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

总结 在严重COVID-19疾病中幸存的患者有发生肺部并发症的风险。虽然这可能 解决后，一些患者会经历疾病的进展，导致严重的肺损伤。虽然T 细胞对于肺部的抗病毒反应至关重要，COVID-19后血液中持续的T细胞改变 疾病使他们陷入持续的疾病。关于是否以及如何传播， T细胞有助于肺部病理学。我们的理解受到肺部疾病的临床性质的影响， 疾病，以及识别血液中的致病性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克服了这些障碍， 强大的机器学习工具，这些工具经过精心定制，可以检测细胞中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， COVID-19的并发症这项研究利用了一个独特的和高度特征化的COVID-19患者队列 根据其急性疾病的严重程度和发展中的纤维化来定义。通过收集数百个蜂窝和 通过对大量患者样本的分子特征进行分析，我们现在准备大大推进这一领域。初步 研究结果揭示了区分严重气道疾病的肺表型， CD 4+和CD 8 + T细胞群，包括产生IFN-γ的病毒特异性细胞，与这些临床疾病相关。 实体.鉴定的T细胞的一个共同特征是它们表达T-bet，T-bet是一种转录因子， 通过组织归巢B细胞在COVID-19疾病后持续存在。此外，我们的数据支持这些之间的相互作用 T细胞和B细胞。因此，我们将检验一个总体假设，即在新的环境中持续的扰动， 表达T-bet的CD 4+和CD 8 + T细胞，包括病毒特异性细胞，标记促纤维化肺表型。 这些细胞通过协调的行动创造了IFN-γ依赖性炎症的持续前馈回路 有B细胞。首先，将定义肺部疾病的免疫程序，并绘制其轨迹， 基于协同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 介体在体内运行超过2年。这将涉及解决蛋白质签名和基因表达 在前所未有的深度研究T细胞的分布，以确定它们的功能和进化（目标1）。接下来 表位特异性T细胞对不同恢复途径的贡献将被区分，以解决如何 进展和消退受病毒表位调节（Aim 2）。为此，组合四聚体方法 将监测每个受试者内多达6个表位特异性的比例和功能。最后我们将 证实来自患有纤维化的受试者的致病性T细胞与T-bet+ B细胞协同作用的能力 通过在体外促进IFN-γ依赖性炎症，通过涉及一种新的潜在生物标志物的过程， 疾病进展，CXCL 13（Aim 3）。组装“T细胞之谜的元素”将确定 这些疾病揭示了新的治疗靶点，可以在COVID-19疾病后停止或逆转肺部炎症。

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.