Abstract
In mouse peritoneal and other serous cavities, the transcription factor GATA6 drives the identity of the major cavity resident population of macrophages, with a smaller subset of cavity-resident macrophages dependent on the transcription factor IRF4. Here we showed that GATA6+ macrophages in the human peritoneum were rare, regardless of age. Instead, more human peritoneal macrophages aligned with mouse CD206+ LYVE1+ cavity macrophages that represent a differentiation stage just preceding expression of GATA6. A low abundance of CD206+ macrophages was retained in C57BL/6J mice fed a high-fat diet and in wild-captured mice, suggesting that differences between serous cavity-resident macrophages in humans and mice were not environmental. IRF4-dependent mouse serous cavity macrophages aligned closely with human CD1c+CD14+CD64+ peritoneal cells, which, in turn, resembled human peritoneal CD1c+CD14−CD64− cDC2. Thus, major populations of serous cavity-resident mononuclear phagocytes in humans and mice shared common features, but the proportions of different macrophage differentiation stages greatly differ between the two species, and dendritic cell (DC2)-like cells were especially prominent in humans.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 /Â 30Â days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
De-identified human scRNA-seq data that support the findings of this study are publicly available in the Gene Expression Omnibus (GEO) database under accession number: GSE228030. Publicly available browser tools to explore the data are found at: https://artyomovlab.wustl.edu/scn/?token=gjrandolph.fig1.adult_peritoneal_mnp; https://artyomovlab.wustl.edu/scn/?token=gjrandolph.fig2.adult_b6_peritoneal_mnp; https://artyomovlab.wustl.edu/scn/?token=gjrandolph.fig3.adult_pediatric_peritoneal_all_immune_cell. Mouse scRNA-seq data can be accessed under the code GSE225668. Human reference genome data are available at https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz and mouse reference genome is available at https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz. The previously published microarray datasets used to generate the Gata6 KO versus wild-type peritoneal macrophage gene signature for the GSEA analysis were accessible at Gene Expression Omnibus (GEO) under accession codes GSE56711, GSE47049 and GSE37448. The remaining gene sets used in the GSEA analysis are accessible at the MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb). Source data are provided with this paper and can be found at https://doi.org/10.6084/m9.figshare.24319603. All other data supporting the findings of this study are available from the corresponding author on reasonable request.
Code availability
Customized code is available at https://github.com/TrmMelanoma/macrophages-and-dendritic-cells-between-mouse-and-human.
References
Gautier, E. L. et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat. Immunol. 13, 1118–1128 (2012).
Jenkins, S. J. et al. Local macrophage proliferation, rather than recruitment from the blood, is a signature of TH2 inflammation. Science 332, 1284–1288 (2011).
Zhang, N. et al. Expression of factor V by resident macrophages boosts host defense in the peritoneal cavity. J. Exp. Med. 216, 1291–1300 (2019).
Chow, A. et al. Tim-4+ cavity-resident macrophages impair anti-tumor CD8+ T cell immunity. Cancer Cell 39, 973–988 e979 (2021).
Jin, H. et al. Genetic fate-mapping reveals surface accumulation but not deep organ invasion of pleural and peritoneal cavity macrophages following injury. Nat. Commun. 12, 2863 (2021).
Vega-Perez, A. et al. Resident macrophage-dependent immune cell scaffolds drive anti-bacterial defense in the peritoneal cavity. Immunity 54, 2578–2594 e2575 (2021).
Zindel, J. et al. Primordial GATA6 macrophages function as extravascular platelets in sterile injury. Science 371, eabe0595 (2021).
Okabe, Y. & Medzhitov, R. Tissue-specific signals control reversible program of localization and functional polarization of macrophages. Cell 157, 832–844 (2014).
Campbell, S. M. et al. Myeloid cell recruitment versus local proliferation differentiates susceptibility from resistance to filarial infection. eLife 7, e30947 (2018).
Gautier, E. L. et al. Gata6 regulates aspartoacylase expression in resident peritoneal macrophages and controls their survival. J. Exp. Med. 211, 1525–1531 (2014).
Rosas, M. et al. The transcription factor Gata6 links tissue macrophage phenotype and proliferative renewal. Science 344, 645–648 (2014).
Ghosn, E. E. et al. Two physically, functionally, and developmentally distinct peritoneal macrophage subsets. Proc. Natl Acad. Sci. USA 107, 2568–2573 (2010).
Salm, L., Shim, R., Noskovicova, N. & Kubes, P. Gata6+ large peritoneal macrophages: an evolutionarily conserved sentinel and effector system for infection and injury. Trends Immunol. 44, 129–145 (2023).
Liu, M., Silva-Sanchez, A., Randall, T. D. & Meza-Perez, S. Specialized immune responses in the peritoneal cavity and omentum. J. Leukoc. Biol. 109, 717–729 (2021).
Epelman, S. et al. Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation. Immunity 40, 91–104 (2014).
Kim, K. W. et al. MHC II+ resident peritoneal and pleural macrophages rely on IRF4 for development from circulating monocytes. J. Exp. Med. 213, 1951–1959 (2016).
Hashimoto, D. et al. Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes. Immunity 38, 792–804 (2013).
Buechler, M. B. et al. A stromal niche defined by expression of the transcription factor WT1 mediates programming and homeostasis of cavity-resident macrophages. Immunity 51, 119–130 e115 (2019).
Deniset, J. F. et al. Gata6+ pericardial cavity macrophages relocate to the injured heart and prevent cardiac fibrosis. Immunity 51, 131–140 e135 (2019).
Bain, C. C. et al. Long-lived self-renewing bone marrow-derived macrophages displace embryo-derived cells to inhabit adult serous cavities. Nat. Commun. 7, ncomms11852 (2016).
Finlay, C. M. et al. T helper 2 cells control monocyte to tissue-resident macrophage differentiation during nematode infection of the pleural cavity. Immunity 56, 1064–1081 e1010 (2023).
Bain, C. C. et al. CD11c identifies microbiota and EGR2-dependent MHCII+ serous cavity macrophages with sexually dimorphic fate in mice. Eur. J. Immunol. 52, 1243–1257 (2022).
Goudot, C. et al. Aryl hydrocarbon receptor controls monocyte differentiation into dendritic cells versus macrophages. Immunity 47, 582–596 e586 (2017).
Liao, C. T. et al. Peritoneal macrophage heterogeneity is associated with different peritoneal dialysis outcomes. Kidney Int. 91, 1088–1103 (2017).
Miller, J. C. et al. Deciphering the transcriptional network of the dendritic cell lineage. Nat. Immunol. 13, 888–899 (2012).
Villani, A. C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).
Dick, S. A. et al. Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles. Sci. Immunol. 7, eabf7777 (2022).
Gundra, U. M. et al. Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct. Blood 123, e110–e122 (2014).
Mair, I. et al. A lesson from the wild: the natural state of eosinophils is Ly6Ghi. Immunology 164, 766–776 (2021).
Irvine, K. M. et al. CRIg-expressing peritoneal macrophages are associated with disease severity in patients with cirrhosis and ascites. JCI Insight 1, e86914 (2016).
Ruiz-Alcaraz, A. J. et al. Characterization of human peritoneal monocyte/macrophage subsets in homeostasis: phenotype, GATA6, phagocytic/oxidative activities and cytokines expression. Sci. Rep. 8, 12794 (2018).
Scott, C. L. et al. Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells. Nat. Commun. 7, 10321 (2016).
Shaw, T. N. et al. Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression. J. Exp. Med. 215, 1507–1518 (2018).
Louwe, P. A. et al. Recruited macrophages that colonize the post-inflammatory peritoneal niche convert into functionally divergent resident cells. Nat. Commun. 12, 1770 (2021).
Jenkins, S. J. & Allen, J. E. The expanding world of tissue-resident macrophages. Eur. J. Immunol. 51, 1882–1896 (2021).
Elpek, K. G. et al. The tumor microenvironment shapes lineage, transcriptional, and functional diversity of infiltrating myeloid cells. Cancer Immunol. Res. 2, 655–667 (2014).
Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003).
Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882–883 (2012).
Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
Acknowledgements
We are very grateful to the patients and families who consented to this study. We thank the members of the Randolph laboratory for their suggestions and critical evaluation of the manuscript. We are indebted to M. Artyomov and M. Terekhova (Washington University, Department of Pathology) for facilitating user-friendly public access to the data. This work was principally funded by NIH grant R37AI049653 to G.J.R. and associated Primary Caregiver Award to E.J.O. J.H. was funded by NIH grant KOOCA264434. N.Z. was funded by NIH grant K99AI151198. R.L.M. is funded by NIH grant F30CA281124 and D.D.L. by NIH grant T32 HL007081. C.V.J. is funded by NIH grants R01 HL115334, R01 HL135001 and R35 HL155458. C.M.F. and J.E.A. were supported by MRC-UK (MR/V011235/1, MR/K01207X/2) and the Wellcome Trust (106898/A/15/Z). We thank the Genome Technology Access Center at the McDonnell Genome Institute at Washington University School of Medicine for help with genomic analysis. The Center is partially supported by NCI Cancer Center Support Grant #P30 CA91842 to the Siteman Cancer Center from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of NCRR or NIH. We thank J. Huecker of the Division of Biostatistics for consultation on statistical analysis, a service funded through Washington University’s Institute for Clinical and Translational Sciences program (NIH grant UL1TR002345). Additional support included use of core services funded by the Digestive Diseases Research Core Center at Washington University # P30 DK052574. B.A.H. is currently affiliated with the Department of Surgical Oncology at the University of Texas MD Anderson Cancer Center in Houston, TX; E.J.O. is now affiliated with Children’s Hospital of Philadelphia; B.A.S. is now affiliated with University of Chicago. The work on the wild mouse population on the Isle of May, UK, was supported by a Joint Biotechnology and Biological Sciences Research Council (grant number BB/P018157/1) awarded to J. Bradley (University of Nottingham) and K.J.E. (University of Manchester). We thank Nature Scotland for permission to carry out work on the Isle of May; D. Steel (Nature Scotland), B. Outram (Nature Scotland) and M. Newell (Centre for Ecology and Hydrology) for support with fieldwork; other members of the full research team (J. Bradley, A. Lowe, A. Bennett, A. Muir and A. Wolfenden) as well as our fieldwork volunteers.
Author information
Authors and Affiliations
Contributions
E.C.E., S.R.E., B.A.H., G.J.R., E.J.O. and N.Z. developed and organized study infrastructure; J.H., E.J.O., B.A.H., S.R.E., F.M.D., B.A.S. and H.M.P. collected samples; B.A.H., J.H., A.G., E.C.E., I.M., X.L., N.Z., R.L.M. and D.D.L. conducted experiments and analyzed data; C.M.F. and J.E.A. advised analyses; M.M.C. and J.D.S. provided key resources; B.A.H., K.J.E., C.V.J., J.D.S. and G.J.R. provided supervision and obtained regulatory compliance and funding; J.H., A.G. and G.J.R. wrote the manuscript with editing input from all authors.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Immunology thanks Charlotte Scott and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Ioana Visan was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Human peritoneal macrophages are heterogenous and have limited population expression GATA6.
(a) Heatmap of differentially expressed genes (rows) of different clusters (columns). Heatmap colors indicate Z-transformed expression of genes in each row, with scale depicted in legend. Annotations (left) highlight representative genes with high differential gene expression within each cluster, relative to other clusters. Colors of gene names indicate corresponding clusters in Fig. 1a. (b) The proportion of cells from each patient contributed to each cluster. Color represents different human samples. (c) Confocal images showing the channels of DAPI and CD14, CD62P and GATA6, separately for the merged image in Fig. 1c. Biological samples were analyzed over two independent experiments. (d) Additional confocal images showing the expression GATA6 and CD62P in human adult peritoneal cells. Biological samples were analyzed over two independent experiments. (e) Violin plot showing the converting macrophage signature score (y-axis) in Fig. 1f for each cluster (x-axis) (n = 3977, 3537, 3504, 2169, 1895, 1571, 1551, 1518, 1001, 351, 347, 283,67,66,28,27 cells respectively). Red bars depict means with error bars representing standard deviation. A one-way ANOVA and post-hoc comparisons using Tukey′s HSD were conducted to compare the means of different groups, **** p < 0.0001. (f) The spliced ratio of GATA6 transcripts in GATA6+ cells versus GATA6- cells in 7 human adult samples. Bars depict means with error bars representing standard deviation. ****p < 0.0001, two-sided t-test. Exact p-value = 2.77028E-05 (g) Principal component analysis showing the distinct transcriptome profiles (microarray) between Gata6 KO and wild-type peritoneal macrophages integrated from three independent studies (GSE56711, GSE47049 and GSE37448).
Extended Data Fig. 2 Human and mouse peritoneal immune cell composition is different.
(a) UMAP projection of all CD45+ cells sequenced from the peritoneal cavity of 7 adults and 3 C57BL6 mice, forming 30 distinct clusters (colored as shown in the legend), with cluster names assigned based on inferred function. (b) UMAP plots showing the distinct immune cell composition of the mouse (right) and human (left) peritoneal cavity. Colors are coded as in a. (c) Feature plots demonstrating the expression of key immune cell markers, including markers for T and B lymphocytes and myeloid cells. Color scale represents the normalized gene expression. (d) Proportion of each cluster out of total immune cells for each sample, grouped by species (n = 7 human adult samples and n = 3 mouse samples). Bars depict means with error bars representing standard deviation. Multiple two-tailed t-tests followed by false discovery rate (FDR) correction; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, n.s. not significant. The exact p-values and FDR corrected q-values are reported as Source Data.
Extended Data Fig. 3 Further analysis of peritoneal MNPs between mouse and human.
(a) Heatmap of differentially expressed genes (rows) of different clusters (columns). Heatmap colors indicate Z-transformed expression of genes in each row, with scale depicted in legend. Annotations (left) highlight representative genes with high differential gene expression within each cluster, relative to other clusters. Colors of gene names indicate corresponding clusters in Fig. 2a. (b) Dot plot showing the average Z-transformed normalized expression of markers for large cavity-, converting- or monocyte like macrophages. The size of each dot indicates the fraction of cells expressing each gene; the color scale represents Z-transformed normalized expression. (c) The projection of cells from each cluster in Fig. 1 in the new UMAP space of Fig. 2. Colors correspond to Fig. 1a. (d) UMAP projection showing the different cell cycle phases of the peritoneal immune cell subsets in mouse or human separately. Colors representing the predicted classification of cell cycle phase based on the S and G2/M scores calculated by the CellCycleScoring function in the Seurat package. (e) The proportions of cells in each cell cycle phase of mouse and human (n = 7 human adult samples and n = 3 mouse samples). Bars depict means with error bars representing standard deviation. * represents p < 0.05, two-tailed t-test.
Extended Data Fig. 4 Summary of patient cohort and patient contributions to each cluster.
(a) Summary for the age, gender and operational procedure of patients we have collected and analyzed in this study. The table was organized by the different experimental approaches performed on the samples collected. (b) Pie charts depicting the proportion of cells from each patient to the total number of cells in each cluster (Fig. 3a). Each color represents one individual patient, with the total number of each cluster labeled at the bottom of each pie chart.
Extended Data Fig. 5 The frequency of various macrophage or DC clusters did not differ based on sex.
(a) Heatmap of differentially expressed genes (rows) of different clusters (columns). Heatmap colors indicate Z-transformed expression of genes in each row, with scale depicted in legend. Annotations (left) highlight representative genes with high differential gene expression within each cluster, relative to other clusters. Colors of gene names indicate corresponding clusters in Fig. 3a. (b) The percentage (x-axis) of each macrophage/DC cluster (y-axis) out of total MNPs in each patient (n = 7 human adult samples, n = 9 human pediatric samples). Black and white squares represent male and female patient, respectively. Bars depict means with error bars representing standard deviation. Multiple two-sided student′s t-test was applied and n.s. represents not significant.
Extended Data Fig. 6 Gating strategies for human and mouse macrophages and dendritic cells subpopulations.
(a) Gating strategy for the different human peritoneal macrophage and DC subsets in Fig. 4. (b) Gating strategy for the mouse counterparts of human peritoneal SCM, cDC1, cDC2 and pDC populations.
Extended Data Fig. 7 . Unsupervised clustering of human peritoneal macrophages based on flow cytometry validates the key macrophage populations.
Extended Data Figure 7 (a) Projection of manually gated CD14+ CCR2+ CM (blue), CD206+ LYVE1+ CCR2- CD62P- CM (orange), CD62P+ CM (red), CD1c+ CD64+ MNPs (green), CD1c+ CD64- MNPs (pink) and cDC1 (purple) over UMAP displayed in Fig. 4a. (b-c) Histograms representing TIMD4 and LYVE1 expression in CD14+ CCR2+ (blue), CD206+ CCR2- CD62P- (Orange) and CCR2- CD62P+ (red) CM across all adult (b, n = 7) or pediatric (c, n = 6) samples.
Extended Data Fig. 8 Gating strategies and flow cytometry plots for the studies in mice to assess impact of environmental triggers on macrophage phenotype.
(a) Gating strategy used for identification of mouse LCM populations based on LYVE1 and CD206 expression. (b) Representative plots of Fig. 5b showing expression of CD206 and LYVE1 by LCMs from control (Gata6fl/fl) and Csf1rERCre x Gata6fl/fl mice 16 days post-tamoxifen administration. (c) Body weight from female mice fed either normal chow diet (n = 6) or high-fat diet (n = 5) for 5 months to induce obesity. Data representative of two similar experiments. A two-sided Mann-Whitney test was used for statistical analysis (p = 0.0087). ** represents p < 0.01 and data are represented as mean value +/− SEM. (d) Isotype controls for CD206 and LYVE1, comparing to the expression of control or high-fat diet mice. (e) Gating strategy used for analysis of LCMs from wild-caught mice.
Supplementary information
Supplementary Table 1
Supplementary Table 1.
Source data
Source Data Fig. 1
Statistical source data.
Source Data Fig. 2
Statistical source data.
Source Data Fig. 3
Statistical source data.
Source Data Fig. 4
Statistical source data.
Source Data Fig. 5
Statistical source data.
Source Data Extended Data Fig. 1
Statistical source data.
Source Data Extended Data Fig. 2
Statistical source data.
Source Data Extended Data Fig. 3
Statistical source data.
Source Data Extended Data Fig. 5
Statistical source data.
Source Data Extended Data Fig. 8
Statistical source data.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Han, J., Gallerand, A., Erlich, E.C. et al. Human serous cavity macrophages and dendritic cells possess counterparts in the mouse with a distinct distribution between species. Nat Immunol 25, 155–165 (2024). https://doi.org/10.1038/s41590-023-01688-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41590-023-01688-7
