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Pisu D, Huang L, Narang V, Theriault M, Lê-Bury G, Lee B, Lakudzala AE, Mzinza DT, Mhango DV, Mitini-Nkhoma SC, Jambo KC, Singhal A, Mwandumba HC, Russell DG. Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung. J Exp Med 2021; 218:e20210615. [PMID: 34292313 PMCID: PMC8302446 DOI: 10.1084/jem.20210615] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/19/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
In this study, we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression, and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis-infected alveolar (AMs) and interstitial macrophages (IMs) in vivo. We identify clusters of pro-inflammatory AMs associated with stressed bacteria, in addition to three different populations of IMs with heterogeneous bacterial phenotypes. Finally, we show that the main macrophage populations in the lung are epigenetically constrained in their response to infection, while inter-species comparison reveals that most AMs subsets are conserved between mice and humans. This conceptual approach is readily transferable to other infectious disease agents with the potential for an increased understanding of the roles that different host cell populations play during the course of an infection.
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MESH Headings
- Animals
- Antitubercular Agents/pharmacology
- Bronchoalveolar Lavage Fluid/microbiology
- CD11 Antigens/immunology
- CD11 Antigens/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Bacterial
- Heme/metabolism
- Host-Pathogen Interactions
- Humans
- Lung/microbiology
- Lung/pathology
- Macrophages, Alveolar/immunology
- Macrophages, Alveolar/microbiology
- Macrophages, Alveolar/pathology
- Mice, Inbred C57BL
- Microorganisms, Genetically-Modified
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/immunology
- Mycobacterium tuberculosis/pathogenicity
- Sequence Analysis, RNA
- Single-Cell Analysis
- Tuberculosis, Pulmonary/genetics
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
- Mice
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Affiliation(s)
- Davide Pisu
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Lu Huang
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
- Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Vipin Narang
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Monique Theriault
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Gabrielle Lê-Bury
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Agnes E. Lakudzala
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - David T. Mzinza
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - David V. Mhango
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - Steven C. Mitini-Nkhoma
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - Kondwani C. Jambo
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amit Singhal
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore
| | - Henry C. Mwandumba
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David G. Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
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