Department of Animal Model, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Department of Infectious Disease, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Front Immunol. 2021 Feb 24;12:625881. doi: 10.3389/fimmu.2021.625881. eCollection 2021.
T cells play a critical role in coronavirus diseases. How they do so in COVID-19 may be revealed by analyzing the epigenetic chromatin accessibility of cis- and trans-regulatory elements and creating transcriptomic immune profiles. We performed single-cell assay for transposase-accessible chromatin (scATAC) and single-cell RNA (scRNA) sequencing (seq) on the peripheral blood mononuclear cells (PBMCs) of severely ill/critical patients (SCPs) infected with COVID-19, moderate patients (MPs), and healthy volunteer controls (HCs). About 76,570 and 107,862 single cells were used, respectively, for analyzing the characteristics of chromatin accessibility and transcriptomic immune profiles by the application of scATAC-seq (nine cases) and scRNA-seq (15 cases). The scATAC-seq detected 28,535 different peaks in the three groups; among these peaks, 41.6 and 10.7% were located in the promoter and enhancer regions, respectively. Compared to HCs, among the peak-located genes in the total T cells and its subsets, CD4 T and CD8 T cells, from SCPs and MPs were enriched with inflammatory pathways, such as mitogen-activated protein kinase (MAPK) signaling pathway and tumor necrosis factor (TNF) signaling pathway. The motifs of TBX21 were less accessible in the CD4 T cells of SCPs compared with those in MPs. Furthermore, the scRNA-seq showed that the proportion of T cells, especially the CD4 T cells, was decreased in SCPs and MPs compared with those in HCs. Transcriptomic results revealed that histone-related genes, and inflammatory genes, such as NFKBIA, S100A9, and PIK3R1, were highly expressed in the total T cells, CD4 T and CD8 T cells, both in the cases of SCPs and MPs. In the CD4 T cells, decreased T helper-1 (Th1) cells were observed in SCPs and MPs. In the CD8T cells, activation markers, such as CD69 and HLA class II genes (HLA-DRA, HLA-DRB1, and HLA-DRB5), were significantly upregulated in SCPs. An integrated analysis of the data from scATAC-seq and scRNA-seq showed some consistency between the approaches. Cumulatively, we have generated a landscape of chromatin epigenetic status and transcriptomic immune profiles of T cells in patients with COVID-19. This has provided a deeper dissection of the characteristics of the T cells involved at a higher resolution than from previously obtained data merely by the scRNA-seq analysis. Our data led us to suggest that the T-cell inflammatory states accompanied with defective functions in the CD4 T cells of SCPs may be the key factors for determining the pathogenesis of and recovery from COVID-19.
T 细胞在冠状病毒疾病中发挥着关键作用。通过分析顺式和反式调控元件的表观遗传染色质可及性，并构建转录组免疫图谱，可能揭示 COVID-19 中 T 细胞的作用机制。我们对感染 COVID-19 的重症/危重症患者（SCPs）、中度患者（MPs）和健康志愿者对照（HCs）的外周血单核细胞（PBMCs）进行了转座酶可及染色质（scATAC）和单细胞 RNA（scRNA）测序（seq）的单细胞分析。分别应用 scATAC-seq（9 例）和 scRNA-seq（15 例）分析染色质可及性和转录组免疫图谱特征，分别使用了约 76570 和 107862 个单细胞。三组中 scATAC-seq 共检测到 28535 个不同的峰；其中，41.6%和 10.7%分别位于启动子和增强子区域。与 HCs 相比，SCPs 和 MPs 中的总 T 细胞及其亚群（CD4 T 和 CD8 T 细胞）中的峰定位基因富集了有丝分裂原激活蛋白激酶（MAPK）信号通路和肿瘤坏死因子（TNF）信号通路等炎症途径。与 MPs 相比，SCPs 中 CD4 T 细胞中 TBX21 基序的可及性较低。此外，scRNA-seq 显示，SCPs 和 MPs 中的 T 细胞，尤其是 CD4 T 细胞的比例低于 HCs。转录组学结果表明，在 SCPs 和 MPs 中，总 T 细胞、CD4 T 和 CD8 T 细胞中组蛋白相关基因和炎症基因（如 NFKBIA、S100A9 和 PIK3R1）的表达水平较高。在 CD4 T 细胞中，SCPs 和 MPs 中 Th1 细胞减少。在 CD8 T 细胞中，SCPs 中 CD69 和 HLA Ⅱ类基因（HLA-DRA、HLA-DRB1 和 HLA-DRB5）等激活标志物的表达显著上调。scATAC-seq 和 scRNA-seq 数据的综合分析显示，这两种方法之间存在一定的一致性。总的来说，我们生成了 COVID-19 患者 T 细胞染色质表观遗传状态和转录组免疫图谱的图谱。这比仅通过 scRNA-seq 分析获得的数据更深入地解析了 T 细胞的特征，分辨率更高。我们的数据表明，SCPs 中 CD4 T 细胞的 T 细胞炎症状态和功能缺陷可能是决定 COVID-19 发病机制和恢复的关键因素。
