The Evolutionary Diversification of CD300s Reveals How Gene Duplication and Structural Innovation Shift the Landscape of Immune Recognition 2257270

Abstract Introduction The CD300 gene cluster encodes activating and inhibitory lipid-binding innate immune receptors that, in humans and mice, play important roles in immune response, including viral entry and autoimmunity. However, their broader evolutionary and functional diversification dynamics across vertebrates remain unresolved. Methods Genomic and transcriptomic analyses were employed to identify CD300 orthologs and paralogs across vertebrates. Numbers and combinations of CD300 genes were quantified and cataloged. AI-based protein folding tools were used to predict changes in protein structures. Recombinant forms of CD300 proteins were generated and subjected to an unbiased lipid-binding assay to identify and quantify ligand binding differences between orthologs and paralogs. Results Our analyses reveal that CD300s are present across jawed vertebrates, with a pronounced pulse of gene duplication coinciding with the origin of placental mammals. Within mammals, the evolutionary trajectory of this cluster is remarkably labile. We observe dramatic lineage-specific expansions and contractions in groups such as chiropterans (bats) and cetaceans (whale and dolphins) that correspond to major events in the evolutionary history of these groups. Structural predictions suggest that these gene duplications are accompanied by corresponding changes in protein shape, including the extracellular domains that mediate lipid binding. Ongoing lipidomics-based ligand screening supports this prediction. Conclusion Our preliminary data show divergent lipid-binding profiles across CD300 paralogs, suggesting functional novelty. Together, these results position CD300s as a tractable model for understanding how the molecular diversification of clustered immune gene families corresponds to their ligand preferences likely reflecting their evolutionary histories. Funding Source NSF IOS 2419126; NSF IOS 2419127; NSF IOS 2419128 Topic Categories Veterinary and Comparative Immunology (VET)