Decoding the cellular mechanisms of COVID-19 severe disease susceptibility in patients with chronic respiratory disease

项目摘要 新型冠状病毒（SARS-CoV-2）及其相关疾病（COVID-19）是全球性的威胁， 经济和公共卫生，因为它的高度传染性和快速传播。开发最佳的 为了制定治疗COVID-19的策略，了解细胞类型和分子机制至关重要， 介导冠状病毒感染、组织繁殖和宿主免疫应答。正如最近报道的那样， SARS-CoV和SARS-CoV-2利用宿主ACE 2受体蛋白和蛋白酶TMPRSS 2获得细胞 入境高通量单细胞RNA测序（scRNA-seq）和转座酶可降解性测定 染色质（scATAC-seq）现在允许我们以前所未有的分辨率询问细胞类型和细胞状态， 这导致了肺组织生物学的突破性发现，包括我们实验室的和人类细胞 Atlas最近对共表达ACE 2和TMPRSS 2的鼻和肺上皮细胞类型的调查与 疾病表型据报道，患有慢性呼吸道疾病的人 易患COVID-19严重疾病。我们建议利用我们在肺生物学、单细胞 分析，并在西奈山从COVID-19慢性呼吸道疾病患者中获得独特的肺组织 疾病合并症，以确定介导COVID-19疾病的细胞类型和调控机制 由于SARS-CoV-2感染、传播和与宿主免疫反应的相互作用而引起的易感性。 为了实现这一目标，我们将进行scRNA-seq，scATAC-seq和空间转录组测序的多个 25-30例COVID-19和慢性阻塞性肺疾病患者的感染和非感染肺区域 尸检后的疾病合并症。单细胞分辨率数据将使我们能够表征 SARS-CoV-2感染细胞及其周围基质和免疫微环境组成，以及它们如何 有助于发展COVID-19严重疾病。来自匹配肺区域的scATAC-seq数据的分析 将确定关键的转录因子和调控机制，驱动相关的表达程序， 病毒感染、宿主免疫应答和严重疾病易感性。最后，配体-受体的整合 对表达和空间转录组学信息将阐明在更大的分辨率和规模如何细胞， 冠状病毒感染后细胞相互作用和组织病理学发生改变。单细胞表征的 细胞类型，免疫反应和感染的调节机制将提高我们对病毒的理解- 慢性呼吸道疾病患者的宿主相互作用和COVID-19严重疾病易感性。这 反过来，将为发现新的治疗靶点提供机制上的见解， 有呼吸系统疾病的COVID-19患者。

PROJECT SUMMARY The new coronavirus (SARS-CoV-2) and associated disease (COVID-19) is a global threat to worldwide economies and public health due to its highly contagious nature and rapid spread. To develop optimal strategies for treatment of COVID-19, it is critical to understand the cell types and molecular mechanisms that mediate coronavirus infection, tissue propagation, and host immune response. As recently reported, both SARS-CoV and SARS-CoV-2 use the host ACE2 receptor protein and protease TMPRSS2 to gain cellular entry. High-throughput single-cell RNA-sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin (scATAC-seq) now allow us to interrogate cell types and cell states at unprecedented resolution, which has led to groundbreaking discoveries in lung tissue biology, including our lab’s and the Human Cell Atlas recent survey of nasal and lung epithelial cell types that co-express ACE2 and TMPRSS2 consistent with disease phenotype. It has been reported that individuals suffering from chronic respiratory diseases are more susceptible to COVID-19 severe disease. We propose to leverage our expertise in lung biology, single-cell analysis, and unique access to lung tissue at Mount Sinai from COVID-19 patients with chronic respiratory disease comorbidities to define the cell types and regulatory mechanisms that mediate COVID-19 disease susceptibility due to SARS-CoV-2 infection, propagation and interplay with the host immune response. Towards this goal, we will perform scRNA-seq, scATAC-seq, and spatial transcriptomic sequencing of multiple infected and non-infected lung regions in 25-30 patients with COVID-19 and chronic obstructive pulmonary disease comorbidity following autopsy. The single-cell resolution data will allow us to characterize the repertoire of SARS-CoV-2 infected cell and surrounding stromal and immune microenvironment and how they contribute to developing COVID-19 severe disease. Analysis of scATAC-seq data from matched lung regions will identify the key transcription factors and regulatory mechanisms driving the expression programs related to viral infection, host immune response, and severe disease susceptibility. Finally, integration of ligand-receptor pair expression and spatial transcriptomics information will elucidate at greater resolution and scale how cell- cell interactions and tissue pathology are altered after coronavirus infection. Single-cell characterization of the cell types, immune response, and regulatory mechanisms of infection will improve our understanding of virus- host interactions and COVID-19 severe disease susceptibility in patients with chronic respiratory disease. This will, in turn, provide mechanistic insight towards discovering new therapeutic targets that specifically benefit COVID-19 patients with pre-existing respiratory conditions.