Tags

Type your tag names separated by a space and hit enter

Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma.
Biomed Res Int. 2019; 2019:2601271.BR

Abstract

Intrahepatic cholangiocarcinoma (ICC) is the second most common lethal liver cancer worldwide. Currently, despite the latest developments in genomics and transcriptomics for ICC in recent years, the molecular pathogenesis promoting ICC remains elusive, especially in regulatory mechanisms of long noncoding RNAs (lncRNAs), which acts as competing endogenous RNA (ceRNA). In order to elucidate the molecular mechanism of functional lncRNA, expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were obtained from The Cancer Genome Atlas (TCGA) database and an integrative analysis of the ICC-associated ceRNA network was performed. Moreover, gene oncology enrichment analyses for the genes in the ceRNA network were implemented and novel prognostic biomarker lncRNA molecules were identified. In total, 6,738 differentially expressed mRNAs (DEmRNAs), 2,768 lncRNAs (DElncRNAs), and 173 miRNAs (DEmiRNAs) were identified in tumor tissues and adjacent nontumor ICC tissues with the thresholds of adjusted P < 0.01 and |logFC| > 2. An ICC-specific ceRNA network was successfully constructed with 30 miRNAs, 16 lncRNAs, and 80 mRNAs. Gene oncology enrichment analyses revealed that they were associated with the adaptive immune response, T cell selection and positive regulation of GTPase activity categories. Among the ceRNA networks, DElncRNAs ARHGEF26-AS1 and MIAT were found to be hub genes in underexpressed and overexpressed networks, respectively. Notably, univariate Cox regression analysis indicated that DElncRNAs HULC significantly correlated with overall survival (OS) in ICC patients (P value < 0.05), and an additional survival analysis for HULC was reconfirmed in an independent ICC cohort from the Gene Expression Omnibus (GEO) database. These findings contribute to a more comprehensive understanding of the ICC-specific ceRNA network and provide novel strategies for subsequent functional studies of lncRNAs in ICC.

Authors+Show Affiliations

Department of Hepatobiliary & Pancreatic Surgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang, China.Department of Hepatobiliary & Pancreatic Surgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang, China.Department of Hepatobiliary & Pancreatic Surgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang, China.Department of Hepatobiliary & Pancreatic Surgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang, China.Department of Hepatobiliary & Pancreatic Surgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, No. 88 Jiefang Road, Hangzhou, Zhejiang, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31886187

Citation

Zhou, Dongkai, et al. "Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma." BioMed Research International, vol. 2019, 2019, p. 2601271.
Zhou D, Gao B, Yang Q, et al. Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma. Biomed Res Int. 2019;2019:2601271.
Zhou, D., Gao, B., Yang, Q., Kong, Y., & Wang, W. (2019). Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma. BioMed Research International, 2019, 2601271. https://doi.org/10.1155/2019/2601271
Zhou D, et al. Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma. Biomed Res Int. 2019;2019:2601271. PubMed PMID: 31886187.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma. AU - Zhou,Dongkai, AU - Gao,Bingqiang, AU - Yang,Qifan, AU - Kong,Yang, AU - Wang,Weilin, Y1 - 2019/11/25/ PY - 2019/08/02/received PY - 2019/10/25/accepted PY - 2019/12/31/entrez PY - 2019/12/31/pubmed PY - 2020/5/15/medline SP - 2601271 EP - 2601271 JF - BioMed research international JO - Biomed Res Int VL - 2019 N2 - Intrahepatic cholangiocarcinoma (ICC) is the second most common lethal liver cancer worldwide. Currently, despite the latest developments in genomics and transcriptomics for ICC in recent years, the molecular pathogenesis promoting ICC remains elusive, especially in regulatory mechanisms of long noncoding RNAs (lncRNAs), which acts as competing endogenous RNA (ceRNA). In order to elucidate the molecular mechanism of functional lncRNA, expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were obtained from The Cancer Genome Atlas (TCGA) database and an integrative analysis of the ICC-associated ceRNA network was performed. Moreover, gene oncology enrichment analyses for the genes in the ceRNA network were implemented and novel prognostic biomarker lncRNA molecules were identified. In total, 6,738 differentially expressed mRNAs (DEmRNAs), 2,768 lncRNAs (DElncRNAs), and 173 miRNAs (DEmiRNAs) were identified in tumor tissues and adjacent nontumor ICC tissues with the thresholds of adjusted P < 0.01 and |logFC| > 2. An ICC-specific ceRNA network was successfully constructed with 30 miRNAs, 16 lncRNAs, and 80 mRNAs. Gene oncology enrichment analyses revealed that they were associated with the adaptive immune response, T cell selection and positive regulation of GTPase activity categories. Among the ceRNA networks, DElncRNAs ARHGEF26-AS1 and MIAT were found to be hub genes in underexpressed and overexpressed networks, respectively. Notably, univariate Cox regression analysis indicated that DElncRNAs HULC significantly correlated with overall survival (OS) in ICC patients (P value < 0.05), and an additional survival analysis for HULC was reconfirmed in an independent ICC cohort from the Gene Expression Omnibus (GEO) database. These findings contribute to a more comprehensive understanding of the ICC-specific ceRNA network and provide novel strategies for subsequent functional studies of lncRNAs in ICC. SN - 2314-6141 UR - https://www.unboundmedicine.com/medline/citation/31886187/Integrative_Analysis_of_ceRNA_Network_Reveals_Functional_lncRNAs_in_Intrahepatic_Cholangiocarcinoma_ L2 - https://doi.org/10.1155/2019/2601271 DB - PRIME DP - Unbound Medicine ER -