综合转录组学分析利用综合生物信息学方法鉴定TNF和IL1B是光滑布鲁氏菌感染巨噬细胞的候选关键早期反应基因。

IF 3.6 3区 生物学 Q1 BIOLOGY
Xiaoyu Yang, Qiang Chen
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引用次数: 0

摘要

光滑布鲁氏菌是威胁人类健康和食品安全的主要致病菌。平滑布鲁氏菌与巨噬细胞相互作用的早期阶段是一个重要的阶段,平滑布鲁氏菌在感染的巨噬细胞中引起了剧烈的转录反应。然而,关键的转录事件仍然不清楚。本研究旨在确定感染光滑布鲁氏菌的巨噬细胞在早期相互作用阶段的关键候选反应途径和基因。从NCBI GEO数据库中检索GSE21117、GSE5202和GSE8385三个基因表达谱,并采用基因集富集分析、差异表达基因分析、蛋白与蛋白相互作用(PPI)网络构建和转录因子预测等综合生物信息学方法进行整合。结果显示,共鉴定出16条上调通路和22条下调通路,其中免疫相关通路上调6条。共鉴定出41个上调基因和4个下调基因,并基于45个异常基因的交互信息构建了包含31个节点和134个边的PPI网络。基于整个PPI网络的拓扑特征,确定了一个包含19个节点和103条边的高度相关模块。7项中心性分析显示,Tnf和Il1b是高度相关模块中的必需基因,并且这两个必需基因同时富集在8条显著上调的通路中(包括2条免疫相关通路)。Bcl3被预测为高度相关模块中的转录因子,并可能在Tnf和Il1b基因的转录中发挥调节作用。本研究确定了Tnf和IL1b作为平滑布鲁氏菌与巨噬细胞相互作用早期感染巨噬细胞的候选关键应答基因,这有助于更深入地了解平滑布鲁氏菌感染巨噬细胞的早期关键转录事件。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Integrative Transcriptomic Profiling Identifies TNF and IL1B as Candidate Key Early-Response Genes in Macrophages Infected with Smooth Brucella Using a Comprehensive Bioinformatic Approach.

Smooth Brucella are the main pathogenic bacteria that threaten human health and food safety. The early stage of smooth Brucella and macrophage interaction is an important phase, and smooth Brucella species elicit a dramatic transcriptional response in infected macrophages. However, the key transcriptional events are still obscure. This study aimed to identify key candidate response pathways and genes in macrophages infected with smooth Brucella at the early interaction stage. Three gene expression profiles including GSE21117, GSE5202, and GSE8385 were retrieved from the NCBI GEO database, and were integrated using comprehensive bioinformatics methods including gene set enrichment analysis, differentially expressed gene analysis, protein and protein interaction (PPI) network construction, and transcription factor prediction. The results showed that 16 up-regulated and 22 down-regulated pathways were identified, including six up-regulated immune-related pathways. A total of 41 up-regulated and four down-regulated genes were identified, and a PPI network including 31 nodes and 134 edges was constructed based on the interactive information of 45 dysregulated genes. A highly correlated module comprising 19 nodes and 103 edges was identified based on the topological features of the whole PPI network. Seven centrality analyses revealed that Tnf and Il1b were essential genes in the highly correlated module, and that the two essential genes were simultaneously enriched in eight significantly up-regulated pathways (including two immune-related pathways). Bcl3 was predicted as a transcription factor in the highly correlated module, and may play regulatory roles in the transcription of Tnf and Il1b genes. The present study identified Tnf and IL1b as candidate key response genes in infected macrophages at the early stage of smooth Brucella and macrophage interaction, which contributes to a deeper understanding of the early key transcriptional events in macrophages infected with smooth Brucella species.

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来源期刊
Biology-Basel
Biology-Basel Biological Science-Biological Science
CiteScore
5.70
自引率
4.80%
发文量
1618
审稿时长
11 weeks
期刊介绍: Biology (ISSN 2079-7737) is an international, peer-reviewed, quick-refereeing open access journal of Biological Science published by MDPI online. It publishes reviews, research papers and communications in all areas of biology and at the interface of related disciplines. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There is no restriction on the length of the papers. The full experimental details must be provided so that the results can be reproduced. Electronic files regarding the full details of the experimental procedure, if unable to be published in a normal way, can be deposited as supplementary material.
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