Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue
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...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Cancer |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12885-019-5983-8 |
| _version_ | 1819145835042045952 |
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| author | Rui-Sheng Zhou En-Xin Zhang Qin-Feng Sun Zeng-Jie Ye Jian-Wei Liu Dai-Han Zhou Ying Tang |
| author_facet | Rui-Sheng Zhou En-Xin Zhang Qin-Feng Sun Zeng-Jie Ye Jian-Wei Liu Dai-Han Zhou Ying Tang |
| author_sort | Rui-Sheng Zhou |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T13:04:20Z |
| format | Article |
| id | doaj.art-3924d7dcdf2c4f4cae1f22202a0ea730 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-12-22T13:04:20Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-3924d7dcdf2c4f4cae1f22202a0ea7302022-12-21T18:24:54ZengBMCBMC Cancer1471-24072019-08-0119111010.1186/s12885-019-5983-8Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongueRui-Sheng Zhou0En-Xin Zhang1Qin-Feng Sun2Zeng-Jie Ye3Jian-Wei Liu4Dai-Han Zhou5Ying Tang6The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese MedicineThe First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese MedicineStomatological Hospital of Shandong UniversityGuangzhou University of Chinese MedicineJinan stomatological hospitalThe First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese MedicineThe First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese MedicineAbstract 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.http://link.springer.com/article/10.1186/s12885-019-5983-8Squamous cell carcinoma of the tongueLong non-coding RNAsCompeting endogenous RNAs networkThe Cancer genome atlasOverall survival |
| spellingShingle | Rui-Sheng Zhou En-Xin Zhang Qin-Feng Sun Zeng-Jie Ye Jian-Wei Liu Dai-Han Zhou Ying Tang Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue BMC Cancer Squamous cell carcinoma of the tongue Long non-coding RNAs Competing endogenous RNAs network The Cancer genome atlas Overall survival |
| title | Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue |
| title_full | Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue |
| title_fullStr | Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue |
| title_full_unstemmed | Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue |
| title_short | Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue |
| title_sort | integrated analysis of lncrna mirna mrna cerna network in squamous cell carcinoma of tongue |
| topic | Squamous cell carcinoma of the tongue Long non-coding RNAs Competing endogenous RNAs network The Cancer genome atlas Overall survival |
| url | http://link.springer.com/article/10.1186/s12885-019-5983-8 |
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