Abstract
Introduction: Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, particularly in Guangdong population, but the prognosis of NPC is poor. Recently microRNA (miR) has been shown to have function in aiding the treatment of cancer. Thus, in this study, miRNAs and genes associated with NPC were analyzed. Methods: mRNA-sequencing and miR-sequencing data were obtained from the Gene Expression Omnibus. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. Then, the gene function annotations about the DEGs were predicted using Gene Ontology (GO) and KEGG pathway. Subsequently, the protein-protein interaction (PPI) network was established based on the STRING database, and function modules were identified using Cytoscape. Finally, DEGs targeted by DEMs were predicted by using the miRDB, miRTarBase, TargetScan and DIANA databases, and the DEM-DEG negative interaction network was built. Results: In all, 704 DEGs (about 49.9% upregulated) were enriched in 234 GO terms and 53 KEGG pathways. Seven hub genes (APP, GNG2, VAV1, RAC2, YES1, EGFR and GNB5) in 6 function modules were found for the PPI network. In addition, 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, moreover, these pairs may potentially contributed to NPC pathogenesis. Conclusion: The constructed miRNA-mRNA negetive regulatory network will give help in elucidating the molecular mechanisms of NPC. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future.
Highlights
Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, in Guangdong population, but the prognosis of NPC is poor
MRNA expression profiles GSE68799 included a collection of 42 Chinese Nasopharyngeal Carcinoma patients tissues and 4 non-NPC nasopharyngeal tissues. mRNA expression profiles GSE118719 and miRNA expression profiles GSE118720 included a collection of 7 NPC samples and 4 normal nasopharyngeal mucosal samples
Bioinformatics methods were applied to analyze three public NPC sequencing data, and found some potential important genes and miRNAs related with the pathogenesis of NPC, the miRNA-mRNA correlation pairs may supply some clues for the molecular mechanisms of NPC pathogenesis
Summary
Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, in Guangdong population, but the prognosis of NPC is poor. In this study, miRNAs and genes associated with NPC were analyzed. The differentially expressed genes (DEGs) and miRNAs (DEMs) were filter out. 86 DEMs were identified containing 56 upregulated and 30 downregulated miRNAs. There were 538 DEM-DEG pairs, of which miR-93-5p/TGFBR2, miR-455-3p/STK17B and miR-766-5p/ITGAV had functions in other cancers, these pairs may potentially contributed to NPC pathogenesis. The important DEGs, DEMs and DEM-DEG pairs associated with NPC may contribute to the diagnosis and treatment of NPC in the future. Nasopharyngeal carcinoma (NPC) is an endemic cancer in southern China, in Guangdong population [1, 2]. By comparing the RNA sequencing results of cancer tissue and normal tissue samples can provide insights into the molecular
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