Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. It is not known what features, if any, of the early viral or cellular gene expression correlate with later processes of viral replication or cell survival. Here we used two fluorescent reporters to visualize innate immune activation of human prostate cancer (PC3) cells against infection by vesicular stomatitis virus. The cells were engineered to express green-fluorescent protein under control of the promoter for IFIT2, an interferon-sensitive component of the anti-viral response, while red-fluorescent protein was expressed as a byproduct of virus infection. To isolate and quantitatively analyze single-cells, we used a unique microwell array device and open-source image processing software. Kinetic analysis of viral and cellular reporter profiles from hundreds of cells revealed novel relationships between gene expression and the outcome of infection. Specifically, the relative timing rather than the magnitude of the viral gene expression and innate immune activation correlated with the infection outcome. Earlier viral or anti-viral gene expression favored or hindered virus growth, respectively. Further, a correlation analysis of kinetic parameters estimated from these data showed a trade-off between robust antiviral signaling and cell death, as indicated by detectable cell lysis. More broadly, we demonstrate how the intrinsic heterogeneity of individual cell behaviors can be exploited to discover features of viral and host gene expression that correlate with single-cell outcomes, which will ultimately impact whether or not infections spread.

中文翻译：

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单细胞中病毒感染引起的先天免疫激活的定量分析


被病毒感染的细胞可以表现出不同的病毒和细胞基因表达模式。这些模式部分源于与少量基因组、酶和其他分子相关的随机或噪声反应动力学，这些分子通常启动病毒复制并激活细胞抗病毒防御。目前尚不清楚早期病毒或细胞基因表达的哪些特征（如果有的话）与后来的病毒复制或细胞存活过程相关。在这里，我们使用两个荧光报告基因来观察人类前列腺癌（PC3）细胞针对水泡性口炎病毒感染的先天免疫激活。这些细胞被设计成在 IFIT2 启动子的控制下表达绿色荧光蛋白，IFIT2 是抗病毒反应的干扰素敏感成分，而红色荧光蛋白则作为病毒感染的副产物表达。为了分离和定量分析单细胞，我们使用了独特的微孔阵列设备和开源图像处理软件。对数百个细胞的病毒和细胞报告基因谱的动力学分析揭示了基因表达与感染结果之间的新关系。具体来说，病毒基因表达和先天免疫激活的相对时间而不是程度与感染结果相关。早期的病毒或抗病毒基因表达分别有利于或阻碍病毒生长。此外，根据这些数据估计的动力学参数的相关分析显示，如可检测到的细胞裂解所示，强大的抗病毒信号传导和细胞死亡之间存在权衡。 更广泛地说，我们展示了如何利用个体细胞行为的内在异质性来发现与单细胞结果相关的病毒和宿主基因表达的特征，这最终将影响感染是否传播。