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Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma.
Cell Physiol Biochem. 2018; 48(5):1953-1967.CP

Abstract

BACKGROUND/AIMS

Hepatocellular carcinoma (HCC) is the most prevalent subtype of primary liver tumor worldwide. Growing evidence has led to a consensus that long non-coding RNAs (lncRNAs) have considerable influence on tumorigenesis and tumor progression of HCC via the mechanism of competing endogenous RNAs (ceRNAs).

METHODS

Here, we systematically investigated the expression landscape and clinical prognostic value of lncRNAs, micorRNAs (miRNAs), and mRNAs from The Cancer Genome Atlas. Differentially expressed RNAs were submitted to Cox regression analysis and the construction of prognostic indexes. A lncRNA-miRNA-mRNA regulatory network was then constructed based on interaction information derived from miRcode, TargetScan, miRTarBase, and miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to reveal and determine the functional roles of the ceRNA network in the prognosis of HCC.

RESULTS

We detected 77 differentially expressed lncRNAs, 29 differentially expressed miRNAs, and 1014 differentially expressed mRNAs in HCC, which were significantly associated with the overall survival of patients with HCC. We developed three prognostic prediction models that showed moderate predicting prognosis performance and were highly correlated with tumor burden, histological grade and pathological stage. Additionally, 10 survival-related lncRNAs, 6 survival-related miRNAs, and 31 survival-related mRNAs were included to develop a ceRNA network. Further functional enrichment analysis suggested that the ceRNA network was associated with a dismal prognosis for patients with HCC by disturbing the homeostasis of the cell cycle.

CONCLUSION

Together, our study highlights the significant roles of lncRNAs in the development and implementation of monitoring surveillance and prognosis of HCC and provides a deeper understanding of the lncRNA-related ceRNA regulatory mechanism in the pathogenesis of HCC.

Authors+Show Affiliations

Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, China.Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, China.Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, China.Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, China.Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, China.Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30092571

Citation

Lin, Peng, et al. "Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma." Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, vol. 48, no. 5, 2018, pp. 1953-1967.
Lin P, Wen DY, Li Q, et al. Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma. Cell Physiol Biochem. 2018;48(5):1953-1967.
Lin, P., Wen, D. Y., Li, Q., He, Y., Yang, H., & Chen, G. (2018). Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma. Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology, 48(5), 1953-1967. https://doi.org/10.1159/000492519
Lin P, et al. Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma. Cell Physiol Biochem. 2018;48(5):1953-1967. PubMed PMID: 30092571.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-Wide Analysis of Prognostic lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Hepatocellular Carcinoma. AU - Lin,Peng, AU - Wen,Dong-Yue, AU - Li,Qing, AU - He,Yun, AU - Yang,Hong, AU - Chen,Gang, Y1 - 2018/08/09/ PY - 2018/02/28/received PY - 2018/07/30/accepted PY - 2018/8/10/pubmed PY - 2018/9/11/medline PY - 2018/8/10/entrez KW - Competing endogenous RNA KW - Hepatocellular carcinoma KW - LncRNA KW - MRNA KW - MiRNA KW - TCGA SP - 1953 EP - 1967 JF - Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology JO - Cell. Physiol. Biochem. VL - 48 IS - 5 N2 - BACKGROUND/AIMS: Hepatocellular carcinoma (HCC) is the most prevalent subtype of primary liver tumor worldwide. Growing evidence has led to a consensus that long non-coding RNAs (lncRNAs) have considerable influence on tumorigenesis and tumor progression of HCC via the mechanism of competing endogenous RNAs (ceRNAs). METHODS: Here, we systematically investigated the expression landscape and clinical prognostic value of lncRNAs, micorRNAs (miRNAs), and mRNAs from The Cancer Genome Atlas. Differentially expressed RNAs were submitted to Cox regression analysis and the construction of prognostic indexes. A lncRNA-miRNA-mRNA regulatory network was then constructed based on interaction information derived from miRcode, TargetScan, miRTarBase, and miRDB. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to reveal and determine the functional roles of the ceRNA network in the prognosis of HCC. RESULTS: We detected 77 differentially expressed lncRNAs, 29 differentially expressed miRNAs, and 1014 differentially expressed mRNAs in HCC, which were significantly associated with the overall survival of patients with HCC. We developed three prognostic prediction models that showed moderate predicting prognosis performance and were highly correlated with tumor burden, histological grade and pathological stage. Additionally, 10 survival-related lncRNAs, 6 survival-related miRNAs, and 31 survival-related mRNAs were included to develop a ceRNA network. Further functional enrichment analysis suggested that the ceRNA network was associated with a dismal prognosis for patients with HCC by disturbing the homeostasis of the cell cycle. CONCLUSION: Together, our study highlights the significant roles of lncRNAs in the development and implementation of monitoring surveillance and prognosis of HCC and provides a deeper understanding of the lncRNA-related ceRNA regulatory mechanism in the pathogenesis of HCC. SN - 1421-9778 UR - https://www.unboundmedicine.com/medline/citation/30092571/Genome_Wide_Analysis_of_Prognostic_lncRNAs_miRNAs_and_mRNAs_Forming_a_Competing_Endogenous_RNA_Network_in_Hepatocellular_Carcinoma_ L2 - https://www.karger.com?DOI=10.1159/000492519 DB - PRIME DP - Unbound Medicine ER -