1. Developmental Biology
  2. Immunology and Inflammation

Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesis

  1. Amir Hossein Kayvanjoo
  2. Iva Splichalova
  3. David Alejandro Bejarano
  4. Hao Huang
  5. Katharina Mauel
  6. Nikola Makdissi
  7. David Heider
  8. Hui Ming Tew
  9. Nora Reka Balzer
  10. Eric Greto
  11. Collins Osei-Sarpong
  12. Kevin Baßler
  13. Joachim L Schultze
  14. Stefan Uderhardt
  15. Eva Kiermaier
  16. Marc Beyer
  17. Andreas Schlitzer
  18. Elvira Mass  Is a corresponding author
  1. Developmental Biology of the Immune System, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany
  2. Quantitative Systems Biology, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany
  3. Department of Internal Medicine 3-Rheumatology and Immunology, Deutsches Zentrum für Immuntherapie (DZI) and FAU Profile Center Immunomedicine (FAU I-MED), Friedrich Alexander University Erlangen-Nuremberg and Universitätsklinikum Erlangen, Germany
  4. Exploratory Research Unit, Optical Imaging Centre Erlangen, Germany
  5. Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Germany
  6. Genomics & Immunoregulation, LIMES Institute, University of Bonn, Germany
  7. Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Germany
  8. PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Germany
  9. Immune and Tumor Biology, Life & Medical Sciences (LIMES) Institute, University of Bonn, Germany
https://doi.org/10.7554/eLife.86493
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Cite this article
  1. Amir Hossein Kayvanjoo
  2. Iva Splichalova
  3. David Alejandro Bejarano
  4. Hao Huang
  5. Katharina Mauel
  6. Nikola Makdissi
  7. David Heider
  8. Hui Ming Tew
  9. Nora Reka Balzer
  10. Eric Greto
  11. Collins Osei-Sarpong
  12. Kevin Baßler
  13. Joachim L Schultze
  14. Stefan Uderhardt
  15. Eva Kiermaier
  16. Marc Beyer
  17. Andreas Schlitzer
  18. Elvira Mass
(2024)
Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesis
eLife 13:e86493.
https://doi.org/10.7554/eLife.86493
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  3. Download .RIS
7 figures, 1 table and 7 additional files

Figures

Figure 1 with 2 supplements
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Characterization of fetal liver macrophage populations.

(A) Single-cell RNA-sequencing (scRNA-seq) analysis of wildtype CD11blow/+ cells isolated from a fetal liver at developmental day (E)14.5. Clusters of possible macrophage subsets identified by a …

Figure 1—source data 1

Quantification of fate-mapped macrophages populations for Figure 1.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig1-data1-v2.xlsx
Figure 1—figure supplement 1
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Sorting and characterization of fetal liver myeloid cells.

(A) Sorting strategy of CD11b+ cell for performing single-cell RNA-sequencing using wildtype E14.5 fetal livers. (B) Subclustering strategy and identification of cell types in the single-cell …

Figure 1—figure supplement 2
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Flow-cytometry analysis of macrophage subpopulations and fate-mapping mouse models.

(A) Flow-cytometry analysis of CD11blow/+ cells with a macrophage signature, isolated from a fetal liver at developmental day E14.5. Cell surface marker expression was used to generate unbiased …

Figure 2
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Transcriptional program and paracrine signaling of fetal liver macrophages.

(A) Gene set enrichment analysis (GSEA) of final macrophage clusters 2, 7, and 8 was performed on the differentially expressed genes of each cluster. (B) Expression of selected ligands in the final …

Figure 3
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Macrophage interaction with CD150+ hematopoietic stem cells (HSCs).

(A) Immunostaining of E14.5 fetal liver sections with antibodies against F4/80, Iba1, CD150, and Ter119. Scale bar represents 50 µm. (B) Immunostaining of E14.5 fetal liver whole-mounts with …

Figure 3—source data 1

Distances measured between CD150+ or CD150− cells and Iba1 cells for Figure 3.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig3-data1-v2.xlsx
Figure 4 with 2 supplements
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Macrophage heterogeneity and their interaction with hematopoietic stem cells (HSCs).

(A, B) A 5-µm frozen section of a fetal liver from an E14.5 wildtype embryo was stained with a 20-plex CODEX antibody panel. Representative image of the entire field of view is shown in (A) and …

Figure 4—source data 1

Number of CD150+ cells within each macrophage subpopulation measured in a 50-μm radius.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
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Spatial CODEX analyses of macrophage clusters in the fetal liver.

(A) Proportions of cells from the macrophage clusters within the total F4/80+ Iba1+ Cx3cr1+ Tim4+ macrophages from the CODEX image in Figure 3B. (B) Single objects detected in Figure 3B were …

Figure 4—figure supplement 1—source data 1

Quantification of macrophage subpopulations and their interaction with Ter119+ cells for Figure 4—figure supplement 1.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig4-figsupp1-data1-v2.xlsx
Figure 4—figure supplement 2
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CODEX-based detection of macrophage heterogeneity and hematopoietic stem cells (HSCs).

(A–C) A 5-µm frozen section of a fetal liver from an E14.5 wildtype embryo was stained with a 20-plex CODEX antibody panel. Representative image of the entire field of view is shown in (A) and …

Figure 4—figure supplement 2—source data 1

Quantification of CD150 and CD41 expression for Figure 4—figure supplement 2.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig4-figsupp2-data1-v2.xlsx
Figure 5
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The effect of macrophage depletion on erythropoiesis.

(A) Quantification of F4/80+ macrophage cells in the E14.5 fetal liver of Tnfrsf11a+/+; Spi1f/f (WT) and Tnfrsf11aCre/+; Spi1f/f (KO) embryos using flow cytometry. n = 16 for WT, n = 10 for KO. (B) …

Figure 5—source data 1

Quantified cell numbers of knockout and wildtype E14.5 embryos for Figure 5.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig5-data1-v2.xlsx
Figure 6 with 1 supplement
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The effect of macrophage depletion on hematopoiesis.

(A) Volcano plot of differentially expressed genes between CD150+ LT-HSCs sorted from Tnfrsf11a+/+; Spi1f/f (WT, n = 4) and Tnfrsf11aCre/+; Spi1f/f (KO, n = 6) embryos. Blue dots are significant …

Figure 6—source data 1

Quantified cell numbers of knockout and wildtype E14.5 livers and cells from serial colony-forming unit (CFU) and proliferation assays for Figure 6.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig6-data1-v2.xlsx
Figure 6—figure supplement 1
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Bulk RNA-sequencing and analysis of long-term hematopoietic stem cell (LT-HSC).

(A) Gating strategy for sorting LT-HSC from Tnfrsf11a+/+; Spi1f/f and Tnfrsf11aCre; Spi1f/f fetal livers at E14.5 for RNA-sequencing. (B) Heatmap of all differentially expressed genes between …

Figure 7 with 1 supplement
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Macrophage depletion shifts hematopoiesis toward the granulocyte–macrophage progenitor (GMP) lineage.

(A) Relative proportions of myeloid cells cells isolated from Tnfrsf11a+/+; Spi1f/f (WT) and Tnfrsf11aCre/+; Spi1f/f (KO) fetal livers at E14.5. Average of n = 11 for WT and n = 5 for KO. (B) …

Figure 7—source data 1

Quantified cell numbers of knockout and wildtype livers and cells from colony-forming unit (CFU) and adoptive transfer assays for Figure 7.

https://cdn.elifesciences.org/articles/86493/elife-86493-fig7-data1-v2.xlsx
Figure 7—figure supplement 1
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Gating strategies for flow-cytometry data.

(A) Gating strategy for quantification of stem and progenitor cells in fetal livers at E14.5. CLP: common lymphoid progenitor; CMP: common myeloid progenitor; GMP: granulocyte–macrophage progenitor; …

Tables

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Commercial assay or kitCODEX conjugation kitAkoya Biosciences7000008
Commercial assay or kitCODEX staining kitAkoya Biosciences7000009
Commercial assay or kitCODEX BufferAkoya Biosciences7000001
Chemical compound, drugBS3 fixativeThermo Fisher Scientific21580
Chemical compound, drugCollagenaseDSigma-Aldrich11088882001
Chemical compound, drugDAPI (4′,6-diamidino-2-phenylindole, dilactate)BioLegend4228011:10,000
Chemical compound, drugDNaseSigma-AldrichDN25-1G
Chemical compound, drugDRAQ7BioLegend4240011:1000
Chemical compound, drugFetal calf serumBio&SellFBS. S 0615HI
Chemical compound, drugGiemsa solutionMerck109204
Chemical compound, drugMay–Grünwald solutionMerck101424
Chemical compound, drugMethoCultStemCell Technologies3434
Chemical compound, drugNormal Goat SerumVWRICNA 08642921
Chemical compound, drugParaformaldehyde (PFA)Thermo Fisher Scientific11586711
Chemical compound, drugProgesteroneSigma-AldrichP3972-5G
Chemical compound, drugQIAzol Lysis ReagentQIAGEN79306
Chemical compound, drugRat serumBio-RadC13SD
Chemical compound, drugRoswell Park Memorial Institute medium (Seahorse XF RPMI medium)Agilent Technologies103576-100
Chemical compound, drugTamoxifenSigma-AldrichT5648
Chemical compound, drugWeise buffer tabletMerck109468
SoftwareCODEX instrument managerAkoya Biosciences
SoftwareCODEX ProcessorAkoya Biosciences
SoftwareCODEX MAVAkoya Biosciences
SoftwareQuPathBankhead et al., 2017
SoftwareImageJSchindelin et al., 2012
SoftwareFlowJoBDv.10.8.1

Additional files

Supplementary file 1

Macrophage subcluster-specific gene set enrichment analysis (GSEA).

https://cdn.elifesciences.org/articles/86493/elife-86493-supp1-v2.xlsx
Supplementary file 2

Ligands expressed by macrophages at E14.5.

https://cdn.elifesciences.org/articles/86493/elife-86493-supp2-v2.xlsx
Supplementary file 3

Differentially expressed genes in knockout versus wildtype long-term hematopoietic stem cells (LT-HSCs).

https://cdn.elifesciences.org/articles/86493/elife-86493-supp3-v2.xlsx
Supplementary file 4

GO term analysis of knockout versus wildtype long-term hematopoietic stem cells (LT-HSCs).

https://cdn.elifesciences.org/articles/86493/elife-86493-supp4-v2.xlsx
Supplementary file 5

Antibody list.

https://cdn.elifesciences.org/articles/86493/elife-86493-supp5-v2.xlsx
Supplementary file 6

Barcodes and reporters for co-detection by indexing CODEX.

https://cdn.elifesciences.org/articles/86493/elife-86493-supp6-v2.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/86493/elife-86493-mdarchecklist1-v2.pdf

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