Single-cell RNA-seq reveals different subsets of non-specific cytotoxic cells in teleost

Niu, Jinzhong; Huang, Yu; Liu, Xinchao; Zhang, Zhiqiang; Tang, Jufen; Wang, Bei; Lu, Yue; Cai, Jia; Jian, Jichang

doi:10.1016/j.ygeno.2020.09.031

Cited by 44 publications

(33 citation statements)

References 64 publications

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“…12,22,34,35 To circumvent some of these inherent issues, we decided to test for the dynamics and conservation of gene co-expression modules in pseudocells. 36–39…”

Section: Discussionmentioning

confidence: 99%

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

Feregrino

Tschopp

2021

Preprint

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Background: During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built - largely - by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. Results: Here, using a paradigm of morphological diversification, the tetrapod limb, and single-cell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. We developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained - to different degrees, in module make-up, density or connectivity - over developmental and evolutionary timescales. Conclusions: We present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification.

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“…12,22,34,35 To circumvent some of these inherent issues, we decided to test for the dynamics and conservation of gene co-expression modules in pseudocells. 36–39…”

Section: Discussionmentioning

confidence: 99%

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

Feregrino

Tschopp

2021

Preprint

View full text Add to dashboard Cite

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“…Lysis of blood cells in the spleen was performed with the Red Blood Cell Lysis Solution (Miltenyi Biotec, Germany). The remaining cells were diluted to a concentration of 1000 cells/μL ( 16 ). Barcode-labeling of these cells and subsequently mixed with reverse transcriptase into a Gel Beads-In-Emulsions (GEMs).…”

Section: Methodsmentioning

confidence: 99%

“…For example, Niu et al. ( 16 ) reported on the first scRNA-seq analysis of Nile tilapia ( Oreochromis niloticus ), an economically farmed fish species rather than a model organism, which revealed different subsets of non-specific cytotoxic cells in fish for the first time ( 16 ).…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome

et al. 2021

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Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/MΦ) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/MΦ including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.

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“…For a long time, the identification of AhR-positive immune cells in fish was hindered by the absence of appropriate cell markers and separation technologies. However, more recently, major progress has been made in techniques for identifying specific immune cell types of fish (e.g., [161][162][163][164][165]), and this opens ample opportunities to advance our knowledge on the cell type-specific distribution and function of the AhR in the fish immune system.…”

Section: The Presence and Xenobiotic Inducibility Of The Ahr In Immune Organs And Cells Of Teleost Fishmentioning

confidence: 99%

Immunotoxicity of Xenobiotics in Fish: A Role for the Aryl Hydrocarbon Receptor (AhR)?

Segner

Bailey²,

Tafalla³

et al. 2021

IJMS

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The impact of anthropogenic contaminants on the immune system of fishes is an issue of growing concern. An important xenobiotic receptor that mediates effects of chemicals, such as halogenated aromatic hydrocarbons (HAHs) and polyaromatic hydrocarbons (PAHs), is the aryl hydrocarbon receptor (AhR). Fish toxicological research has focused on the role of this receptor in xenobiotic biotransformation as well as in causing developmental, cardiac, and reproductive toxicity. However, biomedical research has unraveled an important physiological role of the AhR in the immune system, what suggests that this receptor could be involved in immunotoxic effects of environmental contaminants. The aims of the present review are to critically discuss the available knowledge on (i) the expression and possible function of the AhR in the immune systems of teleost fishes; and (ii) the impact of AhR-activating xenobiotics on the immune systems of fish at the levels of immune gene expression, immune cell proliferation and immune cell function, immune pathology, and resistance to infectious disease. The existing information indicates that the AhR is expressed in the fish immune system, but currently, we have little understanding of its physiological role. Exposure to AhR-activating contaminants results in the modulation of numerous immune structural and functional parameters of fish. Despite the diversity of fish species studied and the experimental conditions investigated, the published findings rather uniformly point to immunosuppressive actions of xenobiotic AhR ligands in fish. These effects are often associated with increased disease susceptibility. The fact that fish populations from HAH- and PAH-contaminated environments suffer immune disturbances and elevated disease susceptibility highlights that the immunotoxic effects of AhR-activating xenobiotics bear environmental relevance.

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Single-cell RNA-seq reveals different subsets of non-specific cytotoxic cells in teleost

Cited by 44 publications

References 64 publications

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

Full-Length Transcriptome: A Reliable Alternative for Single-Cell RNA-Seq Analysis in the Spleen of Teleost Without Reference Genome

Immunotoxicity of Xenobiotics in Fish: A Role for the Aryl Hydrocarbon Receptor (AhR)?

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