Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma.

Abstract

BACKGROUND:

The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy.

METHODS:

We investigated two microarray profile datasets GSE64634 and GSE12452 to screen the potential differentially expressed genes (DEGs) in NPC. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were also performed. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized by Cytoscape software. The associated transcriptional factor regulatory network of the DEGs was also constructed.

RESULTS:

A total of 152 DEGs were identified from the GSE64634 and GSE12452 datasets, including 10 upregulated and 142 downregulated genes. Gene functional enrichment analysis indicated that these DEGs were enriched in the cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, carbohydrate transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Five hub genes (DNALI1, RSPH4A, RSPH9, DNAI2, and ALDH3A1) and one significant module (score = 5.6) were obtained from the PPI network. Key transcriptional factors, such as SPI1, SIN3B, and GATA2, were identified with close interactions with these five hub DEGs from the gene-transcriptional factor network.

CONCLUSIONS:

With the integrated bioinformatic analysis, numerous DEGs related to NPC were screened, and the hub DEGs we identified may be potential biomarkers for NPC.

• Authors: Zhimin Ye, Fangzheng Wang, Fengqin Yan, Lei Wang, Bin Li, Tongxin Liu, Fujun Hu, Mingxiang Jiang, Weiyang Li, Zhenfu Fu
• Journal: World journal of surgical oncology (World J Surg Oncol) Vol. 17 Issue 1 Pg. 60 (Apr 01 2019) ISSN: 1477-7819 [Electronic] England
• PMID: 30935420 (Publication Type: Journal Article)

Chemical References

• Biomarkers, Tumor
• Transcription Factors

Topics

• Biomarkers, Tumor (genetics, metabolism)
• Computational Biology (methods)
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Gene Ontology
• Gene Regulatory Networks
• Humans
• Nasopharyngeal Carcinoma (genetics, metabolism, pathology)
• Prognosis
• Protein Interaction Maps
• Software
• Transcription Factors (genetics, metabolism)