Project 2: Dissection of Type-III Interferon Signaling in iPSC-Derived Hepatocytes

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Project 2 – Project Summary Type-III interferons (IFNs), also called lambda IFNs (IFNLs), are key modulators of innate immunity at mucosal and epithelial surfaces. Single-nucleotide polymorphisms (SNPs) at IFNL loci associate with odds of spontaneous hepatitis C virus (HCV) clearance during acute infection and the likelihood of cure upon treatment of chronic infection. Insight gained from studies of HCV has prompted clinical trials using IFNL to treat not only HCV, but also hepatitis B (HBV) and hepatitis D virus infections. Modulation of IFN signaling has emerged as an attractive component of HIV cure strategies. While HCV infection is now readily curable with antivirals, HBV and HIV are not, and available treatments are suppressive and lifelong. Although type-I and type-III IFN signaling pathways share multiple signaling proteins, our understanding of how these pathways intersect and communicate in the clinical context is incomplete. Given the interest in modulating IFN signaling during the treatment of chronic viral infections, it is essential to further understand the protective, pathologic, and relational roles of IFNs. Using clinical samples and in vitro models, we previously showed that hepatic IFNL expression correlates with inflammation during HCV infection and declines during antiviral suppression of HCV, which parallels changes in immunity that correlate with treatment outcome. We now seek to expand our mechanistic insight of how type-I and type-III IFNs interact and are balanced. Based on our preliminary data, we believe that type-III IFNL signaling exerts negative control over the host type-I IFN response through induction of negative regulators of IFN signaling. We propose that the efficiency of IFN-III signaling is influenced by the relative expression of canonical and non-canonical isoforms of the IFNL receptor (IFNLR1). Because a dinucleotide polymorphism at the rs368234815 locus imparts differential capacity to produce IFNL4 ligand and correlates with HCV clinical outcomes, we also predict that cells capable of IFNL4 production induce a heightened type-III IFN response that dampens type-I IFN signaling and inhibits viral clearance. To overcome limitations of studies conducted in cell lines and primary human hepatocytes, we will use inducible pluripotent stem cell (iPSC) derived hepatocytes as a model system. iPSCs can be genetically manipulated, cultured long-term, differentiated into hepatocyte-like cells, support HCV and HBV infection, and have intact IFN-signaling pathways, and thus are extremely well-suited to test our hypotheses. In Aim 1, we will test the hypothesis that signaling through IFNLR1, and relative expression of canonical and non-canonical isoforms, functionally impacts the nature and magnitude of type-I IFN signaling. In Aim 2, we will test the hypothesis that the rs368234815 polymorphism, which modulates the capacity to make IFNL4, is responsible for heterogeneity in the innate hepatocyte response to viral infection. These findings will have broad relevance when considering therapeutic modulation of IFN signaling for other chronic infections, such as HBV and HIV, that impact the liver and gut and cause chronic inflammation via mechanisms that are both infectious and non-infectious.