Severe COVID-19 patients can show respiratory failure, T-cell reduction, and cytokine release syndrome (CRS), which can be fatal in both young and aged patients and is a major concern of the pandemic. However, the pathogenetic mechanisms of CRS in COVID-19 are poorly understood. Here we show single cell-level mechanisms for T-cell dysregulation in severe SARS-CoV-2 infection, and thereby demonstrate the mechanisms underlying T-cell hyperactivation and paralysis in severe COVID-19 patients. By in silico sorting CD4+ T-cells from a single cell RNA-seq dataset, we found that CD4+ T-cells were highly activated and showed unique differentiation pathways in the lung of severe COVID-19 patients. Notably, those T-cells in severe COVID-19 patients highly expressed immunoregulatory receptors and CD25, whilst repressing the expression of the transcription factor FOXP3 and interestingly, both the differentiation of regulatory T-cells (Tregs) and Th17 was inhibited. Meanwhile, highly activated CD4+ T-cells express PD-1 alongside macrophages that express PD-1 ligands in severe patients, suggesting that PD-1-mediated immunoregulation was partially operating. Furthermore, we show that CD25+ hyperactivated T-cells differentiate into multiple helper T-cell lineages, showing multifaceted effector T-cells with Th1 and Th2 characteristics. Lastly, we show that CD4+ T-cells, particularly CD25-expressing hyperactivated T-cells, produce the protease Furin, which facilitates the viral entry of SARS- CoV-2. Collectively, CD4+ T-cells from severe COVID-19 patients are hyperactivated and FOXP3-mediated negative feedback mechanisms are impaired in the lung, while activated CD4+ T-cells continue to promote further viral infection through the production of Furin. Therefore, our study proposes a new model of T-cell hyperactivation and paralysis that drives pulmonary damage, systemic CRS and organ failure in severe COVID-19 patients.

中文翻译：

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单细胞分析显示严重COVID-19感染中的T细胞过度活化和麻痹

严重的COVID-19患者可表现出呼吸衰竭，T细胞减少和细胞因子释放综合症（CRS），这对年轻和老年患者均可能是致命的，是大流行的主要关注因素。但是，对COVID-19中CRS的致病机理了解甚少。在这里，我们显示了严重SARS-CoV-2感染中T细胞失调的单细胞水平机制，从而证明了在严重COVID-19患者中T细胞过度活化和麻痹的潜在机制。通过对单个细胞RNA-seq数据集中的CD4 + T细胞进行计算机分选，我们发现CD4 + T细胞被高度激活并在重症COVID-19患者的肺中显示出独特的分化途径。值得注意的是，严重COVID-19患者中的那些T细胞高表达免疫调节受体和CD25，有趣的是，在抑制转录因子FOXP3的表达的同时，抑制了调节性T细胞（Tregs）和Th17的分化。同时，在重症患者中，高度活化的CD4 + T细胞与表达PD-1配体的巨噬细胞一起表达PD-1，表明PD-1介导的免疫调节部分起作用。此外，我们显示CD25 +过度活化的T细胞分化为多个辅助性T细胞谱系，显示出具有Th1和Th2特征的多面效应T细胞。最后，我们表明CD4 + T细胞，特别是表达CD25的超活化T细胞，产生了蛋白酶弗林蛋白酶，它促进了SARS-CoV-2的病毒进入。集体而言，来自严重COVID-19患者的CD4 + T细胞过度活化，而FOXP3介导的负反馈机制在肺中受损，而活化的CD4 + T细胞则通过产生弗林蛋白酶继续促进进一步的病毒感染。因此，我们的研究提出了一种重度COVID-19患者的T细胞过度活化和麻痹的新模型，该模型可驱动肺部损伤，全身性CRS和器官衰竭。