RAPID: Single-cell dissection of the cell types and mechanisms underlying SARS-CoV-2 entry in host cells via the ACE2 receptor and protease TMPRSS2

新的冠状病毒(SARS-CoV-2)具有高度传染性和快速传播的特点，是对全球经济和公共卫生的全球性威胁。为了制定控制和治疗冠状病毒流行的最佳战略，关键是要了解介导病毒进入和在人类群体中传播的细胞类型和生物学机制。单细胞技术的最新进展现在使以细胞类型的分辨率测量基因的表达成为可能。该项目旨在全面调查SARS-CoV-2病毒通过鼻呼吸道、肺和肠道组织进入的细胞类型，并了解年龄、性别和吸烟史可能使健康人容易感染的生理学基础。鉴定含有两种已知介导病毒进入的蛋白质[受体蛋白血管紧张素转换酶-2(ACE2)和跨膜丝氨酸蛋白酶2(TMPRSS2)]的细胞将阐明与新型冠状病毒用于宿主进入的细胞相关的基因表达程序和信号通路。对来自肺的单细胞染色质可及性(scATAC-seq)数据的分析将识别与这些基因表达程序相关的细胞类型的特定转录因子和调节区。这种对冠状病毒感染细胞的信号通路、基因表达程序和调控机制的深入了解可能会导致针对患者和区域的新的治疗靶点，以对抗SARS-CoV-2的传播。单细胞数据将可供下载、分析和可视化，从而为科学界提供宝贵的资源。除了传播研究结果并为控制冠状病毒感染的潜在治疗策略做出贡献外，该项目还将支持一名数据科学家和一名计算研究人员的培训和专业发展。由新型冠状病毒(SARS-CoV-2)引起的新冠肺炎大流行的灾难性影响突显了迫切需要提高对病毒进入和传播的潜在机制的科学理解。SARS-CoV-2利用宿主ACE2受体蛋白和蛋白酶TMPRSS2进入细胞；然而，哪些器官和细胞类型表达这些基因，以及它们如何与宿主免疫系统相互作用仍不清楚。单细胞技术的最新进展现在允许以前所未有的分辨率解剖细胞类型和细胞状态，这导致了组织生物学的突破性发现。该项目将整合多个个体的单细胞RNA测序数据，以评估ACE2和TMPRSS2在肺部的表达模式如何与个人的年龄、性别和吸烟史有关。肺部是与冠状病毒感染有关的主要器官。它还将提供肺和肠道中表达ACE2和TMPRSS2的不同细胞类型的更广泛的背景，并阐明与健康个体的病毒进入相关的基因表达程序和信号通路。最后，对来自不同肺部区域的单细胞染色质可及性数据的分析将确定驱动与病毒进入相关的表达程序的关键转录因子和调控机制。综上所述，该项目将有助于更好地了解冠状病毒的感染机制。这一快速奖项是由综合组织系统生物部的生理机制和生物力学项目以及共生、防御和自我认可项目颁发的，资金来自冠状病毒援助、救济和经济安全(CARE)法案。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

The new coronavirus (SARS-CoV-2) is a global threat to worldwide economies and public health due to its highly contagious nature and rapid spread. To develop optimal strategies for containment and treatment of the coronavirus epidemic, it is critical to understand the cell types and biological mechanisms that mediate viral entry and propagation across the human population. Recent advancements in single-cell technologies now make it possible to measure the expression of genes at a cell-type resolution. This project aims to provide a comprehensive survey of the cell types used by SARS-CoV-2 for viral entry across the nasal airways, lung, and gut tissue and to understand physiological basis of how age, gender, and smoking history may predispose healthy individuals to infection. Identification of cells containing the two proteins known to mediate viral entry [the receptor protein angiotensin-converting enzyme-2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2)] will elucidate the gene expression programs and signaling pathways associated with cells used by the novel coronavirus for host entry. Analysis of single-cell chromatin accessibility (scATAC-seq) data from the lung will identify the cell-type specific transcription factors and regulatory regions associated with these gene expression programs. This improved understanding of the signaling pathways, gene expression programs, and regulatory mechanisms of coronavirus infection of cells may lead to novel, patient- and region-specific therapeutic targets to combat the spread of SARS-CoV-2. The single-cell data will be made available for download, analysis, and visualization, thus providing a valuable resource to the scientific community.In addition to dissemination of the findings and contributing to potential treatment strategies for the control of coronavirus infection, the project will support the training and professional development of a data scientist and of a computational research associate.The catastrophic effects of the COVID-19 pandemic caused by the novel coronavirus (SARS-CoV-2) highlights an urgent need for improving scientific understanding of the underlying mechanisms of viral entry and propagation. SARS-CoV-2 uses the host ACE2 receptor protein and protease TMPRSS2 to gain cellular entry; however, what organs and cell types express these genes and how they interact with the host immune system remain obscure. Recent advancements in single-cell technologies now allow for the dissection of cell types and cell states at unprecedented resolution, which has led to groundbreaking discoveries in tissue biology. This project will integrate single-cell RNA-sequencing data across multiple individuals to assess how expression patterns of ACE2 and TMPRSS2 in the lung, the primary organ linked to coronavirus infection, are associated with an individual’s age, gender and smoking history. It will also provide a broader context of the distinct cell types in the lung and gut expressing ACE2 and TMPRSS2 and elucidate the gene expression programs and signaling pathways that are associated with viral entry in healthy individuals. Finally, analysis of single-cell chromatin accessibility data from different lung regions will identify the key transcription factors and regulatory mechanisms driving the expression programs related to viral entry. Taken together, this project will lead to a better understanding of coronavirus infection mechanisms. This RAPID award is made by the Physiological Mechanisms and Biomechanics Program and the Symbiosis, Defense, and Self-recognition Program in the BIO Division of Integrative Organismal Systems, using funds from the Coronavirus Aid, Relief, and Economic Security (CARES) Act.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.