Dissection of influenza infection in vivo by single-cell RNA-sequencing

The influenza virus is a major cause of morbidity and mortality worldwide, yet, the impact of intracellular viral invasion and the cellular response diversity remain uncharacterized. By massively parallel single-cell RNA-seq we comprehensively mapped the host lung response to in-vivo influenza infection in wild-type and Irf7-knockout mice across nine immune and non-immune cell types. We found an unexpected high prevalence of infected cells in all cell types, showed that infection is a characteristic property of cell types that is independent of type-I interferon activity, and demonstrated that all cell types responded primarily with a robust generic transcriptional response. Analysis of the viral and host transcriptomes in the same single cell enabled us to resolve the heterogeneity of bystander (exposed but uninfected) as compared to viral-infected cells. Our results highlight novel markers specific for influenza-infected as opposed to bystander cells, opening new avenues for targeted therapy aimed exclusively at infected cells. Overall design: We used Massively parallel single-cell RNA-seq (MARS-seq) to characterize single cell RNA-seq of immune (CD45+) and non-immune (CD45-) cells derived from the lungs of influenza-treated and PBS-treated mice.流行性感冒病毒是全球范围内引发高发病率与高死亡率的主要病原体之一，然而细胞内病毒侵袭过程及细胞应答多样性的相关机制仍未得到系统阐明。本研究通过大规模平行单细胞RNA测序（massively parallel single-cell RNA-seq），对野生型与干扰素调节因子7敲除（Irf7-knockout）小鼠的体内流感感染模型，全面绘制了肺部宿主应答的细胞图谱，涵盖9种免疫细胞与非免疫细胞类型。研究团队观测到所有细胞类型中均存在出乎意料的高比例感染细胞，证实感染是细胞类型固有的特征属性，且该属性不依赖于I型干扰素（type-I interferon）活性；同时发现所有细胞类型主要呈现出强烈的通用转录应答模式。通过对同一单细胞内的病毒与宿主转录组进行联合分析，本研究得以解析病毒感染细胞与旁观（暴露但未感染）细胞之间的异质性。本研究结果鉴定出流感感染细胞相较于旁观细胞的特异性新型标志物，为仅靶向感染细胞的精准治疗开辟了全新研究方向。整体实验设计：本研究采用大规模平行单细胞RNA测序（Massively parallel single-cell RNA-seq, MARS-seq）技术，对流感处理组与磷酸盐缓冲液（PBS）处理组小鼠肺部来源的免疫细胞（CD45+）与非免疫细胞（CD45-）开展单细胞转录组测序分析。