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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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2
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Simonson AW, Zeppa JJ, Bucsan AN, Chao MC, Pokkali S, Hopkins F, Chase MR, Vickers AJ, Sutton MS, Winchell CG, Myers AJ, Ameel CL, Kelly R, Krouse B, Hood LE, Li J, Lehman CC, Kamath M, Tomko J, Rodgers MA, Donlan R, Chishti H, Jacob Borish H, Klein E, Scanga CA, Fortune S, Lin PL, Maiello P, Roederer M, Darrah PA, Seder RA, Flynn JL. CD4 T cells and CD8α+ lymphocytes are necessary for intravenous BCG-induced protection against tuberculosis in macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594183. [PMID: 38798646 PMCID: PMC11118459 DOI: 10.1101/2024.05.14.594183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Tuberculosis (TB) is a major cause of morbidity and mortality worldwide despite widespread intradermal (ID) BCG vaccination in newborns. We previously demonstrated that changing the route and dose of BCG vaccination from 5×105 CFU ID to 5×107 CFU intravenous (IV) resulted in prevention of infection and disease in a rigorous, highly susceptible non-human primate model of TB. Identifying the immune mechanisms of protection for IV BCG will facilitate development of more effective vaccines against TB. Here, we depleted select lymphocyte subsets in IV BCG vaccinated macaques prior to Mtb challenge to determine the cell types necessary for that protection. Depletion of CD4 T cells or all CD8α expressing lymphoycytes (both innate and adaptive) resulted in loss of protection in most macaques, concomitant with increased bacterial burdens (~4-5 log10 thoracic CFU) and dissemination of infection. In contrast, depletion of only adaptive CD8αβ+ T cells did not significantly reduce protection against disease. Our results demonstrate that CD4 T cells and innate CD8α+ lymphocytes are critical for IV BCG-induced protection, supporting investigation of how eliciting these cells and their functions can improve future TB vaccines.
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Affiliation(s)
- Andrew W. Simonson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Joseph J. Zeppa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Allison N. Bucsan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Michael C. Chao
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Supriya Pokkali
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Forrest Hopkins
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Michael R. Chase
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Andrew J. Vickers
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Matthew S. Sutton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Caylin G. Winchell
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Amy J. Myers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Cassaundra L. Ameel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Ryan Kelly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Ben Krouse
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Luke E. Hood
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Jiaxiang Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Chelsea C. Lehman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Jaime Tomko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Mark A. Rodgers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Rachel Donlan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Harris Chishti
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - H. Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Edwin Klein
- Division of Animal Laboratory Resources, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Charles A. Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Sarah Fortune
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Philana Ling Lin
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Department of Pediatrics, Children’s Hospital of the University of Pittsburgh of UPMC; Pittsburgh, PA, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Patricia A. Darrah
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); Bethesda, MD, USA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
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3
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Michael CT, Almohri SA, Linderman JJ, Kirschner DE. A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons. FRONTIERS IN SYSTEMS BIOLOGY 2024; 3:1283341. [PMID: 39310676 PMCID: PMC11415237 DOI: 10.3389/fsysb.2023.1283341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Computational models of disease progression have been constructed for a myriad of pathologies. Typically, the conceptual implementation for pathology-related in-silico intervention studies has been ad-hoc and similar in design to experimental studies. We introduce a multi-scale interventional design (MID) framework toward two key goals: tracking of disease dynamics from within-body to patient to population scale; and tracking impact(s) of interventions across these same spatial scales. Our MID framework prioritizes investigation of impact on individual patients within virtual pre-clinical trials, instead of replicating the design of experimental studies. We apply a MID framework to develop, organize, and analyze a cohort of virtual patients for the study of tuberculosis (TB) as an example disease. For this study, we use HostSim: our next-generation whole patient-scale computational model of individuals infected with Mycobacterium tuberculosis. HostSim captures infection within lungs by tracking multiple granulomas, together with dynamics occurring with blood and lymph node compartments, the compartments involved during pulmonary TB. We extend HostSim to include a simple drug intervention as an example of our approach and use our MID framework to quantify the impact of treatment at cellular and tissue (granuloma), patient (lungs, lymph nodes and blood), and population scales. Sensitivity analyses allow us to determine which features of virtual patients are the strongest predictors of intervention efficacy across scales. These insights allow us to identify patient-heterogeneous mechanisms that drive outcomes across scales.
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Affiliation(s)
- Christian T. Michael
- Department of Microbiology & Immunology, University of Michigan - Michigan Medicine, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sayed Ahmad Almohri
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Denise E. Kirschner
- Department of Microbiology & Immunology, University of Michigan - Michigan Medicine, Ann Arbor, MI, USA
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4
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Bromley JD, Ganchua SKC, Nyquist SK, Maiello P, Chao M, Borish HJ, Rodgers M, Tomko J, Kracinovsky K, Mugahid D, Nguyen S, Wang D, Rosenberg JM, Klein EC, Gideon HP, Floyd-O’Sullivan R, Berger B, Scanga CA, Lin PL, Fortune SM, Shalek AK, Flynn JL. CD4 + T cells are homeostatic regulators during Mtb reinfection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572669. [PMID: 38187598 PMCID: PMC10769325 DOI: 10.1101/2023.12.20.572669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Immunological priming - either in the context of prior infection or vaccination - elicits protective responses against subsequent Mycobacterium tuberculosis (Mtb) infection. However, the changes that occur in the lung cellular milieu post-primary Mtb infection and their contributions to protection upon reinfection remain poorly understood. Here, using clinical and microbiological endpoints in a non-human primate reinfection model, we demonstrate that prior Mtb infection elicits a long-lasting protective response against subsequent Mtb exposure and that the depletion of CD4+ T cells prior to Mtb rechallenge significantly abrogates this protection. Leveraging microbiologic, PET-CT, flow cytometric, and single-cell RNA-seq data from primary infection, reinfection, and reinfection-CD4+ T cell depleted granulomas, we identify differential cellular and microbial features of control. The data collectively demonstrate that the presence of CD4+ T cells in the setting of reinfection results in a reduced inflammatory lung milieu characterized by reprogrammed CD8+ T cell activity, reduced neutrophilia, and blunted type-1 immune signaling among myeloid cells, mitigating Mtb disease severity. These results open avenues for developing vaccines and therapeutics that not only target CD4+ and CD8+ T cells, but also modulate innate immune cells to limit Mtb disease.
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Affiliation(s)
- Joshua D. Bromley
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sharie Keanne C. Ganchua
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Sarah K. Nyquist
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
| | - Michael Chao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - H. Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Mark Rodgers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Jaime Tomko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Kara Kracinovsky
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Douaa Mugahid
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Son Nguyen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dennis Wang
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacob M. Rosenberg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edwin C. Klein
- Division of Laboratory Animal Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Roisin Floyd-O’Sullivan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles A Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
| | - Philana Ling Lin
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
- Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine
| | - Sarah M. Fortune
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex K. Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh PA USA
- Lead contact
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5
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Winchell CG, Nyquist SK, Chao MC, Maiello P, Myers AJ, Hopkins F, Chase M, Gideon HP, Patel KV, Bromley JD, Simonson AW, Floyd-O’Sullivan R, Wadsworth M, Rosenberg JM, Uddin R, Hughes T, Kelly RJ, Griffo J, Tomko J, Klein E, Berger B, Scanga CA, Mattila J, Fortune SM, Shalek AK, Lin PL, Flynn JL. CD8+ lymphocytes are critical for early control of tuberculosis in macaques. J Exp Med 2023; 220:e20230707. [PMID: 37843832 PMCID: PMC10579699 DOI: 10.1084/jem.20230707] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/31/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
The functional role of CD8+ lymphocytes in tuberculosis remains poorly understood. We depleted innate and/or adaptive CD8+ lymphocytes in macaques and showed that loss of all CD8α+ cells (using anti-CD8α antibody) significantly impaired early control of Mycobacterium tuberculosis (Mtb) infection, leading to increased granulomas, lung inflammation, and bacterial burden. Analysis of barcoded Mtb from infected macaques demonstrated that depletion of all CD8+ lymphocytes allowed increased establishment of Mtb in lungs and dissemination within lungs and to lymph nodes, while depletion of only adaptive CD8+ T cells (with anti-CD8β antibody) worsened bacterial control in lymph nodes. Flow cytometry and single-cell RNA sequencing revealed polyfunctional cytotoxic CD8+ lymphocytes in control granulomas, while CD8-depleted animals were unexpectedly enriched in CD4 and γδ T cells adopting incomplete cytotoxic signatures. Ligand-receptor analyses identified IL-15 signaling in granulomas as a driver of cytotoxic T cells. These data support that CD8+ lymphocytes are required for early protection against Mtb and suggest polyfunctional cytotoxic responses as a vaccine target.
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Affiliation(s)
- Caylin G. Winchell
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sarah K. Nyquist
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, MIT, Cambridge, MA, USA
| | - Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amy J. Myers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Forrest Hopkins
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Michael Chase
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kush V. Patel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua D. Bromley
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, MIT, Cambridge, MA, USA
| | - Andrew W. Simonson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roisin Floyd-O’Sullivan
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Marc Wadsworth
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Jacob M. Rosenberg
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Travis Hughes
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Ryan J. Kelly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Josephine Griffo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jaime Tomko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Edwin Klein
- Division of Laboratory Animal Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bonnie Berger
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, MIT, Cambridge, MA, USA
| | - Charles A. Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joshua Mattila
- Department of Infectious Disease and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah M. Fortune
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Alex K. Shalek
- Broad Institute, Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Institute for Medical Engineering and Science, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Philana Ling Lin
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatrics, Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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6
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Grant NL, Kelly K, Maiello P, Abbott H, O’Connor S, Lin PL, Scanga CA, Flynn JL. Mycobacterium tuberculosis-Specific CD4 T Cells Expressing Transcription Factors T-Bet or RORγT Associate with Bacterial Control in Granulomas. mBio 2023; 14:e0047723. [PMID: 37039646 PMCID: PMC10294621 DOI: 10.1128/mbio.00477-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/12/2023] Open
Abstract
Despite the extensive research on CD4 T cells within the context of Mycobacterium tuberculosis (Mtb) infections, few studies have focused on identifying and investigating the profile of Mtb-specific T cells within lung granulomas. To facilitate the identification of Mtb-specific CD4 T cells, we identified immunodominant epitopes for two Mtb proteins, namely, Rv1196 and Rv0125, using a Mauritian cynomolgus macaque model of Mtb infection, thereby providing data for the synthesis of MHC class II tetramers. Using tetramers, we identified Mtb-specific cells within different immune compartments, postinfection. We found that granulomas were enriched sites for Mtb-specific cells and that tetramer+ cells had increased frequencies of the activation marker CD69 as well as the transcription factors T-bet and RORγT, compared to tetramer negative cells within the same sample. Our data revealed that while the frequency of Rv1196 tetramer+ cells was positively correlated with the granuloma bacterial burden, the frequency of RORγT or T-bet within tetramer+ cells was inversely correlated with the granuloma bacterial burden, thereby highlighting the importance of having activated, polarized, Mtb-specific cells for the control of Mtb in lung granulomas. IMPORTANCE Tuberculosis, caused by the bacterial pathogen Mycobacterium tuberculosis, kills 1.5 million people each year, despite the existence of effective drugs and a vaccine that is given to infants in most countries. Clearly, we need better vaccines against this disease. However, our understanding of the immune responses that are necessary to prevent tuberculosis is incomplete. This study seeks to understand the functions of T cells that are specific for M. tuberculosis at the site of the disease in the lungs. For this, we developed specialized tools called MHC class II tetramers to identify those T cells that can recognize M. tuberculosis and applied the tools to the study of this infection in nonhuman primate models that mimic human tuberculosis. We demonstrate that M. tuberculosis-specific T cells in lung lesions are associated with control of the bacteria only when those T cells are expressing certain functions, thereby highlighting the importance of combining the identification of specific T cells with functional analyses. Thus, we surmise that these functions of specific T cells are critical to the control of infection and should be considered as a part of the development of vaccines against tuberculosis.
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Affiliation(s)
- Nicole L. Grant
- Department of Infectious Disease and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Kristen Kelly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Helena Abbott
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shelby O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison Wisconsin, USA
| | - Philana Ling Lin
- Department of Pediatrics, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles A. Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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7
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Mott D, Yang J, Baer C, Papavinasasundaram K, Sassetti CM, Behar SM. High Bacillary Burden and the ESX-1 Type VII Secretion System Promote MHC Class I Presentation by Mycobacterium tuberculosis-Infected Macrophages to CD8 T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1531-1542. [PMID: 37000471 PMCID: PMC10159937 DOI: 10.4049/jimmunol.2300001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/21/2023] [Indexed: 04/01/2023]
Abstract
We used a mouse model to study how Mycobacterium tuberculosis subverts host defenses to persist in macrophages despite immune pressure. CD4 T cells can recognize macrophages infected with a single bacillus in vitro. Under identical conditions, CD8 T cells inefficiently recognize infected macrophages and fail to restrict M. tuberculosis growth, although they can inhibit M. tuberculosis growth during high-burden intracellular infection. We show that high intracellular M. tuberculosis numbers cause macrophage death, leading other macrophages to scavenge cellular debris and cross-present the TB10.4 Ag to CD8 T cells. Presentation by infected macrophages requires M. tuberculosis to have a functional ESX-1 type VII secretion system. These data indicate that phagosomal membrane damage and cell death promote MHC class I presentation of the immunodominant Ag TB10.4 by macrophages. Although this mode of Ag presentation stimulates cytokine production that we presume would be host beneficial, killing of uninfected cells could worsen immunopathology. We suggest that shifting the focus of CD8 T cell recognition to uninfected macrophages would limit the interaction of CD8 T cells with infected macrophages and impair CD8 T cell-mediated resolution of tuberculosis.
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Affiliation(s)
- Daniel Mott
- Immunology and Microbiology Program, Graduate School of Biomedical Science, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jason Yang
- Immunology and Microbiology Program, Graduate School of Biomedical Science, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christina Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher M. Sassetti
- Immunology and Microbiology Program, Graduate School of Biomedical Science, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Samuel M. Behar
- Immunology and Microbiology Program, Graduate School of Biomedical Science, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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8
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Qin Y, Wang Q, Shi J. Immune checkpoint modulating T cells and NK cells response to Mycobacterium tuberculosis infection. Microbiol Res 2023; 273:127393. [PMID: 37182283 DOI: 10.1016/j.micres.2023.127393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/07/2023] [Accepted: 04/22/2023] [Indexed: 05/16/2023]
Abstract
Many subversive mechanisms promote the occurrence and development of chronic infectious diseases and cancer, among which the down-regulated expression of immune-activating receptors and the enhanced expression of immune-inhibitory receptors accelerate the occurrence and progression of the disease. Recently, the use of immune checkpoint inhibitors has shown remarkable efficacy in the treatment of tumors in multiple organs. However, the expression of immune checkpoint molecules on natural killer (NK) cells by Mycobacterium tuberculosis (Mtb) infection and its impact on NK cell effector functions have been poorly studied. In this review, we focus on what is currently known about the expression of various immune checkpoints in NK cells following Mtb infection and how it alters NK cell-mediated host cytotoxicity and cytokine secretion. Unraveling the function of NK cells after the infection of host cells by Mtb is crucial for a comprehensive understanding of the innate immune mechanism of NK cells involved in tuberculosis and the evaluation of the efficacy of immunotherapies using immune checkpoint inhibitors to treat tuberculosis. In view of some similarities in the immune characteristics of T cells and NK cells, we reviewed the molecular mechanism of the interaction between T cells and Mtb, which can help us to further understand and explore the specific interaction mechanism between NK cells and Mtb.
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Affiliation(s)
- Yongwei Qin
- Department of Pathogen Biology, Medical College, Nantong University, No. 19 Qixiu Road, Nantong 226001, China.
| | - Qinglan Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong 226001, China
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9
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Ashenafi S, Brighenti S. Reinventing the human tuberculosis (TB) granuloma: Learning from the cancer field. Front Immunol 2022; 13:1059725. [PMID: 36591229 PMCID: PMC9797505 DOI: 10.3389/fimmu.2022.1059725] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in the world and every 20 seconds a person dies from TB. An important attribute of human TB is induction of a granulomatous inflammation that creates a dynamic range of local microenvironments in infected organs, where the immune responses may be considerably different compared to the systemic circulation. New and improved technologies for in situ quantification and multimodal imaging of mRNA transcripts and protein expression at the single-cell level have enabled significantly improved insights into the local TB granuloma microenvironment. Here, we review the most recent data on regulation of immunity in the TB granuloma with an enhanced focus on selected in situ studies that enable spatial mapping of immune cell phenotypes and functions. We take advantage of the conceptual framework of the cancer-immunity cycle to speculate how local T cell responses may be enhanced in the granuloma microenvironment at the site of Mycobacterium tuberculosis infection. This includes an exploratory definition of "hot", immune-inflamed, and "cold", immune-excluded TB granulomas that does not refer to the level of bacterial replication or metabolic activity, but to the relative infiltration of T cells into the infected lesions. Finally, we reflect on the current knowledge and controversy related to reactivation of active TB in cancer patients treated with immune checkpoint inhibitors such as PD-1/PD-L1 and CTLA-4. An understanding of the underlying mechanisms involved in the induction and maintenance or disruption of immunoregulation in the TB granuloma microenvironment may provide new avenues for host-directed therapies that can support standard antibiotic treatment of persistent TB disease.
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Affiliation(s)
- Senait Ashenafi
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, ANA Futura, Huddinge, Sweden,Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Susanna Brighenti
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, ANA Futura, Huddinge, Sweden,*Correspondence: Susanna Brighenti,
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10
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Immune cell interactions in tuberculosis. Cell 2022; 185:4682-4702. [PMID: 36493751 DOI: 10.1016/j.cell.2022.10.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Despite having been identified as the organism that causes tuberculosis in 1882, Mycobacterium tuberculosis has managed to still evade our understanding of the protective immune response against it, defying the development of an effective vaccine. Technology and novel experimental models have revealed much new knowledge, particularly with respect to the heterogeneity of the bacillus and the host response. This review focuses on certain immunological elements that have recently yielded exciting data and highlights the importance of taking a holistic approach to understanding the interaction of M. tuberculosis with the many host cells that contribute to the development of protective immunity.
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