Immune Programs and Related T Cell Mechanisms of Pulmonary Complications After COVID-19 Illness

摘要 在严重的新冠肺炎疾病中幸存下来的患者有发生肺部并发症的风险。虽然这可能会 解决，一些患者经历他们的疾病的进展，导致严重的肺损伤。虽然T 细胞是肺部抗病毒反应的关键，新冠肺炎后血液中持续的T细胞变化 疾病使他们陷入持续的疾病之中。关于是否以及如何流通，存在着重大的知识差距 T细胞在肺部病理中起作用。由于肺炎性疾病的临床性质多种多样，我们的认识受到了阻碍。 疾病，以及在识别血液中的致病T细胞和确定与 病程。目前的项目通过应用创新的单细胞方法和 强大的机器学习工具，经过精心定制，可检测与疾病相关的细胞群 血液，并定义构成免疫程序的细胞和分子动力学 新冠肺炎的并发症。这项研究利用了一组独特且具有高度特征性的新冠肺炎患者 根据他们急性疾病的严重程度和发展中的纤维化来定义。通过收集数百个手机和手机上的数据 在大样本患者的分子特征方面，我们现在已经准备好显著推进这一领域。初步 研究结果显示，肺表型可以区分严重的呼吸道疾病和离散的扰动 T细胞亚群，包括产生干扰素-γ的病毒特异性细胞，与这些临床相关 实体。已发现的T细胞的一个共同特征是它们表达T-bet，T-bet是一种也表达的转录因子 通过组织归巢的B细胞，这些细胞在新冠肺炎病后仍然存在。此外，我们的数据支持这些因素之间的相互作用 T细胞和B细胞。因此，我们将检验小说中持续的扰动这一首要假设 表达T-bet的CD4和CD8T细胞，包括病毒特异性细胞，标志着促纤维化的肺表型。 这些细胞通过协调作用产生干扰素-γ依赖的炎症的持续前馈回路。 B细胞。首先，将定义肺部疾病的免疫程序，并绘制其轨迹图 协同T细胞、其他免疫细胞和炎性细胞与疾病进展和恢复的关系 在活体内工作的调解人超过2年。这将涉及解决蛋白质签名和基因表达 以前所未有的深度分析T细胞，以确定其功能和进化(目标1)。接下来， 将区分表位特异性T细胞对不同恢复路径的贡献，以解决如何 进展和分解由病毒表位调节(目标2)。为此，一种组合四聚体方法 将监测每个对象中最多6个表位特异性的比例和功能。最后，我们会 确认发展中的纤维化患者的致病T细胞与T-bet B细胞协同作用的能力 通过在体外促进干扰素-γ依赖的炎症，通过涉及一个新的潜在的生物标志物的过程 疾病进展，CXCL13(目标3)。组装“T细胞拼图的元素”将确定 显示新冠肺炎病后肺部炎症停止或逆转的新治疗靶点的疾病。

SUMMARY Patients who survive severe COVID-19 illness are at risk of developing pulmonary complications. While this may resolve, some patients experience progression of their disease, resulting in severe lung damage. Although T cells are critical to anti-viral responses in the lungs, sustained T-cell alterations in the blood after COVID-19 illness implicates them in persistent disease. There is a major knowledge gap regarding if, and how, circulating T cells contribute to lung pathology. Our understanding is hampered by the variable clinical nature of pulmonary disease, as well as the challenges to identifying pathogenic T cells in the blood and defining relationships to disease course. The current project overcomes these barriers by applying innovative single-cell methods and powerful machine learning tools that are exquisitely tailored to detect disease-relevant cell populations in the blood, and to define the cellular and molecular dynamics that constitute immune programs governing pulmonary complications of COVID-19. The study leverages a unique and highly characterized cohort of COVID-19 patients defined by their severity of acute illness and developing fibrosis. By garnering data on hundreds of cellular and molecular features in a large sample of patients, we are now poised to significantly advance the field. Preliminary findings reveal pulmonary phenotypes that discriminate severe airway disease, and perturbations in discrete CD4+ and CD8+ T-cell populations, including IFN-γ-producing virus-specific cells, related to these clinical entities. A shared feature of T cells identified is their expression of T-bet, a transcription factor also expressed by tissue-homing B cells that persist after COVID-19 illness. Further, our data support an interplay between these T cells and B cells. Accordingly, we will test the overarching hypothesis that sustained perturbations in novel CD4+ and CD8+ T cells expressing T-bet, including virus-specific cells, mark pro-fibrotic pulmonary phenotypes. These cells create a persistent feedforward circuit of IFN-γ-dependent inflammation through coordinated actions with B cells. First, immune programs of pulmonary disease will be defined and their trajectories mapped in relation to progression and recovery on the basis of concerted T cells, other immune cells and inflammatory mediators operating in vivo over 2 years. This will involve resolving protein signatures and gene expression profiles of T cells at unprecedented depth to determine their functions and evolution (Aim 1). Next, the contributions of epitope-specific T cells to divergent recovery paths will be distinguished in order to address how progression and resolution is regulated by virus epitopes (Aim 2). To this end, a combinatorial tetramer method will monitor the proportions and functions of up to 6 epitope specificities within each subject. Finally, we will confirm the ability for pathogenic T cells from subjects with developing fibrosis, to synergize with T-bet+ B cells by promoting IFN-γ-dependent inflammation in vitro, through a process involving a novel potential biomarker of disease progression, CXCL13 (Aim 3). Assembling “elements of the T-cell puzzle” will identify mechanisms of disease that reveal new therapeutic targets for halting or reversing lung inflammation after COVID-19 illness.