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

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 immunecell-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.

A population of stress-like cancer cells in melanoma promotes tumorigenesis and confers drug resistance

“…RMW is a consultant to N-of-One Therapeutics, a subsidiary of Qiagen, Inc. Table S1. Marker genes used in analysis are indicated for each cell type hBRAF, crestin, sox10, mitfa, tyrp1a, tyrp1b, dct, pmela (Kaufman et al, 2016) Keratinocytes tp63, krt4 (Eisenhoffer et al, 2017) Fibroblasts fn1a, col1a1a, fstl1b, s100a10b (Gistelinck et al, 2016;Maruyama et al, 2016) Erythrocytes ba1, hbaa1 (Kulkeaw and Sugiyama, 2012) Natural Killers nkl.2, ccl38.6 (Carmona et al, 2017) Neutrophils mpx, mmp9, ncf1 (Carmona et al, 2017) Macrophages ctss2.1, ctss2,2, mhc2dab (Carmona et al, 2017)…”

“…This process initially revealed five clusters: cancer, immune, keratinocytes, fibroblasts and erythrocytes. After examining the immune cluster using recently published markers (Carmona et al, 2017) we could separate the immune cluster into three sub-clusters: macrophages, natural killers and neutrophils. To identify each cluster, we obtained a list of marker genes by examining genes that are differentially expressed ( P <10 -6 , Kolmogorov-Smirnov test; effect size >0.2, Cohen's d).…”

Single-cell transcriptomics to explore the immune system in health and disease

“…For example, T-cells, NK cells and myeloid-like cell transcriptomes were characterized in zebrafish, a vertebrate model organism (36). In another example, scRNA-seq profiled the cell intrinsic innate immune response of fibroblasts across four mammalian species stimulated with dsRNA (18).…”

Single-cell transcriptional analysis reveals naïve helper ILC-like cells in zebrafish

“…These approaches have confirmed the presence of erythrocytes, thrombocytes, neutrophils, macrophages, eosinophils, T cells, B cells and NK cells in zebrafish. Comprehensive transcriptome atlases exist for many of these cell types (Athanasiadis et al, 2017;Carmona et al, 2017;Tang et al, 2017). Because these studies focused on steady state conditions, they were limited in their ability to characterise the response mechanisms following immune challenge.…”