Molecular basis of fish antiviral responses

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Viral pathogens threaten both cultured and wild fish, yet little is known about comparative aspects of fish antiviral responses, and how early life stage fish defend themselves against viruses. My research program uses transcriptomics (i.e. global gene expression) and complementary methods to study the genes and molecular pathways involved in fish defense responses. Fish are key models for comparative and developmental immunology, and for studying the molecular evolution of immune genes and gene families. Over the next 5 years we will study and compare the genes and mechanisms involved in antiviral immune responses of teleost fish of different life stages from embryo to adult. Four evolutionarily diverged species - Atlantic salmon, Atlantic cod, zebrafish and lumpfish - all with sequenced genomes and 3 of which are important for aquaculture/fisheries (salmon, cod, lumpfish), will be used as models. We will fully characterize key antiviral genes in all 4 species, facilitating research on gene expression, regulation and function. Macrophages play central roles in vertebrate immune (e.g. antiviral) responses. I hypothesize that evolutionarily conserved and lineage-specific genes and miRNAs involved in macrophage antiviral responses will be identified using studies with the 4 model species. To test this hypothesis, salmon, cod, zebrafish and lumpfish head kidney macrophages will be isolated and immune stimulated with pIC, a synthetic RNA that elicits an antiviral response. Macrophage antiviral responses will be assessed by RNA sequencing (mRNA, miRNA), and expression of selected antiviral genes and miRNAs will be further studied using techniques such as real-time quantitative polymerase chain reaction (qPCR) and in situ hybridization (ISH). In addition, we will study the expression and function of antiviral genes and miRNAs during fish development. Based on our recent results [e.g. dynamic expression of irf7, viperin and other key interferon (IFN) pathway genes during cod embryogenesis], I hypothesize that the IFN pathway plays important roles during fish development. To test this hypothesis, we will study the expression of IFN pathway mRNAs and miRNAs in immune-stimulated (e.g. pIC) and control salmon, cod, zebrafish and lumpfish embryos using various techniques (e.g. qPCR, ISH); irf7 and viperin gene function during embryonic development will be investigated using target gene knockdown and characterization of the resulting phenotypes. Comparison of our results across species will shed light on the antiviral defences in macrophages and embryos of the last common ancestor of salmon, cod, zebrafish and lumpfish (i.e. early Teleost, ~ 250 million years ago), as well as lineage-specific mechanisms of antiviral defense (e.g. present in cod but not salmon). A more complete understanding of the genes and molecular pathways involved in these fish species will be valuable to many research areas including evolutionary biology, fisheries, and aquaculture.