Modeling early SARS-CoV-2 pathogenesis in human lung organoids and slice cultures

PROJECT SUMMARY COVID-19 remains an ongoing global health crisis, in part due to emerging variants. Fundamental questions remain about the mechanisms by which SARS-CoV-2 infection drives inflammation in the lower lung, in part due to the lack of in vitro infection models. Better understanding of variant biology and the immune pathways involved in early SARS-CoV-2 infection could offer insights for the development of novel therapeutic strategies. The antiviral cytokines type I interferons and their downstream effects have been implicated in COVID-19. SARS-CoV-2 may inhibit or promote interferon effects in some cell types in the lung, and this may differ between viral variants. My preliminary work shows that organoids and lung slice cultures can be used to study these early events in SARS-CoV-2 infection and identifies macrophages as a cell type that activates the interferon pathway in infected cultures. Thus, I propose using quantitative PCR, single-cell RNA sequencing, and flow cytometry to study viral variants and to deeply profile the changes to viral and host gene and protein expression during infection. I will study highly relevant cell types that can interact with each other in a similar fashion to the in vivo lung. I will study the interferon stimulated gene response and identify the cell types in which it is being modulated or would be good targets for therapeutic intervention. This knowledge will be critical to our efforts to combat the COVID-19 pandemic. I am currently a fellow in Dr. Catherine Blish's lab in the Division of Infectious Diseases at Stanford University and I am in the process of being promoted to a full time Instructor position. Stanford University offers an outstanding scientific environment, where all the resources necessary to the success of this project are made available to me. My long-term goal is to become an independent physician-scientist, with a research focus in respiratory viral pathogenesis. I aim to establish a research program focused on modeling established and emerging infections in primary lung tissue with a goal of developing new treatments. To achieve this goal, I have designed a tailored career development plan that comprises both formal and informal training. This training will enhance my expertise in lung biology, immunology, and sequencing analysis. Informal training in these topics will be provided by my mentor, Dr. Catherine Blish, and by the rest of my advisory committee, Dr. Calvin Kuo, Dr. Mark Krasnow, Dr. Susan Holmes, and Dr. Ben Pinsky. With their guidance, I will complete the proposed project, submit research manuscripts, obtain further funding, and obtain an independent research position.