1
|
Petrone L, Peruzzu D, Altera AMG, Salmi A, Vanini V, Cuzzi G, Coppola A, Mellini V, Gualano G, Palmieri F, Panda S, Peters B, Sette A, Arlehamn CL, Goletti D. Therapy modulates the response to T cell epitopes over the spectrum of tuberculosis infection. J Infect 2024:106295. [PMID: 39343243 DOI: 10.1016/j.jinf.2024.106295] [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: 08/05/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND Identifying stage-specific antigens is essential for developing tuberculosis (TB) diagnostics and vaccines. In a low TB endemic country, we characterized, the Mycobacterium tuberculosis (Mtb)-specific immune response to a pool of Mtb-derived epitopes (ATB116), demonstrated as associated with TB disease. METHODS In this prospective observational cross-sectional study, we enrolled healthy donors (HD), subjects with TB disease, and TB infection (TBI) at baseline and therapy completion. T-cell response after whole blood stimulation with the peptide pools was characterized by ELISA, flow cytometry, and multiplex assay. RESULTS ATB116-specific IFN-γ response (by ELISA) significantly associates with Mtb regardless of infection/disease (p<0.0001) and decreases during TB therapy (p=0.0002). Flow cytometry confirms that ATB116-specific CD4+ T-cell response associated with Mtb regardless of infection/disease (p<0.0001) and shows a significantly higher frequency of IFN-γ/IL-2 and central memory T-cells in TBI compared to TB (p=0.016; p=0.0242, respectively). CD4+ T cell-specific response decreases after TB therapy completion. The antigen-specific CD8+ T-cell response mirrors the CD4+ response. Finally, the multiplex assay analysis showed that ATB116 induces several immune factors in both TB and TBI. CONCLUSION We characterized the immune response to Mtb peptide pools that is modulated by TB therapy. These results are important for our understanding of TB immunopathogenesis and vaccine design. DATA AVAILABILITY STATEMENT The raw data generated and/or analyzed within the present study will be available in INMI institutional repository (rawdata.inmi.it), subject to registration. The data can be found by selecting the article of interest from a list of articles ordered by year of publication. No charge for granting access to data is required. In the event of a malfunction of the application, the request can be sent directly by e-mail to biblioteca@inmi.it.
Collapse
Affiliation(s)
- Linda Petrone
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Daniela Peruzzu
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Anna Maria Gerarda Altera
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Andrea Salmi
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Valentina Vanini
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy; UOS Professioni Sanitarie Tecniche, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Gilda Cuzzi
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Andrea Coppola
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Valeria Mellini
- Respiratory Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Gina Gualano
- Respiratory Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Fabrizio Palmieri
- Respiratory Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy
| | - Sudhasini Panda
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Bjoern Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, University of California San Diego (UCSD), La Jolla, CA 92093, USA
| | | | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Rome, Italy.
| |
Collapse
|
2
|
Church EC, Bishop E, Fiore-Gartland A, Yu KKQ, Chang M, Jones RM, Brache JK, Ballweber Fleming L, Phan JM, Makatsa MS, Heptinstall J, Chiong K, Dintwe O, Naidoo A, Voillet V, Mayer-Blackwell K, Nwanne G, Andersen-Nissen E, Vary JC, Tomaras GD, McElrath MJ, Sherman DR, Murphy SC, Kublin JG, Seshadri C. Probing Dermal Immunity to Mycobacteria through a Controlled Human Infection Model. Immunohorizons 2024; 8:695-711. [PMID: 39283647 PMCID: PMC11447685 DOI: 10.4049/immunohorizons.2400053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/22/2024] Open
Abstract
Cutaneous mycobacterial infections cause substantial morbidity and are challenging to diagnose and treat. An improved understanding of the dermal immune response to mycobacteria may inspire new therapeutic approaches. We conducted a controlled human infection study with 10 participants who received 2 × 106 CFUs of Mycobacterium bovis bacillus Calmette-Guérin (Tice strain) intradermally and were randomized to receive isoniazid or no treatment. Peripheral blood was collected at multiple time points for flow cytometry, bulk RNA sequencing (RNA-seq), and serum Ab assessments. Systemic immune responses were detected as early as 8 d postchallenge in this M. bovis bacillus Calmette-Guérin-naive population. Injection-site skin biopsies were performed at days 3 and 15 postchallenge and underwent immune profiling using mass cytometry and single-cell RNA-seq, as well as quantitative assessments of bacterial viability and burden. Molecular viability testing and standard culture results correlated well, although no differences were observed between treatment arms. Single-cell RNA-seq revealed various immune and nonimmune cell types in the skin, and communication between them was inferred by ligand-receptor gene expression. Day 3 communication was predominantly directed toward monocytes from keratinocyte, muscle, epithelial, and endothelial cells, largely via the migration inhibitory factor pathway and HLA-E-KLRK1 interaction. At day 15, communication was more balanced between cell types. These data reveal the potential role of nonimmune cells in the dermal immune response to mycobacteria and the utility of human challenge studies to augment our understanding of mycobacterial infections.
Collapse
Affiliation(s)
- E Chandler Church
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Seattle-King County Public Health, Seattle, WA
| | - Emma Bishop
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | | | - Krystle K Q Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Ming Chang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Richard M Jones
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Justin K Brache
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Jolie M Phan
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Mohau S Makatsa
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Jack Heptinstall
- Duke Center for Human Systems Immunology, Duke University, Durham, NC
| | - Kelvin Chiong
- Duke Center for Human Systems Immunology, Duke University, Durham, NC
| | - One Dintwe
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Anneta Naidoo
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Valentin Voillet
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | | | - Gift Nwanne
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Jay C Vary
- Department of Dermatology, University of Washington School of Medicine, Seattle, WA
| | - Georgia D Tomaras
- Duke Center for Human Systems Immunology, Duke University, Durham, NC
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| |
Collapse
|
3
|
Nelson CE, Foreman TW, Fukutani ER, Kauffman KD, Sakai S, Fleegle JD, Gomez F, Gould ST, Le Nouën C, Liu X, Burdette TL, Garza NL, Lafont BAP, Brooks K, Lindestam Arlehamn CS, Weiskopf D, Sette A, Hickman HD, Buchholz UJ, Johnson RF, Brenchley JM, Oberman JP, Quieroz ATL, Andrade BB, Via LE, Barber DL. IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques. PLoS Pathog 2024; 20:e1012339. [PMID: 38950078 PMCID: PMC11244803 DOI: 10.1371/journal.ppat.1012339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/12/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024] Open
Abstract
The regulation of inflammatory responses and pulmonary disease during SARS-CoV-2 infection is incompletely understood. Here we examine the roles of the prototypic pro- and anti-inflammatory cytokines IFNγ and IL-10 using the rhesus macaque model of mild COVID-19. We find that IFNγ drives the development of 18fluorodeoxyglucose (FDG)-avid lesions in the lungs as measured by PET/CT imaging but is not required for suppression of viral replication. In contrast, IL-10 limits the duration of acute pulmonary lesions, serum markers of inflammation and the magnitude of virus-specific T cell expansion but does not impair viral clearance. We also show that IL-10 induces the subsequent differentiation of virus-specific effector T cells into CD69+CD103+ tissue resident memory cells (Trm) in the airways and maintains Trm cells in nasal mucosal surfaces, highlighting an unexpected role for IL-10 in promoting airway memory T cells during SARS-CoV-2 infection of macaques.
Collapse
Affiliation(s)
- Christine E. Nelson
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Taylor W. Foreman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eduardo R. Fukutani
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Keith D. Kauffman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shunsuke Sakai
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joel D. Fleegle
- Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Felipe Gomez
- Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - NIAID/DIR Tuberculosis Imaging Program
- Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sydnee T. Gould
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xueqiao Liu
- RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tracey L. Burdette
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicole L. Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bernard A. P. Lafont
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kelsie Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, California, United States of America
| | - Heather D. Hickman
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Reed F. Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James P. Oberman
- Holy Cross Germantown Hospital, Affiliate of National Breathe Free Sinus and ENT Center, Frederick Breathe Free Sinus and ENT Center, Frederick, Maryland, United States of America
| | - Artur T. L. Quieroz
- Laboratório de Pesquisa Clínica e Translacional, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Bruno B. Andrade
- Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura E. Via
- Division of Intramural Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
- Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Daniel L. Barber
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
4
|
Ogongo P, Tran A, Marzan F, Gingrich D, Krone M, Aweeka F, Lindestam Arlehamn CS, Martin JN, Deeks SG, Hunt PW, Ernst JD. High-parameter phenotypic characterization reveals a subset of human Th17 cells that preferentially produce IL-17 against M. tuberculosis antigen. Front Immunol 2024; 15:1378040. [PMID: 38698866 PMCID: PMC11064812 DOI: 10.3389/fimmu.2024.1378040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/28/2024] [Indexed: 05/05/2024] Open
Abstract
Background Interleukin-17-producing CD4 T cells contribute to the control of Mycobacterium tuberculosis (Mtb) infection in humans; whether infection with human immunodeficiency virus (HIV) disproportionately affects distinct Th17-cell subsets that respond to Mtb is incompletely defined. Methods We performed high-definition characterization of circulating Mtb-specific Th17 cells by spectral flow cytometry in people with latent TB and treated HIV (HIV-ART). We also measured kynurenine pathway activity by liquid chromatography-mass spectrometry (LC/MS) on plasma and tested the hypothesis that tryptophan catabolism influences Th17-cell frequencies in this context. Results We identified two subsets of Th17 cells: subset 1 defined as CD4+Vα7.2-CD161+CD26+and subset 2 defined as CD4+Vα7.2-CCR6+CXCR3-cells of which subset 1 was significantly reduced in latent tuberculosis infection (LTBI) with HIV-ART, yet Mtb-responsive IL-17-producing CD4 T cells were preserved; we found that IL-17-producing CD4 T cells dominate the response to Mtb antigen but not cytomegalovirus (CMV) antigen or staphylococcal enterotoxin B (SEB), and tryptophan catabolism negatively correlates with both subset 1 and subset 2 Th17-cell frequencies. Conclusions We found differential effects of ART-suppressed HIV on distinct subsets of Th17 cells, that IL-17-producing CD4 T cells dominate responses to Mtb but not CMV antigen or SEB, and that kynurenine pathway activity is associated with decreases of circulating Th17 cells that may contribute to tuberculosis immunity.
Collapse
Affiliation(s)
- Paul Ogongo
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
- Department of Tropical and Infectious Diseases, Institute of Primate Research, Nairobi, Kenya
| | - Anthony Tran
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Florence Marzan
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA, United States
| | - David Gingrich
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA, United States
| | - Melissa Krone
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Francesca Aweeka
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA, United States
| | | | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joel D. Ernst
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
5
|
Ogongo P, Tran A, Marzan F, Gingrich D, Krone M, Aweeka F, Lindestam Arlehamn CS, Martin JN, Deeks SG, Hunt PW, Ernst JD. High-parameter phenotypic characterization reveals a subset of human Th17 cells that preferentially produce IL17 against M. tuberculosis antigen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.06.523027. [PMID: 36711855 PMCID: PMC9881994 DOI: 10.1101/2023.01.06.523027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Interleukin 17 producing CD4 T cells contribute to the control of Mycobacterium tuberculosis (Mtb) infection in humans; whether infection with Human Immunodeficiency Virus (HIV) disproportionately affects distinct Th17 cell subsets that respond to Mtb is incompletely defined. Methods We performed high-definition characterization of circulating Mtb-specific Th17 cells by spectral flow cytometry in people with latent TB and treated HIV (HIV-ART). We also measured kynurenine pathway activity by LC/MS on plasma and tested the hypothesis that tryptophan catabolism influences Th17 cell frequencies in this context. Results We identified two subsets of Th17 cells: subset 1 defined as CD4+Vα7.2-CD161+CD26+ and subset 2 defined as CD4+Vα7.2-CCR6+CXCR3- cells of which subset 1 was significantly reduced in LTBI with HIV-ART, yet Mtb-responsive IL17-producing CD4 T cells were preserved; we found that IL17-producing CD4 T cells dominate the response to Mtb antigen but not CMV antigen or staphylococcal enterotoxin B (SEB); and tryptophan catabolism negatively correlates with both subset 1 and subset 2 Th17 cell frequencies. Conclusions We found differential effects of ART-suppressed HIV on distinct subsets of Th17 cells, that IL17-producing CD4 T cells dominate responses to Mtb but not CMV antigen or SEB, and that kynurenine pathway activity is associated with decreases of circulating Th17 cells that may contribute to tuberculosis immunity.
Collapse
Affiliation(s)
- Paul Ogongo
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
- Department of Tropical and Infectious Diseases, Institute of Primate Research, Nairobi, Kenya
| | - Anthony Tran
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Florence Marzan
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, CA, USA
| | - David Gingrich
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Melissa Krone
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Francesca Aweeka
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, CA, USA
| | | | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Joel D. Ernst
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| |
Collapse
|
6
|
Panda S, Morgan J, Cheng C, Saito M, Gilman RH, Ciobanu N, Crudu V, Catanzaro DG, Catanzaro A, Rodwell T, Perera JSB, Chathuranga T, Gunasena B, DeSilva AD, Peters B, Sette A, Lindestam Arlehamn CS. Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection. Nat Commun 2024; 15:765. [PMID: 38278794 PMCID: PMC10817963 DOI: 10.1038/s41467-024-45058-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
There is still incomplete knowledge of which Mycobacterium tuberculosis (Mtb) antigens can trigger distinct T cell responses at different stages of infection. Here, a proteome-wide screen of 20,610 Mtb-derived peptides in 21 patients mid-treatment for active tuberculosis (ATB) reveals IFNγ-specific T cell responses against 137 unique epitopes. Of these, 16% are recognized by two or more participants and predominantly derived from cell wall and cell processes antigens. There is differential recognition of antigens, including TB vaccine candidate antigens, between ATB participants and interferon-gamma release assay (IGRA + /-) individuals. We developed an ATB-specific peptide pool (ATB116) consisting of epitopes exclusively recognized by ATB participants. This pool can distinguish patients with pulmonary ATB from IGRA + /- individuals from various geographical locations, with a sensitivity of over 60% and a specificity exceeding 80%. This proteome-wide screen of T cell reactivity identified infection stage-specific epitopes and antigens for potential use in diagnostics and measuring Mtb-specific immune responses.
Collapse
Affiliation(s)
- Sudhasini Panda
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeffrey Morgan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Catherine Cheng
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Baltimore, MD, USA
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Judy S B Perera
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Teshan Chathuranga
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | - Aruna D DeSilva
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | |
Collapse
|
7
|
Gress AR, Ronayne CE, Thiede JM, Meyerholz DK, Okurut S, Stumpf J, Mathes TV, Ssebambulidde K, Meya DB, Cresswell FV, Boulware DR, Bold TD. Recently activated CD4 T cells in tuberculosis express OX40 as a target for host-directed immunotherapy. Nat Commun 2023; 14:8423. [PMID: 38110410 PMCID: PMC10728168 DOI: 10.1038/s41467-023-44152-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
After Mycobacterium tuberculosis (Mtb) infection, many effector T cells traffic to the lungs, but few become activated. Here we use an antigen receptor reporter mouse (Nur77-GFP) to identify recently activated CD4 T cells in the lungs. These Nur77-GFPHI cells contain expanded TCR clonotypes, have elevated expression of co-stimulatory genes such as Tnfrsf4/OX40, and are functionally more protective than Nur77-GFPLO cells. By contrast, Nur77-GFPLO cells express markers of terminal exhaustion and cytotoxicity, and the trafficking receptor S1pr5, associated with vascular localization. A short course of immunotherapy targeting OX40+ cells transiently expands CD4 T cell numbers and shifts their phenotype towards parenchymal protective cells. Moreover, OX40 agonist immunotherapy decreases the lung bacterial burden and extends host survival, offering an additive benefit to antibiotics. CD4 T cells from the cerebrospinal fluid of humans with HIV-associated tuberculous meningitis commonly express surface OX40 protein, while CD8 T cells do not. Our data thus propose OX40 as a marker of recently activated CD4 T cells at the infection site and a potential target for immunotherapy in tuberculosis.
Collapse
Affiliation(s)
- Abigail R Gress
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
- Center for Immunology, 2101 6th St SE, WMBB 2-118, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christine E Ronayne
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
- Center for Immunology, 2101 6th St SE, WMBB 2-118, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Joshua M Thiede
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
- Center for Immunology, 2101 6th St SE, WMBB 2-118, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David K Meyerholz
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, 1165 Medical Laboratories (ML), 51 Newton Rd, University of Iowa, Iowa City, IA, 52242, USA
| | - Samuel Okurut
- Infectious Diseases Institute, P.O. Box 22418, Makerere University, Kampala, Uganda
| | - Julia Stumpf
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
| | - Tailor V Mathes
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
- Center for Immunology, 2101 6th St SE, WMBB 2-118, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - David B Meya
- Infectious Diseases Institute, P.O. Box 22418, Makerere University, Kampala, Uganda
| | - Fiona V Cresswell
- Infectious Diseases Institute, P.O. Box 22418, Makerere University, Kampala, Uganda
- MRC/UVRI and London School of Hygiene and Tropical Medicine Uganda Research Unit, PO Box 49, Plot 51-59, Nakiwogo Road Entebbe, Entebbe, Uganda
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton, East Sussex, BN1 9PX, UK
| | - David R Boulware
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA
| | - Tyler D Bold
- Department of Medicine, University of Minnesota, 420 Delaware Street, SE MMC 250, Minneapolis, MN, 55455, USA.
- Center for Immunology, 2101 6th St SE, WMBB 2-118, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
8
|
da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [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] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
Collapse
Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| |
Collapse
|
9
|
Gong W, Du J. Excluding Participants With Mycobacteria Infections From Clinical Trials: A Critical Consideration in Evaluating the Efficacy of BCG Against COVID-19. J Korean Med Sci 2023; 38:e343. [PMID: 37904656 PMCID: PMC10615642 DOI: 10.3346/jkms.2023.38.e343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/01/2023] [Indexed: 11/01/2023] Open
Abstract
In the context of the coronavirus disease 2019 (COVID-19) pandemic, Bacillus Calmette-Guérin (BCG), a tuberculosis (TB) vaccine, has been investigated for its potential to prevent COVID-19 with conflicting outcomes. Currently, over 50 clinical trials have been conducted to assess the effectiveness of BCG in preventing COVID-19, but the results have shown considerable variations. After scrutinizing the data, it was discovered that some trials had enrolled individuals with active TB, latent TB infection, or a history of TB. This finding raises concerns about the reliability and validity of the trial outcomes. In this study, we explore the potential consequences of including these participants in clinical trials, including impaired host immunity, immune exhaustion, and the potential masking of the BCG vaccine's protective efficacy against COVID-19 by persistent mycobacterial infections. We also put forth several suggestions for future clinical trials. Our study underscores the criticality of excluding individuals with active or latent TB from clinical trials evaluating the efficacy of BCG in preventing COVID-19.
Collapse
Affiliation(s)
- Wenping Gong
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China.
| | - Jingli Du
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China.
| |
Collapse
|
10
|
Gail DP, Suzart VG, Du W, Kaur Sandhu A, Jarvela J, Nantongo M, Mwebaza I, Panigrahi S, Freeman ML, Canaday DH, Boom WH, Silver RF, Carpenter SM. Mycobacterium tuberculosis impairs human memory CD4 + T cell recognition of M2 but not M1-like macrophages. iScience 2023; 26:107706. [PMID: 37694142 PMCID: PMC10485162 DOI: 10.1016/j.isci.2023.107706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/24/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Direct recognition of Mycobacterium tuberculosis (Mtb)-infected cells is required for protection by CD4+ T cells. While impaired T cell recognition of Mtb-infected macrophages was demonstrated in mice, data are lacking for humans. Using T cells and monocyte-derived macrophages (MDMs) from individuals with latent Mtb infection (LTBI), we quantified the frequency of memory CD4+ T cell activation in response to autologous MDMs infected with virulent Mtb. We observed robust T cell activation in response to Mtb infection of M1-like macrophages differentiated using GM-CSF, while M2-like macrophages differentiated using M-CSF were poorly recognized. However, non-infected GM-CSF and M-CSF MDMs loaded with exogenous antigens elicited similar CD4+ T cell activation. IL-10 was preferentially secreted by infected M-CSF MDMs, and neutralization improved T cell activation. These results suggest that preferential infection of macrophages with an M2-like phenotype limits T cell-mediated protection against Mtb. Vaccine development should focus on T cell recognition of Mtb-infected macrophages.
Collapse
Affiliation(s)
- Daniel P. Gail
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Vinicius G. Suzart
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Weinan Du
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Avinaash Kaur Sandhu
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jessica Jarvela
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Medicine, The Louis Stokes Cleveland V.A. Medical Center, Cleveland, OH 44106, USA
| | - Mary Nantongo
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ivan Mwebaza
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Soumya Panigrahi
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael L. Freeman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - David H. Canaday
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Medicine, The Louis Stokes Cleveland V.A. Medical Center, Cleveland, OH 44106, USA
| | - W. Henry Boom
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44139, USA
| | - Richard F. Silver
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Medicine, The Louis Stokes Cleveland V.A. Medical Center, Cleveland, OH 44106, USA
| | - Stephen M. Carpenter
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Biomedical Sciences Training Program, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44139, USA
| |
Collapse
|
11
|
Lai R, Gong DN, Williams T, Ogunsola AF, Cavallo K, Lindestam Arlehamn CS, Acolatse S, Beamer GL, Ferris MT, Sassetti CM, Lauffenburger DA, Behar SM. Host genetic background is a barrier to broadly effective vaccine-mediated protection against tuberculosis. J Clin Invest 2023; 133:e167762. [PMID: 37200108 PMCID: PMC10313364 DOI: 10.1172/jci167762] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/11/2023] [Indexed: 05/20/2023] Open
Abstract
Heterogeneity in human immune responses is difficult to model in standard laboratory mice. To understand how host variation affects Bacillus Calmette Guerin-induced (BCG-induced) immunity against Mycobacterium tuberculosis, we studied 24 unique collaborative cross (CC) mouse strains, which differ primarily in the genes and alleles they inherit from founder strains. The CC strains were vaccinated with or without BCG and challenged with aerosolized M. tuberculosis. Since BCG protects only half of the CC strains tested, we concluded that host genetics has a major influence on BCG-induced immunity against M. tuberculosis infection, making it an important barrier to vaccine-mediated protection. Importantly, BCG efficacy is dissociable from inherent susceptibility to tuberculosis (TB). T cell immunity was extensively characterized to identify components associated with protection that were stimulated by BCG and recalled after M. tuberculosis infection. Although considerable diversity is observed, BCG has little impact on the composition of T cells in the lung after infection. Instead, variability is largely shaped by host genetics. BCG-elicited protection against TB correlated with changes in immune function. Thus, CC mice can be used to define correlates of protection and to identify vaccine strategies that protect a larger fraction of genetically diverse individuals instead of optimizing protection for a single genotype.
Collapse
Affiliation(s)
- Rocky Lai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diana N. Gong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Travis Williams
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Abiola F. Ogunsola
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kelly Cavallo
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Sarah Acolatse
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Samuel M. Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
12
|
Darrah PA, Zeppa JJ, Wang C, Irvine EB, Bucsan AN, Rodgers MA, Pokkali S, Hackney JA, Kamath M, White AG, Borish HJ, Frye LJ, Tomko J, Kracinovsky K, Lin PL, Klein E, Scanga CA, Alter G, Fortune SM, Lauffenburger DA, Flynn JL, Seder RA, Maiello P, Roederer M. Airway T cells are a correlate of i.v. Bacille Calmette-Guerin-mediated protection against tuberculosis in rhesus macaques. Cell Host Microbe 2023; 31:962-977.e8. [PMID: 37267955 PMCID: PMC10355173 DOI: 10.1016/j.chom.2023.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/04/2023]
Abstract
Bacille Calmette-Guerin (BCG), the only approved Mycobacterium tuberculosis (Mtb) vaccine, provides limited durable protection when administered intradermally. However, recent work revealed that intravenous (i.v.) BCG administration yielded greater protection in macaques. Here, we perform a dose-ranging study of i.v. BCG vaccination in macaques to generate a range of immune responses and define correlates of protection. Seventeen of 34 macaques had no detectable infection after Mtb challenge. Multivariate analysis incorporating longitudinal cellular and humoral immune parameters uncovered an extensive and highly coordinated immune response from the bronchoalveolar lavage (BAL). A minimal signature predicting protection contained four BAL immune features, of which three remained significant after dose correction: frequency of CD4 T cells producing TNF with interferon γ (IFNγ), frequency of those producing TNF with IL-17, and the number of NK cells. Blood immune features were less predictive of protection. We conclude that CD4 T cell immunity and NK cells in the airway correlate with protection following i.v. BCG.
Collapse
Affiliation(s)
- Patricia A Darrah
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph J Zeppa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chuangqi Wang
- Department of Immunology and Microbiology, University of Colorado, Anschuntz Medical Campus, Aurora, CO 80045, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Edward B Irvine
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA 02139, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Allison N Bucsan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A Rodgers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Supriya Pokkali
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Hackney
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander G White
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - H Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - L James Frye
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jaime Tomko
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Kara Kracinovsky
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Philana Ling Lin
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15620, USA
| | - Edwin Klein
- Division of Animal Laboratory Resources, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Charles A Scanga
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA 02139, USA
| | - Sarah M Fortune
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Cambridge, MA 02139, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
13
|
Dijkman K, Lindenstrøm T, Rosenkrands I, Søe R, Woodworth JS, Lindestam Arlehamn CS, Mortensen R. A protective, single-visit TB vaccination regimen by co-administration of a subunit vaccine with BCG. NPJ Vaccines 2023; 8:66. [PMID: 37160970 PMCID: PMC10169149 DOI: 10.1038/s41541-023-00666-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
The only licensed tuberculosis (TB) vaccine, Bacillus Calmette Guerin (BCG), fails to reliably protect adolescents and adults from pulmonary TB, resulting in ~1.6 million deaths annually. Protein subunit vaccines have shown promise against TB in clinical studies. Unfortunately, most subunit vaccines require multiple administrations, which increases the risk of loss to follow-up and necessitates more complex and costly logistics. Given the well-documented adjuvant effect of BCG, we hypothesized that BCG co-administration could compensate for a reduced number of subunit vaccinations. To explore this, we developed an expression-optimized version of our H107 vaccine candidate (H107e), which does not cross-react with BCG. In the CAF®01 adjuvant, a single dose of H107e induced inferior protection compared to three H107e/CAF®01 administrations. However, co-administering a single dose of H107e/CAF®01 with BCG significantly improved protection, which was equal to BCG co-administered with three H107e/CAF®01 doses. Importantly, combining BCG with a single H107e/CAF®01 dose also increased protection in previously BCG-primed animals. Overall, a single dose of H107e/CAF®01 with BCG induced long-lived immunity and triggered BCG-specific Th17 responses. These data support co-administration of BCG and subunit vaccines in both BCG naïve and BCG-primed individuals as an improved TB vaccine strategy with reduced number of vaccination visits.
Collapse
Affiliation(s)
- Karin Dijkman
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
- Janssen Vaccines & Prevention, Leiden, the Netherlands
| | - Thomas Lindenstrøm
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Rikke Søe
- Department of Vaccine Development, Statens Serum Institut, Copenhagen, Denmark
| | - Joshua S Woodworth
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Rasmus Mortensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark.
| |
Collapse
|
14
|
Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
Collapse
|
15
|
Panda S, Morgan J, Cheng C, Saito M, Gilman RH, Ciobanu N, Crudu V, Catanzaro DG, Catanzaro A, Rodwell T, Perera JS, Chathuranga T, Gunasena B, DeSilva AD, Peters B, Sette A, Lindestam Arlehamn CS. Identification of differentially recognized T cell epitopes in the spectrum of Mtb infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536550. [PMID: 37090558 PMCID: PMC10120689 DOI: 10.1101/2023.04.12.536550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis is one of the leading causes of death from a single infectious agent. Identifying dominant epitopes and comparing their reactivity in different tuberculosis (TB) infection states can help design diagnostics and vaccines. We performed a proteome-wide screen of 20,610 Mtb derived peptides in 21 Active TB (ATB) patients 3-4 months post-diagnosis of pulmonary TB (mid-treatment) using an IFNγ and IL-17 Fluorospot assay. Responses were mediated exclusively by IFNγ and identified a total of 137 unique epitopes, with each patient recognizing, on average, 8 individual epitopes and 22 epitopes (16%) recognized by 2 or more participants. Responses were predominantly directed against antigens part of the cell wall and cell processes category. Testing 517 peptides spanning TB vaccine candidates and ESAT-6 and CFP10 antigens also revealed differential recognition between ATB participants mid-treatment and healthy IGRA+ participants of several vaccine antigens. An ATB-specific peptide pool consisting of epitopes exclusively recognized by participants mid-treatment, allowed distinguishing participants with active pulmonary TB from healthy interferon-gamma release assay (IGRA)+/- participants from diverse geographical locations. Analysis of longitudinal samples indicated decreased reactivity during treatment for pulmonary TB. Together, these results show that a proteome-wide screen of T cell reactivity identifies epitopes and antigens that are differentially recognized depending on the Mtb infection stage. These have potential use in developing diagnostics and vaccine candidates and measuring correlates of protection.
Collapse
Affiliation(s)
- Sudhasini Panda
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeffrey Morgan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Catherine Cheng
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Johns Hopkins School of Public Health, Baltimore, MD, USA
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Judy S.B. Perera
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Teshan Chathuranga
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | - Aruna D. DeSilva
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | |
Collapse
|
16
|
Imprinting of Gut-Homing Receptors on Mtb-Specific Th1* Cells Is Associated with Reduced Lung Homing after Gavage BCG Vaccination of Rhesus Macaques. mBio 2023; 14:e0022023. [PMID: 36880755 PMCID: PMC10127997 DOI: 10.1128/mbio.00220-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Alternative delivery routes of the current Mycobacterium tuberculosis (Mtb) vaccine, intradermally (ID) delivered BCG, may provide better protection against tuberculosis, and be more easily administered. Here, we use rhesus macaques to compare the airway immunogenicity of BCG delivered via either ID or intragastric gavage vaccination. Ag-specific CD4 T cell responses in the blood were similar after BCG vaccination via gavage or ID injection. However, gavage BCG vaccination induced significantly lower T cell responses in the airways compared to intradermal BCG vaccination. Examining T cell responses in lymph node biopsies showed that ID vaccination induced T cell priming in skin-draining lymph nodes, while gavage vaccination induced priming in the gut-draining nodes, as expected. While both delivery routes induced highly functional Ag-specific CD4 T cells with a Th1* phenotype (CXCR3+CCR6+), gavage vaccination induced the co-expression of the gut-homing integrin α4β7 on Ag-specific Th1* cells, which was associated with reduced migration into the airways. Thus, in rhesus macaques, the airway immunogenicity of gavage BCG vaccination may be limited by the imprinting of gut-homing receptors on Ag-specific T cells primed in intestinal lymph nodes. IMPORTANCE Mycobacterium tuberculosis (Mtb) is a leading cause of global infectious disease mortality. The vaccine for Mtb, Bacillus Calmette-Guérin (BCG), was originally developed as an oral vaccine, but is now given intradermally. Recently, clinical studies have reevaluated oral BCG vaccination in humans and found that it induces significant T cell responses in the airways. Here, we use rhesus macaques to compare the airway immunogenicity of BCG delivered intradermally or via intragastric gavage. We find that gavage BCG vaccination induces Mtb-specific T cell responses in the airways, but to a lesser extent than intradermal vaccination. Furthermore, gavage BCG vaccination induces the gut-homing receptor a4ß7 on Mtb-specific CD4 T cells, which was associated with reduced migration into the airways. These data raise the possibility that strategies to limit the induction of gut-homing receptors on responding T cells may enhance the airway immunogenicity of oral vaccines.
Collapse
|
17
|
Musvosvi M, Huang H, Wang C, Xia Q, Rozot V, Krishnan A, Acs P, Cheruku A, Obermoser G, Leslie A, Behar SM, Hanekom WA, Bilek N, Fisher M, Kaufmann SHE, Walzl G, Hatherill M, Davis MM, Scriba TJ. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat Med 2023; 29:258-269. [PMID: 36604540 PMCID: PMC9873565 DOI: 10.1038/s41591-022-02110-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/25/2022] [Indexed: 01/07/2023]
Abstract
Antigen-specific, MHC-restricted αβ T cells are necessary for protective immunity against Mycobacterium tuberculosis, but the ability to broadly study these responses has been limited. In the present study, we used single-cell and bulk T cell receptor (TCR) sequencing and the GLIPH2 algorithm to analyze M. tuberculosis-specific sequences in two longitudinal cohorts, comprising 166 individuals with M. tuberculosis infection who progressed to either tuberculosis (n = 48) or controlled infection (n = 118). We found 24 T cell groups with similar TCR-β sequences, predicted by GLIPH2 to have common TCR specificities, which were associated with control of infection (n = 17), and others that were associated with progression to disease (n = 7). Using a genome-wide M. tuberculosis antigen screen, we identified peptides targeted by T cell similarity groups enriched either in controllers or in progressors. We propose that antigens recognized by T cell similarity groups associated with control of infection can be considered as high-priority targets for future vaccine development.
Collapse
Affiliation(s)
- Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiong Xia
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Akshaya Krishnan
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA
| | - Peter Acs
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA
| | - Abhilasha Cheruku
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA
| | | | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Infection and Immunity, University College London, London, UK
| | - Samuel M Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Willem A Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, USA
| | - Gerhard Walzl
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
| |
Collapse
|
18
|
Brito-Sierra CA, Lannan MB, Siegel RW, Malherbe LP. The HLA class-II immunopeptidomes of AAV capsids proteins. Front Immunol 2022; 13:1067399. [PMID: 36605211 PMCID: PMC9807805 DOI: 10.3389/fimmu.2022.1067399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Gene therapies are using Adeno-associated viruses (AAVs) as vectors, but immune responses against the capsids pose challenges to their efficiency and safety. Helper T cell recognition of capsid-derived peptides bound to human leukocyte antigen (HLA) class II molecules is an essential step in the AAV-specific adaptive immunity. Methods Using MHC-associated peptide proteomics, we identified the HLA-DR and HLA-DQ immunopeptidomes of the capsid proteins of three different AAV serotypes (AAV2, AAV6, and AAV9) from a panel of healthy donors selected to represent a majority of allele usage. Results The identified sequences span the capsids of all serotypes, with AAV2 having the highest peptide count. For all the serotypes, multiple promiscuous peptides were identified and displayed by both HLA-DR and -DQ. However, despite high sequence homology, there were few identical peptides among AAV2, AAV6, and AAV9 immunopeptidomes, and none were promiscuous. Discussion Results from this work represent a comprehensive immunopeptidomics research of potential CD4+ T cell epitopes and provide the basis for immunosurveillance efforts for safer and more efficient AAV-based gene therapies.
Collapse
Affiliation(s)
| | | | - Robert W. Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Laurent P. Malherbe
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| |
Collapse
|
19
|
Du Bruyn E, Ruzive S, Howlett P, Cerrone M, Jacobs A, Arlehamn CSL, Sette A, Sher A, Mayer-Barber KD, Barber DL, Mayosi B, Ntsekhe M, Wilkinson RJ, Riou C. Comparison of the frequency and phenotypic profile of Mycobacterium tuberculosis-specific CD4 T cells between the site of disease and blood in pericardial tuberculosis. Front Immunol 2022; 13:1009016. [PMID: 36439130 PMCID: PMC9692124 DOI: 10.3389/fimmu.2022.1009016] [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: 08/01/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Studies of the immune response at the site of disease in extra-pulmonary tuberculosis (EPTB) disease are scarce. In this study, we compared the cellular profile of Mycobacterium tuberculosis (Mtb)-specific T cells in pericardial fluid and peripheral blood in patients with pericardial TB (PCTB). Whole blood and pericardial fluid (PCF) samples were collected at the time of diagnostic sampling, with repeat blood sampling after completion of anti-tubercular treatment (ATT) in 16 PCTB patients, most of them being HIV-1 infected (n=14). These samples were stimulated ex vivo and the phenotypic and functional cellular profile of PCF and blood was assessed by flow cytometry. We found that lymphocytes were the predominant cell type in PCF in PCTB, with a preferential influx of CD4 T cells. The frequencies of TNF-α producing Mtb-specific granulocytes and Mtb-specific CD4 T cells were significantly higher in PCF compared to blood. Mtb-specific CD4 T cells in PCF exhibited a distinct phenotype compared to those in blood, with greater GrB expression and lower CD27 and KLRG1 expression. We observed no difference in the production IFNγ, TNF or IL-2 by Mtb-specific CD4 T cells between the two compartments, but MIP-1β production was lower in the PCF T cells. Bacterial loads were not associated with alterations in the phenotype or function of Mtb-specific CD4 T cells. Upon ATT completion, HLA-DR, Ki-67 and GrB expression was significantly decreased, and relative IL-2 production was increased in peripheral Mtb-specific CD4 T cells. Overall, using an ex vivo assay to compare the immune response towards Mtb in PCF and in blood, we identified significant difference in the phenotypic profile of Mtb-specific CD4 T response between these two compartments. Moreover, we show that the activation profile of peripheral Mtb-specific CD4 T cells could be used to monitor treatment response in PCTB.
Collapse
Affiliation(s)
- Elsa Du Bruyn
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sheena Ruzive
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Patrick Howlett
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Maddalena. Cerrone
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Department of Infectious Diseases, Imperial College London, London, United Kingdom,Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ashley J. Jacobs
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bongani Mayosi
- Department of Medicine, University of Cape Town, Cape Town, South Africa,Division of Cardiology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Mpiko Ntsekhe
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Department of Medicine, University of Cape Town, Cape Town, South Africa,Division of Cardiology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert J. Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Department of Infectious Diseases, Imperial College London, London, United Kingdom,Tuberculosis Laboratory, The Francis Crick Institute, London, United Kingdom,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Catherine Riou
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa,*Correspondence: Catherine Riou,
| |
Collapse
|
20
|
Kairuz D, Samudh N, Ely A, Arbuthnot P, Bloom K. Advancing mRNA technologies for therapies and vaccines: An African context. Front Immunol 2022; 13:1018961. [PMID: 36353641 PMCID: PMC9637871 DOI: 10.3389/fimmu.2022.1018961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/10/2022] [Indexed: 09/26/2023] Open
Abstract
Synthetic mRNA technologies represent a versatile platform that can be used to develop advanced drug products. The remarkable speed with which vaccine development programs designed and manufactured safe and effective COVID-19 vaccines has rekindled interest in mRNA technology, particularly for future pandemic preparedness. Although recent R&D has focused largely on advancing mRNA vaccines and large-scale manufacturing capabilities, the technology has been used to develop various immunotherapies, gene editing strategies, and protein replacement therapies. Within the mRNA technologies toolbox lie several platforms, design principles, and components that can be adapted to modulate immunogenicity, stability, in situ expression, and delivery. For example, incorporating modified nucleotides into conventional mRNA transcripts can reduce innate immune responses and improve in situ translation. Alternatively, self-amplifying RNA may enhance vaccine-mediated immunity by increasing antigen expression. This review will highlight recent advances in the field of synthetic mRNA therapies and vaccines, and discuss the ongoing global efforts aimed at reducing vaccine inequity by establishing mRNA manufacturing capacity within Africa and other low- and middle-income countries.
Collapse
Affiliation(s)
| | | | | | | | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
21
|
Lindestam Arlehamn CS, Benson B, Kuan R, Dill-McFarland KA, Peterson GJ, Paul S, Nguyen FK, Gilman RH, Saito M, Taplitz R, Arentz M, Goss CH, Aitken ML, Horne DJ, Shah JA, Sette A, Hawn TR. T-cell deficiency and hyperinflammatory monocyte responses associate with Mycobacterium avium complex lung disease. Front Immunol 2022; 13:1016038. [PMID: 36263044 PMCID: PMC9574438 DOI: 10.3389/fimmu.2022.1016038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Immunological mechanisms of susceptibility to nontuberculous mycobacterial (NTM) disease are poorly understood. To understand NTM pathogenesis, we evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex (MAC) in asymptomatic individuals with a previous history of MAC lung disease (MACDZ). We hypothesized that Mav-specific immune responses are associated with susceptibility to MAC lung disease. We measured MAC-, NTM-, or MAC/Mtb-specific T-cell responses by cytokine production, expression of surface markers, and analysis of global gene expression in 27 MACDZ individuals and 32 healthy controls. We also analyzed global gene expression in Mycobacterium avium-infected and uninfected peripheral blood monocytes from 17 MACDZ and 17 healthy controls. We were unable to detect increased T-cell responses against MAC-specific reagents in MACDZ compared to controls, while the responses to non-mycobacteria derived antigens were preserved. MACDZ individuals had a lower frequency of Th1 and Th1* T-cell populations. In addition, MACDZ subjects had lower transcriptional responses in PBMCs stimulated with a mycobacterial peptide pool (MTB300). By contrast, global gene expression analysis demonstrated upregulation of proinflammatory pathways in uninfected and M. avium-infected monocytes, i.e. a hyperinflammatory in vitro response, derived from MACDZ subjects compared to controls. Together, these data suggest a novel immunologic defect which underlies MAC pathogenesis and includes concurrent innate and adaptive dysregulation which persists years after completion of treatment.
Collapse
Affiliation(s)
- Cecilia S. Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- *Correspondence: Cecilia S. Lindestam Arlehamn,
| | - Basilin Benson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Rebecca Kuan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Glenna J. Peterson
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Sinu Paul
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Felicia K. Nguyen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Robert H. Gilman
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States
- Department of Microbiology, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA, United States
| | - Matthew Arentz
- Department of Global Health, University of Washington, Seattle, WA, United States
- FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Christopher H. Goss
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Moira L. Aitken
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - David J. Horne
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Javeed A. Shah
- Department of Medicine, University of Washington, Seattle, WA, United States
- VA Puget Sound Healthcare System, Seattle, WA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Thomas R. Hawn
- Department of Medicine, University of Washington, Seattle, WA, United States
| |
Collapse
|
22
|
Sitoe N, Ahmed MIM, Enosse M, Bakuli A, Chissumba RM, Held K, Hoelscher M, Nhassengo P, Khosa C, Rachow A, Geldmacher C. Tuberculosis Treatment Response Monitoring by the Phenotypic Characterization of MTB-Specific CD4+ T-Cells in Relation to HIV Infection Status. Pathogens 2022; 11:pathogens11091034. [PMID: 36145465 PMCID: PMC9506022 DOI: 10.3390/pathogens11091034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
HIV infection causes systemic immune activation, impacts TB disease progression and hence may influence the diagnostic usability of Mycobacterium tuberculosis-specific T cell profiling. We investigated changes of activation and maturation markers on MTB-specific CD4+ T-cells after anti-tuberculosis treatment initiation in relation to HIV status and the severity of lung impairment. Thawed peripheral blood mononuclear cells from TB patients with (n = 27) and without HIV (n = 17) were analyzed using an intracellular IFN-γ assay and flow cytometry 2 and 6 months post-TB treatment initiation. H37Rv antigen was superior to the profile MTB-specific CD4+ T-cells phenotype when compared to PPD and ESAT6/CFP10. Regardless of HIV status and the severity of lung impairment, activation markers (CD38, HLA-DR and Ki67) on MTB-specific CD4+ T-cells declined after TB treatment initiation (p < 0.01), but the expression of the maturation marker CD27 did not change over the course of TB treatment. The MTB-specific T cell phenotype before, during and after treatment completion was similar between people living with and without HIV, as well as between subjects with severe and mild lung impairment. These data suggest that the assessment of activation and maturation markers on MTB-specific CD4+ T-cells can be useful for TB treatment monitoring, regardless of HIV status and the severity of lung disease.
Collapse
Affiliation(s)
- Nádia Sitoe
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
- CIH LMU Center for International Health, Ludwig-Maximilians University, 80802 Munich, Germany
- Correspondence: ; Tel.: +258-840784833
| | - Mohamed I. M. Ahmed
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | - Maria Enosse
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | - Abhishek Bakuli
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | | | - Kathrin Held
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | | | - Celso Khosa
- Instituto Nacional de Saúde, Marracuene 3943, Mozambique
| | - Andrea Rachow
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Klinikum of the University of Munich (LMU), 80802 Munich, Germany
- German Center for Infection Research, Partner Site Munich, 80802 Munich, Germany
| | | |
Collapse
|
23
|
Lee YH, Hyun YS, Jo HA, Baek IC, Kim SM, Sohn HJ, Kim TG. Comprehensive analysis of mycobacterium tuberculosis antigen-specific CD4+ T cell responses restricted by single HLA class II allotype in an individual. Front Immunol 2022; 13:897781. [PMID: 35967347 PMCID: PMC9366214 DOI: 10.3389/fimmu.2022.897781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis infection is generally asymptomatic as latent tuberculosis, but it is still known as the world’s leading bacterial cause of death. The diagnosis of latent tuberculosis infection relies on the evidence of cellular immunity to mycobacterial antigens. Since the association between HLA class II and tuberculosis infection has been reported in several population groups, a detailed study on the CD4+ T cell response to major tuberculosis antigens is needed. To elucidate which HLA class II allotypes in an individual are preferentially used in tuberculosis, CD4+ T cells specific to TB10.4, Ag85b, ESAT-6, and CFP-10 of Mycobacterium tuberculosis antigens were analyzed comprehensively. A total of 33 healthy donors were analyzed by ex vivo and cultured ELISPOT using panels of artificial antigen-presenting cells expressing a single HLA class II allotype. The CD4+ T cell responses were increased by an average of 39-fold in cultured ELISPOT compared with ex vivo ELISPOT. In ex vivo and cultured ELISPOT, CD4+ T cell responses showed significantly higher by HLA-DR than those of HLA-DQ and HLA-DP locus. In cultured ELISPOT, 9 HLA-DR allotypes, 4 HLA-DQ allotypes, and 3 HLA-DP allotypes showed positive CD4+ T cell responses. Among ten donors with positive CD4+ T cell responses when tested for mixed Mycobacterium tuberculosis antigens, seven donors were positive for only a single allotype, and three were positive for two allotypes in an individual. However, only one allotype was used for a single antigen-specific response when a single tuberculosis antigen was used individually. These results on the distribution of HLA class II allotypes showing high CD4+ T-cell responses to Mycobacterium tuberculosis antigens and the intra-individual allotype dominance will provide valuable information for understanding the immunobiology and immunogenetics of tuberculosis, which can contribute to the development of more effective vaccines.
Collapse
Affiliation(s)
- Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- *Correspondence: Tai-Gyu Kim,
| |
Collapse
|
24
|
Khan Z, Ualiyeva D, Amissah OB, Sapkota S, Hameed HMA, Zhang T. Insight Into Novel Anti-tuberculosis Vaccines by Using Immunoinformatics Approaches. Front Microbiol 2022; 13:866873. [PMID: 35722321 PMCID: PMC9201507 DOI: 10.3389/fmicb.2022.866873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 01/26/2023] Open
Abstract
Tuberculosis (TB), an infectious disease, has been a leading cause of morbidity and mortality for decades. The causative agent of TB is the Mycobacterium tuberculosis (Mtb) which can infects various parts of the body, mainly the lungs in pulmonary TB cases. Mycobacterium bovis Bacillus Calmette–Guerin (BCG) is the only approved vaccine for TB, but its efficiency to combat pulmonary TB is limited. Multidrug-resistant (MDR) TB and extensive drug-resistant (XDR) TB requires the evolution of more potent vaccines. Therefore, this research aims to generate a universal TB subunit vaccine using advanced immunoinformatics techniques. In generating a novel multiepitope subunit vaccine, we selected the conserved and experimentally confirmed antigens Rv0058, Rv0101, and Rv3343. After a rigorous evaluation, the top candidates from predicted Helper T-lymphocytes (HTL), Cytotoxic T-lymphocytes (CTL), and B-cell epitopes were considered potential vaccine candidates. Immunogenicity was enhanced by the addition of an adjuvant to the ultimate construct of the vaccine. B-cell epitopes predictions guaranteed the eventual induction of a humoral response. Thereafter, dynamics simulations and molecular docking validated the vaccine-receptor complex’s stability and high affinity for the immune receptor TLR-3. Also, immune simulations revealed the significantly elevated levels of immunoglobulins such as IgM, cytokines such as interleukin-2, helper T (Th) cells, and cytotoxic T-cell populations. These results agreed with the actual inflammatory response and showed rapid antigen clearance after manifold exposure. Finally, the E. coli K12 strain was confirmed via in-silico cloning for quality expression. Nevertheless, in vivo experiments should be performed to validate the safety of the proposed vaccine and its inherent ability to prevent TB infection.
Collapse
Affiliation(s)
- Zafran Khan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Daniya Ualiyeva
- University of Chinese Academy of Sciences, Beijing, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Obed Boadi Amissah
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Sanjeep Sapkota
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| |
Collapse
|
25
|
Ansari A, Sachan S, Jit BP, Sharma A, Coshic P, Sette A, Weiskopf D, Gupta N. An efficient immunoassay for the B cell help function of SARS-CoV-2-specific memory CD4 + T cells. CELL REPORTS METHODS 2022; 2:100224. [PMID: 35571764 PMCID: PMC9085463 DOI: 10.1016/j.crmeth.2022.100224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/27/2021] [Accepted: 04/28/2022] [Indexed: 04/30/2023]
Abstract
The B cell "help" function of CD4+ T cells is an important mechanism of adaptive immunity. Here, we describe improved antigen-specific T-B cocultures for quantitative measurement of T cell-dependent B cell responses, with as few as ∼90 T cells. Utilizing M. tuberculosis (Mtb), we show that early priming and activation of CD4+ T cells is important for productive interaction between T and B cells and that similar effects are achieved by supplementing cocultures with monocytes. We find that monocytes promote survivability of B cells via BAFF and stem cell growth factor (SCGF)/C-type lectin domain family 11 member A (CLEC11A), but this alone does not fully recapitulate the effects of monocyte supplementation. Importantly, we demonstrate improved activation and immunological output of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific memory CD4+ T-B cell cocultures with the inclusion of monocytes. This method may therefore provide a more sensitive assay to evaluate the B cell help quality of memory CD4+ T cells, for example, after vaccination or natural infection.
Collapse
Affiliation(s)
- Asgar Ansari
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Shilpa Sachan
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Poonam Coshic
- Department of Transfusion Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Nimesh Gupta
- Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi 110067, India
| |
Collapse
|
26
|
Coppola M, Lai RPJ, Wilkinson RJ, Ottenhoff THM. The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung. Front Immunol 2022; 12:763364. [PMID: 35003075 PMCID: PMC8727759 DOI: 10.3389/fimmu.2021.763364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genes encoding proteins targeted by vaccines and drugs should be expressed in the lung, the main organ affected by Mtb, for these to be effective. However, the pulmonary expression of most Mtb genes and their proteins remains poorly characterized. The aim of this study is to fill this knowledge gap. We analyzed large scale transcriptomic datasets from specimens of Mtb-infected humans, TB-hypersusceptible (C3H/FeJ) and TB-resistant (C57BL/6J) mice and compared data to in vitro cultured Mtb gene-expression profiles. Results revealed high concordance in the most abundantly in vivo expressed genes between pulmonary Mtb transcriptomes from different datasets and different species. As expected, this contrasted with a lower correlation found with the highest expressed Mtb genes from in vitro datasets. Among the most consistently and highly in vivo expressed genes, 35 have not yet been explored as targets for vaccination or treatment. More than half of these genes are involved in protein synthesis or metabolic pathways. This first lung-oriented multi-study analysis of the in vivo expressed Mtb-transcriptome provides essential data that considerably increase our understanding of pulmonary TB infection biology, and identifies novel molecules for target-based TB-vaccine and drug development.
Collapse
Affiliation(s)
- Mariateresa Coppola
- Department Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Rachel P-J Lai
- The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Infectious Diseases, Imperial College London, London, United Kingdom.,Department of Medicine, Institute of Infectious Disease and Molecular Medicine, Wellcome Centre for Infectious Diseases Research in Africa, Cape Town, South Africa
| | - Tom H M Ottenhoff
- Department Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, Netherlands
| |
Collapse
|
27
|
Ukey R, Bruiners N, Mishra H, Mishra PK, McCloskey D, Onyuka A, Chen F, Pinter A, Weiskopf D, Sette A, Roy J, Gaur S, Gennaro ML. Dichotomy between the humoral and cellular responses elicited by mRNA and adenoviral vector vaccines against SARS-CoV-2. BMC Med 2022; 20:32. [PMID: 35073931 PMCID: PMC8786593 DOI: 10.1186/s12916-022-02252-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protection from severe disease and hospitalization by SARS-CoV-2 vaccination has been amply demonstrated by real-world data. However, the rapidly evolving pandemic raises new concerns. One pertains efficacy of adenoviral vector-based vaccines, particularly the single-dose Ad26.COV2.S, relative to mRNA vaccines. MAIN BODY We investigated the immunogenicity of Ad26.COV2.S and mRNA vaccines in 33 subjects vaccinated with either vaccine class 5 months earlier on average. After controlling for the time since vaccination, Spike-binding antibody and neutralizing antibody levels were higher in the mRNA-vaccinated subjects, while no significant differences in antigen-specific B cell and T cell responses were observed between the two groups. CONCLUSIONS A dichotomy exists between the humoral and cellular responses elicited by the two vaccine classes. Testing only for humoral responses to compare the durability of SARS-CoV-2 vaccine-induced responses, as typically performed for public health and research purposes, is insufficient.
Collapse
Affiliation(s)
- Rahul Ukey
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Natalie Bruiners
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
- Department of Medicine, Rutgers New Jersey Medical School, ICPH building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Hridesh Mishra
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Pankaj K Mishra
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Deborah McCloskey
- Clinical Research Center, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alberta Onyuka
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, ICPH building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Fei Chen
- Clinical Research Center, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Abraham Pinter
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
- Department of Medicine, Rutgers New Jersey Medical School, ICPH building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Jason Roy
- Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ, USA
| | - Sunanda Gaur
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, ICPH Building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA.
- Department of Medicine, Rutgers New Jersey Medical School, ICPH building, W250Q, 225 Warren Street, Newark, NJ, 07103, USA.
| |
Collapse
|
28
|
Hyun YS, Lee YH, Jo HA, Baek IC, Kim SM, Sohn HJ, Kim TG. Comprehensive Analysis of CD4 + T Cell Response Cross-Reactive to SARS-CoV-2 Antigens at the Single Allele Level of HLA Class II. Front Immunol 2022; 12:774491. [PMID: 35069546 PMCID: PMC8770530 DOI: 10.3389/fimmu.2021.774491] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Common human coronaviruses have been circulating undiagnosed worldwide. These common human coronaviruses share partial sequence homology with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); therefore, T cells specific to human coronaviruses are also cross-reactive with SARS-CoV-2 antigens. Herein, we defined CD4+ T cell responses that were cross-reactive with SARS-CoV-2 antigens in blood collected in 2016–2018 from healthy donors at the single allele level using artificial antigen-presenting cells (aAPC) expressing a single HLA class II allotype. We assessed the allotype-restricted responses in the 42 individuals using the aAPCs matched 22 HLA-DR alleles, 19 HLA-DQ alleles, and 13 HLA-DP alleles. The response restricted by the HLA-DR locus showed the highest magnitude, and that by HLA-DP locus was higher than that by HLA-DQ locus. Since two alleles of HLA-DR, -DQ, and -DP loci are expressed co-dominantly in an individual, six different HLA class II allotypes can be used to the cross-reactive T cell response. Of the 16 individuals who showed a dominant T cell response, five, one, and ten showed a dominant response by a single allotype of HLA-DR, -DQ, and -DP, respectively. The single allotype-restricted T cells responded to only one antigen in the five individuals and all the spike, membrane, and nucleocapsid proteins in the six individuals. In individuals heterozygous for the HLA-DPA and HLA-DPB loci, four combinations of HLA-DP can be expressed, but only one combination showed a dominant response. These findings demonstrate that cross-reactive T cells to SARS-CoV-2 respond with single-allotype dominance.
Collapse
Affiliation(s)
- You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| |
Collapse
|
29
|
Singhania A, Dubelko P, Kuan R, Chronister WD, Muskat K, Das J, Phillips EJ, Mallal SA, Seumois G, Vijayanand P, Sette A, Lerm M, Peters B, Lindestam Arlehamn C. CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature. EBioMedicine 2021; 74:103746. [PMID: 34902786 PMCID: PMC8671872 DOI: 10.1016/j.ebiom.2021.103746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The century-old Mycobacterium bovis Bacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. METHODS We investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or a Mycobacterium tuberculosis (Mtb)-derived peptide pool. FINDINGS Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* (CXCR3+CCR6+) and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects. INTERPRETATION The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.
Collapse
Affiliation(s)
- Akul Singhania
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Paige Dubelko
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Rebecca Kuan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - William D Chronister
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kaylin Muskat
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Jyotirmoy Das
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Grégory Seumois
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria Lerm
- Division of Infection and Inflammation, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Cecilia Lindestam Arlehamn
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
| |
Collapse
|
30
|
Woodworth JS, Clemmensen HS, Battey H, Dijkman K, Lindenstrøm T, Laureano RS, Taplitz R, Morgan J, Aagaard C, Rosenkrands I, Lindestam Arlehamn CS, Andersen P, Mortensen R. A Mycobacterium tuberculosis-specific subunit vaccine that provides synergistic immunity upon co-administration with Bacillus Calmette-Guérin. Nat Commun 2021; 12:6658. [PMID: 34795205 PMCID: PMC8602668 DOI: 10.1038/s41467-021-26934-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
Given the encouraging clinical results of both candidate subunit vaccines and revaccination with Bacillus Calmette-Guérin (BCG) against tuberculosis (TB), there is support for combining BCG and subunit vaccination for increased efficacy. BCG and Mycobacterium tuberculosis (Mtb) share ~98% of their genome and current subunit vaccines are almost exclusively designed as BCG boosters. The goal of this study is to design a TB subunit vaccine composed of antigens not shared with BCG and explore the advantages of this design in a BCG + subunit co-administration vaccine strategy. Eight protective antigens are selected to create an Mtb-specific subunit vaccine, named H107. Whereas traditional vaccines containing BCG-shared antigens exhibit in vivo cross-reactivity to BCG, H107 shows no cross-reactivity and does not inhibit BCG colonization. Instead, co-administering H107 with BCG leads to increased adaptive responses against both H107 and BCG. Importantly, rather than expanding BCG-primed T cells, H107 broadens the overall vaccine repertoire with new T cell clones and introduces ‘adjuvant-imprinted’ qualities including Th17 responses and less-differentiated Th1 cells. Collectively, these features of H107 are associated with a substantial increase in long-term protection. Tuberculosis (TB) subunit vaccines have been investigated as boosters for BCG-induced immunity. Here, the authors design a TB subunit vaccine that doesn't share antigens with BCG and show that co-administration of the two vaccines broadens the T cell response to TB and increases protection.
Collapse
Affiliation(s)
- Joshua S Woodworth
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Strand Clemmensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hannah Battey
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Karin Dijkman
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Lindenstrøm
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Randy Taplitz
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | - Jeffrey Morgan
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Claus Aagaard
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peter Andersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark.,Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Mortensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark.
| |
Collapse
|
31
|
Risk assessment of latent tuberculosis infection through a multiplexed cytokine biosensor assay and machine learning feature selection. Sci Rep 2021; 11:20544. [PMID: 34654869 PMCID: PMC8520014 DOI: 10.1038/s41598-021-99754-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/21/2021] [Indexed: 11/09/2022] Open
Abstract
Accurate detection and risk stratification of latent tuberculosis infection (LTBI) remains a major clinical and public health problem. We hypothesize that multiparameter strategies that probe immune responses to Mycobacterium tuberculosis can provide new diagnostic insights into not only the status of LTBI infection, but also the risk of reactivation. After the initial proof-of-concept study, we developed a 13-plex immunoassay panel to profile cytokine release from peripheral blood mononuclear cells stimulated separately with Mtb-relevant and non-specific antigens to identify putative biomarker signatures. We sequentially enrolled 65 subjects with various risk of TB exposure, including 32 subjects with diagnosis of LTBI. Random Forest feature selection and statistical data reduction methods were applied to determine cytokine levels across different normalized stimulation conditions. Receiver Operator Characteristic (ROC) analysis for full and reduced feature sets revealed differences in biomarkers signatures for LTBI status and reactivation risk designations. The reduced set for increased risk included IP-10, IL-2, IFN-γ, TNF-α, IL-15, IL-17, CCL3, and CCL8 under varying normalized stimulation conditions. ROC curves determined predictive accuracies of > 80% for both LTBI diagnosis and increased risk designations. Our study findings suggest that a multiparameter diagnostic approach to detect normalized cytokine biomarker signatures might improve risk stratification in LTBI.
Collapse
|
32
|
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PLoS Comput Biol 2021; 17:e1009459. [PMID: 34613979 PMCID: PMC8523066 DOI: 10.1371/journal.pcbi.1009459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/18/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022] Open
Abstract
Recent technological advances have made the gathering of comprehensive gene expression datasets a commodity. This has shifted the limiting step of transcriptomic studies from the accumulation of data to their analyses and interpretation. The main problem in analyzing transcriptomics data is that the number of independent samples is typically much lower (<100) than the number of genes whose expression is quantified (typically >14,000). To address this, it would be desirable to reduce the gathered data’s dimensionality without losing information. Clustering genes into discrete modules is one of the most commonly used tools to accomplish this task. While there are multiple clustering approaches, there is a lack of informative metrics available to evaluate the resultant clusters’ biological quality. Here we present a metric that incorporates known ground truth gene sets to quantify gene clusters’ biological quality derived from standard clustering techniques. The GECO (Ground truth Evaluation of Clustering Outcomes) metric demonstrates that quantitative and repeatable scoring of gene clusters is not only possible but computationally lightweight and robust. Unlike current methods, it allows direct comparison between gene clusters generated by different clustering techniques. It also reveals that current cluster analysis techniques often underestimate the number of clusters that should be formed from a dataset, which leads to fewer clusters of lower quality. As a test case, we applied GECO combined with k-means clustering to derive an optimal set of co-expressed gene modules derived from PBMC, which we show to be superior to previously generated modules generated on whole-blood. Overall, GECO provides a rational metric to test and compare different clustering approaches to analyze high-dimensional transcriptomic data. Next-generation sequencing has spurred the creation of many techniques that attempt to distill large datasets down to a more manageable size without losing valuable information, more simply referred to as dimensionality reduction. We have sought to contribute to this effort by focusing not directly on dimensionality reduction but on interpreting the results of the most common technique used for dimensionality reduction of sequencing data: gene clustering. While methods to generate gene clusters have been well explored, the evaluation of cluster quality has not, i.e., answering the question "Have we made biologically significant clusters?" We have developed a metric that can be used to answer this question. Our metric incorporates prior biological knowledge about the data to determine if the clustering process was optimal by looking at how genes are grouped in gene clusters and determine if they make sense biologically. Our metric can also be used to provide a discrete range of values that indicate how to generate clusters with the highest potential biological information content. This metric can be utilized by any -omics level study to generate study-specific gene clusters while reducing the time spent validating gene clusters and improving confidence in the resultant clusters.
Collapse
|
33
|
Ukey R, Bruiners N, Mishra H, Mishra PK, McCloskey D, Onyuka A, Chen F, Pinter A, Weiskopf D, Sette A, Roy J, Gaur S, Gennaro ML. Dichotomy between the humoral and cellular responses elicited by mRNA and adenoviral vector vaccines against SARS-CoV-2. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.09.17.21263528. [PMID: 34580675 PMCID: PMC8475964 DOI: 10.1101/2021.09.17.21263528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protection from severe disease and hospitalization by SARS-CoV-2 vaccination has been amply demonstrated by real-world data. However, the rapidly evolving pandemic raises new concerns. One pertains efficacy of adenoviral vector-based vaccines, particularly the single-dose Ad26.COV2.S, relative to mRNA vaccines. We investigated the immunogenicity of Ad26.COV2.S and mRNA vaccines in 33 subjects vaccinated with either vaccine class five months earlier on average. After controlling for time since vaccination, Spike-binding antibody and neutralizing antibody levels were higher in the mRNA-vaccinated subjects, while no significant differences in antigen-specific B cell and T cell responses were observed between the two groups. Thus, a dichotomy exists between humoral and cellular responses elicited by the two vaccine classes. Our results have implications for the need of booster doses in vaccinated subjects and might explain the dichotomy reported between the waning protection from symptomatic infection by SARS-CoV-2 vaccination and its persisting efficacy in preventing hospitalization and death.
Collapse
Affiliation(s)
- Rahul Ukey
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
| | - Natalie Bruiners
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ
| | - Hridesh Mishra
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
| | - Pankaj K. Mishra
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
| | - Deborah McCloskey
- Clinical Research Center, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alberta Onyuka
- Global Tuberculosis Institute, Rutgers New Jersey Medical School, Newark, NJ
| | - Fei Chen
- Clinical Research Center, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Abraham Pinter
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
| | - Jason Roy
- Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ
| | - Sunanda Gaur
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Maria Laura Gennaro
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark, NJ
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ
| |
Collapse
|
34
|
Abstract
Despite the prevalence and medical significance of human cytomegalovirus (HCMV) infections, a systematic analysis of the targets of T cell recognition in humans that spans the entire genome and includes recently described potential novel ORFs is not available. Here, we screened a library of epitopes predicted to bind HLA class II that spans over 350 different HCMV ORFs and includes ∼150 previously described and ∼200 recently described potential novel ORFs using an ex vivo IFNγ fluorospot assay. We identified 235 unique HCMV specific epitopes derived from 100 ORFs, some previously described as immunodominant and others that were not previously described to be immunogenic. Of those, 41 belong to the set of recently reported novel ORFs, thus providing evidence that at least some of these are actually expressed in vivo in humans. These data reveal that the breadth of the human T cell response to HCMV is much greater than previously thought. The ORFs and epitopes identified will help elucidate how T cell immunity relates to HCMV pathogenesis and instruct ongoing HCMV vaccine research. Importance To understand the crucial role of adaptive immunity in controlling cytomegalovirus infection and disease, we systematically analyzed the CMV 'ORFeome' to identify new CMV epitopes targeted primarily by CD4 T cells in humans. Our study identified >200 new T cell epitopes derived from both canonical and novel ORFs, highlighting the substantial breadth of anti-CMV T cell response and providing new targets for vaccine design.
Collapse
|
35
|
Tippalagama R, Singhania A, Dubelko P, Lindestam Arlehamn CS, Crinklaw A, Pomaznoy M, Seumois G, deSilva AD, Premawansa S, Vidanagama D, Gunasena B, Goonawardhana NDS, Ariyaratne D, Scriba TJ, Gilman RH, Saito M, Taplitz R, Vijayanand P, Sette A, Peters B, Burel JG. HLA-DR Marks Recently Divided Antigen-Specific Effector CD4 T Cells in Active Tuberculosis Patients. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:523-533. [PMID: 34193602 PMCID: PMC8516689 DOI: 10.4049/jimmunol.2100011] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023]
Abstract
Upon Ag encounter, T cells can rapidly divide and form an effector population, which plays an important role in fighting acute infections. In humans, little is known about the molecular markers that distinguish such effector cells from other T cell populations. To address this, we investigated the molecular profile of T cells present in individuals with active tuberculosis (ATB), where we expect Ag encounter and expansion of effector cells to occur at higher frequency in contrast to Mycobacterium tuberculosis-sensitized healthy IGRA+ individuals. We found that the frequency of HLA-DR+ cells was increased in circulating CD4 T cells of ATB patients, and was dominantly expressed in M. tuberculosis Ag-specific CD4 T cells. We tested and confirmed that HLA-DR is a marker of recently divided CD4 T cells upon M. tuberculosis Ag exposure using an in vitro model examining the response of resting memory T cells from healthy IGRA+ to Ags. Thus, HLA-DR marks a CD4 T cell population that can be directly detected ex vivo in human peripheral blood, whose frequency is increased during ATB disease and contains recently divided Ag-specific effector T cells. These findings will facilitate the monitoring and study of disease-specific effector T cell responses in the context of ATB and other infections.
Collapse
Affiliation(s)
- Rashmi Tippalagama
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Akul Singhania
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Paige Dubelko
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | | | - Austin Crinklaw
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Mikhail Pomaznoy
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Gregory Seumois
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
| | - Aruna D deSilva
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | | | | | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | | | - Dinuka Ariyaratne
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Baltimore, MD
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Randy Taplitz
- Department of Medicine, City of Hope National Medical Center, Duarte, CA; and
| | - Pandurangan Vijayanand
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Alessandro Sette
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Bjoern Peters
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA;
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Julie G Burel
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA;
| |
Collapse
|
36
|
Martín C, Marinova D, Aguiló N, Gonzalo-Asensio J. MTBVAC, a live TB vaccine poised to initiate efficacy trials 100 years after BCG. Vaccine 2021; 39:7277-7285. [PMID: 34238608 DOI: 10.1016/j.vaccine.2021.06.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 01/06/2023]
Abstract
At its 100th birthday of its first administration to a newborn, BCG has been (and continues being) an inspiration for the construction and development of hundreds of new TB vaccine candidates in the last two and a half decades. Today, 14 candidates are in clinical development inside the global TB vaccine pipeline. MTBVAC is one of these candidates. Based on a live-attenuated Mycobacterium tuberculosis clinical isolate, MTBVAC's 25 years of vaccine discovery, construction and characterisation have followed Pasteur principles, and in the process, BCG has served as a reference gold standard for establishing the safety and protective efficacy of new TB vaccine candidates. MTBVAC, which contains the antigen repertoire of M. tuberculosis, is now poised to initiate Phase 3 efficacy trials in newborns in TB-endemic countries. BCG's efficacy extends beyond that against TB, shown to confer heterologous non-specific immunity to other diseases and reduce all-cause mortality in the first months of life. Today, WHO recognises the importance that any new TB vaccine designed for administration at birth, should show similar non-specific benefits as BCG vía mechanisms of trained immunity and/or cross-reactivity of adaptive immune responses to other pathogens. Key recent studies provide strong support for MTBVAC's ability of inducing trained immunity and conferring non-specific heterologous protection similar to BCG. Research on alternative delivery routes of MTBVAC, such as a clinically feasible aerosol route, could facilitate vaccine administration for long-term TB eradication programmes in the future.
Collapse
Affiliation(s)
- Carlos Martín
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Miguel Servet, ISS Aragón, Zaragoza, Spain.
| | - Dessislava Marinova
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
37
|
Riou C, du Bruyn E, Stek C, Daroowala R, Goliath RT, Abrahams F, Said-Hartley Q, Allwood BW, Hsiao NY, Wilkinson KA, Arlehamn CSL, Sette A, Wasserman S, Wilkinson RJ. Relationship of SARS-CoV-2-specific CD4 response to COVID-19 severity and impact of HIV-1 and tuberculosis coinfection. J Clin Invest 2021; 131:149125. [PMID: 33945513 PMCID: PMC8203446 DOI: 10.1172/jci149125] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
T cells are involved in control of coronavirus disease 2019 (COVID-19), but limited knowledge is available on the relationship between antigen-specific T cell response and disease severity. Here, we used flow cytometry to assess the magnitude, function, and phenotype of SARS coronavirus 2-specific (SARS-CoV-2-specific) CD4+ T cells in 95 hospitalized COVID-19 patients, 38 of them being HIV-1 and/or tuberculosis (TB) coinfected, and 38 non-COVID-19 patients. We showed that SARS-CoV-2-specific CD4+ T cell attributes, rather than magnitude, were associated with disease severity, with severe disease being characterized by poor polyfunctional potential, reduced proliferation capacity, and enhanced HLA-DR expression. Moreover, HIV-1 and TB coinfection skewed the SARS-CoV-2 T cell response. HIV-1-mediated CD4+ T cell depletion associated with suboptimal T cell and humoral immune responses to SARS-CoV-2, and a decrease in the polyfunctional capacity of SARS-CoV-2-specific CD4+ T cells was observed in COVID-19 patients with active TB. Our results also revealed that COVID-19 patients displayed reduced frequency of Mycobacterium tuberculosis-specific CD4+ T cells, with possible implications for TB disease progression. These results corroborate the important role of SARS-CoV-2-specific T cells in COVID-19 pathogenesis and support the concept of altered T cell functions in patients with severe disease.
Collapse
Affiliation(s)
- Catherine Riou
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Division of Medical Virology, Department of Pathology, and
| | - Elsa du Bruyn
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Cari Stek
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Remy Daroowala
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Rene T. Goliath
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
| | - Fatima Abrahams
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
| | | | - Brian W. Allwood
- Division of Pulmonology, Department of Medicine, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Department of Pathology, and
- National Health Laboratory Service, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Katalin A. Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, United Kingdom
| | | | - Alessandro Sette
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Sean Wasserman
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert J. Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine
- Department of Medicine, University of Cape Town, Cape Town, South Africa
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | |
Collapse
|
38
|
Nathan A, Beynor JI, Baglaenko Y, Suliman S, Ishigaki K, Asgari S, Huang CC, Luo Y, Zhang Z, Lopez K, Lindestam Arlehamn CS, Ernst JD, Jimenez J, Calderón RI, Lecca L, Van Rhijn I, Moody DB, Murray MB, Raychaudhuri S. Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease. Nat Immunol 2021; 22:781-793. [PMID: 34031617 PMCID: PMC8162307 DOI: 10.1038/s41590-021-00933-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
Multimodal T cell profiling can enable more precise characterization of elusive cell states underlying disease. Here, we integrated single-cell RNA and surface protein data from 500,089 memory T cells to define 31 cell states from 259 individuals in a Peruvian tuberculosis (TB) progression cohort. At immune steady state >4 years after infection and disease resolution, we found that, after accounting for significant effects of age, sex, season and genetic ancestry on T cell composition, a polyfunctional type 17 helper T (TH17) cell-like effector state was reduced in abundance and function in individuals who previously progressed from Mycobacterium tuberculosis (M.tb) infection to active TB disease. These cells are capable of responding to M.tb peptides. Deconvoluting this state-uniquely identifiable with multimodal analysis-from public data demonstrated that its depletion may precede and persist beyond active disease. Our study demonstrates the power of integrative multimodal single-cell profiling to define cell states relevant to disease and other traits.
Collapse
Affiliation(s)
- Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jessica I Beynor
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kattya Lopez
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | | | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Roger I Calderón
- Socios En Salud Sucursal Peru, Lima, Peru
- Programa Acadêmico de Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
- Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
| |
Collapse
|
39
|
Ogongo P, Tezera LB, Ardain A, Nhamoyebonde S, Ramsuran D, Singh A, Ng’oepe A, Karim F, Naidoo T, Khan K, Dullabh KJ, Fehlings M, Lee BH, Nardin A, Lindestam Arlehamn CS, Sette A, Behar SM, Steyn AJ, Madansein R, Kløverpris HN, Elkington PT, Leslie A. Tissue-resident-like CD4+ T cells secreting IL-17 control Mycobacterium tuberculosis in the human lung. J Clin Invest 2021; 131:142014. [PMID: 33848273 PMCID: PMC8121523 DOI: 10.1172/jci142014] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
T cell immunity is essential for the control of tuberculosis (TB), an important disease of the lung, and is generally studied in humans using peripheral blood cells. Mounting evidence, however, indicates that tissue-resident memory T cells (Trms) are superior at controlling many pathogens, including Mycobacterium tuberculosis (M. tuberculosis), and can be quite different from those in circulation. Using freshly resected lung tissue, from individuals with active or previous TB, we identified distinct CD4+ and CD8+ Trm-like clusters within TB-diseased lung tissue that were functional and enriched for IL-17-producing cells. M. tuberculosis-specific CD4+ T cells producing TNF-α, IL-2, and IL-17 were highly expanded in the lung compared with matched blood samples, in which IL-17+ cells were largely absent. Strikingly, the frequency of M. tuberculosis-specific lung T cells making IL-17, but not other cytokines, inversely correlated with the plasma IL-1β levels, suggesting a potential link with disease severity. Using a human granuloma model, we showed the addition of either exogenous IL-17 or IL-2 enhanced immune control of M. tuberculosis and was associated with increased NO production. Taken together, these data support an important role for M. tuberculosis-specific Trm-like, IL-17-producing cells in the immune control of M. tuberculosis in the human lung.
Collapse
Affiliation(s)
- Paul Ogongo
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Liku B. Tezera
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, and
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Amanda Ardain
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shepherd Nhamoyebonde
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Alveera Singh
- Africa Health Research Institute, Durban, South Africa
| | | | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
| | - Taryn Naidoo
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
| | - Kaylesh J. Dullabh
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Samuel M. Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Adrie J.C. Steyn
- Africa Health Research Institute, Durban, South Africa
- Department of Microbiology and
- Center for AIDS Research and Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rajhmun Madansein
- Department of Cardiothoracic Surgery, Nelson Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Henrik N. Kløverpris
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Paul T. Elkington
- National Institute for Health Research Southampton Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, and
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|
40
|
Morgan J, Muskat K, Tippalagama R, Sette A, Burel J, Lindestam Arlehamn CS. Classical CD4 T cells as the cornerstone of antimycobacterial immunity. Immunol Rev 2021; 301:10-29. [PMID: 33751597 PMCID: PMC8252593 DOI: 10.1111/imr.12963] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 12/13/2022]
Abstract
Tuberculosis is a significant health problem without an effective vaccine to combat it. A thorough understanding of the immune response and correlates of protection is needed to develop a more efficient vaccine. The immune response against Mycobacterium tuberculosis (Mtb) is complex and involves all aspects of the immune system, however, the optimal protective, non‐pathogenic T cell response against Mtb is still elusive. This review will focus on discussing CD4 T cell immunity against mycobacteria and its importance in Mtb infection with a primary focus on human studies. We will in particular discuss the large heterogeneity of immune cell subsets that have been revealed by recent immunological investigations at an unprecedented level of detail. These studies have identified specific classical CD4 T cell subsets important for immune responses against Mtb in various states of infection. We further discuss the functional attributes that have been linked to the various subsets such as upregulation of activation markers and cytokine production. Another important topic to be considered is the antigenic targets of Mtb‐specific immune responses, and how antigen reactivity is influenced by both disease state and environmental exposure(s). These are key points for both vaccines and immune diagnostics development. Ultimately, these factors are holistically considered in the definition and investigations of what are the correlates on protection and resolution of disease.
Collapse
Affiliation(s)
- Jeffrey Morgan
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kaylin Muskat
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Rashmi Tippalagama
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Julie Burel
- Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | |
Collapse
|
41
|
Farrell D. epitopepredict: a tool for integrated MHC binding prediction. GIGABYTE 2021; 2021:gigabyte13. [PMID: 36824339 PMCID: PMC9631954 DOI: 10.46471/gigabyte.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics, which allows in silico screening of peptides before experiments are performed. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from https://github.com/dmnfarrell/epitopepredict.
Collapse
Affiliation(s)
- Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Ireland
| |
Collapse
|
42
|
Wood MP, Wood LF, Templeton M, Fisher B, Lippy A, Jones CI, Lindestam Arlehamn CS, Sette A, Fuller JT, Murapa P, Jaspan HB, Fuller DH, Sodora DL. Transient Immune Activation in BCG-Vaccinated Infant Rhesus Macaques Is Not Sufficient to Influence Oral Simian Immunodeficiency Virus Infection. J Infect Dis 2021; 222:44-53. [PMID: 31605528 DOI: 10.1093/infdis/jiz382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
BCG vaccination has been demonstrated to increase levels of activated CD4+ T cells, thus potentially influencing mother-to-child transmission of human immunodeficiency virus (HIV). To assess the risk of BCG vaccination in HIV infection, we randomly assigned newborn rhesus macaques to receive BCG vaccine or remain unvaccinated and then undergo oral simian immunodeficiency virus (SIV) challenges 3 weeks later. We observed elevated levels of activated peripheral CD4+ T cells (ie, HLA-DR+CD38+CCR5+ CD4+ T cells) by week 3 after vaccination. BCG was also associated with an altered immune gene expression profile, as well as with monocyte activation in both peripheral blood and the draining axillary lymph node, indicating significant BCG vaccine-induced immune activation. Despite these effects, BCG vaccination did not increase the rate of SIV oral transmission or disease progression. Our findings therefore identify patterns of T-cell and monocyte activation that occur after BCG vaccination but do not support the hypothesis that BCG vaccination is a risk factor for postnatal HIV transmission or increased pathogenesis in infants.
Collapse
Affiliation(s)
- Matthew P Wood
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Lianna F Wood
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Megan Templeton
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Bridget Fisher
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Adriana Lippy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Chloe I Jones
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, San Diego.,Department of Medicine, University of California-San Diego, La Jolla, California
| | - James T Fuller
- Department of Microbiology, Seattle, Washington; and University of Washington.,Washington National Primate Research Center, Seattle, Washington
| | - Patience Murapa
- Department of Microbiology, Seattle, Washington; and University of Washington.,Washington National Primate Research Center, Seattle, Washington
| | - Heather B Jaspan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Deborah H Fuller
- Department of Microbiology, Seattle, Washington; and University of Washington.,Washington National Primate Research Center, Seattle, Washington
| | - Donald L Sodora
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| |
Collapse
|
43
|
Hyun YS, Jo HA, Lee YH, Kim SM, Baek IC, Sohn HJ, Cho HI, Kim TG. Comprehensive Analysis of CD4 + T Cell Responses to CMV pp65 Antigen Restricted by Single HLA-DR, -DQ, and -DP Allotype Within an Individual. Front Immunol 2021; 11:602014. [PMID: 33658991 PMCID: PMC7917246 DOI: 10.3389/fimmu.2020.602014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/15/2020] [Indexed: 01/18/2023] Open
Abstract
Within an individual, six different HLA class II heterodimers are expressed co-dominantly by two alleles of HLA-DR, -DQ, and -DP loci. However, it remained unclear which HLA allotypes were used in T cell responses to a given antigen. For the measurement of the CD4+ T cell responses restricted by a single HLA allotype, we established a panel of artificial antigen-presenting cells (aAPCs) expressing each single HLA allele of 20 HLA-DRB1, 16 HLA-DQ, and 13 HLA-DP alleles. CD4+ T cell responses to cytomegalovirus (CMV) pp65 restricted by single HLA class II allotype defined in 45 healthy donors. The average magnitude of CD4+ T cell responses by HLA-DR allotypes was higher than HLA-DQ and HLA-DP allotypes. CD4+ T cell responses by DRA*01:01/DRB1*04:06, DQA1*01:02/DQB1*06:02, DPA1*02:02/DPB1*05:01 were higher among the other alleles in each HLA-DR, -DQ, and -DP locus. Interestingly, the frequencies of HLA-DR alleles and the positivity of specific allotypes showed an inverse correlation. One allotype within individuals is dominantly used in CD4+ T cell response in 49% of donors, and two allotypes showed that in 7% of donors, and any positive response was detected in 44% of donors. Even if one individual had several dominant alleles, CD4+ T cell responses tended to be restricted by only one of them. Furthermore, CD8+ and CD4+ T cell responses by HLA class I and class II were correlated. Our results demonstrate that the CD4+ T cell preferentially use a few dominant HLA class II allotypes within individuals, similar to CD8+ T cell response to CMV pp65.
Collapse
Affiliation(s)
- You-Seok Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyeong-A Jo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yong-Hun Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sun-Mi Kim
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Hyun-Il Cho
- Translational and Clinical Division, ViGenCell Inc., Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| |
Collapse
|
44
|
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. CELL REPORTS MEDICINE 2021; 2:100204. [PMID: 33521695 PMCID: PMC7837622 DOI: 10.1016/j.xcrm.2021.100204] [Citation(s) in RCA: 322] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/17/2020] [Accepted: 01/20/2021] [Indexed: 12/19/2022]
Abstract
T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens and precisely measure virus-specific CD4+ and CD8+ T cells, we study epitope-specific T cell responses of 99 convalescent coronavirus disease 2019 (COVID-19) cases. The SARS-CoV-2 proteome is probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of human leukocyte antigen (HLA) alleles for class II responses. For HLA class I, we study an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identify several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance are observed, which differ for CD4+ T cells, CD8+ T cells, and antibodies. The class I and class II epitopes are combined into epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+ and CD8+ T cells.
Collapse
|
45
|
da Silva Antunes R, Pallikkuth S, Williams E, Yu ED, Mateus J, Quiambao L, Wang E, Rawlings SA, Stadlbauer D, Jiang K, Amanat F, Arnold D, Andrews D, Fuego I, Dan JM, Grifoni A, Weiskopf D, Krammer F, Crotty S, Hoffer ME, Pahwa SG, Sette A. Differential T cell reactivity to seasonal coronaviruses and SARS-CoV-2 in community and health care workers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.12.21249683. [PMID: 33469594 PMCID: PMC7814840 DOI: 10.1101/2021.01.12.21249683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Herein we measured CD4+ T cell responses against common cold corona (CCC) viruses and SARS-CoV-2 in high-risk health care workers (HCW) and community controls. We observed higher levels of CCC reactive T cells in SARS-CoV-2 seronegative HCW compared to community donors, consistent with potential higher occupational exposure of HCW to CCC. We further show that SARS-CoV-2 reactivity of seronegative HCW was higher than community controls and correlation between CCC and SARS-CoV-2 responses is consistent with cross-reactivity and not associated with recent in vivo activation. Surprisingly, CCC reactivity was decreased in SARS-CoV-2 infected HCW, suggesting that exposure to SARS-CoV-2 might interfere with CCC responses, either directly or indirectly. This result was unexpected, but consistently detected in independent cohorts derived from Miami and San Diego.
Collapse
Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Erin Williams
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Lorenzo Quiambao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Eric Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaijun Jiang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Arnold
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - David Andrews
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Irma Fuego
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Michael E. Hoffer
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA
- Department of Neurological Surgery, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Savita G. Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| |
Collapse
|
46
|
Kauffman KD, Sakai S, Lora NE, Namasivayam S, Baker PJ, Kamenyeva O, Foreman TW, Nelson CE, Oliveira-de-Souza D, Vinhaes CL, Yaniv Z, Lindestam Arleham CS, Sette A, Freeman GJ, Moore R, Sher A, Mayer-Barber KD, Andrade BB, Kabat J, Via LE, Barber DL. PD-1 blockade exacerbates Mycobacterium tuberculosis infection in rhesus macaques. Sci Immunol 2021; 6:6/55/eabf3861. [PMID: 33452107 DOI: 10.1126/sciimmunol.abf3861] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]
Abstract
Boosting immune cell function by targeting the coinhibitory receptor PD-1 may have applications in the treatment of chronic infections. Here, we examine the role of PD-1 during Mycobacterium tuberculosis (Mtb) infection of rhesus macaques. Animals treated with anti-PD-1 monoclonal antibody developed worse disease and higher granuloma bacterial loads compared with isotype control-treated monkeys. PD-1 blockade increased the number and functionality of granuloma Mtb-specific CD8 T cells. In contrast, Mtb-specific CD4 T cells in anti-PD-1-treated macaques were not increased in number or function in granulomas, expressed increased levels of CTLA-4, and exhibited reduced intralesional trafficking in live imaging studies. In granulomas of anti-PD-1-treated animals, multiple proinflammatory cytokines were elevated, and more cytokines correlated with bacterial loads, leading to the identification of a role for caspase 1 in the exacerbation of tuberculosis after PD-1 blockade. Last, increased Mtb bacterial loads after PD-1 blockade were found to associate with the composition of the intestinal microbiota before infection in individual macaques. Therefore, PD-1-mediated coinhibition is required for control of Mtb infection in macaques, perhaps because of its role in dampening detrimental inflammation and allowing for normal CD4 T cell responses.
Collapse
Affiliation(s)
- Keith D Kauffman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shunsuke Sakai
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nickiana E Lora
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul J Baker
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Olena Kamenyeva
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Taylor W Foreman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christine E Nelson
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Deivide Oliveira-de-Souza
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Intituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Caian L Vinhaes
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Intituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Ziv Yaniv
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Rashida Moore
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Intituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Juraj Kabat
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura E Via
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel L Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
47
|
Bibi S, Ullah I, Zhu B, Adnan M, Liaqat R, Kong WB, Niu S. In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology. Sci Rep 2021; 11:1249. [PMID: 33441913 PMCID: PMC7807040 DOI: 10.1038/s41598-020-80899-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/29/2020] [Indexed: 01/29/2023] Open
Abstract
Tuberculosis (TB) kills more individuals in the world than any other disease, and a threat made direr by the coverage of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Bacillus Calmette-Guérin (BCG) is the single TB vaccine licensed for use in human beings and effectively protects infants and children against severe military and meningeal TB. We applied advanced computational techniques to develop a universal TB vaccine. In the current study, we select the very conserved, experimentally confirmed Mtb antigens, including Rv2608, Rv2684, Rv3804c (Ag85A), and Rv0125 (Mtb32A) to design a novel multi-epitope subunit vaccine. By using the Immune Epitopes Database (IEDB), we predicted different B-cell and T-cell epitopes. An adjuvant (Griselimycin) was also added to vaccine construct to improve its immunogenicity. Bioinformatics tools were used to predict, refined, and validate the 3D structure and then docked with toll-like-receptor (TLR-3) using different servers. The constructed vaccine was used for further processing based on allergenicity, antigenicity, solubility, different physiochemical properties, and molecular docking scores. The in silico immune simulation results showed significant response for immune cells. For successful expression of the vaccine in E. coli, in-silico cloning and codon optimization were performed. This research also sets out a good signal for the design of a peptide-based tuberculosis vaccine. In conclusion, our findings show that the known multi-epitope vaccine may activate humoral and cellular immune responses and maybe a possible tuberculosis vaccine candidate. Therefore, more experimental validations should be exposed to it.
Collapse
Affiliation(s)
- Shaheen Bibi
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China
- Lanzhou Center for Tuberculosis Research and Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, 730000, China
- Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Inayat Ullah
- Lanzhou Center for Tuberculosis Research and Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, 730000, China
- Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Bingdong Zhu
- Lanzhou Center for Tuberculosis Research and Gansu Provincial Key Laboratory of Evidence Based Medicine and Clinical Translation, Lanzhou University, Lanzhou, 730000, China
- Institute of Pathogen Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Muhammad Adnan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 99 Lincheng west Road, Guanshan Lake District, Guiyang, 550081, Guizhou, China
| | - Romana Liaqat
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Wei-Bao Kong
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Shiquan Niu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China.
| |
Collapse
|
48
|
Sakai S, Lora NE, Kauffman KD, Dorosky DE, Oh S, Namasivayam S, Gomez F, Fleegle JD, Arlehamn CSL, Sette A, Sher A, Freeman GJ, Via LE, Barry III CE, Barber DL. Functional inactivation of pulmonary MAIT cells following 5-OP-RU treatment of non-human primates. Mucosal Immunol 2021; 14:1055-1066. [PMID: 34158594 PMCID: PMC8217205 DOI: 10.1038/s41385-021-00425-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/28/2021] [Accepted: 06/06/2021] [Indexed: 02/04/2023]
Abstract
Targeting MAIT cells holds promise for the treatment of different diseases and infections. We previously showed that treatment of Mycobacterium tuberculosis infected mice with 5-OP-RU, a major antigen for MAIT cells, expands MAIT cells and enhances bacterial control. Here we treated M. tuberculosis infected rhesus macaques with 5-OP-RU intratracheally but found no clinical or microbiological benefit. In fact, after 5-OP-RU treatment MAIT cells did not expand, but rather upregulated PD-1 and lost the ability to produce multiple cytokines, a phenotype resembling T cell exhaustion. Furthermore, we show that vaccination of uninfected macaques with 5-OP-RU+CpG instillation into the lungs also drives MAIT cell dysfunction, and PD-1 blockade during vaccination partly prevents the loss of MAIT cell function without facilitating their expansion. Thus, in rhesus macaques MAIT cells are prone to the loss of effector functions rather than expansion after TCR stimulation in vivo, representing a significant barrier to therapeutically targeting these cells.
Collapse
Affiliation(s)
- Shunsuke Sakai
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Nickiana E. Lora
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Keith D. Kauffman
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Danielle E. Dorosky
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Sangmi Oh
- grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Sivaranjani Namasivayam
- grid.419681.30000 0001 2164 9667Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Felipe Gomez
- grid.419681.30000 0001 2164 9667Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Joel D. Fleegle
- grid.419681.30000 0001 2164 9667Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | | | | | - Alessandro Sette
- grid.185006.a0000 0004 0461 3162Center for Infectious Disease, La Jolla Institute for Immunology, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Alan Sher
- grid.419681.30000 0001 2164 9667Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| | - Gordon J. Freeman
- grid.38142.3c000000041936754XDepartment of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA USA
| | - Laura E. Via
- grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA ,grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Clifton E. Barry III
- grid.419681.30000 0001 2164 9667Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA ,grid.7836.a0000 0004 1937 1151Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniel L. Barber
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD USA
| |
Collapse
|
49
|
Du Bruyn E, Ruzive S, Lindestam Arlehamn CS, Sette A, Sher A, Barber DL, Wilkinson RJ, Riou C. Mycobacterium tuberculosis-specific CD4 T cells expressing CD153 inversely associate with bacterial load and disease severity in human tuberculosis. Mucosal Immunol 2021; 14:491-499. [PMID: 32678272 PMCID: PMC7855386 DOI: 10.1038/s41385-020-0322-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 02/04/2023]
Abstract
Recent data from mice and non-human primate models of tuberculosis suggested that CD153, a TNF super family member, plays an important role in Mycobacterium tuberculosis (Mtb) control. However, this molecule has not been comprehensively evaluated in humans. Here, we show that the proportion of Mtb-specific CD4 T cells expressing CD153 was significantly reduced in active TB patients compared to latently infected persons. Importantly, the CD153+ Mtb-specific CD4 response inversely correlated with lung bacterial load, inferred by Xpert cycle threshold, irrespective of HIV status. Antitubercular treatment partially restored CD153 expression on Mtb-specific CD4 T cells. This is the first report of a subset of Mtb-specific CD4 T cells showing strong negative correlation with bacterial burden. Building on substantial evidence from animal models implicating CD153 as a mediator of host protection, our findings suggest it may play a similar role in humans and its measurement may be useful to evaluate TB vaccine efficacy.
Collapse
Affiliation(s)
- Elsa Du Bruyn
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa
| | - Sheena Ruzive
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa
| | | | - Alessandro Sette
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Alan Sher
- grid.419681.30000 0001 2164 9667Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Daniel L. Barber
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Robert J. Wilkinson
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.7445.20000 0001 2113 8111Department of Infectious Diseases, Imperial College London, London, W2 1PG UK ,grid.7836.a0000 0004 1937 1151Department of Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, NW1 1AT UK
| | - Catherine Riou
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.7836.a0000 0004 1937 1151Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
50
|
Yang R, Mele F, Worley L, Langlais D, Rosain J, Benhsaien I, Elarabi H, Croft CA, Doisne JM, Zhang P, Weisshaar M, Jarrossay D, Latorre D, Shen Y, Han J, Ogishi M, Gruber C, Markle J, Al Ali F, Rahman M, Khan T, Seeleuthner Y, Kerner G, Husquin LT, Maclsaac JL, Jeljeli M, Errami A, Ailal F, Kobor MS, Oleaga-Quintas C, Roynard M, Bourgey M, El Baghdadi J, Boisson-Dupuis S, Puel A, Batteux F, Rozenberg F, Marr N, Pan-Hammarström Q, Bogunovic D, Quintana-Murci L, Carroll T, Ma CS, Abel L, Bousfiha A, Di Santo JP, Glimcher LH, Gros P, Tangye SG, Sallusto F, Bustamante J, Casanova JL. Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria. Cell 2020; 183:1826-1847.e31. [PMID: 33296702 PMCID: PMC7770098 DOI: 10.1016/j.cell.2020.10.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Inborn errors of human interferon gamma (IFN-γ) immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. The patient has extremely low counts of circulating Mycobacterium-reactive natural killer (NK), invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of Mycobacterium-non reactive classic TH1 lymphocytes, with the residual populations of these cells also producing abnormally small amounts of IFN-γ. Other lymphocyte subsets develop normally but produce low levels of IFN-γ, with the exception of CD8+ αβ T and non-classic CD4+ αβ TH1∗ lymphocytes, which produce IFN-γ normally in response to mycobacterial antigens. Human T-bet deficiency thus underlies mycobacterial disease by preventing the development of innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells) and IFN-γ production by them, with mycobacterium-specific, IFN-γ-producing, purely adaptive CD8+ αβ T, and CD4+ αβ TH1∗ cells unable to compensate for this deficit.
Collapse
Affiliation(s)
- Rui Yang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA.
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Lisa Worley
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - David Langlais
- Department of Human Genetics, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada; McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Ibithal Benhsaien
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Houda Elarabi
- Pediatrics Department, Hassan II Hospital, 80030 Dakhla, Morocco
| | - Carys A Croft
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France; University of Paris, 75006 Paris, France
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Peng Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Marc Weisshaar
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - David Jarrossay
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Daniela Latorre
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yichao Shen
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Jing Han
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Masato Ogishi
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Janet Markle
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | | | - Taushif Khan
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Lucas T Husquin
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France
| | - Julia L Maclsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mohamed Jeljeli
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Abderrahmane Errami
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Manon Roynard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Mathieu Bourgey
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics, Montreal, QC H3A 0G1, Canada
| | | | - Stéphanie Boisson-Dupuis
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Fréderic Batteux
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Flore Rozenberg
- University of Paris, 75006 Paris, France; Virology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, PO 34110, Qatar
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, 75005 Paris, France
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Gros
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Federica Sallusto
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland; Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jacinta Bustamante
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Study Center for Primary Immunodeficiencies, Necker Children Hospital, AP-HP, 75015 Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
| |
Collapse
|