Abstract
Background Nasopharyngeal carcinoma (NPC) is a rare but highly aggressive tumor that is predominantly encountered in Southeast Asia and China in particular. Aside from radiotherapy, no effective therapy that specifically treats NPC is available, including targeted drugs. Finding more sensitive biomarkers is important for new drug discovery and for evaluating patient prognosis. Methods mRNA expression datasets from the Gene Expression Omnibus database (GSE53819, GSE64634, and GSE40290) were selected. After all samples in each dataset were subjected to quality control using principal component analyses, the qualified samples were used for additional analyses. The genes that were significantly expressed in each dataset were intersected to identify the most significant of these. Gene functional enrichment analyses were performed on these genes, using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses. The protein–protein interaction network of selected genes was analyzed using the Search Tool for the Retrieval of Interacting Genes database. Significantly, differentially expressed genes were further verified with two RNA-seq datasets (GSE68799 and GSE12452), as well as in clinical samples. Results In all, 34 (8 upregulated genes and 26 downregulated) genes were identified as significantly differentially expressed. The immune response and the regulation of cell proliferation were the most enriched biological GO terms. Using reverse transcription quantitative real-time PCR (RT-qPCR), the genes MMP1, AQP9, and TNFAIP6 were detected to be upregulated, and FAM3D, CR2, and LTF were downregulated in NPC tissue samples. Conclusion This study provides information on the genes that may be involved in the development of NPC and suggests possible druggable targets and biomarkers for diagnosing and evaluating the prognosis of NPC.
Highlights
Nasopharyngeal carcinoma (NPC), which originates in the nasopharynx epithelium, is often observed in the pharyngeal recess
Each study in the database was reviewed for whether it met the following criteria: data are from the mRNA expression sequencing or microarray analyses of NPC; datasets are available for download and reanalysis, and data include an NPC sample and a control sample, as well as detailed information on the technique and platform used for each
The downregulated genes that we have identified in NPC, such as Microseminoprotein beta (MSMB), UPK1B, and Forkhead box protein J1 (FOXJ1), may be associated with the development or progression of NPC and may play different roles from their roles in other cancers
Summary
Nasopharyngeal carcinoma (NPC), which originates in the nasopharynx epithelium, is often observed in the pharyngeal recess. NPC is an aggressive head and neck cancer that is highly prevalent in Southeast Asia, in South China [1]. Studying changes in the gene expression in NPC is an important way to identify biomarkers of early clinical diagnosis, improve evaluation of prognosis, and most importantly, target molecules that can effectively target NPC. The genes that were significantly expressed in each dataset were intersected to identify the most significant of these. Differentially expressed genes were further verified with two RNA-seq datasets (GSE68799 and GSE12452), as well as in clinical samples.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
