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Khuzwayo S, Mthembu M, Meermeier EW, Prakadan SM, Kazer SW, Bassett T, Nyamande K, Khan DF, Maharaj P, Mitha M, Suleman M, Mhlane Z, Ramjit D, Karim F, Shalek AK, Lewinsohn DM, Ndung'u T, Wong EB. MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection. Front Immunol 2021; 12:631410. [PMID: 33897687 PMCID: PMC8062704 DOI: 10.3389/fimmu.2021.631410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Mucosal associated invariant T (MAIT) cells are a class of innate-like T cells that utilize a semi-invariant αβ T cell receptor to recognize small molecule ligands produced by bacteria and fungi. Despite growing evidence that immune cells at mucosal surfaces are often phenotypically and functionally distinct from those in the peripheral circulation, knowledge about the characteristics of MAIT cells at the lung mucosal surface, the site of exposure to respiratory pathogens, is limited. HIV infection has been shown to have a profound effect on the number and function of MAIT cells in the peripheral blood, but its effect on lung mucosal MAIT cells is unknown. We examined the phenotypic, functional, and transcriptomic features of major histocompatibility complex (MHC) class I-related (MR1)-restricted MAIT cells from the peripheral blood and bronchoalveolar compartments of otherwise healthy individuals with latent Mycobacterium tuberculosis (Mtb) infection who were either HIV uninfected or HIV infected. Peripheral blood MAIT cells consistently co-expressed typical MAIT cell surface markers CD161 and CD26 in HIV-negative individuals, while paired bronchoalveolar MAIT cells displayed heterogenous expression of these markers. Bronchoalveolar MAIT cells produced lower levels of pro-inflammatory cytokine IFN-γ and expressed higher levels of co-inhibitory markers PD-1 and TIM-3 than peripheral MAIT cells. HIV infection resulted in decreased frequencies and pro-inflammatory function of peripheral blood MAIT cells, while in the bronchoalveolar compartment MAIT cell frequency was decreased but phenotype and function were not significantly altered. Single-cell transcriptomic analysis demonstrated greater heterogeneity among bronchoalveolar compared to peripheral blood MAIT cells and suggested a distinct subset in the bronchoalveolar compartment. The transcriptional features of this bronchoalveolar subset were associated with MAIT cell tissue repair functions. In summary, we found previously undescribed phenotypic and transcriptional heterogeneity of bronchoalveolar MAIT cells in HIV-negative people. In HIV infection, we found numeric depletion of MAIT cells in both anatomical compartments but preservation of the novel phenotypic and transcriptional features of bronchoalveolar MAIT cells.
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Affiliation(s)
- Sharon Khuzwayo
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maphe Mthembu
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Erin W Meermeier
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Sanjay M Prakadan
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Samuel W Kazer
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thierry Bassett
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Kennedy Nyamande
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Dilshaad Fakey Khan
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Priya Maharaj
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Mohammed Mitha
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Moosa Suleman
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa.,Department of Pulmonology and Critical Care, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zoey Mhlane
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Dirhona Ramjit
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Alex K Shalek
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - David M Lewinsohn
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States.,Department of Research, VA Portland Health Care Center, Portland, OR, United States
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Emily B Wong
- Africa Health Research Institute (AHRI), Durban, South Africa.,Division of Infection and Immunity, University College London, London, United Kingdom.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States.,Division of Infectious Diseases, University of Alabama Birmingham, Birmingham, AL, United States
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Muema DM, Mthembu M, Schiff AE, Singh U, Corleis B, Chen D, Bassett T, Rasehlo SS, Nyamande K, Khan DF, Maharaj P, Mitha M, Suleman M, Mhlane Z, Naidoo T, Ramjit D, Karim F, Kwon DS, Ndung'u T, Wong EB. Contrasting Inflammatory Signatures in Peripheral Blood and Bronchoalveolar Cells Reveal Compartment-Specific Effects of HIV Infection. Front Immunol 2020; 11:864. [PMID: 32508817 PMCID: PMC7248324 DOI: 10.3389/fimmu.2020.00864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/15/2020] [Indexed: 01/07/2023] Open
Abstract
The mechanisms by which HIV increases susceptibility to tuberculosis and other respiratory infections are incompletely understood. We used transcriptomics of paired whole bronchoalveolar lavage cells (BLCs) and peripheral blood mononuclear cells to compare the effect of HIV at the lung mucosal surface and in peripheral blood. The majority of HIV-induced differentially expressed genes (DEGs) were specific to either the peripheral or lung mucosa compartments (1,307/1,404, 93%). Type I interferon signaling was the dominant signature of DEGs in HIV-positive blood but not in HIV-positive BLCs. DEGs in the HIV-positive BLCs were significantly enriched for infiltration with cytotoxic CD8+ T cells. Higher expression of type 1 interferon transcripts in peripheral CD8+ T cells and representative transcripts and proteins in BLCs-derived CD8+ T cells during HIV infection, including IFNG (IFN-gamma), GZMB (Granzyme B), and PDCD1 (PD-1), was confirmed by cell-subset specific transcriptional analysis and flow cytometry. Thus, we report that a whole transcriptomic approach revealed qualitatively distinct effects of HIV in blood and bronchoalveolar compartments. Further work exploring the impact of distinct type I interferon programs and functional features of CD8+ T cells infiltrating the lung mucosa during HIV infection may provide novel insights into HIV-induced susceptibility to respiratory pathogens.
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Affiliation(s)
- Daniel M. Muema
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Maphe Mthembu
- African Health Research Institute, Durban, South Africa
| | - Abigail E. Schiff
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Urisha Singh
- African Health Research Institute, Durban, South Africa
| | - Björn Corleis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Institute of Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Isle of Riems, Germany
| | - Dongquan Chen
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | | | | | - Kennedy Nyamande
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Dilshaad Fakey Khan
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Priya Maharaj
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mohammed Mitha
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Moosa Suleman
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zoey Mhlane
- African Health Research Institute, Durban, South Africa
| | - Taryn Naidoo
- African Health Research Institute, Durban, South Africa
| | | | - Farina Karim
- African Health Research Institute, Durban, South Africa
| | - Douglas S. Kwon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Thumbi Ndung'u
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Emily B. Wong
- African Health Research Institute, Durban, South Africa
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
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Fakey Khan D, Suleman M, Baijnath P, Perumal R, Moodley V, Mhlane Z, Naidoo T, Ndung'u T, Wong EB. Multiple microbiologic tests for tuberculosis improve diagnostic yield of bronchoscopy in medically complex patients. AAS Open Res 2019; 2:25. [PMID: 32382702 PMCID: PMC7194149 DOI: 10.12688/aasopenres.12980.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 01/09/2023] Open
Abstract
Background: Bronchoalveolar lavage (BAL) is indicated for medical evaluation of complex cases of lung disease. There is limited data on the performance of tuberculosis (TB) microbiologic tests on BAL in such patients, particularly in human immunodeficiency virus (HIV) and TB endemic areas. Methods: We evaluated the performance of Mycobacterium tuberculosis (Mtb) culture and up to two simultaneous Xpert MTB/RIF tests on BAL fluid against a consensus clinical diagnosis in 98 medically complex patients undergoing bronchoscopy over a two-year period in Durban, South Africa. Results: TB was the most frequently diagnosed lung disease, found in 19 of 98 participants (19%) and was microbiologically proven in 14 of these (74%); 9 (47%) were culture positive and 5 were positive on at least one Xpert MTB/RIF assay. Immunosuppression prevalence was high (26% HIV-infected, 29% on immunosuppressive therapy and 4% on chemotherapy). Xpert MTB/RIF had low sensitivity (45%) and high specificity (99%) when assessed against the consensus clinical diagnosis. Compared to TB culture, a single Xpert MTB/RIF increased the diagnostic yield by 11% and a second Xpert MTB/RIF by a further 16%. Conclusion: Although Xpert MTB/RIF had a low sensitivity, sending two tests improved the microbiologically-proven diagnostic yield of bronchoscopy from 47% to 74% compared to culture alone.
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Affiliation(s)
- Dilshaad Fakey Khan
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, KZN, 4000, South Africa
| | - Moosa Suleman
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, KZN, 4000, South Africa
| | - Prinita Baijnath
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, KZN, 4000, South Africa
| | - Rubeshan Perumal
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, KZN, 4000, South Africa
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Vedanthi Moodley
- Department of Pulmonology, Inkosi Albert Luthuli Central Hospital, Durban, KZN, 4000, South Africa
| | - Zoey Mhlane
- Africa Health Research Institute, Durban, South Africa
| | - Taryn Naidoo
- Africa Health Research Institute, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
- HIV Pathogenesis programme, Doris Duke Medical Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Massachusetts, USA
| | - Emily B. Wong
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, USA
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