Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion.
Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion.
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DOI：
10.12688/wellcomeopenres.17946.1
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发表时间：
2022
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背景资料：定量蛋白质组学能够对病毒感染引起的细胞变化提供全面、公正的描述，但由于感染和未感染的“旁观者”细胞的差异变化或使用非生理细胞模型，解释可能会变得复杂。 研究方法：在本文中，我们使用荧光激活细胞分选术（FACS）和定量蛋白质组学分析真实的SARS冠状病毒-2感染的呼吸道上皮细胞，病毒感染的主要目标在体内引起的细胞自主的变化。首先，我们确定了在气液界面分化的原代人气道上皮细胞（基底细胞、分泌细胞和纤毛细胞）中蛋白质的相对丰度。接下来，我们专门研究了SARS-CoV-2感染纤毛细胞引起的变化。最后，我们比较了感染和未感染的“旁观者”Calu-3肺上皮细胞的时间蛋白质组变化，并比较了B.29和B.1.1.7（Alpha）变体的感染。 结果如下：在原代人气道纤毛细胞中的5，709种定量蛋白质中，226种蛋白质的丰度在SARS-CoV-2感染的存在下发生显著变化（q <0.05 and >1.5倍）。值得注意的是，病毒复制在不诱导I型干扰素应答的情况下进行。在Calu-3细胞中的6，996种定量蛋白质中，645种蛋白质的丰度在SARS-CoV-2感染的存在下显著改变（q < 0.05 and >1.5倍）。与原代细胞模型相反，观察到明显的I型干扰素（IFN）应答。尽管如此，与未感染的“旁观者”细胞相比，IFN诱导蛋白的诱导在感染细胞中明显减弱。用B.29和B.1.1.7（α）变体感染得到类似的结果。 结论：总之，我们的数据提供了一个详细的蛋白质组学图谱的变化，在SARS冠状病毒2感染的呼吸道上皮细胞在两个广泛使用的，生理相关的感染模型。以及确定失调的细胞蛋白质和过程，SARS-CoV-2所采用的策略，以避免I型干扰素反应的有效性在两个模型中说明。
Background: Quantitative proteomics is able to provide a comprehensive, unbiased description of changes to cells caused by viral infection, but interpretation may be complicated by differential changes in infected and uninfected ‘bystander’ cells, or the use of non-physiological cellular models. Methods: In this paper, we use fluorescence-activated cell sorting (FACS) and quantitative proteomics to analyse cell-autonomous changes caused by authentic SARS-CoV-2 infection of respiratory epithelial cells, the main target of viral infection in vivo. First, we determine the relative abundance of proteins in primary human airway epithelial cells differentiated at the air-liquid interface (basal, secretory and ciliated cells). Next, we specifically characterise changes caused by SARS-CoV-2 infection of ciliated cells. Finally, we compare temporal proteomic changes in infected and uninfected ‘bystander’ Calu-3 lung epithelial cells and compare infection with B.29 and B.1.1.7 (Alpha) variants. Results: Amongst 5,709 quantified proteins in primary human airway ciliated cells, the abundance of 226 changed significantly in the presence of SARS-CoV-2 infection (q <0.05 and >1.5-fold). Notably, viral replication proceeded without inducing a type-I interferon response. Amongst 6,996 quantified proteins in Calu-3 cells, the abundance of 645 proteins changed significantly in the presence of SARS-CoV-2 infection (q < 0.05 and > 1.5-fold). In contrast to the primary cell model, a clear type I interferon (IFN) response was observed. Nonetheless, induction of IFN-inducible proteins was markedly attenuated in infected cells, compared with uninfected ‘bystander’ cells. Infection with B.29 and B.1.1.7 (Alpha) variants gave similar results. Conclusions: Taken together, our data provide a detailed proteomic map of changes in SARS-CoV-2-infected respiratory epithelial cells in two widely used, physiologically relevant models of infection. As well as identifying dysregulated cellular proteins and processes, the effectiveness of strategies employed by SARS-CoV-2 to avoid the type I IFN response is illustrated in both models.