通过生物信息学分析和机器学习鉴定牙周炎和动脉粥样硬化的串音通路和panoptosis相关基因

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics Pub Date : 2025-09-10 DOI:10.1016/j.ygeno.2025.111106

Nan Yang , Shiqun Sun , Xiantao Chen , Tongtong Yan , Nan Gu , Zhihui Liu

{"title":"通过生物信息学分析和机器学习鉴定牙周炎和动脉粥样硬化的串音通路和panoptosis相关基因","authors":"Nan Yang , Shiqun Sun , Xiantao Chen , Tongtong Yan , Nan Gu , Zhihui Liu","doi":"10.1016/j.ygeno.2025.111106","DOIUrl":null,"url":null,"abstract":"<div><h3>Background and objectives</h3><div>Periodontitis(PD) is a chronic inflammatory disease that poses a serious threat to oral health and is one of the risk factors for atherosclerosis(AS). A growing body of evidence suggests that the two diseases are closely related. However, current studies have yet to fully understand the common genes and common mechanisms between PD and AS. This study aimed to screen the tandem genes of PD and AS and the potential relationship between the tandem genes and pan-apoptosis-related genes. By analyzing the relationship between the core genes and immune cells, it will provide new targets for clinical treatment.</div></div><div><h3>Materials and methods</h3><div>The PD and AS datasets were downloaded from the GEO database and differential expression analysis was performed to obtain DEGs. AS-related genes were downloaded from the GeneCards database, and PANoptosis-related genes were obtained through literature review. AS-related genes were merged into AS DEGs, and overlapping DEGs were cross-talk genes for PD and AS. Protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Pearson coefficients were used to calculate the correlation between cross-talk genes and PANoptosis-related genes in the PD and AS datasets. The intersection of cross-talk genes and PANoptosis-related genes was defined as cross-talk-PANoptosis genes. Core genes were screened using ROC analysis and XGBoost. PPI sub-network, gene-biological processes and gene-pathway networks were constructed based on the core genes. In addition, immune infiltration on the PD and AS datasets was analyzed using the CIBERSORT algorithm.</div></div><div><h3>Results</h3><div>285 cross-talk genes overlapped between PD DEGs and AS DEGs. The intersection of cross-talk genes with 109 PANoptosis-related genes was defined as cross-talk-PAoptosis genes. ROC and XGBoost showed that MLKL, ZBP1, CD14, and IL6 were more accurate than the other cross-talk-PAoptosis genes in predicting the diseases, and were better in terms of the overall characteristics. GO and KEGG analyses showed that these four core genes were involved in the immune and inflammatory response of the organism. The results of immune infiltration showed that Monocytes and Mast cells resting were altered to a greater extent in PD and AS patients. Finally, 24 drugs related to the core genes were retrieved from the DGIDB database.</div></div><div><h3>Conclusions</h3><div>This study reveals the joint mechanism between PD and AS associated with PANoptosis. Analyzing the four core genes and immune cells may provide new therapeutic directions for the pathogenesis of PD combined with AS.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 6","pages":"Article 111106"},"PeriodicalIF":3.0000,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification of cross-talk pathways and PANoptosis-related genes in periodontitis and atherosclerosis by bioinformatics analysis and machine learning\",\"authors\":\"Nan Yang , Shiqun Sun , Xiantao Chen , Tongtong Yan , Nan Gu , Zhihui Liu\",\"doi\":\"10.1016/j.ygeno.2025.111106\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background and objectives</h3><div>Periodontitis(PD) is a chronic inflammatory disease that poses a serious threat to oral health and is one of the risk factors for atherosclerosis(AS). A growing body of evidence suggests that the two diseases are closely related. However, current studies have yet to fully understand the common genes and common mechanisms between PD and AS. This study aimed to screen the tandem genes of PD and AS and the potential relationship between the tandem genes and pan-apoptosis-related genes. By analyzing the relationship between the core genes and immune cells, it will provide new targets for clinical treatment.</div></div><div><h3>Materials and methods</h3><div>The PD and AS datasets were downloaded from the GEO database and differential expression analysis was performed to obtain DEGs. AS-related genes were downloaded from the GeneCards database, and PANoptosis-related genes were obtained through literature review. AS-related genes were merged into AS DEGs, and overlapping DEGs were cross-talk genes for PD and AS. Protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Pearson coefficients were used to calculate the correlation between cross-talk genes and PANoptosis-related genes in the PD and AS datasets. The intersection of cross-talk genes and PANoptosis-related genes was defined as cross-talk-PANoptosis genes. Core genes were screened using ROC analysis and XGBoost. PPI sub-network, gene-biological processes and gene-pathway networks were constructed based on the core genes. In addition, immune infiltration on the PD and AS datasets was analyzed using the CIBERSORT algorithm.</div></div><div><h3>Results</h3><div>285 cross-talk genes overlapped between PD DEGs and AS DEGs. The intersection of cross-talk genes with 109 PANoptosis-related genes was defined as cross-talk-PAoptosis genes. ROC and XGBoost showed that MLKL, ZBP1, CD14, and IL6 were more accurate than the other cross-talk-PAoptosis genes in predicting the diseases, and were better in terms of the overall characteristics. GO and KEGG analyses showed that these four core genes were involved in the immune and inflammatory response of the organism. The results of immune infiltration showed that Monocytes and Mast cells resting were altered to a greater extent in PD and AS patients. Finally, 24 drugs related to the core genes were retrieved from the DGIDB database.</div></div><div><h3>Conclusions</h3><div>This study reveals the joint mechanism between PD and AS associated with PANoptosis. Analyzing the four core genes and immune cells may provide new therapeutic directions for the pathogenesis of PD combined with AS.</div></div>\",\"PeriodicalId\":12521,\"journal\":{\"name\":\"Genomics\",\"volume\":\"117 6\",\"pages\":\"Article 111106\"},\"PeriodicalIF\":3.0000,\"publicationDate\":\"2025-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0888754325001223\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0888754325001223","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

背景与目的牙周炎（periodontitis， PD）是一种严重威胁口腔健康的慢性炎症性疾病，是动脉粥样硬化（AS）的危险因素之一。越来越多的证据表明这两种疾病密切相关。然而，目前的研究尚未完全了解PD和AS之间的共同基因和共同机制。本研究旨在筛选PD和AS的串联基因，以及串联基因与泛凋亡相关基因之间的潜在关系。通过分析核心基因与免疫细胞的关系，将为临床治疗提供新的靶点。材料和方法从GEO数据库中下载PD和AS数据集，进行差异表达分析，获得deg。从GeneCards数据库下载as相关基因，通过文献查阅获得panoptosis相关基因。将AS相关基因合并为AS deg，重叠deg为PD与AS的串扰基因。利用STRING数据库和Cytoscape软件构建蛋白-蛋白相互作用（PPI）网络。使用Pearson系数计算PD和AS数据集中相声基因与panoptosis相关基因之间的相关性。将相声基因与panoptosis相关基因的交集定义为相声- panoptosis基因。采用ROC分析和XGBoost筛选核心基因。以核心基因为基础构建PPI子网络、基因生物学过程和基因通路网络。此外，使用CIBERSORT算法分析PD和AS数据集上的免疫浸润。结果PD - deg与AS - deg间有285个串音基因重叠。将相声基因与109个panoptosis相关基因的交集定义为相声- panoptosis基因。ROC和XGBoost结果显示，MLKL、ZBP1、CD14和IL6在预测疾病方面比其他串音- paoptosis基因更准确，在整体特征方面也更好。GO和KEGG分析表明，这四个核心基因参与了机体的免疫和炎症反应。免疫浸润结果显示，PD和AS患者单核细胞和肥大细胞静息改变程度更大。最后，从DGIDB数据库中检索到与核心基因相关的24种药物。结论本研究揭示了帕金森病与AS合并PANoptosis的联合机制。分析这四个核心基因和免疫细胞可能为PD合并AS的发病机制提供新的治疗方向。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

Identification of cross-talk pathways and PANoptosis-related genes in periodontitis and atherosclerosis by bioinformatics analysis and machine learning

Background and objectives

Periodontitis(PD) is a chronic inflammatory disease that poses a serious threat to oral health and is one of the risk factors for atherosclerosis(AS). A growing body of evidence suggests that the two diseases are closely related. However, current studies have yet to fully understand the common genes and common mechanisms between PD and AS. This study aimed to screen the tandem genes of PD and AS and the potential relationship between the tandem genes and pan-apoptosis-related genes. By analyzing the relationship between the core genes and immune cells, it will provide new targets for clinical treatment.

Materials and methods

The PD and AS datasets were downloaded from the GEO database and differential expression analysis was performed to obtain DEGs. AS-related genes were downloaded from the GeneCards database, and PANoptosis-related genes were obtained through literature review. AS-related genes were merged into AS DEGs, and overlapping DEGs were cross-talk genes for PD and AS. Protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Pearson coefficients were used to calculate the correlation between cross-talk genes and PANoptosis-related genes in the PD and AS datasets. The intersection of cross-talk genes and PANoptosis-related genes was defined as cross-talk-PANoptosis genes. Core genes were screened using ROC analysis and XGBoost. PPI sub-network, gene-biological processes and gene-pathway networks were constructed based on the core genes. In addition, immune infiltration on the PD and AS datasets was analyzed using the CIBERSORT algorithm.

Results

285 cross-talk genes overlapped between PD DEGs and AS DEGs. The intersection of cross-talk genes with 109 PANoptosis-related genes was defined as cross-talk-PAoptosis genes. ROC and XGBoost showed that MLKL, ZBP1, CD14, and IL6 were more accurate than the other cross-talk-PAoptosis genes in predicting the diseases, and were better in terms of the overall characteristics. GO and KEGG analyses showed that these four core genes were involved in the immune and inflammatory response of the organism. The results of immune infiltration showed that Monocytes and Mast cells resting were altered to a greater extent in PD and AS patients. Finally, 24 drugs related to the core genes were retrieved from the DGIDB database.

Conclusions

This study reveals the joint mechanism between PD and AS associated with PANoptosis. Analyzing the four core genes and immune cells may provide new therapeutic directions for the pathogenesis of PD combined with AS.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.