Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, 90095, USA.
Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Mol Syst Biol. 2024 Aug;20(8):898-932. doi: 10.1038/s44320-024-00047-4. Epub 2024 Jun 13.
Macrophages sense pathogens and orchestrate specific immune responses. Stimulus specificity is thought to be achieved through combinatorial and dynamical coding by signaling pathways. While NFκB dynamics are known to encode stimulus information, dynamical coding in other signaling pathways and their combinatorial coordination remain unclear. Here, we established live-cell microscopy to investigate how NFκB and p38 dynamics interface in stimulated macrophages. Information theory and machine learning revealed that p38 dynamics distinguish cytokine TNF from pathogen-associated molecular patterns and high doses from low, but contributed little to information-rich NFκB dynamics when both pathways are considered. This suggests that immune response genes benefit from decoding immune signaling dynamics or combinatorics, but not both. We found that the heterogeneity of the two pathways is surprisingly uncorrelated. Mathematical modeling revealed potential sources of uncorrelated heterogeneity in the branched pathway network topology and predicted it to drive gene expression variability. Indeed, genes dependent on both p38 and NFκB showed high scRNAseq variability and bimodality. These results identify combinatorial signaling as a mechanism to restrict NFκB-AND-p38-responsive inflammatory cytokine expression to few cells.
巨噬细胞感知病原体并协调特定的免疫反应。人们认为通过信号通路的组合和动态编码来实现刺激特异性。虽然已知 NFκB 动力学可以编码刺激信息,但其他信号通路的动态编码及其组合协调仍不清楚。在这里,我们建立了活细胞显微镜技术来研究 NFκB 和 p38 动力学在受刺激的巨噬细胞中如何相互作用。信息论和机器学习表明,p38 动力学可以区分细胞因子 TNF 与病原体相关分子模式,以及高剂量与低剂量,但当同时考虑两条途径时,对富含信息的 NFκB 动力学贡献不大。这表明免疫反应基因受益于解码免疫信号动力学或组合,但不是两者兼而有之。我们发现两条途径的异质性出人意料地没有相关性。数学模型揭示了分支途径网络拓扑中不相关异质性的潜在来源,并预测它会驱动基因表达的可变性。事实上,依赖 p38 和 NFκB 的基因表现出高的 scRNAseq 可变性和双峰性。这些结果确定了组合信号作为一种机制,将 NFκB-AND-p38 反应性炎症细胞因子的表达限制在少数细胞中。