A Multifaceted Approach to Study Tissue and Cell Type Specific Molecular Mechanisms of the Host Response to Acute/Chronic Viral Infection

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Project Abstract Very few viruses manifest as pathogenic chronic infections in humans and most are cleared acutely. The cell- intrinsic innate antiviral response provides a first line of defense against invading viruses. Unfortunately, in the case of chronic viral infections, these initial responses that were ineffective at controlling virus replication can subsequently cause disease due to chronic inflammation. In most organs, epithelial cells are some of the first cells to encounter viruses and host defense responses in these cells are paramount to facilitating viral eradication. Interestingly, epithelial cells predominantly produce type III interferons (IFNs) in response to viral infection whereas immune cells produce Type II (γ) while Type I (α/β) IFNs are produced by most cells in the body. The mechanism underlying cell type and organ specific expression of the IFNs are unknown and likely involve regulation of epigenetic modifications (e.g. SOCS1), gene expression of pattern recognition receptors (e.g. TLR3, cGAS), associated signaling molecules (e.g. STING) and pertinent transcription factors (e.g. IRF7). In drosophila, the fat body is the innate immune organ producing antimicrobial peptides in response to pathogens. In humans, the liver is functionally equivalent to the drosophila fat body while utilizing Type III IFN responses to fight viral infection and it likely possesses other unique properties with respect to innate immunity when compared to other organs. We have developed rigorous, novel and exciting in vitro models that utilize primary epithelial cells from several organs that have intact innate antiviral responses when compared to immortalized or transformed cell lines. We and others have demonstrated that these cells are of critical importance in the development of disease since they directly detect components of viral pathogens. We therefore assert that primary cells are the optimal model to use for studies on innate immunity and we propose a novel approach to rigorously study this based on the signaling pathways that we have demonstrated to be important for viral clearance and pathogenesis. In addition, we have developed novel models incorporating primary epithelial cells, iPSC-derived epithelial cells and 3-dimensional chip and microfluidic-based platforms for studies involving multiple cell types. The use of iPSC- derived cells facilitates the identification of changes in gene expression and epigenetic or post-translational modifications, which occur during differentiation, that contribute to the unique innate immune system in epithelial cells. The specific goals of this program are to functionally characterize the innate immune response, to multiple viral pathogen associated patterns including both DNA and RNA sensing pathways, and to elucidate the underlying molecular mechanisms through which innate immunity manifests in epithelial cells using sophisticated models. Furthermore, organ specific and associated developmental changes in the functional expression of specific signaling pathways will be addressed through studies on epigenetic mechanism underlying tissue specific antiviral responses. Completion of these ambitious studies would offer in depth characterization of innate immunity while allowing us to develop new paradigms for its contribution to human disease in multiple organs.