Next Generation Resolution of Antiviral Gene Networks

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SUMMARY As the primary mediators of the innate response to viral infection, type I interferons (IFN-I) establish an antiviral state in both infected and uninfected bystander cells through the induction of several hundreds of interferon stimulated genes (ISGs). The mechanisms by which the coordinated activities of these ISGs confer resistance to diverse viruses, and the regulatory circuits that modulate their expression remain poorly understood. Working with unique samples from individuals with hereditary syndromes of dysregulated IFN-I responsiveness, we have identified a collection of thirty ISGs that confer resistance to diverse viruses (increased protection against RNA and DNA viruses with both high and low pathogenic burden). We have also uncovered previously unappreciated negative feedback mechanisms of IFN-I signaling. We have found that these regulatory circuits, as well as ISG expression patterns, vary significantly across different cell types at steady state and upon IFN-I stimulation. Recent technological advances now enable us to explore these cooperative ISG antiviral functions and negative feedback mechanisms at unprecedented depth and resolution. In the studies proposed here, we will identify subsets of ISGs sufficient to confer broad protection against multiple viruses using a novel single cell RNA-Seq strategy. This approach provides the throughput required to conduct complex combinatorial experiments while maintaining the high resolution to test specific hypotheses. Results may offer new broad spectrum antiviral therapeutic strategies, which would be of particular value against emerging viral pathogens. We will also investigate in detail the mechanisms by which IFN-I signaling establishes a lasting imprint on cellular responsiveness to subsequent IFN-I stimulation. This recently described but incompletely characterized phenomenon likely has important implications for successive infectious challenges and viral susceptibilities. Combining a unique collection of clinical samples, cutting edge technologies, and diverse and complementary expertise in immunovirology from our two laboratories, these studies are expected to address long standing, fundamental questions in innate antiviral immunity, as well as to pioneer new directions for developing antiviral therapies.