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

  • Carmona SJ Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
  • Teichmann SA European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
  • Ferreira L Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom.
  • Macaulay IC Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom.
  • Stubbington MJ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
  • Cvejic A Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom.
  • Gfeller D Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
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  • 2017-01-15
Published in:
  • Genome research. - 2017
Animals
Cells, Cultured
Conserved Sequence
Evolution, Molecular
Humans
Killer Cells, Natural
Mice
Receptors, IgG
Single-Cell Analysis
Transcriptome
Zebrafish
Zebrafish Proteins
English 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.
Language
  • English
Open access status
hybrid
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/259525
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