Objective: To explore differentially expressed genes (DEG) and pathways between human papilloma virus (HPV) positive and negative head and neck squamous cell carcinoma (HNSCC) and to search gene targets for diagnosis and treatment of HPV-related HNSCC. Methods: HPV-related HNSCC expression profile chips of GSE3292 (including 8 HPV-positive and 28 HPV-negative HNSCC tissues, of which 15 collected from oral cavity cancer, 9 from oropharyngeal cancer, 9 from laryngeal cancer and 3 from hypopharyngeal cancer) were selected from Gene Expression Omnibus (GEO) database of National Center for Biotechnology Information and DEG were screened out using Gene-Cloud of Biotechnology Informs (GCBI). Gene ontology and pathway enrichment analysis were performed using DAVID and protein-to-protein interaction (PPI) network was constructed by STRING. Hub genes were identified by Cytoscape and then performed pathway enrichment analysis. Finally, expression differences of hub genes in the cancer genome atlas (TCGA) database were checked using UALCAN. Results: Five hundred and seventy-three DEG were screened out from more than 25 000 genes detected in the chips including 539 up-regulated genes and 34 down regulated ones. Twenty-seven hub genes including cyclin-dependent kinases 1(CDK1), proliferating cell nuclear antigen (PCNA), minichromosome maintenance proteins (MCM) family (MCM2, MCM3, MCM6 and MCM7), replication factor C subunit 4 (RFC4) and kinesin family member 11 (KIF11) were identified after two rounds of Cytoscape screening. Gene ontology and pathway analysis showed that DEG were mainly distributed in chromosome, nucleoplasm, nuclear lumen and membrane-enclosed lumen and participated in biological processes such as DNA replication, DNA metabolism, cell cycle and cell division, and also 6 major signaling pathways centered on p53 signaling pathway （P<0.01）. All hub genes were expressed differently between HPV-positive and negative HNSCC in TCGA database（P<0.01）. Conclusions: Hub genes including CDK1, PCNA, MCM family (MCM2, MCM3, MCM6 and MCM7) act as an important part on HPV-induced HNSCC and the p53 pathway is the key of this process and plays different regulatory roles between two subtypes of HNSCC. CDK1, MCM7 and RFC4 are expected to be potential treatment targets for HPV-positive HNSCC while MCM2, MCM3, PCNA and KIF11 may be employed as biomarkers for diagnosis and prognosis.
目的： 探索人乳头状瘤病毒（human papilloma virus，HPV）阳性和阴性头颈部鳞状细胞癌（head and neck squamous cell carcinoma，HNSCC）的差异表达基因及关键通路，为HPV相关HNSCC的诊断和治疗提供候选基因靶点。 方法： 从美国国立生物技术信息中心(Gene Expression Omnibus,GEO）数据库中检索获得序号为GSE3292的HPV相关HNSCC表达谱芯片研究系列（其中HPV 阳性癌组织8例、阴性28例，含口腔癌15例、口咽癌9例、喉癌9例、下咽癌3例），通过Gene-Cloud of Biotechnology Information（GCBI）分析平台筛选得到差异表达基因，运用DAVID数据库进行基因本体分析和信号通路富集分析。通过STRING数据库构建蛋白相互作用网络后，利用Cytoscape软件筛选关键基因并进一步行信号通路富集分析，最后使用UALCAN数据分析工具检验关键基因在癌症基因组图谱（the cancer genome atlas，TCGA）数据库中的表达差异性。 结果： 从芯片检测的25 000多个基因中筛选得到573个差异表达基因，其中上调基因539个，下调基因34个，经Cytoscape两轮筛选确定细胞周期蛋白依赖性激酶1（cyclin-dependent kinases 1，CDK1）、增殖细胞核抗原（proliferating cell nuclear antigen，PCNA）、微小染色体维持蛋白（minichromosome maintenance proteins，MCM）家族（MCM2、MCM3、MCM6、MCM7）、复制因子C4（replication factor C subunit 4，RFC4）、驱动蛋白家族成员11（kinesin family member 11，KIF11）等27个基因为关键基因。基因本体分析和信号通路富集分析显示差异表达基因主要分布于染色体及核质、核内腔、膜包围内腔等部位，并参与DNA复制、DNA代谢、细胞周期、细胞分裂等生物学过程以及以p53信号通路为核心的6个主要信号通路（P<0.01）。经TCGA数据库检验证实27个关键基因在HPV阳性及阴性HNSCC中的表达差异均有统计学意义（P<0.01）。 结论： CDK1、PCNA、MCM家族等关键基因在HPV诱发HNSCC的过程中发挥重要作用，而p53通路是此过程的核心通路，且在HNSCC两个亚型中的调控作用存在差异。CDK1、MCM7、RFC4有望成为治疗HPV阳性HNSCC的潜在靶点，而MCM2、MCM3、PCNA、KIF11可能作为HPV阳性HNSCC诊断及预后的标志物。.
Keywords: Biomarkers, tumor; Computational biology; Papillomavirus infections; Squamous cell carcinoma of head and neck.