The innate antiviral response in airway epithelium: a cell type-resolved, functional genomics approach

PROJECT SUMMARY Beyond its role in conducting the air required for respiration, the airway epithelium plays a critical role in host defense through its physical and immunological properties. Specialized secretory cells present in the epithelium secrete airway mucins, which form a viscous hydrogel protecting the epithelial surface, and the coordinated beating of multiciliated cells propels this surface liquid and trapped foreign material away from the lower airways. TP63+ airway basal cells serve as the progenitor cell to replenish all other epithelial cell populations. Additional rare cell types with as-of-yet incompletely defined functions include FOXI1+ ionocytes and POU2F3+ tuft-like cells. All epithelial cell types constitute a selectively permeable physical barrier by forming cell-cell junctions with neighboring cells, such that an electrochemical gradient can be maintained across epithelial boundary. Besides these physical functions, airway epithelial cells participate in both innate and adaptive immune mechanisms through pathogen sensing, release of cytokines, and crosstalk with immune cells. The type I interferon (IFN-I) response is a broad-spectrum, first-line innate immune defense against viruses. While traditionally viewed as relatively uniform across cell types, preliminary data from our lab and collaborators show that IFN-I induces distinct gene expression programs across airway cell types, hinting at possible functional heterogeneity in the IFN-I response on a per-cell type basis. However, it is unclear whether these altered gene expression patterns and associated transcriptional regulators have functional significance in the context of respiratory virus infection. A diverse group of respiratory viruses infect the airway epithelium, including influenza viruses, rhinoviruses, “common-cold” coronaviruses, and SARS-CoV-2. These can be important triggers for acute exacerbations of chronic airway disease states. The proposed project will develop state-of-the-art CRISPRa/i functional genomics approaches to perturb IFN-induced regulators and effectors of innate immunity in a human, physiologically relevant model of the human airway epithelium. This will enable precise functional profiling of the IFN-I response in individual airway epithelial cell types. Altogether, this work will shed light on how the airway epithelium functions as an integrated unit to mediate host defense against respiratory viruses and strike a balance between effective host defense and immune homeostasis (using influenza A virus as a clinically relevant model respiratory pathogen), with the ultimate goal of developing novel host-directed antiviral therapeutic strategies. More generally, I anticipate the proposed experimental system developed here will be broadly valuable for precise genetic characterization of other airway disease states and their interaction with respiratory virus infection, including COPD, cystic fibrosis, and asthma. This project also presents a unique opportunity for training in both experimental and computational research approaches relevant to airway biology and respiratory virus infection.