Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis

Abstract

Background: Nasopharyngeal carcinoma (NPC) is an epithelial malignancy with high morbidity rates in the east and southeast Asia. The molecular mechanisms of NPC remain largely unknown. We explored the pathogenesis, potential biomarkers, and prognostic indicators of NPC. Methods: We analyzed mRNAs, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) in the whole transcriptome sequencing dataset of our hospital (five normal tissues vs. five NPC tissues) and six microarray datasets (62 normal tissues vs. 334 NPC tissues) downloaded from the Gene Expression Omnibus (GSE12452, GSE13597, GSE95166, GSE126683, and GSE70970, GSE43039). Differential expression analyses, gene ontology (GO) enrichment, kyoto encyclopedia of genes and genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were conducted. The lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks were constructed using the miRanda and Tar-getScan database, and a protein-protein interaction (PPI) network of differentially expressed genes (DEGs) was built using Search Tool for the Retrieval of Interacting Genes (STRING) software. Hub genes were identified using Molecular Complex Detection (MCODE), NetworkAnalyzer, and CytoHubba. Results: We identified 61 mRNAs, 14miRNAs, and 10 lncRNAs as shared DEGs related to NPC in seven datasets. Changes in NPC were enriched in the chromosomal region, sister chromatid segregation, and nuclear chromosome segregation. GSEA indicated that the mitogen-activated protein kinase (MAPK) pathway, phosphatidylinositol-3 OH kinase/protein kinase B (PI3K-Akt) pathway, apoptotic pathway, and tumor necrosis factor (TNF) were involved in the initiation and development of NPC. Finally, 20 hub genes were screened out via the PPI network. Conclusions: Several DEGs and their biological processes, pathways, and interrelations were found in our current study by bioinformatics analyses. Our findings may offer insights into the biological mechanisms underlying NPC and identify potential therapeutic targets for NPC.

A Novel Three-MicroRNA Signature for Predicting Survival in Patients with Nasopharyngeal Carcinoma

“…In the subsequent GO enrichment analysis, the results showed that the biological process and cellular components of these target genes were related to the nuclear chromosome segregation and centromeric region of chromosome, respectively, suggesting that chromosomal abnormalities are important factors for poor prognosis of NPC. At present, studies have shown that chromosomal aberration, loss of heterozygosity, chromosome rearrangements and chromosomal imbalances can play important role in the occurrence and development of NPC [42]. We speculated that during NPC resistance to radiotherapy or chemotherapy, these post-transcriptional target genes were regulated by the 3 miRNAs, resulting in chromosomal rearrangements and causing distant metastasis or recurrence of tumor.…”

Identification of a five-miRNA signature as a novel potential prognostic biomarker in patients with nasopharyngeal carcinoma

“…Clinical data and gene expression data of NPC were downloaded from the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ) database [ 25 ] including the GSE32960 [ 26 ], GSE70970 [ 27 ], GSE36682 [ 28 ], GSE118721, and GSE102349 [ 29 ] datasets. The GSE32960, GSE70970, and GSE36682 datasets were miRNA data containing clinical survival information; the GSE118721 dataset contained miRNA and mRNA data but without clinical survival information; and the GSE102349 dataset was mRNA data containing clinical survival information.…”

Identification and Validation of Immune-Related Biomarker Gene and Construction of ceRNA Networks in Septic Cardiomyopathy

“…Therefore, we used these five datasets for the acquisition of SCM immune-related biomarker genes and the construction of ceRNA networks. It is important to note that our technique is achievable and accepted, and gene expression under pathophysiological conditions has been studied by scholars ( Xu et al., 2020 ; Cheng et al., 2021 ).…”