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Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue.
BMC Cancer. 2019 Aug 07; 19(1):779.BC

Abstract

BACKGROUND

Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and target genes. These lncRNA-associated ceRNAs have been theorized to play a significant role in cancer initiation and progression. However, the roles and functions of the lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of the tongue (SCCT) are still unclear.

METHODS

The miRNA, mRNA and lncRNA expression profiles from 138 patients with SCCT were downloaded from The Cancer Genome Atlas database. We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the limma package of R software. We used the clusterProfiler package for GO and KEGG pathway annotations. The survival package was used to estimate survival analysis according to the Kaplan-Meier curve. Finally, the GDCRNATools package was used to construct the lncRNA-miRNA-mRNA ceRNA network.

RESULTS

In total, 1943 SCCT-specific mRNAs, 107 lncRNAs and 100 miRNAs were explored. Ten mRNAs (CSRP2, CKS2, ADGRG6, MB21D1, GMNN, RIPOR3, RAD51, PCLAF, ORC1, NAGS), 9 lncRNAs (LINC02560, HOXC13 - AS, FOXD2 - AS1, AC105277.1, AC099850.3, STARD4 - AS1, SLC16A1 - AS1, MIR503HG, MIR100HG) and 8 miRNAs (miR - 654, miR - 503, miR - 450a, miR - 379, miR - 369, miR - 190a, miR - 101, and let-7c) were found to be significantly associated with overall survival (log-rank p < 0.05). Based on the analysis of the lncRNA-miRNA-mRNA ceRNA network, one differentially expressed (DE) lncRNA, five DEmiRNAs, and three DEmRNAs were demonstrated to be related to the pathogenesis of SCCT.

CONCLUSIONS

In this study, we described the gene regulation by the lncRNA-miRNA-mRNA ceRNA network in the progression of SCCT. We propose a new lncRNA-associated ceRNA that could help in the diagnosis and treatment of SCCT.

Authors+Show Affiliations

The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.Stomatological Hospital of Shandong University, Shandong, China.Guangzhou University of Chinese Medicine, Guangzhou, China.Jinan stomatological hospital, Shandong, China.The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China. 18825144748@163.com. Guangzhou University of Chinese Medicine, Guangzhou, China. 18825144748@163.com. Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China. 18825144748@163.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31391008

Citation

Zhou, Rui-Sheng, et al. "Integrated Analysis of lncRNA-miRNA-mRNA ceRNA Network in Squamous Cell Carcinoma of Tongue." BMC Cancer, vol. 19, no. 1, 2019, p. 779.
Zhou RS, Zhang EX, Sun QF, et al. Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue. BMC Cancer. 2019;19(1):779.
Zhou, R. S., Zhang, E. X., Sun, Q. F., Ye, Z. J., Liu, J. W., Zhou, D. H., & Tang, Y. (2019). Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue. BMC Cancer, 19(1), 779. https://doi.org/10.1186/s12885-019-5983-8
Zhou RS, et al. Integrated Analysis of lncRNA-miRNA-mRNA ceRNA Network in Squamous Cell Carcinoma of Tongue. BMC Cancer. 2019 Aug 7;19(1):779. PubMed PMID: 31391008.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue. AU - Zhou,Rui-Sheng, AU - Zhang,En-Xin, AU - Sun,Qin-Feng, AU - Ye,Zeng-Jie, AU - Liu,Jian-Wei, AU - Zhou,Dai-Han, AU - Tang,Ying, Y1 - 2019/08/07/ PY - 2019/01/09/received PY - 2019/07/26/accepted PY - 2019/8/9/entrez PY - 2019/8/9/pubmed PY - 2020/1/10/medline KW - Competing endogenous RNAs network KW - Long non-coding RNAs KW - Overall survival KW - Squamous cell carcinoma of the tongue KW - The Cancer genome atlas SP - 779 EP - 779 JF - BMC cancer JO - BMC Cancer VL - 19 IS - 1 N2 - BACKGROUND: Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and target genes. These lncRNA-associated ceRNAs have been theorized to play a significant role in cancer initiation and progression. However, the roles and functions of the lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of the tongue (SCCT) are still unclear. METHODS: The miRNA, mRNA and lncRNA expression profiles from 138 patients with SCCT were downloaded from The Cancer Genome Atlas database. We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the limma package of R software. We used the clusterProfiler package for GO and KEGG pathway annotations. The survival package was used to estimate survival analysis according to the Kaplan-Meier curve. Finally, the GDCRNATools package was used to construct the lncRNA-miRNA-mRNA ceRNA network. RESULTS: In total, 1943 SCCT-specific mRNAs, 107 lncRNAs and 100 miRNAs were explored. Ten mRNAs (CSRP2, CKS2, ADGRG6, MB21D1, GMNN, RIPOR3, RAD51, PCLAF, ORC1, NAGS), 9 lncRNAs (LINC02560, HOXC13 - AS, FOXD2 - AS1, AC105277.1, AC099850.3, STARD4 - AS1, SLC16A1 - AS1, MIR503HG, MIR100HG) and 8 miRNAs (miR - 654, miR - 503, miR - 450a, miR - 379, miR - 369, miR - 190a, miR - 101, and let-7c) were found to be significantly associated with overall survival (log-rank p < 0.05). Based on the analysis of the lncRNA-miRNA-mRNA ceRNA network, one differentially expressed (DE) lncRNA, five DEmiRNAs, and three DEmRNAs were demonstrated to be related to the pathogenesis of SCCT. CONCLUSIONS: In this study, we described the gene regulation by the lncRNA-miRNA-mRNA ceRNA network in the progression of SCCT. We propose a new lncRNA-associated ceRNA that could help in the diagnosis and treatment of SCCT. SN - 1471-2407 UR - https://www.unboundmedicine.com/medline/citation/31391008/Integrated_analysis_of_lncRNA_miRNA_mRNA_ceRNA_network_in_squamous_cell_carcinoma_of_tongue_ L2 - https://bmccancer.biomedcentral.com/articles/10.1186/s12885-019-5983-8 DB - PRIME DP - Unbound Medicine ER -