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Khan N, Downey J, Sanz J, Kaufmann E, Blankenhaus B, Pacis A, Pernet E, Ahmed E, Cardoso S, Nijnik A, Mazer B, Sassetti C, Behr MA, Soares MP, Barreiro LB, Divangahi M. M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity. Cell 2020; 183:752-770.e22. [PMID: 33125891 PMCID: PMC7599081 DOI: 10.1016/j.cell.2020.09.062] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 06/23/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting protective versus detrimental immunity to pathogens that cause chronic infections such as Mycobacterium tuberculosis (Mtb). We have shown that systemic administration of Bacille Calmette-Guérin (BCG) or β-glucan reprograms HSCs in the bone marrow (BM) via a type II interferon (IFN-II) or interleukin-1 (IL1) response, respectively, which confers protective trained immunity against Mtb. Here, we demonstrate that, unlike BCG or β-glucan, Mtb reprograms HSCs via an IFN-I response that suppresses myelopoiesis and impairs development of protective trained immunity to Mtb. Mechanistically, IFN-I signaling dysregulates iron metabolism, depolarizes mitochondrial membrane potential, and induces cell death specifically in myeloid progenitors. Additionally, activation of the IFN-I/iron axis in HSCs impairs trained immunity to Mtb infection. These results identify an unanticipated immune evasion strategy of Mtb in the BM that controls the magnitude and intrinsic anti-microbial capacity of innate immunity to infection.
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Affiliation(s)
- Nargis Khan
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Jeffrey Downey
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Joaquin Sanz
- Department of Theoretical Physics, University of Zaragoza, Institute BIFI for Bio-computation and Physics of Complex Systems, University of Zaragoza, Zaragoza, Spain
| | - Eva Kaufmann
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | | | - Alain Pacis
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Erwan Pernet
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Eisha Ahmed
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada
| | | | - Anastasia Nijnik
- Department of Physiology, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Bruce Mazer
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada
| | - Christopher Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marcel A Behr
- McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | | | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology, McGill University, Montreal, QC, Canada; McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada.
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May G, Soneji S, Tipping A, Teles J, McGowan S, Wu M, Guo Y, Fugazza C, Brown J, Karlsson G, Pina C, Olariu V, Taylor S, Tenen D, Peterson C, Enver T. Dynamic analysis of gene expression and genome-wide transcription factor binding during lineage specification of multipotent progenitors. Cell Stem Cell 2013; 13:754-68. [PMID: 24120743 PMCID: PMC3878573 DOI: 10.1016/j.stem.2013.09.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/06/2013] [Accepted: 09/12/2013] [Indexed: 12/30/2022]
Abstract
We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (1) differential complexity of sequence motifs bound by GATA1, GATA2, and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression; and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. This rubric exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis. Cross-platform resource for TF-network regulation of multipotent blood cell fate DNA motif dependence and changing specificity of GATA factors in lineage choice Modeling-based inference identifies GATA2 repression of PU.1 in multipotent cells Priming, recruitment, and switching modes of GATA interplay during differentiation
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Affiliation(s)
- Gillian May
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Shamit Soneji
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alex J. Tipping
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jose Teles
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Simon J. McGowan
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mengchu Wu
- Cancer Science Institute, National University of Singapore, Singapore 117599
| | - Yanping Guo
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Cristina Fugazza
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - John Brown
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Göran Karlsson
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Cristina Pina
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Victor Olariu
- Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Stephen Taylor
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daniel G. Tenen
- Cancer Science Institute, National University of Singapore, Singapore 117599
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Carsten Peterson
- Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Tariq Enver
- Stem Cell Group, UCL Cancer Institute, University College London, London WC1E 6BT, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Corresponding author
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