1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [4].
1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2].
Nature. 2014 Jun 19;510(7505):363-9. doi: 10.1038/nature13437. Epub 2014 Jun 11.
High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.
高通量单细胞转录组学为理解看似相同的细胞之间基因表达变异的程度、基础和功能提供了一种无偏倚的方法。在这里，我们对来自超过 1700 个原代小鼠骨髓来源树突状细胞的单细胞 RNA-seq 文库进行了测序，这些细胞跨越了几种实验条件。我们发现，在相同刺激的树突状细胞之间，无论是可检测到特定信使 RNA 表达的细胞比例，还是表达细胞内转录本的水平，都存在着大量的变异。不同的基因模块具有不同的时间异质性特征。特别是，抗病毒基因的“核心”模块在受到致病成分的均匀刺激时，少数“早熟”细胞会很早表达，但后来所有细胞都会被激活。通过在密封的微流控腔中单独刺激细胞、分析敲除小鼠的树突状细胞、以及调节分泌和细胞外信号，我们表明这种反应是由这些早熟细胞通过干扰素介导的旁分泌信号协调的。值得注意的是，阻止细胞间通讯也会显著降低早期诱导的“峰”炎症模块在细胞间表达的可变性，这表明旁分泌信号还会抑制炎症程序的一部分。我们的研究强调了细胞间通讯在控制细胞异质性中的重要性，并揭示了多细胞群体可以用来建立复杂动态反应的一般策略。
