Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types
- Santiago J. Carmona1,2,
- Sarah A. Teichmann3,4,8,
- Lauren Ferreira4,5,6,
- Iain C. Macaulay7,
- Michael J.T. Stubbington3,
- Ana Cvejic4,5,6,8 and
- David Gfeller1,2,8
- 1Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- 2Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland;
- 3European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom;
- 4Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom;
- 5Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
- 6Wellcome Trust–Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom;
- 7Sanger Institute–EBI Single-Cell Genomics Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom
- Corresponding authors: saraht{at}ebi.ac.uk, as889{at}cam.ac.uk, david.gfeller{at}unil.ch
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↵8 Joint senior authors.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.207704.116.
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Freely available online through the Genome Research Open Access option.
- Received March 31, 2016.
- Accepted January 12, 2017.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
