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, analysis of kinetic parameters estimated from these data suggests a trade-off between robust antiviral signaling and cell death, as indicated by a higher rate of detectable cell lysis in infected cells with a detectable immune response. In short, cells that activate an immune response lyse at a higher rate. 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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单个细胞中病毒感染对先天性免疫激活的定量分析

被病毒感染的细胞可以表现出病毒和细胞基因表达的多种模式。该模式部分源于与少数基因组，酶和其他通常引发病毒复制并激活细胞抗病毒防御作用的分子相关的随机或嘈杂的反应动力学。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）与病毒复制或细胞存活的后期过程相关。在这里，我们使用了两个荧光报告器来可视化人类前列腺癌（PC3）细胞针对水泡性口炎病毒感染的先天免疫激活。这些细胞经过改造后可以在IFIT2（抗病毒应答的干扰素敏感成分）启动子的控制下表达绿色荧光蛋白，而红色荧光蛋白被表达为病毒感染的副产物。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。对来自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型关系。具体而言，病毒基因表达和先天性免疫激活的相对时机而不是其大小与感染的结果相关。较早的病毒或抗病毒基因表达分别有利于或阻碍病毒的生长。此外，根据这些数据估算的动力学参数分析表明，在强大的抗病毒信号传导与细胞死亡之间需要权衡取舍，如在具有可检测的免疫应答的感染细胞中可检测的细胞裂解率更高。简而言之，激活免疫反应的细胞裂解率更高。更广泛地说，我们证明了如何利用单个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扩散。