鉴定头颈部鳞癌中异常甲基化的差异表达基因及其通路

目的基于头颈部鳞癌(HNSCC)的生物标记物及其通路尚不明确的现状,研究旨在分析和鉴定HNSCC中异常甲基化的差异表达基因,探讨其关键基因和潜在通路。方法从GEO数据库下载基因表达的数据集GSE107591和甲基化数据集GSE33202。通过R软件筛选异常甲基化基因和差异表达基因,两者取交集后获得低甲基化高表达基因(Hypo-HGs)和高甲基化低表达基因(Hyper-LGs)。利用Enrichr对两组基因进行功能富集分析。蛋白互作(PPI)网络由STRING构建并在Cytoscape中可视化,最后利用生存分析来鉴定出关键基因。此外,还进行了免疫组化分析,利用CMap寻找可能逆转HNSCC基因表达的候选小分子。结果共鉴定出28个低甲基化高表达基因,GO富集分析显示其主要参与T细胞趋化性的正调节,表皮发育、细胞-基底连接组件及调节T细胞趋化性等方面。Wiki通路分析的结果表明,其主要参与典型和非典型TGF-β信号传导、血液凝结级联反应、α6β4信号通路、补体和凝血级联反应及癌症中的衰老和自噬途径。同时,发现了24个高甲基化低表达基因,主要富集于血管生成及发育的调节,对干扰素-γ反应的负调节,对干扰素-γ介导的信号通路的负调节和上皮发育的生物学过程。Wiki通路分析显示其主要参与哺乳动物含黄素单加氧酶(FMOs)的催化循环,HIF1A和PPARG调节糖酵解以及苯和黄曲霉毒素B1的代谢。此外,鉴定出与HNSCC预后相关的关键基因,分别是SERPINE1、PLAU、MMRN1、LAMB3、LAMC2、PDPN和CXCL13。结论通过生物信息学分析并鉴定出HNSCC中异常甲基化差异表达的基因和作用途径,为揭示HNSCC发病机制提供了重要的分子学基础。包括SERPINE1、PLAU、MMRN1、LAMB3、LAMC2、PDPN和CXCL13在内的关键基因可能作为基于甲基化的异常生物标志物,为未来寻找HNSCC诊断和治疗靶点提供了新的思路。

Identification of differentially expressed genes and pathways for abnormal methylation in squamous cell carcinoma of the head and neck

Objective The biomarkers and pathways of head and neck squamous cell carcinoma(HNSCC)are yet to be identified. The purpose of this study is to analyze differentially expressed genes associated with abnormal methylation in HNSCC and identify key genes and potential pathways. Methods The gene expression data set, GSE107591, and methylation data set, GSE33202, were obtained from the GEO database. The abnormally methylated genes and differentially expressed genes were screened using R, and the low methylation-high expression genes(Hypo-HGs)and high methylation-low expression genes(Hyper-LGs)were identified using the intersect function. Enrichr was used for functional and enrichment analysis of the two groups of genes. The protein-protein interaction(PPI)network was constructed using STRING and visualized using Cytoscape. Finally, we used survival analysis to identify key genes. We performed immunohistochemical analysis using CMap to identify small candidate molecules that may reverse HNSCC gene expression. Results A total of 28 hypomethylated, highly expressed genes were identified and GO enrichment analysis showed that they were mainly involved in the positive regulation of T cell chemotaxis, epidermal development, and cell-basal junction components. The results of WikiPathway analysis indicate that these genes are mainly involved in typical and atypical TGF-β signaling, blood clotting cascade, α6β4 signaling pathway, complementation and coagulation cascade, and aging and autophagy in cancer. Additionally, we found 24 genes with high methylation and low expression, which are mainly involved in GO biological processes including the regulation of angiogenesis and development, negative regulation of the interferon-γ response, negative regulation of the interferon-γ-mediated signaling pathway, and epithelial development. WikiPathway analysis further showed that these genes are mainly involved in the catalytic cycle of mammalian riboflavin monooxygenases(FMOs). Specifically, HIF1A and PPARG regulate glycolysis and metabolism of benzene and aflatoxin B1. Furthermore, key genes related to the prognosis of HNSCC were identified, namely SERPINE1, PLAU, MMRN1, LAMB3, LAMC2, PDPN, and CXCL13. Conclusion In this study, we have identified differentially expressed genes and pathways of abnormal methylation in HNSCC through biological analysis, thereby providing an important molecular basis for exploring the pathogenesis of HNSCC. Key genes, including SERPINE1, PLAU, MMRN1, LAMB3, LAMC2, PDPN, and CXCL13 can be used as abnormal methylation-based biomarkers and therapeutic targets for future diagnosis and treatment of HNSCC.