Description

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

Santiago J. Carmona^1,2, S. A. Teichmann^3,4, L. Ferreira^4,5,6, I. C. Macaulay⁷, M. J.T. Stubbington³, A. Cvejic^4,5,6 and D. Gfeller^1,2

¹Ludwig Center for Cancer Research, University of Lausanne, Switzerland; ²Swiss Institute of Bioinformatics (SIB), Switzerland; ³European Molecular Biology Laboratory European Bioinformatics Institute, UK; ⁴Wellcome Trust Sanger Institute, UK; ⁵Department of Haematology, University of Cambridge, UK; ⁶Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, UK; ⁷Sanger Institute–EBI Single-Cell Genomics Centre, UK

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 analysed 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 to 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 non-mammalian 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 to T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.