Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma
Background. Oral squamous cell carcinoma (OSCC) severely affects the quality of life and the 5-year survival rate is low. Exploring the potential miRNA-mRNA regulatory network and analyzing hub genes and clinical data can provide a theoretical basis for further elucidating the pathogenesis of OSCC....
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| Format: | Article |
| Language: | English |
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Palacký University Olomouc, Faculty of Medicine and Dentistry
2022-09-01
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| Series: | Biomedical Papers |
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| Online Access: | https://biomed.papers.upol.cz/artkey/bio-202203-0006_construction-of-the-mirna-mrna-regulatory-network-and-analysis-of-hub-genes-in-oral-squamous-cell-carcinoma.php |
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| author | Zifeng Cui Qiwen Song Yanping Chen Kaicheng Yang |
| author_facet | Zifeng Cui Qiwen Song Yanping Chen Kaicheng Yang |
| author_sort | Zifeng Cui |
| collection | DOAJ |
| description | Background. Oral squamous cell carcinoma (OSCC) severely affects the quality of life and the 5-year survival rate is low. Exploring the potential miRNA-mRNA regulatory network and analyzing hub genes and clinical data can provide a theoretical basis for further elucidating the pathogenesis of OSCC. Methods. The miRNA expression datasets of GSE113956 and GSE124566 and mRNA expression datasets of GSE31056, GSE37991 and GSE13601 were obtained from the Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and mRNAs (DEGs) were screened using GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by DAVID database. The PPI network was established through STRING database and the hub genes were preliminarily screened out by Cytoscape software. After identifying the hub genes in the TCGA database, we predicted the potential DEM transcription factors, constructed a miRNA-mRNA regulatory network, and analyzed the relationship between the hub genes and clinical data. Results. A total of 28 DEMs and 764 DEGs were screened out, which were composed of 285 up-regulated genes and 479 down-regulated genes. Enrichment analysis showed that up-regulation of DEGs were mainly enriched in extracellular matrix organization and cancer-related pathway, while down-regulation of DEGs were mainly enriched in muscular system process and adrenaline signal transduction. After preliminary screening by PPI network and identification in TCGA, the up-regulated FN1, COL1A1, COL1A2, AURKA, CCNB1, CCNA2, SPP1, CDC6, and down-regulated ACTN2, TTN, IGF1, CAV3, MYL2, DMD, LDB3, CSRP3, ACTA1, PPARG were identified as hub genes. The miRNA-mRNA regulation network showed that hsa-miR-513b was the DEM with the most regulation, and COL1A1 was the DEG with the most regulation. In addition, CDC6, AURKA, CCNB1 and CCNA2 were related to overall survival and tumor differentiation. Conclusions. The regulatory relationship of hsa-miR-513b/ CDC6, CCNB1, CCNA2 and the regulatory relationship of hsa-miR-342-5p /AURKA were not only verified in the miRNA-mRNA regulatory network but also related to overall survival and tumor differentiation. These results indicated that they participated in the cellular regulatory process, and provided a molecular mechanism model for the study of pathogenesis. |
| first_indexed | 2024-04-11T21:09:21Z |
| format | Article |
| id | doaj.art-fd10e445ae1542aab68c0ed0681b9131 |
| institution | Directory Open Access Journal |
| issn | 1213-8118 1804-7521 |
| language | English |
| last_indexed | 2024-04-11T21:09:21Z |
| publishDate | 2022-09-01 |
| publisher | Palacký University Olomouc, Faculty of Medicine and Dentistry |
| record_format | Article |
| series | Biomedical Papers |
| spelling | doaj.art-fd10e445ae1542aab68c0ed0681b91312022-12-22T04:03:04ZengPalacký University Olomouc, Faculty of Medicine and DentistryBiomedical Papers1213-81181804-75212022-09-01166328028910.5507/bp.2022.001bio-202203-0006Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinomaZifeng Cui0Qiwen Song1Yanping Chen2Kaicheng Yang3Department of Stomatology, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang 050000, Hebei, ChinaOral and Maxillofacial Surgery, Hebei Provincial Stomatological Hospital, No. 383, East Zhongshan Road, Shijiazhuang 050000, Hebei, ChinaDepartment of Stomatology, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang 050000, Hebei, ChinaDepartment of Stomatology, The Fourth Hospital of Hebei Medical University, No. 12, Jiankang Road, Shijiazhuang 050000, Hebei, ChinaBackground. Oral squamous cell carcinoma (OSCC) severely affects the quality of life and the 5-year survival rate is low. Exploring the potential miRNA-mRNA regulatory network and analyzing hub genes and clinical data can provide a theoretical basis for further elucidating the pathogenesis of OSCC. Methods. The miRNA expression datasets of GSE113956 and GSE124566 and mRNA expression datasets of GSE31056, GSE37991 and GSE13601 were obtained from the Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and mRNAs (DEGs) were screened using GEO2R. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by DAVID database. The PPI network was established through STRING database and the hub genes were preliminarily screened out by Cytoscape software. After identifying the hub genes in the TCGA database, we predicted the potential DEM transcription factors, constructed a miRNA-mRNA regulatory network, and analyzed the relationship between the hub genes and clinical data. Results. A total of 28 DEMs and 764 DEGs were screened out, which were composed of 285 up-regulated genes and 479 down-regulated genes. Enrichment analysis showed that up-regulation of DEGs were mainly enriched in extracellular matrix organization and cancer-related pathway, while down-regulation of DEGs were mainly enriched in muscular system process and adrenaline signal transduction. After preliminary screening by PPI network and identification in TCGA, the up-regulated FN1, COL1A1, COL1A2, AURKA, CCNB1, CCNA2, SPP1, CDC6, and down-regulated ACTN2, TTN, IGF1, CAV3, MYL2, DMD, LDB3, CSRP3, ACTA1, PPARG were identified as hub genes. The miRNA-mRNA regulation network showed that hsa-miR-513b was the DEM with the most regulation, and COL1A1 was the DEG with the most regulation. In addition, CDC6, AURKA, CCNB1 and CCNA2 were related to overall survival and tumor differentiation. Conclusions. The regulatory relationship of hsa-miR-513b/ CDC6, CCNB1, CCNA2 and the regulatory relationship of hsa-miR-342-5p /AURKA were not only verified in the miRNA-mRNA regulatory network but also related to overall survival and tumor differentiation. These results indicated that they participated in the cellular regulatory process, and provided a molecular mechanism model for the study of pathogenesis.https://biomed.papers.upol.cz/artkey/bio-202203-0006_construction-of-the-mirna-mrna-regulatory-network-and-analysis-of-hub-genes-in-oral-squamous-cell-carcinoma.phpbioinformaticsoral squamous cell carcinoma (oscc)regulatory network |
| spellingShingle | Zifeng Cui Qiwen Song Yanping Chen Kaicheng Yang Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma Biomedical Papers bioinformatics oral squamous cell carcinoma (oscc) regulatory network |
| title | Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| title_full | Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| title_fullStr | Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| title_full_unstemmed | Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| title_short | Construction of the miRNA-mRNA regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| title_sort | construction of the mirna mrna regulatory network and analysis of hub genes in oral squamous cell carcinoma |
| topic | bioinformatics oral squamous cell carcinoma (oscc) regulatory network |
| url | https://biomed.papers.upol.cz/artkey/bio-202203-0006_construction-of-the-mirna-mrna-regulatory-network-and-analysis-of-hub-genes-in-oral-squamous-cell-carcinoma.php |
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