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Mulder K, Patel AA, Kong WT, Piot C, Halitzki E, Dunsmore G, Khalilnezhad S, Irac SE, Dubuisson A, Chevrier M, Zhang XM, Tam JKC, Lim TKH, Wong RMM, Pai R, Khalil AIS, Chow PKH, Wu SZ, Al-Eryani G, Roden D, Swarbrick A, Chan JKY, Albani S, Derosa L, Zitvogel L, Sharma A, Chen J, Silvin A, Bertoletti A, Blériot C, Dutertre CA, Ginhoux F. Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease. Immunity 2021; 54:1883-1900.e5. [PMID: 34331874 DOI: 10.1016/j.immuni.2021.07.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/05/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022]
Abstract
Mononuclear phagocytes (MNPs) encompass dendritic cells, monocytes, and macrophages (MoMac), which exhibit antimicrobial, homeostatic, and immunoregulatory functions. We integrated 178,651 MNPs from 13 tissues across 41 datasets to generate a MNP single-cell RNA compendium (MNP-VERSE), a publicly available tool to map MNPs and define conserved gene signatures of MNP populations. Next, we generated a MoMac-focused compendium that revealed an array of specialized cell subsets widely distributed across multiple tissues. Specific pathological forms were expanded in cancer and inflammation. All neoplastic tissues contained conserved tumor-associated macrophage populations. In particular, we focused on IL4I1+CD274(PD-L1)+IDO1+ macrophages, which accumulated in the tumor periphery in a T cell-dependent manner via interferon-γ (IFN-γ) and CD40/CD40L-induced maturation from IFN-primed monocytes. IL4I1_Macs exhibited immunosuppressive characteristics through tryptophan degradation and promoted the entry of regulatory T cell into tumors. This integrated analysis provides a robust online-available platform for uniform annotation and dissection of specific macrophage functions in healthy and pathological states.
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Affiliation(s)
- Kevin Mulder
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Amit Ashok Patel
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Wan Ting Kong
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Cécile Piot
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Evelyn Halitzki
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore; Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Garett Dunsmore
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Shabnam Khalilnezhad
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Sergio Erdal Irac
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Agathe Dubuisson
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Marion Chevrier
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Xiao Meng Zhang
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - John Kit Chung Tam
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Tony Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, 20 College Road, Singapore 169856, Singapore
| | - Regina Men Men Wong
- Genome Institute of Singapore, A(∗)STAR, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Rhea Pai
- Genome Institute of Singapore, A(∗)STAR, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | | | - Pierce Kah Hoe Chow
- Division of Surgical Oncology, National Cancer Centre, Singapore 169610, Singapore
| | - Suny Z Wu
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ghamdan Al-Eryani
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Daniel Roden
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore 169857, Singapore; Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
| | - Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France; Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Cancer Medicine Department, Gustave Roussy, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS), 1428 Villejuif, France
| | - Ankur Sharma
- Genome Institute of Singapore, A(∗)STAR, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore; Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia; School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Institute, Curtin University, Perth, WA 6102, Australia
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore
| | - Aymeric Silvin
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Antonio Bertoletti
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Camille Blériot
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Charles-Antoine Dutertre
- Gustave Roussy Cancer Campus, Villejuif, France; Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore; Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore.
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A(∗)STAR, 8A Biomedical Grove, Immunos Building, Singapore 138648, Singapore; Translational Immunology Institute, SingHealth/Duke-NUS Academic Medical Centre, the Academia, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore; Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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3
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See P, Dutertre CA, Chen J, Günther P, McGovern N, Irac SE, Gunawan M, Beyer M, Händler K, Duan K, Sumatoh HRB, Ruffin N, Jouve M, Gea-Mallorquí E, Hennekam RCM, Lim T, Yip CC, Wen M, Malleret B, Low I, Shadan NB, Fen CFS, Tay A, Lum J, Zolezzi F, Larbi A, Poidinger M, Chan JKY, Chen Q, Rénia L, Haniffa M, Benaroch P, Schlitzer A, Schultze JL, Newell EW, Ginhoux F. Mapping the human DC lineage through the integration of high-dimensional techniques. Science 2017; 356:science.aag3009. [PMID: 28473638 DOI: 10.1126/science.aag3009] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 04/25/2017] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here, we combine two high-dimensional technologies-single-cell messenger RNA sequencing (scmRNAseq) and cytometry by time-of-flight (CyTOF)-to identify human blood CD123+CD33+CD45RA+ DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC. Tracing the differentiation of DC from the bone marrow to the peripheral blood revealed that the pre-DC compartment contains distinct lineage-committed subpopulations, including one early uncommitted CD123high pre-DC subset and two CD45RA+CD123low lineage-committed subsets exhibiting functional differences. The discovery of multiple committed pre-DC populations opens promising new avenues for the therapeutic exploitation of DC subset-specific targeting.
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Affiliation(s)
- Peter See
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Patrick Günther
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Naomi McGovern
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Sergio Erdal Irac
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Merry Gunawan
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Marc Beyer
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Hermi Rizal Bin Sumatoh
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nicolas Ruffin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Mabel Jouve
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Ester Gea-Mallorquí
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Raoul C M Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Tony Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Chan Chung Yip
- Department of Health Promotion Board (HPB) and Transplant Surgery, Singapore General Hospital, Singapore
| | - Ming Wen
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ivy Low
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charlene Foong Shu Fen
- Singapore Health Services Flow Cytometry Core Platform, 20 College Road, The Academia, Discovery Tower Level 10, Singapore 169856, Singapore
| | - Alicia Tay
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Jerry K Y Chan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Reproductive Medicine, Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore.,Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Philippe Benaroch
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Andreas Schlitzer
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Myeloid Cell Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.
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