholangiocarcinoma. Biochem Biophys Res Commun. 2018;506(4):1004-1012.
Song, W., Miao, D. L., & Chen, L. (2018). Comprehensive analysis of long noncoding RNA-associated competing endogenous RNA network in cholangiocarcinoma. Biochemical and Biophysical Research Communications, 506(4), 1004-1012. https://doi.org/10.1016/j.bbrc.2018.10.186
Song W, Miao DL, Chen L. Comprehensive Analysis of Long Noncoding RNA-associated Competing Endogenous RNA Network in Cholangiocarcinoma. Biochem Biophys Res Commun. 2018 12 2;506(4):1004-1012. PubMed PMID: 30404735.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive analysis of long noncoding RNA-associated competing endogenous RNA network in cholangiocarcinoma. AU - Song,Wei, AU - Miao,Dong-Liu, AU - Chen,Lei, Y1 - 2018/11/04/ PY - 2018/10/18/received PY - 2018/10/29/accepted PY - 2018/11/9/pubmed PY - 2019/5/18/medline PY - 2018/11/9/entrez KW - Cholangiocarcinoma KW - Competitive endogenous RNA KW - LncRNA KW - Survival analysis KW - The Cancer Genome Atlas SP - 1004 EP - 1012 JF - Biochemical and biophysical research communications JO - Biochem. Biophys. Res. Commun. VL - 506 IS - 4 N2 - BACKGROUND: Long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) as a competing endogenous RNA (ceRNA) to regulate the expression of target genes, which can largely influence on tumorigenesis and tumor progression. However, the role of lncRNA-mediated ceRNAs in cholangiocarcinoma (CCA) remains unknown. This study aimed to develop novel lncRNAs as well as their action mechanisms in CCA. METHODS: The expression profiles of lncRNAs, miRNAs, and mRNAs of 36 CCA tissues and 9 non-tumor bile duct tissues were obtained from The Cancer Genome Atlas (TCGA) database. The differentially expressed RNAs werre identified using the DESeq package in R. The ceRNA network was constructed in CCA based on bioinformatics generated from miRcode, miRTarBase, miRDB, and TargetScan. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using "DAVID 6.8" and R packages "Clusterprofile". Survival analysis was performed based on Kaplan-Meier curve analysis. RESULTS: We identified a total of 1411 differentially expressed lncRNAs, 3494 mRNAs, and 64 miRNAs between CCA and matched normal tissues. By combining the data predicted by databases with intersection RNAs, a lncRNA-miRNA-mRNA ceRNA network consisting of 116 lncRNAs, 14 miRNAs and 59 mRNAs was established. According to the survival analysis, we detected 11 DElncRNA to have a significant impact on the overall survival in patients with CCA (P < 0.05). CONCLUSIONS: Our study identified novel lncRNAs associated with CCA progression and prognosis and provided data to further understand lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of CCA. SN - 1090-2104 UR - https://www.unboundmedicine.com/medline/citation/30404735/Comprehensive_analysis_of_long_noncoding_RNA_associated_competing_endogenous_RNA_network_in_cholangiocarcinoma_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0006-291X(18)32374-X DB - PRIME DP - Unbound Medicine ER -