Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity
- College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, China
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, China
- Department of Genetic and Metabolic Disease, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, China
Figures
Figure 1 with 2 supplements
Categorization of the hematopoietic stem/progenitor cells (HSPCs) and immune cell types in zebrafish kidney.
(A) Nonlinear t-SNE clustering visually categorized populations of zebrafish kidney leukocytes. Principal component analysis (PCA) was performed following expression data normalization, with …
Figure 1—figure supplement 1
Single-cell sequencing quality control.
(A) Identification of the effective cell number of the sample. The x-axis is the number of barcodes, and the y-axis is the UMI counts. Blue line is the effective cells corresponding to barcodes, and …
Figure 1—figure supplement 2
Violin plots showing the expression of marker genes for per immune cell and renal cell categories at the single cell level.
(A) neutrophil; (B) macrophage/myeloid cells; (C) B cells; (D) T cells; (E) Kidney multiciliated cells; (F) Kidney distal tubule cells; (G) Kidney mucin cells; (H) hematopoietic stem/progenitor …
Figure 2
Hematopoietic stem/progenitor cells (HSPCs) subtype analysis based on single-cell gene expression.
(A) Graph-based clustering revealed 11 subclusters of HSPCs within both the control group (PBS) and the spring viremia of carp virus (SVCV)-infected group. (B) Heatmap presenting marker gene …
Figure 3
Pseudotemporal and RNA velocity analyses of zebrafish kidney hematopoietic stem/progenitor cells (HSPCs) development.
(A) Pseudotime single-cell trajectory of HSPCs reconstructed using Monocle2. Pseudotime is represented in a gradient from dark to light blue, with its starting point indicated. (B–C) Distribution of …
Figure 4
Integrated clustering and pseudotemporal analysis of zebrafish kidney and spleen hematopoietic stem/progenitor cells (HSPCs) and immune cells development.
(A) Nonlinear t-distributed stochastic neighbor embedding (t-SNE) clustering illustrated the divergence in classification outcomes of zebrafish leukocyte populations between the kidney and spleen. (B…
Figure 5
T/NK cell subtype analysis based on single-cell gene expression.
(A) Graph-based clustering unveiled 23T/NK cell subclusters within the control group. Nonlinear t-distributed stochastic neighbor embedding (t-SNE) clustering highlighted the differing …
Figure 6 with 2 supplements
B-cell subtype and pseudotemporal analysis based on single-cell gene expression.
(A) Graph-based clustering disclosed nine B cell subclusters in both the control group (PBS) and spring viremia of carp virus (SVCV)-infected group. (B) Dot plots of differentially expressed …
Figure 6—figure supplement 1
Identification of B cell subtype clusters and the expression patterns of marker genes.
(A) Histogram presenting differences in cell numbers within each cluster between the control group and the spring viremia of carp virus (SVCV)-infected group. (B) The top 10 differently expressed …
Figure 6—figure supplement 2
GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of each cluster of B subset cells.
(A–D) The top 20 most significant Gene Ontology (GO) terms within the biological process (BP) category for pre/pro B, immature/mature B cells (im/mat. B), activated B cell and plasmablasts (act. …
Figure 7
Identification of macrophage/myeloid cell subtypes.
(A) Graph-based clustering identified 10 macrophage/myeloid cell subclusters within the control group. (B) Heatmap displaying marker genes for each cluster. (C) Dot plots illustrating marker gene …
Figure 8 with 1 supplement
Neutrophil subtype analysis based on single-cell gene expression.
(A) Graph-based clustering of neutrophils revealed six subclusters within both the control group (PBS) and the spring viremia of carp virus (SVCV)-infected group. Increased and decreased neutrophil …
Figure 8—figure supplement 1
Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of neutrophil subsets (N2–N5).
(A–D) Top 20 most significant KEGG pathways of neutrophil subclusters (Cluster 2, 3, 4, 5).
Figure 9
Zebrafish kidney immune-cell and T/NK cell subtype changes upon spring viremia of carp virus (SVCV) infection.
(A) Nonlinear t-distributed stochastic neighbor embedding (t-SNE) clustering depicted variations in zebrafish kidney leukocyte classification between control (PBS) and SVCV-infected groups. (B) …
Figure 10 with 1 supplement
Analysis of interferons (IFN)-producing cell types and key virus-responsive genes upon spring viremia of carp virus (SVCV) infection.
(A) Dot plots illustrating five significantly up-/down-regulated IFNs during viral infection in zebrafish kidney immune cells. (B) Dot plots showing five differentially expressed IFN genes in each …
Figure 10—figure supplement 1
Volcano plots showing the differentially expressed genes (DEGs) in zebrafish kidney immune-cell and renal cell categories between control (PBS) and spring viremia of carp virus (SVCV)-infected groups (up-regulated: red; down-regulated: blue).
(A) Neutrophils 1; (B) Macrophage/myeloid cells; (C) Neutrophils 2; (D) B cells; (E) hematopoietic stem/progenitor cells (HSPCs) 1; (F) T/NK cells; (G) HSPCs 2; (H) Kidney multiciliated cells; (I) …
Figure 11 with 1 supplement
Induction of trained immunity in hematopoietic stem/progenitor cells (HSPCs) through zebrafish vaccination with inactivated spring viremia of carp virus (SVCV).
(A) Nonlinear t-distributed stochastic neighbor embedding (t-SNE) clustering displayed the proportions of HSPCs 1 (H0) in the PBS-administered (control), SVCV-infected (infected), and …
Figure 11—figure supplement 1
Percentage and number changes in zebrafish kidney hematopoietic stem/progenitor cells (HSPCs) and immune-cell categories in response to spring viremia of carp virus (SVCV) infection.
(A) Histogram showing the differences in cell ratios between the control group, the SVCV-infected group and the SVCV-vaccinated plus SVCV-infected group. (B) Histogram presenting the differences in …
Figure 12
Single-cell sequencing reveals spring viremia of carp virus (SVCV)-infected cells in kidney tissue.
(A) Nonlinear t-distributed stochastic neighbor embedding (t-SNE) clustering depicted the zebrafish kidney leukocyte classification results after integrating SVCV genes into the zebrafish genome. …
Figure 13
Examination of zebrafish kidney acting as a secondary immune organ involved in the antiviral immune response.
(A) In vivo proliferation assessment of CD4+ and CD8+ T cells in the kidney of zebrafish stimulated with inactivated spring viremia of carp virus (SVCV) (106 TCID50), determined by CD4+EdU+ and CD8+E…
Additional files
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Supplementary file 1
Gene sets for all immune cell and HSPCs annotation.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp1-v1.xlsx
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Supplementary file 2
Marker gene list and gene expression tables of 13 immune-cell and renal cell categories.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp2-v1.xlsx
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Supplementary file 3
Marker gene list and gene expression tables of HSPC subsets.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp3-v1.xlsx
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Supplementary file 4
Marker gene list and gene expression tables of T/NK cell subsets.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp4-v1.xlsx
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Supplementary file 5
Marker gene list and gene expression tables of B cell subsets.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp5-v1.xlsx
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Supplementary file 6
Marker gene list and gene expression tables of macrophages/myeloid cell subsets.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp6-v1.xlsx
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Supplementary file 7
Marker gene list and gene expression tables of neutrophil subsets.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp7-v1.xlsx
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Supplementary file 8
Similarities and differences in HSPC and immune cell populations between zebrafish and human.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp8-v1.xlsx
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Supplementary file 9
Primers used in this study for Real-time quantitative PCR and IgM antibody repertoire analysis.
- https://cdn.elifesciences.org/articles/92424/elife-92424-supp9-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/92424/elife-92424-mdarchecklist1-v1.docx
