基于生物信息学和体外实验筛选头颈鳞癌生物标志物

Comprehensive bioinformatics analysis combined with experimental validation to screen biomarkers for head and neck squamous cell carcinoma

目的:筛选头颈部鳞状细胞癌(head and neck squamous cell carcinoma,HNSCC)潜在的分子生物标志物,并确定其功能和临床意义。方法:从基因综合表达(Gene Expression Omnibus,GEO)数据库下载GSE58911数据集,筛选正常样本和头颈鳞癌样本中的差异表达基因(differentially expressed genes,DEGs)。使用GeneCards和比较毒理学基因组(Comparative Toxicogenomics Database,CTD)数据库,进一步筛选HNSCC潜在生物标志物,针对HNSCC潜在生物标志物进行生物信息学分析。利用癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据库作为外部验证,并用ssGSEA评估免疫细胞浸润情况。通过CCK-8、集落形成实验及实时荧光定量PCR(RT-PCR)验证数据库分析结果的准确性。结果:在GSE58911数据集中得到605个DEGs,从中开发并验证了SERPINE1、PLAU、PLAUR和SERPINB2为HNSCC核心基因。与正常对照相比,HNSCC中SERPINE1,PLAU和PLAUR表达量显著上调,而SERPINB2表达量显著下调。核心基因与免疫细胞浸润关系,进一步提高对HNSCC免疫治疗的理解。RT-PCR结果与4个核心基因在数据集中的结果一致,体外实验结果表明,SERPINE1能促进HNSCC的进展。结论:SERPINE1、PLAU、PLAUR和SERPINB2可作为诊断HNSCC的潜在生物标志物,但需进一步体外和体内研究,明确其在HNSCC中的作用及具体机制。

PURPOSE:This study was aimed to identify potential molecular biomarkers in head and neck squamous cell carcinoma(HNSCC) and to determine their functional and clinical significance.METHODS:The GSE58911 dataset was downloaded from Gene Expression Omnibus(GEO) database to screen differentially expressed genes(DEGs) in normal and HNSCC samples.GeneCards and Comparative Toxicogenomics Database(CTD) were used to further determine potential biomarkers of HNSCC.A series of bioinformatic analyses were performed for potential biomarkers of HNSCC.The Cancer Genome Atlas(TCGA) database was then used as an external validation and the infiltration of immune cells was assessed using ssGSEA.Finally,the accuracy of the database analysis results was verified by cell CCK-8,flat panel cloning and RT-PCR experiments.RESULTS:In total,605 DEGs were screened out of the GSE58911 microarray dataset.Out of these DEGs,SERPINE1,PLAU,PLAUR,and SERPINB2 were developed and validated as hub genes for HNSCC.Compared with normal controls,SERPINE1,PLAU,and PLAUR expression levels were significantly up-regulated,while SERPINB2 expression level was significantly down-regulated in HNSCC.Moreover,the relationship between hub genes and immune cell infiltration may improve the understanding of HNSCC immunotherapy.In addition,RT-PCR results were consistent with the results of the four hub genes in the dataset.In vitro results also showed that SERPINE1 could promote the progression of HNSCC.CONCLUSIONS:SERPINE1,PLAU,PLAUR and SERPINB2 can be used as potential biomarkers for the diagnosis of HNSCC,but further in vitro and in vivo studies are needed to clarify their roles and specific mechanisms in HNSCC.