Tongue immune compartment analysis reveals spatial macrophage heterogeneity
- Max-Delbrück-Center for Molecular Medicine Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, Germany
- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Microbiology, Infectious Diseases and Immunology, Charité Berlin, Germany
- Weizmann Institute of Science, Israel
- Institute of Dental Sciences, The Hebrew University of Jerusalem, Israel
- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charité Berlin, Germany
- Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Otorhinolaryngology, Charité Berlin, Germany
- InFLAMES Research Flagship Center, University of Turku, Finland
- Institute of Biomedicine, Medicity, University of Turku, Finland
Figures
Figure 1 with 1 supplement
Single-cell sequencing characterization of leukocytes in the mouse tongue.
(a) UMAP representation of 6773 sequenced tongue leukocytes from adult, female Bl6 mice (pool of n=8 mice). Data from a biologically and technically independent experiment is shown in Figure …
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Figure 1—source data 1
Marker genes for the 19 identified clusters.
Listed are the marker genes for each cluster of the scRNA-seq experiments 1–4 together with the respective test statistics. Each cluster can be found in separated tabs. As test method we used MAST, the log2fc threshold was set to 0.25 and a Bonferroni mutiple testing correction was applied. We only considered genes that were expressed in at least 20% of the cells in at least one of the groups. Note that cluster 11 is not represented due to low cell numbers and cluster 16 could only be detected in experiment 3 (LPS). These data sets belong to Figures 1, 4 and 6.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig1-data1-v1.xlsx
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Figure 1—source data 2
Average expression matrix of scRNA-seq data.
The file contains the average expression value for each cluster based on the normalized counts of the cells in the respective sample. Additionally, a column for each cluster indicates, whether a gene is a conserved marker for this cluster (see Figure 1—source data 1).
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig1-data2-v1.xlsx
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Figure 1—source data 3
Core gene signatures.
Listed are the core gene signatures of cDC (tab 1), macrophages (tab 2), cDC1 (tab 3), and cDC2 (tab 4). The gene lists were derived from Gautier et al., 2012; Schlitzer et al., 2015.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig1-data3-v1.xlsx
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Figure 1—source data 4
GO enrichment of myeloid clusters.
Represented are the full GO lists for the myeloid clusters 0, 1, 3, 5, 6, 7, and 10.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig1-data4-v1.xlsx
Figure 1—figure supplement 1
Characterization of adult tongue leukocytes.
(a) Biological and technical replication (experiment 2, right graph) of the scRNA-seq experiment depicted in Figure 1 (experiment 1, left graph). For experiment 2, CD45+ tongue leukocytes were …
Figure 2 with 2 supplements
Tissue-specific transcriptomic identity of tongue macrophages.
(a) Exemplary flow cytometry analysis and gating for tCX3CR1-MF and tFOLR2-MF in Cx3cr1Gfp/+ mice. See Figure 2—figure supplement 1 for isolation tissue procedure. (b) Shown are histogram expression …
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Figure 2—source data 1
Read count table bluk RNA-Seq.
This table includes the full bulk RNA-seq read counts for all isolated tissue resident macrophage populations that are shown in Figure 2.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig2-data1-v1.xlsx
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Figure 2—source data 2
GO enrichment for myeloid populations.
Listed are the upregulated genes that could be extracted from the bulk RNA-seq data. These genes were used for GO annotations represented in Figure 2. Each subset is represented in a separate tab. Note that heart macrophages were not separated into MHCII- and MHCII+ cells for this analysis.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig2-data2-v1.xlsx
Figure 2—figure supplement 1
Different isolation methods for the identification of tongue leukocytes.
(a) Digestion of tongues from PBS perfused mice with Collagenase IV, Hyaluronidase and DNase. Shown are examples for Bl6 mice (left) and Cx3cr1Gfp/+ mice (right). Note the almost complete absence of …
Figure 2—figure supplement 2
Gating strategy for the isolation of tissue resident macrophages.
Shown are the gating strategies that allow the identification of (a) Langerhans cells from the skin, (b) splenic macrophages, (c) Cx3cr1+ colonic macrophages, (d) MHCII+ and MHCII- Cx3cr1+ heart …
Figure 3 with 1 supplement
Distinct localization of mouse tongue macrophages.
(a) Panoramic image of a tongue sagittal section from a perfused Cx3cr1Gfp/+ mouse. The tongue was stained for anti-GFP (CX3CR1; green) and anti-LYVE1 (violet). (b) Magnification of the area …
Figure 3—figure supplement 1
Quantification of tongue macrophages.
(a) Panoramic image of an adult tongue counterstained with DAPI (white). The insets represent different areas of the tongue that were quantified. (b) Imaris-based mask for the identification of …
Figure 4
Inflammatory response of tongue macrophages to systemic LPS challenge.
(a) Female Bl6 mice were intraperitonally injected with 1 mg/kg LPS and analyzed 6 hr after injection by flow cytometry. Note the absence of LYVE1 surface expression in CD11b+ CD64+ tongue …
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Figure 4—source data 1
List of differential expressed genes between untreated and LPS treated myeloid cells.
Listed are all significant differential expressed genes between untreated and LPS-treated tFOLR2-MF (tab1) and tCX3CR1-MF (tab2).
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig4-data1-v1.xlsx
Figure 5
Tongue macrophage distribution during development.
(a) Representative flow cytometry analysis of tongue leukocytes isolated from Cx3cr1Gfp/+ mice at different embryonic (E) and postnatal (p) days of development and 8 week-old adults. Cells were …
Figure 6 with 3 supplements
Transcriptomic analysis of hematopoietic tongue cells from newborn mice.
(a) CD45+ tongue leukocytes were isolated by FACS from newborn p3 mice. The purified cells were subjected to scRNA-seq and a total of 13,898 cells were sequenced. The early postnatal data was …
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Figure 6—source data 1
3D UMAP.
This html file shows the 3D representation of the postnatal day 3 UMAP represented in Figure 6.
- https://cdn.elifesciences.org/articles/77490/elife-77490-fig6-data1-v1.zip
Figure 6—figure supplement 1
Gene expression differences in tongue macrophages at p3 and adult stages.
(a) Differentially expressed genes between p3 and adult tFOLR2-MF. Shown are all significantly changed genes that passed variance analysis. No fold-change filter was applied to the analysis. (b) GO …
Figure 6—figure supplement 2
The maturation pattern of tFOLR2-MF and tCX3CR1-MF in adult tongues.
(a) Latent time analysis reveals distinct gene expression patterns in adult tFOLR2-MF. Note the gradual down-regulation of MHC-related genes (for example, H2–Ab1, H2–Aa, Cd74), …
Figure 6—figure supplement 3
Irf8-deficiency does not affect the tongue leukocyte composition.
(a) Exemplary flow cytometry analysis of Irf8-deficient tongue leukocytes and their respective controls. The cells were pre-gated as CD11b+ CD64+. (b) Ratio analysis of Ly6C- monocytes / Ly6C+ …
