DataSheet_1_Increased Expression of Tim-3 Is Associated With Depletion of NKT Cells In SARS-CoV-2 Infection.docx

In the ongoing coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), natural killer T (NKT) cells act as primary initiators of immune responses. However, a decrease of circulating NKT cells has been observed in COVID-19 different stages, of which the underlying mechanism remains to be elucidated. Here, by performing single-cell RNA sequencing analysis in three large cohorts of COVID-19 patients, we found that increased expression of Tim-3 promotes depletion of NKT cells during the progression stage of COVID-19, which is associated with disease severity and outcome of patients with COVID-19. Tim-3+ NKT cells also expressed high levels of CD147 and CD26, which are potential SARS-CoV-2 spike binding receptors. In the study, Tim-3+ NKT cells showed high enrichment of apoptosis, higher expression levels of mitochondrial genes and caspase genes, with a larger pseudo time value. In addition, Tim-3+ NKT cells in COVID-19 presented a stronger capacity to secrete IFN-γ, IL-4 and IL-10 compared with healthy individuals, they also demonstrated high expression of co-inhibitory receptors such as PD-1, CTLA-4, and LAG-3. Moreover, we found that IL-12 secreted by dendritic cells (DCs) was positively correlated with up-regulated expression of Tim-3 in NKT cells in COVID-19 patients. Overall, this study describes a novel mechanism by which up-regulated Tim-3 expression induced the depletion and dysfunction of NKT cells in COVID-19 patients. These findings not only have possible implications for the prediction of severity and prognosis in COVID-19 but also provide a link between NKT cells and future new therapeutic strategies in SARS-CoV-2 infection.

在当前由严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）引起的冠状病毒疾病2019（COVID-19）疫情中，自然杀伤T细胞（NKT细胞）充当免疫反应的主要启动者。然而，在COVID-19的不同阶段，循环中NKT细胞的减少已被观察到，但其潜在机制尚待阐明。在本研究中，通过对三个大型COVID-19患者队列进行单细胞RNA测序分析，我们发现Tim-3表达的增加促进了COVID-19进展阶段NKT细胞的耗竭，这与疾病的严重程度和COVID-19患者的预后相关。Tim-3+ NKT细胞还表达了高水平的CD147和CD26，这些是潜在的SARS-CoV-2刺突结合受体。在研究中，Tim-3+ NKT细胞显示出高度富集的细胞凋亡、线粒体基因和caspase基因的高表达水平，以及更大的伪时间值。此外，与健康个体相比，COVID-19中的Tim-3+ NKT细胞表现出更强的分泌干扰素-γ（IFN-γ）、白细胞介素-4（IL-4）和白细胞介素-10（IL-10）的能力，同时它们也显示出高表达共抑制受体，如程序性死亡受体1（PD-1）、细胞毒性T淋巴细胞相关蛋白4（CTLA-4）和淋巴细胞激活基因3（LAG-3）。此外，我们发现树突状细胞（DCs）分泌的IL-12与COVID-19患者中NKT细胞Tim-3上调表达呈正相关。总体而言，本研究描述了一种新的机制，即上调的Tim-3表达诱导COVID-19患者中NKT细胞的耗竭和功能障碍。这些发现不仅对预测COVID-19的严重程度和预后具有潜在影响，而且为NKT细胞与SARS-CoV-2感染未来新治疗策略之间的联系提供了桥梁。