Molecular Mechanisms of Human Interferon System Deficiency

The human type I interferon (IFN-I) system is a critical cytokine-mediated innate immune barrier that protects against viral disease. Inborn errors of several IFN-I system components (or autoantibodies that neutralize the function of IFN-I cytokines) are associated with defects in innate immune function, and can result in the increased susceptibility of individuals to severe viral infections. However, the precise molecular mechanisms governing how some inborn errors of immunity impact IFN-I system activity are unclear, and this unavailability of detailed knowledge prevents the potential application of tailored therapies. Furthermore, while most studies to date focus on developing our understanding of how IFN-I system deficiencies exacerbate an individual's disease, there are limited insights into how these deficiencies might impact the biology of the infecting virus, particularly with respect to promoting virus persistence and the likelihood of adaptive evolution, something that could have broader consequences for the wider population beyond single affected individuals. Research advances in both these important areas are currently hampered by a lack of appropriate physiologically-relevant cell models that can be used to translate findings and observations from affected patients into actionable experimental systems for molecular studies.In a first aim, we will study the pathogenic mechanism of action of a recently-identified and uncharacterized human variant in a gene of the IFN-I system. This gene variant has been associated with an increased risk of critical COVID-19, but it is unclear how a single mutation in this gene can contribute to severe viral disease susceptibility given widespread redundancy within the system. In preliminary work, we have found that overexpression of the variant gene activates the cell's unfolded protein response (UPR). We now aim to implement state-of-the-art CRISPR/Cas9-mediated gene-editing and iPSC technologies to generate various physiologically-relevant human immune-cell models where the endogenous gene has been modified to the disease-associated variant. We will then have the possibility to use these in vitro models to define the molecular, cellular, and immunological consequences of this single variant. A key goal will be to mechanistically dissect pathways (such as the UPR) that contribute to pathogenesis, and to investigate proof-of-concept therapies to reverse the effects.In a second aim, we will attempt to integrate viral genome sequence analysis with new in vitro infection models (inc. primary human airway epithelial cells) to test the hypothesis that IFN-I system deficiencies, including those caused by autoantibodies neutralizing IFN-Is, can lead to persistent virus replication and contribute to the evolution of viral variants, particularly those with immune-escape properties. The goal will be to investigate the concept of whether those who harbor these deficiencies are likely to be potential sources of viral genetic variation, thus validating the idea that prioritizing these individuals for prophylactic and therapeutic treatments could have community-wide benefits.Outcomes from our project should re-frame our fundamental understanding of how individual mutations can have broadly-acting immunological consequences through unanticipated mechanisms, as well as define previously unappreciated virological ramifications of an individual's compromised immunity. These insights will be critical to develop new frameworks for both future therapeutic concepts and risk assessments.