Infectious diseases are an enormous burden on global health. However, we only poorly understand the many mechanisms that hosts have evolved to defend against pathogens and that pathogens have counter-evolved to defeat those defenses. Importantly, the result of these host-pathogen evolutionary conflicts (i.e. whether the host or the pathogen is successful) ultimately determine our susceptibility to infection. It is therefore of paramount importance that we address the following questions: what are the critical genes and mechanisms that protect us from infection, how do pathogens counteract those defenses, and how does host genetic variation affect susceptibility to infection? Our research brings an evolution-guided perspective to answering these questions by exploiting the fact that the interests of pathogens and their hosts are necessarily at odds with one another. That is, if the host successfully defends against a pathogen, there is evolutionary pressure on the pathogen to evolve a way to overcome that defense. Likewise, if the pathogen establishes a successful infection, the host is pressured to adapt. These back and forth dynamics drive constant innovation on both sides of host-pathogen molecular interactions, resulting in the wide genetic and functional diversity we see today. Our research explicitly leverages this diversity to discover which host proteins have been driven to rapidly evolve by genetic conflicts with pathogens, in effect allowing pathogens to lead us to the host genes, mechanisms and pathways that are most important for fitness. Based on this evolution-guided approach, our current work focuses on the importance of several incompletely understood post-transcriptional and post- translational regulatory mechanisms in host antiviral defense. One current area of focus is investigating the antiviral mechanisms and evolutionary consequences of a dynamically evolving family of genes, known as IFITs, that distinguish host from viral mRNAs based on mRNA modifications. Another aim is to determine the immune functions of a poorly characterized but rapidly evolving family of genes known as PARPs that catalyze the post-translational addition of ADP-ribose to proteins. Using diverse virology models, coupled with genetic and biochemical approaches, these studies aim to not only determine the consequences of IFIT and PARP gene evolution on susceptibility to viral infection, but also to reveal the broader mechanistic roles for mRNA modifications and ADP-ribosylation in host antiviral defense and cellular regulation. Finally, we are developing genome wide tools to identify other rapidly evolving but understudied regulatory mechanisms that we hypothesize are additional determinants of human susceptibility to viral infection. The overall mission of our work is to use this evolution-guided approach to provide unique insights into mechanisms of host defense and pathogen immune evasion, species-specific barriers to pathogen replication, and pathogen-driven evolution of cellular functions.

Public Health Relevance

Viral infections are an enormous burden on global health, yet we incompletely understand the many ways that our immune system defends against viruses, and the ways that viruses evolve to avoid or defeat our defenses. This project takes an evolution-guided approach to discover new critical mechanisms that underlie host susceptibility to viral infection by identifying and characterizing human genes that have repeatedly evolved to contend with pathogen infections in the past. Such an unbiased approach will allow us to discover new players in the ongoing conflict between hosts and viruses, and leverage the diversity that is already found in nature to develop ways to diagnose, prevent and treat infectious diseases. !

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Unknown (R35)
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Special Emphasis Panel (ZGM1)
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Janes, Daniel E
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University of California, San Diego
Schools of Arts and Sciences
La Jolla
United States
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