Zou Zhenning, Gan Siyuan, Liu Shuguang, Li Rujia, Huang Jian
Department of Pathology, Guangdong Medical University, Zhanjiang, Guangdong 524023, P.R. China.
Department of Pathology, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518033, P.R. China.
Oncol Lett. 2019 Jul;18(1):916-926. doi: 10.3892/ol.2019.10382. Epub 2019 May 21.
Nasopharyngeal carcinoma (NPC) is a common malignancy of the head and neck. The aim of the present study was to conduct an integrated bioinformatics analysis of differentially expressed genes (DEGs) and to explore the molecular mechanisms of NPC. Two profiling datasets, GSE12452 and GSE34573, were downloaded from the Gene Expression Omnibus database and included 44 NPC specimens and 13 normal nasopharyngeal tissues. R software was used to identify the DEGs between NPC and normal nasopharyngeal tissues. Distributions of DEGs in chromosomes were explored based on the annotation file and the CYTOBAND database of DAVID. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied. Additionally, a protein-protein interaction (PPI) network, constructed using the STRING database and visualized by Cytoscape, was used to identify hub genes, key modules and important transcription factors (TFs). A total of 906 DEGs were identified; 434 (47.90%) DEGs were upregulated and 472 (52.10%) were downregulated. The DEGs were demonstrated to be enriched in chromosome 7p15-p14, 2q31, 1q21-q22, 1q21, 4q21 and 1p31-p22. DEGs were mainly enriched for the following GO terms: 'Cilium movement', 'microtubule bundle formation' and 'axoneme assembly'. KEGG pathway enrichment analysis revealed that pathways for 'cell cycle', 'DNA replication', 'interleukin-17 signaling', 'amoebiasis' and 'glutathione metabolism' were enriched. In addition, a PPI network comprising 867 nodes and 1,241 edges was constructed. Finally, five hub genes (aurora kinase A, cell division cycle 6, mitotic arrest deficient 2-like 1, DNA topoisomerase 2α and TPX2 microtubule nucleation factor), 8 modules, and 14 TFs were identified. Modules analysis revealed that cyclin-dependent kinase 1 and exportin 1 were involved in the pathway of Epstein-Barr virus infection. In summary, the hub genes, key modules and TFs identified in this study may promote our understanding of the pathogenesis of NPC and require further in-depth investigation.
鼻咽癌（NPC）是头颈部常见的恶性肿瘤。本研究的目的是对差异表达基因（DEGs）进行综合生物信息学分析，并探索鼻咽癌的分子机制。从基因表达综合数据库下载了两个基因表达谱数据集GSE12452和GSE34573，其中包括44个鼻咽癌标本和13个正常鼻咽组织。使用R软件鉴定鼻咽癌组织与正常鼻咽组织之间的差异表达基因。基于注释文件和DAVID的CYTOBAND数据库探索差异表达基因在染色体上的分布。进行基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路富集分析。此外，利用STRING数据库构建并通过Cytoscape可视化的蛋白质-蛋白质相互作用（PPI）网络，用于鉴定枢纽基因、关键模块和重要转录因子（TFs）。共鉴定出906个差异表达基因；其中434个（47.90%）差异表达基因上调，472个（52.10%）下调。这些差异表达基因在7号染色体p15-p14、2号染色体q31、1号染色体q21-q22、1号染色体q21、4号染色体q21和1号染色体p31-p22区域富集。差异表达基因主要富集于以下GO术语：“纤毛运动”、“微管束形成”和“轴丝组装”。KEGG通路富集分析显示，“细胞周期”、“DNA复制”、“白细胞介素-17信号通路”、“阿米巴病”和“谷胱甘肽代谢”通路富集。此外，构建了一个包含867个节点和1241条边的PPI网络。最后，鉴定出5个枢纽基因（极光激酶A、细胞分裂周期6、有丝分裂阻滞缺陷2样1、DNA拓扑异构酶2α和TPX2微管成核因子）、8个模块和14个转录因子。模块分析显示，细胞周期蛋白依赖性激酶1和输出蛋白1参与了爱泼斯坦-巴尔病毒感染途径。总之，本研究中鉴定出的枢纽基因、关键模块和转录因子可能有助于我们理解鼻咽癌的发病机制，需要进一步深入研究。
