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Comprehensive analysis of differentially expressed profiles of lncRNAs, mRNAs, and miRNAs in laryngeal squamous cell carcinoma in order to construct a ceRNA network and identify potential biomarkers.
J Cell Biochem. 2019 10; 120(10):17963-17974.JC

Abstract

OBJECTIVE

This study aimed to uncover a regulatory network comprised of long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in laryngeal squamous cell carcinoma (LSCC), to explore its underlying mechanisms and development, and to identify key genetic biomarkers for the prognosis of LSCC.

METHODS

Here, we compared mRNA, lncRNA, and miRNA expression profiles between 111 LSCC and 12 adjacent normal tissues using RNA sequencing (RNA-Seq) data from the Cancer Genome Atlas (TCGA) database. Based on the interaction information obtained from miRcode, TargetScan, miRTarBase, and miRDB, a lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network was constructed using differentially expressed lncRNAs (DElncRNA), miRNAs (DEmiRNA), and mRNAs (DEmRNA). By assessing the functional enrichment of DEmRNAs in this network, the potential underlying mechanisms were explored. In addition, Kaplan-Meier survival analysis was used to assess genetic biomarkers related to the prognosis of LSCC patients.

RESULTS

Upon comparing LSCC and control tissues, 1640 DElncRNAs, 75 DEmiRNAs, and 3217 DEmRNAs were identified. Based on the prediction between lncRNA-miRNA and miRNA-mRNA relationships, we constructed a ceRNA network comprised of 93 lncRNAs, nine miRNAs, and nine mRNAs. This network predicted that two lncRNAs (AC016773.1 and C00299), two mRNAs (DIO1 and STC2), and two miRNAs (hsa-mir-137 and hsa-mir-210) were significant biomarkers of LSCC prognosis according to thorough topological and survival analyses (P < .05).

CONCLUSION

Through a ceRNA network analysis, our study identifies new lncRNAs, miRNAs, and mRNAs, which can be used as potential biomarkers of LSCC and as therapeutic targets for treating LSCC, thus laying a foundation for future clinical studies.

Authors+Show Affiliations

Clinical Medical College, Weifang Medical University, Weifang, P.R. China.Clinical Medical College, Weifang Medical University, Weifang, P.R. China.Clinical Medical College, Weifang Medical University, Weifang, P.R. China.Hainan Hospital of Chinese PLA General Hospital, Sanya, P.R. China.Central Lab, Hainan Hospital of Chinese PLA General Hospital, Sanya, P.R. China.Clinical Medical College, Weifang Medical University, Weifang, P.R. China.Hainan Hospital of Chinese PLA General Hospital, Sanya, P.R. China.Hainan Hospital of Chinese PLA General Hospital, Sanya, P.R. China. Clinical Medical Research Center for Otolaryngology Head and Neck Diseases of Hainan Province, Sanya, P.R. China.Department of Otorhinolaryngology, Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, P.R. China.

Pub Type(s)

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

Language

eng

PubMed ID

31127661

Citation

Kong, Xinru, et al. "Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs, mRNAs, and miRNAs in Laryngeal Squamous Cell Carcinoma in Order to Construct a ceRNA Network and Identify Potential Biomarkers." Journal of Cellular Biochemistry, vol. 120, no. 10, 2019, pp. 17963-17974.
Kong X, Qi J, Yan Y, et al. Comprehensive analysis of differentially expressed profiles of lncRNAs, mRNAs, and miRNAs in laryngeal squamous cell carcinoma in order to construct a ceRNA network and identify potential biomarkers. J Cell Biochem. 2019;120(10):17963-17974.
Kong, X., Qi, J., Yan, Y., Chen, L., Zhao, Y., Fang, Z., Fan, J., Liu, M., & Liu, Y. (2019). Comprehensive analysis of differentially expressed profiles of lncRNAs, mRNAs, and miRNAs in laryngeal squamous cell carcinoma in order to construct a ceRNA network and identify potential biomarkers. Journal of Cellular Biochemistry, 120(10), 17963-17974. https://doi.org/10.1002/jcb.29063
Kong X, et al. Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs, mRNAs, and miRNAs in Laryngeal Squamous Cell Carcinoma in Order to Construct a ceRNA Network and Identify Potential Biomarkers. J Cell Biochem. 2019;120(10):17963-17974. PubMed PMID: 31127661.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive analysis of differentially expressed profiles of lncRNAs, mRNAs, and miRNAs in laryngeal squamous cell carcinoma in order to construct a ceRNA network and identify potential biomarkers. AU - Kong,Xinru, AU - Qi,Jixia, AU - Yan,Yao, AU - Chen,Liwei, AU - Zhao,Yali, AU - Fang,Zhongju, AU - Fan,Junda, AU - Liu,Mingbo, AU - Liu,Yehai, Y1 - 2019/05/24/ PY - 2019/02/21/received PY - 2019/04/18/revised PY - 2019/04/29/accepted PY - 2019/5/28/pubmed PY - 2020/9/15/medline PY - 2019/5/26/entrez KW - LSCC KW - biomarkers KW - ceRNA network KW - expression profiles KW - overall survival SP - 17963 EP - 17974 JF - Journal of cellular biochemistry JO - J. Cell. Biochem. VL - 120 IS - 10 N2 - OBJECTIVE: This study aimed to uncover a regulatory network comprised of long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in laryngeal squamous cell carcinoma (LSCC), to explore its underlying mechanisms and development, and to identify key genetic biomarkers for the prognosis of LSCC. METHODS: Here, we compared mRNA, lncRNA, and miRNA expression profiles between 111 LSCC and 12 adjacent normal tissues using RNA sequencing (RNA-Seq) data from the Cancer Genome Atlas (TCGA) database. Based on the interaction information obtained from miRcode, TargetScan, miRTarBase, and miRDB, a lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network was constructed using differentially expressed lncRNAs (DElncRNA), miRNAs (DEmiRNA), and mRNAs (DEmRNA). By assessing the functional enrichment of DEmRNAs in this network, the potential underlying mechanisms were explored. In addition, Kaplan-Meier survival analysis was used to assess genetic biomarkers related to the prognosis of LSCC patients. RESULTS: Upon comparing LSCC and control tissues, 1640 DElncRNAs, 75 DEmiRNAs, and 3217 DEmRNAs were identified. Based on the prediction between lncRNA-miRNA and miRNA-mRNA relationships, we constructed a ceRNA network comprised of 93 lncRNAs, nine miRNAs, and nine mRNAs. This network predicted that two lncRNAs (AC016773.1 and C00299), two mRNAs (DIO1 and STC2), and two miRNAs (hsa-mir-137 and hsa-mir-210) were significant biomarkers of LSCC prognosis according to thorough topological and survival analyses (P < .05). CONCLUSION: Through a ceRNA network analysis, our study identifies new lncRNAs, miRNAs, and mRNAs, which can be used as potential biomarkers of LSCC and as therapeutic targets for treating LSCC, thus laying a foundation for future clinical studies. SN - 1097-4644 UR - https://www.unboundmedicine.com/medline/citation/31127661/Comprehensive_analysis_of_differentially_expressed_profiles_of_lncRNAs_mRNAs_and_miRNAs_in_laryngeal_squamous_cell_carcinoma_in_order_to_construct_a_ceRNA_network_and_identify_potential_biomarkers_ L2 - https://doi.org/10.1002/jcb.29063 DB - PRIME DP - Unbound Medicine ER -