Identification Of The Key Micrornas And The MiRNA-mRNA Regulatory Pathways In Nasopharyngeal Carcinoma By Bioinformatics Methods

Objective: By using gene chip technology and bioinformatics a-nalysis method,we identify key microRNAs(miRNAs)and their r-egulatatory networks in nasopharyngeal carcinoma(NPC)and explo-e the pathogenesis of NPC.Methods: 1.NPC gene expression profiling datasets and miRNA microarray datasets were downloaded from the Gene Expression Omnibus(GEO)database of the National Center for Biotechnology Information.The "limma R package" was used to screen differentially expressed miRNAs(DEMs)and mRNAs(DEGs)in NPC and normal tissues.2.The differential miRNAs in the miRNA microarray datasets were overlapped with each other through the "Venny" R language.Only those appeared in two or more datasets were considered as the key DEMs.3.The target genes regulated by key miRNAs were predicted by multiple target gene prediction websites 4.The intersection genes of target genes and DEGs,which were defined as the significant DEGs,were finded by "Venn" R software package.5.Gene ontology and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of the DEGs were also performed by DAVID and R software.6.The significant DEGs' protein-protein interaction(PPI)network was constructed from the STRING database and visualized by the Cytoscape software.7.The miRNA-mRNA regulatory network was constructed using Cytoscape software.8.The distant metastasis-free survival(DMFS)of patients with nasopharyngeal carcinoma was analyzed using R software.Results: 1.The miRNA microarray datasets GSE70970,GSE32960,and GSE43039 were downloaded from the GEO database through screening criteria,including a total of 578 nasopharyngeal cancer tissue samples and 55 nasopharyngeal normal tissue samples.The gene expression profile of GSE53819 was downloaded from the GEO database,which contained 18 NPC samples and 18 normal NPC samples.2.A total of 142 differentially expressed miRNAs were identified in the GSE70970,of which 127 miRNAs were up-regulated and 15 miRNAs were down-regulated.A total of 80 DEMs were identified from the GSE32960 datasets,including 32 upregulated and 48 downregulated DEMs.And a total of 95 DEMs were identified from the GSE43039 datasets,including 40 upregulated and 55 downregulated DEMs.There were 4507 differential expressed genes in GSE53819 dataset,of which 2011 genes were up-regulated and 2496 genes were down-regulated.3.4 up-regulated and 12 down-regulated common DEMs were identified,respectively.4.Through multiple target gene prediction websites,737 protein-coding genes targeted by 16 miRNAs were found.These target genes were overlapped with DEGs to obtain 160 the significant DEGs.5.GO analysis indicated that the up-regulated intersection genes were mainly concentrated in extracellular matrix tissues,extracellular structural tissues,collagen trimer complexes,extracellular matrix components,and collagen catabolism(p <0.05);The down-regulated genes were mainly concentrated in positive regulation of wound healing,positive response to injury,regulation of wound healing,regulation of response to injury,positive regulation of I-kappaB kinase / NF-kappaB signal(p <0.05).KEGG pathway analysis revealed that the up-regulated genes were mainly concentrated in PI3K-Akt signaling pathway,ECM-receptor interaction,protein digestion and absorption,human papillomavirus infection,and small cell lung cancer(p<0.05),while the down-regulated genes were mainly concentrated in axons Guidance,type II diabetes pathway(p <0.05).6.According to the PPI network of intersecting genes,two central genes were identified: MYC and VEGFA.7.Survival analysis of key DEMs showed that low hsa-miR-29 c level was associated with worse DMFS in nasopharyngeal carcinoma patients(p=0.00036),whlie low hsa-miR-93 level was associated with better DMFS in nasopharyngeal carcinoma patients(p=0.00048).Conclusion: The study identified 16 key miRNAs between NPC and normal tissues by bioinformatics,which may be involved in the progression of NPC.Among them,hsa-miR-29c?hsa-miR-93 were significantly related to the prognosis of nasopharyngeal carcinoma.These findings improve our understanding of the pathogenesis of NPC and the underlying molecular mechanisms.However,the specific functions of key miRNAs in the NPC should be confirmed by further molecular biological experiments.