牙源性角化囊肿中心基因和氧化应激相关途径的生物信息学分析。

IF 2 3区医学 Q2 DENTISTRY, ORAL SURGERY & MEDICINE

Journal of Stomatology Oral and Maxillofacial Surgery Pub Date : 2025-10-01 DOI:10.1016/j.jormas.2025.102423

Hao Zhou , Rui-Fang Li , Qi-Wen Man

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引用次数: 0

摘要

目的：研究牙源性角化囊肿（odontogenic kerat囊肿，OKCs）的中枢基因和氧化应激相关通路，并预测中枢基因相关的转录因子。方法：从Gene Expression Omnibus （GEO）数据库中检索GSE38494数据集，包括12个OKC组织和4个正常口腔黏膜组织。利用R编程语言中的limma包识别差异表达基因（DEGs）。此外，还对氧化应激相关基因进行了基因本体（GO）分析。利用Database for Annotation， Visualization, and Integrated Discovery (DAVID)， metscape和Gene Set Enrichment Analysis (GSEA)，我们全面分析了氧化石墨烯术语和与氧化应激相关的信号通路。利用Cytoscape中的Degree算法对枢纽基因进行鉴定。利用STRING数据库构建蛋白-蛋白相互作用（PPI）网络。最后，使用NetworkAnalyst网络工具鉴定中心基因的转录因子（tf）。利用OKC （GSE176351）的scRNA数据，采用Pearson相关分析对氧化应激相关枢纽基因与IL-β基因进行相关性分析。结果：GSE38494和GO数据库共鉴定出465个与氧化应激相关的基因，其中60个基因存在显著差异表达。这些基因大多参与多种信号通路，如癌症中的microrna、化学致癌作用、活性氧、花生四烯酸代谢信号通路等。10个最重要的枢纽基因是MAPK3、HMOX1、GPX6、GPX7、GCLM、COL1A1、TXN、PDGFRB、NQO1和MMP2。FOXC1、HNF4A和GATA2可能是枢纽基因的关键调控因子。氧化应激相关基因与OKC上皮细胞中IL-1β呈弱正相关（R = 0.26）。结论：通过生物信息学分析，我们在OKC中发现了几个与IL-1β表达相关的氧化应激相关枢纽基因和信号通路。

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Bioinformatics analysis of hub genes and oxidative stress-related pathways in odontogenic keratocysts

Objective

The study aimed to examine the hub genes and oxidative stress-related pathways in odontogenic keratocysts (OKCs) and predict transcription factors associated with the hub genes.

Methods

The GSE38494 dataset, which includes 12 OKC tissues and 4 normal oral mucosa tissues, was retrieved from the Gene Expression Omnibus (GEO) database. The limma package in the R programming language was utilized to identify differentially expressed genes (DEGs). In addition, Gene Ontology (GO) analysis was performed specifically for genes associated with oxidative stress. Utilizing Database for Annotation, Visualization, and Integrated Discovery (DAVID), Metascape, and Gene Set Enrichment Analysis (GSEA), we comprehensively analyzed the GO terms and signaling pathways related to oxidative stress. The Degree algorithm in Cytoscape was employed to identify hub genes. The STRING database was leveraged to construct the protein-protein interaction (PPI) network. Finally, the transcription factors (TFs) of the hub genes were identified using the NetworkAnalyst web tool. scRNA data of OKC (GSE176351) was used for correlation analysis between oxidative stress-related hub genes and IL-β gene by Pearson correlation analysis.

Results

A total of 465 genes associated with oxidative stress were identified in the GSE38494 and GO databases, and 60 genes were significantly differentially expressed. The majority of these genes were involved in multiple signaling pathways, such as microRNAs in cancers, chemical carcinogenesis, reactive oxygen species, and the arachidonic acid metabolism signaling pathway. The ten most important hub genes were MAPK3, HMOX1, GPX6, GPX7, GCLM, COL1A1, TXN, PDGFRB, NQO1, and MMP2. FOXC1, HNF4A, and GATA2 may be the key regulatory factors of the hub genes. Additionally, there is a weak postitive correlation between oxidative stress-related genes and IL-1β in epithelial cells of OKC (R = 0.26).

Conclusions

Through bioinformatics analysis, we identified several oxidative stress-related hub genes and signaling pathways in OKC which was related to IL-1β expression.

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来源期刊

Journal of Stomatology Oral and Maxillofacial Surgery Surgery, Dentistry, Oral Surgery and Medicine, Otorhinolaryngology and Facial Plastic Surgery

CiteScore

2.30

自引率

9.10%

发文量

审稿时长

23 days