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Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

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Carmona, SJ 
Teichmann, SA 
Ferreira, L 
Macaulay, IC 
Stubbington, MJT 


The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analyzed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared with other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a nonmammalian species. Unsupervised clustering and single-cell TCR locus reconstruction identified three cell populations, T cells, a novel type of NK-like cells, and a smaller population of myeloid-like cells. Differential expression analysis uncovered new immune-cell–specific genes, including novel immunoglobulin-like receptors, and neofunctionalization of recently duplicated paralogs. Evolutionary analyses confirmed the higher gene turnover of trans-membrane proteins in NK cells compared with T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.



Animals, Cells, Cultured, Conserved Sequence, Evolution, Molecular, Humans, Killer Cells, Natural, Mice, Receptors, IgG, Single-Cell Analysis, Transcriptome, Zebrafish, Zebrafish Proteins

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Genome Research

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Cold Spring Harbor Laboratory Press
Medical Research Council (MC_PC_12009)
European Research Council (677501)
This work was supported by SystemsX (MelanomX grant for S.J.C.), Cancer Research UK grant number C45041/A14953 to A.C. and L.F., European Research Council project 677501–ZF_Blood to A.C., and a core support grant from the Wellcome Trust and MRC to the Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute.