Key genes affecting the progression of nasopharyngeal carcinoma identified by RNA-sequencing and bioinformatic analysis

Abstract

Background: The present work was conducted to screen the potential biomarkers affecting nasopharyngeal carcinoma (NPC) progression through RNA-sequencing (RNA-seq), bioinformatic analysis and functional experiments. Materials and Methods: Six normal samples and five NPC clinical samples were collected for RNA-seq analysis. The expression levels in both groups were determined through student’s t -test. We identified genes of P < 0.01 as the differentially expressed genes (DEGs). In addition, gene set enrichment analysis (GSEA) was conducted. Afterwards, STRING V10 database was employed to extract protein interactions among the DEGs. Later, we established a protein-protein interaction (PPI) network, and used the Cytoscape software for network visualization. qRT-PCR was conducted to verify hub genes from clinical samples. Then, the function of CXCL10 in cell proliferation, apoptosis, invasion and migration was evaluated. Results: A total of 2024 DEGs were identified, among which, 1449 were down-regulated and 575 were up-regulated. The PPI was constructed, and the hub genes including Insulin Like Growth Factor 1 ( IGF1 ), C-X-C Motif Chemokine Ligand 10 ( CXCL10 ), Interleukin 13 ( IL13 ), Intercellular Adhesion Molecule 1 ( ICAM1 ), G Protein Subunit Gamma Transducin 1 ( GNGT1 ), Matrix Metallopeptidase 1 ( MMP1 ), Neurexin 1 ( NRXN1 ) and Matrix Metallopeptidase 3 ( MMP3 ) were obtained. The expression levels of CXCL10, IGF1, MMP3, MMP1, ICAM1, and IL-13 were significantly up-regulated in tumor tissues. High expression levels of CXCL10, MMP3 and ICAM1 predicted poor prognosis of NPC patients. CXCL10 silencing suppressed NPC cell proliferation and migration. Conclusions: CXCL10 may serve as a potential key gene affecting NPC genesis and progression.

Epstein–Barr Virus Epithelial Cancers—A Comprehensive Understanding to Drive Novel Therapies

“…IL-18 polymorphisms at the promoter region have also been associated with variable risk of nasopharyngeal carcinoma (113). NPC patients with elevated levels of CXCL10 have also been observed to have poorer prognosis (114), suggesting that despite their pro-inflammatory role, CXCL10 and IL-18 are unlikely to result in tumour-suppressive effects.…”

Identification of GNG7 as a novel biomarker and potential therapeutic target for gastric cancer via bioinformatic analysis and in vitro experiments

“…Through high-throughput sequencing and gene microarray technologies, bioinformatic analysis has recently been increasingly used to search for molecular markers or targets involved in tumor development and progression [7][8][9][10]. In the present study, the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo) and The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD, https://portal.gdc.cancer.gov/) databases were used to screen the common differentially expressed genes (DEGs) between GC tissues and normal controls.…”