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Silvin A, Uderhardt S, Piot C, Da Mesquita S, Yang K, Geirsdottir L, Mulder K, Eyal D, Liu Z, Bridlance C, Thion MS, Zhang XM, Kong WT, Deloger M, Fontes V, Weiner A, Ee R, Dress R, Hang JW, Balachander A, Chakarov S, Malleret B, Dunsmore G, Cexus O, Chen J, Garel S, Dutertre CA, Amit I, Kipnis J, Ginhoux F. Dual ontogeny of disease-associated microglia and disease inflammatory macrophages in aging and neurodegeneration. Immunity 2022; 55:1448-1465.e6. [PMID: 35931085 DOI: 10.1016/j.immuni.2022.07.004] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [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: 02/18/2022] [Revised: 04/18/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022]
Abstract
Brain macrophage populations include parenchymal microglia, border-associated macrophages, and recruited monocyte-derived cells; together, they control brain development and homeostasis but are also implicated in aging pathogenesis and neurodegeneration. The phenotypes, localization, and functions of each population in different contexts have yet to be resolved. We generated a murine brain myeloid scRNA-seq integration to systematically delineate brain macrophage populations. We show that the previously identified disease-associated microglia (DAM) population detected in murine Alzheimer's disease models actually comprises two ontogenetically and functionally distinct cell lineages: embryonically derived triggering receptor expressed on myeloid cells 2 (TREM2)-dependent DAM expressing a neuroprotective signature and monocyte-derived TREM2-expressing disease inflammatory macrophages (DIMs) accumulating in the brain during aging. These two distinct populations appear to also be conserved in the human brain. Herein, we generate an ontogeny-resolved model of brain myeloid cell heterogeneity in development, homeostasis, and disease and identify cellular targets for the treatment of neurodegeneration.
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Affiliation(s)
- Aymeric Silvin
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - Stefan Uderhardt
- Department of Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; Deutsches Zentrum für Immuntherapie, FAU, 91054 Erlangen, Germany; Exploratory Research Unit, Optical Imaging Centre Erlangen, FAU, 91058 Erlangen, Germany
| | - Cecile Piot
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Sandro Da Mesquita
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia, Charlottesville, VA 22908, USA; Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Katharine Yang
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Laufey Geirsdottir
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kevin Mulder
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - David Eyal
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Cecile Bridlance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Morgane Sonia Thion
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Xiao Meng Zhang
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Wan Ting Kong
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Marc Deloger
- INSERM US23, CNRS UMS 3655, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - Vasco Fontes
- Department of Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany; Deutsches Zentrum für Immuntherapie, FAU, 91054 Erlangen, Germany; Exploratory Research Unit, Optical Imaging Centre Erlangen, FAU, 91058 Erlangen, Germany
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rachel Ee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Regine Dress
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Jing Wen Hang
- Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore
| | - Akhila Balachander
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Svetoslav Chakarov
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Benoit Malleret
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Department of Microbiology and Immunology, Immunology Translational Research Programme, Yong Loo Lin School of Medicine, Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117543, Singapore
| | - Garett Dunsmore
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - Olivier Cexus
- INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France; School Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Jinmiao Chen
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Sonia Garel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Charles Antoine Dutertre
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jonathan Kipnis
- Department of Neuroscience, Center for Brain Immunology and Glia, University of Virginia, Charlottesville, VA 22908, USA; Center for Brain Immunology and Glia, Department of Pathology and Immunology, School of Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; INSERM U1015, Gustave Roussy Cancer Campus, Villejuif 94800, France; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore.
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Subramanian S, Busch CJL, Molawi K, Geirsdottir L, Maurizio J, Vargas Aguilar S, Belahbib H, Gimenez G, Yuda RAA, Burkon M, Favret J, Gholamhosseinian Najjar S, de Laval B, Kandalla PK, Sarrazin S, Alexopoulou L, Sieweke MH. Long-term culture-expanded alveolar macrophages restore their full epigenetic identity after transfer in vivo. Nat Immunol 2022; 23:458-468. [PMID: 35210623 DOI: 10.1038/s41590-022-01146-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/20/2022] [Indexed: 12/31/2022]
Abstract
Alveolar macrophages (AMs) are lung tissue-resident macrophages that can be expanded in culture, but it is unknown to what extent culture affects their in vivo identity. Here we show that mouse long-term ex vivo expanded AMs (exAMs) maintained a core AM gene expression program, but showed culture adaptations related to adhesion, metabolism and proliferation. Upon transplantation into the lung, exAMs reacquired full transcriptional and epigenetic AM identity, even after several months in culture and could self-maintain long-term in the alveolar niche. Changes in open chromatin regions observed in culture were fully reversible in transplanted exAMs and resulted in a gene expression profile indistinguishable from resident AMs. Our results indicate that long-term proliferation of AMs in culture did not compromise cellular identity in vivo. The robustness of exAM identity provides new opportunities for mechanistic analysis and highlights the therapeutic potential of exAMs.
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Affiliation(s)
- Sethuraman Subramanian
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.,Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France.,Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), Berlin, Germany
| | - Clara Jana-Lui Busch
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Kaaweh Molawi
- Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France.,Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), Berlin, Germany
| | | | | | - Stephanie Vargas Aguilar
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.,Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France.,Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), Berlin, Germany
| | | | - Gregory Gimenez
- Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France
| | - Ridzky Anis Advent Yuda
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Michaela Burkon
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Jérémy Favret
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | | | | | - Prashanth Kumar Kandalla
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Sandrine Sarrazin
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.,Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France
| | | | - Michael H Sieweke
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany. .,Aix-Marseille University, CNRS, INSERM, CIML, Marseille, France.
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3
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Geirsdottir L, David E, Keren-Shaul H, Weiner A, Bohlen SC, Neuber J, Balic A, Giladi A, Sheban F, Dutertre CA, Pfeifle C, Peri F, Raffo-Romero A, Vizioli J, Matiasek K, Scheiwe C, Meckel S, Mätz-Rensing K, van der Meer F, Thormodsson FR, Stadelmann C, Zilkha N, Kimchi T, Ginhoux F, Ulitsky I, Erny D, Amit I, Prinz M. Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program. Cell 2020; 179:1609-1622.e16. [PMID: 31835035 DOI: 10.1016/j.cell.2019.11.010] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [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: 03/12/2019] [Revised: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 02/08/2023]
Abstract
Microglia, the brain-resident immune cells, are critically involved in many physiological and pathological brain processes, including neurodegeneration. Here we characterize microglia morphology and transcriptional programs across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to humans, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, whereas human microglia display significant heterogeneity. In addition, we observed notable differences in several gene modules of rodents compared with primate microglia, including complement, phagocytic, and susceptibility genes to neurodegeneration, such as Alzheimer's and Parkinson's disease. Our study provides an essential resource of conserved and divergent microglia pathways across evolution, with important implications for future development of microglia-based therapies in humans.
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Affiliation(s)
- Laufey Geirsdottir
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel; Life Science Core Facility-Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Jana Neuber
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, United Kingdom
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Fadi Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, Singapore
| | - Christine Pfeifle
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Ploen, Germany
| | - Francesca Peri
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Antonella Raffo-Romero
- Universite Lille, Inserm, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France
| | - Jacopo Vizioli
- Universite Lille, Inserm, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Scheiwe
- Clinic for Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Meckel
- Department of Neuroradiology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kerstin Mätz-Rensing
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | | | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Noga Zilkha
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Kimchi
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, Singapore, Singapore
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Erny
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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4
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Geirsdottir L, David E, Keren-Shaul H, Weiner A, Bohlen SC, Neuber J, Balic A, Giladi A, Sheban F, Dutertre CA, Pfeifle C, Peri F, Raffo-Romero A, Vizioli J, Matiasek K, Scheiwe C, Meckel S, Mätz-Rensing K, van der Meer F, Thormodsson FR, Stadelmann C, Zilkha N, Kimchi T, Ginhoux F, Ulitsky I, Erny D, Amit I, Prinz M. Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program. Cell 2020; 181:746. [PMID: 32359440 DOI: 10.1016/j.cell.2020.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Sankowski R, Böttcher C, Masuda T, Geirsdottir L, Sagar, Sindram E, Seredenina T, Muhs A, Scheiwe C, Shah MJ, Heiland DH, Schnell O, Grün D, Priller J, Prinz M. Mapping microglia states in the human brain through the integration of high-dimensional techniques. Nat Neurosci 2019; 22:2098-2110. [PMID: 31740814 DOI: 10.1038/s41593-019-0532-y] [Citation(s) in RCA: 249] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
Abstract
Microglia are tissue-resident macrophages of the CNS that orchestrate local immune responses and contribute to several neurological and psychiatric diseases. Little is known about human microglia and how they orchestrate their highly plastic, context-specific adaptive responses during pathology. Here we combined two high-dimensional technologies, single-cell RNA-sequencing and time-of-flight mass cytometry, to identify microglia states in the human brain during homeostasis and disease. This approach enabled us to identify and characterize a previously unappreciated spectrum of transcriptional states in human microglia. These transcriptional states are determined by their spatial distribution, and they further change with aging and brain tumor pathology. This description of multiple microglia phenotypes in the human CNS may open promising new avenues for subset-specific therapeutic interventions.
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Affiliation(s)
- Roman Sankowski
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Takahiro Masuda
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laufey Geirsdottir
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sagar
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Elena Sindram
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | | | - Christian Scheiwe
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mukesch Johannes Shah
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Schnell
- Department of Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominic Grün
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- DZNE and BIH, Berlin, Germany.
- University of Edinburgh and UK DRI, Edinburgh, UK.
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany.
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