Understanding of the molecular regulatory mechanisms underlying the inflammatory response is incomplete. The present study focuses on characterizing the proteome in a model of inflammation in macrophages treated with lipopolysaccharide (LPS). A total of 3597 proteins are identified in macrophages with the data-independent acquisition (DIA) method. Bioinformatic analyses reveal discrete modules and the underlying molecular mechanisms, as well as the signaling network that modulates the development of inflammation. It is found that a total of 87 differentially expressed proteins are shared by all stages of LPS-induced inflammation in macrophages and that 18 of these proteins participate in metabolic processes by forming a tight interaction network. Data support the hypothesis that ribosome proteins play a key role in regulating the macrophage response to LPS. Interestingly, conjoint analyses of the transcriptome and proteome in macrophages treated with LPS reveal that the genes upregulated at both the mRNA and protein levels are mainly involved in inflammation and the immune response, whereas the genes downregulated are significantly enriched in metabolism-related processes. These results not only provide a more comprehensive understanding of the molecular mechanisms of inflammation mediated by bacterial infection but also provide a dynamic proteomic resource for further studies.

中文翻译：

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基于数据的基于采集的定量蛋白质组学分析揭示了巨噬细胞炎症反应过程中的动态网络概况。

对炎症反应的分子调控机制的了解还不完全。本研究的重点是在用脂多糖（LPS）处理的巨噬细胞的炎症模型中表征蛋白质组。使用数据独立获取（DIA）方法在巨噬细胞中鉴定出总共3597种蛋白质。生物信息学分析揭示了离散的模块和潜在的分子机制，以及调节炎症发展的信号网络。发现在巨噬细胞中，LPS诱导的炎症的所有阶段共有87种差异表达的蛋白质，这些蛋白质中的18种通过形成紧密的相互作用网络而参与代谢过程。数据支持以下假设：核糖体蛋白在调节巨噬细胞对LPS的反应中起关键作用。有趣的是，对用LPS处理的巨噬细胞的转录组和蛋白质组进行的联合分析显示，在mRNA和蛋白水平上调的基因主要参与炎症和免疫反应，而下调的基因则在代谢相关过程中显着丰富。这些结果不仅提供了对细菌感染介导的炎症分子机制的更全面的了解，而且为进一步的研究提供了动态的蛋白质组学资源。LPS处理的巨噬细胞的转录组和蛋白质组的联合分析显示，在mRNA和蛋白质水平上调的基因主要参与炎症和免疫反应，而下调的基因则在代谢相关过程中显着丰富。这些结果不仅提供了对细菌感染介导的炎症分子机制的更全面的了解，而且为进一步的研究提供了动态的蛋白质组学资源。LPS处理的巨噬细胞的转录组和蛋白质组的联合分析显示，在mRNA和蛋白质水平上调的基因主要参与炎症和免疫反应，而下调的基因则在代谢相关过程中显着丰富。这些结果不仅提供了对细菌感染介导的炎症分子机制的更全面的了解，而且为进一步的研究提供了动态的蛋白质组学资源。