Understanding T cell responses and T cell signaling in human airway organoids with SARS-CoV-2 infection

The SARS coronavirus-2 (SARS-CoV-2) has rapidly emerged over the past four months leading to a criticalpandemic of coronavirus disease (COVID-19) with over 1.4M cases worldwide(https://coronavirus.jhu.edu/map.html) and roughly 100,000 projected fatalities in the US alone by August2020 (See https://covid19.healthdata.org/projections). SARS-CoV-2 causes a lethal ARDS. Despite ourimproved mechanistic understanding of ARDS, intervention clinically is challenging. NOT-AI-20-31 indicatedseveral needs, such as development of reagents and assays for virus characterization, understand criticalaspects of viral infection, replication, pathogenesis, and transmission, identification and evaluation of thecellular and humoral immune responses to SARS-CoV-2, which we address in this proposal. Indeed, there is an urgent need to understand the immunopathology of COVID-19 and study theinteractions of the lung epithelium and tissue, the immune system and the virus to understand the biology ofthis multipartite interaction. We need to better understand the immunopathology of COVID-19 to explorenovel therapeutic approaches that have the potential to work in COVID-19 patients. Our proposal addresses this need from the perspective of the lung epithelium response to SARS-CoV-2 infection and from a T cell perspective in COVID-19. Simultaneously, or efforts will also provide asharable research platform of lung airway organoids/SARS-CoV-2/immune cells that will expedite testing ofexperimental therapeutics. Results from my supplement program will be shared with Drs. Gordon, Looney,and Krummel in our 'RapidPath' program (see supporting letter) to promote rapid discovery and progressand will be compared to insights from COVID-19 patient immune systems, being simultaneously profiled inthe UCSF IMPACC project. In this this Administrative Supplement we will capitalize on my lab's establishedexpertise in T cell signaling, T cell activation, antigen recognition, inflammation, and autoimmune diseases.Those are broad topics of the parent P01 (2P01AI091580, Weiss). Uniquely, we will combine our T cellexpertise with our expertise in the generation and studies of epithelial cell organoids. We already have an"Airway Organoid Biobank" that we will expand as a resource for the community. We will characterize theepithelial response to six different SARS-CoV-2 strains compared to H1N1pdm virus, using airwayorganoid-, single cell RNAseq-, and CyTOF- technology (Aim 1). In order to better understand SARS-CoV-2and adaptive immunity, we will obtain mechanistic insights into T cell activation and T cell signaling in thecontext of SARS-CoV-2- and H1N1pdm- infection of seven, diverse Airway Organoids and two NSCLCorganoids (Aim 2). High-resolution imaging and CyTOF analysis of these "virus-T cell-organoids" willprovide much needed immunological insights into SARS-CoV-2 and its T cell biology as indicated in NOT-AI-20-31 and will synergize with other projects in 'RapidPath' and in UCSF IMPACC programs.