口腔鳞状细胞癌淋巴转移关键基因的筛选与鉴定

Screening and identification of key genes involved in lymphatic metastasis of oral squamous cell carcinoma

目的筛选口腔鳞状细胞癌(oral squamous cell carcinoma,OSCC)发生淋巴转移的关键基因,并对其进行生物信息学分析及鉴定。方法从基因表达数据库(gene expression omnibus,GEO)中下载OSCC表达谱芯片GSE2280,利用在线工具GEO2R对表达差异基因(differentially expressed genes,DEGs)进行筛选。基于DAVID数据库对DEGs进行GO分析及KEGG通路分析,运用STRING数据库及Cytoscape软件构建蛋白相互作用网络。使用CytoHubba插件鉴定枢纽基因,并使用肿瘤基因图谱数据库(the cancer genome atlas,TCGA)在口腔肿瘤病例中进行枢纽基因突变的生存分析比较。结果在OSCC发生淋巴转移与未发生淋巴转移的患者中共筛选出131个DEGs,其中74个上调基因,57个下调基因。上调基因GO功能主要富集在消化降解(GO:0007586)、中间丝细胞骨架(GO:0045111)、受损的DNA结合(GO:0003684),主要参与胰腺分泌(hsa04972)和代谢途径(hsa01100),下调基因GO功能富集在细胞外基质组成(GO:0030198)、胶原三聚体(GO:0005581)和细胞外基质结构成分(GO:0005201),主要参与细胞外基质受体相互作用(hsa04512)及蛋白质消化吸收(hsa04974)。关键的枢纽基因包括:DHCR24、ALDH3A1、COL5A1、HSPG2、APOE、TP63、VCAN。枢纽基因分析结果显示:TP63突变的患者出现生存率降低的趋势(P=0.717),VCAN突变的患者呈现生存率升高的趋势(P=0.568),但生存率差异均无统计学意义。结论 DHCR24、ALDH3A1、COL5A1、HSPG2、APOE、TP63、VCAN关键基因在OSCC淋巴转移中具有潜在的基础和临床研究价值。

Objective To screen the key genes associated with lymphatic metastasis of oral squamous cell carcinoma(OSCC) and analyze their roles and the impact of their mutations on the patients’ survival through a bioinformatics approach. Methods The OSCC expression profile chip GSE2280 was downloaded from GEO database, and the differentially expressed genes(DEGs) were screened using the online tool GEO2 R. Based on DAVID database, GO analysis and KEGG pathway analysis of the DEGs were carried out, and the protein interaction network was constructed using STRING database and Cytoscape software. CytoHubba Plug-in was used to identify the hub genes, and The Cancer Genome Atlas(TCGA) database was used to analyze the survival outcomes of oral cancer patients with mutations of these hub genes. Results We identified a total of 131 DEGs, including 74 up-regulated and 57 down-regulated genes, between OSCC patients with lymphatic metastasis and those without lymphatic metastasis. The up-regulated genes were enriched in digestion and degradation(GO:0007586), intermediate filament cytoskeleton(GO:0045111), and impaired DNA binding(GO:0003684), and participated mainly in pancreatic secretion(hsa04972) and metabolic pathway(hsa01100). The down-regulated genes were enriched in extracellular matrix composition(GO:0030198), collagen trimer(GO:0005581) and extracellular matrix structural components(GO:0005201), and participated in extracellular matrix receptor interaction(hsa04512) and protein digestion and absorption(hsa04974). The key hub genes involved in lymphatic metastasis of OSCC included DHCR24, ALDH3 A1, COL5 A1, HSPG2, APOE, TP63 and VCAN. Analysis of the data from TCGA database showed that the survival rate of patients with TP63 mutation was significantly decreased(P=0.717), and the patients with VCAN mutation appeared to have an increased survival rate, but this increase was not statistically significant(P=0.568). Conclusion DHCR24, ALDH3 A1, COL5 A1, HSPG2, APOE, TP63 and VCAN genes may have potential values in both preclinical and clinical studies of lymphatic metastasis of OSCC.