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Casanova JL, MacMicking JD, Nathan CF. Interferon- γ and infectious diseases: Lessons and prospects. Science 2024; 384:eadl2016. [PMID: 38635718 DOI: 10.1126/science.adl2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
Infectious diseases continue to claim many lives. Prevention of morbidity and mortality from these diseases would benefit not just from new medicines and vaccines but also from a better understanding of what constitutes protective immunity. Among the major immune signals that mobilize host defense against infection is interferon-γ (IFN-γ), a protein secreted by lymphocytes. Forty years ago, IFN-γ was identified as a macrophage-activating factor, and, in recent years, there has been a resurgent interest in IFN-γ biology and its role in human defense. Here we assess the current understanding of IFN-γ, revisit its designation as an "interferon," and weigh its prospects as a therapeutic against globally pervasive microbial pathogens.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, 75015 Paris, France
- Imagine Institute, Paris Cité University, 75015 Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, 75015 Paris, France
| | - John D MacMicking
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, Yale University, West Haven, CT 06477, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carl F Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
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2
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Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Alekseev Y, Ma Q, Dayama G, Lau NC, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I. Myc Dysregulation in Activated Macrophages Initiates Iron-Mediated Lipid Peroxidation that Fuels Type I Interferon and Compromises TB Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583602. [PMID: 38496444 PMCID: PMC10942339 DOI: 10.1101/2024.03.05.583602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
A quarter of human population is infected with Mycobacterium tuberculosis, but less than 10% of those infected develop clinical, mostly pulmonary, TB. To dissect mechanisms of susceptibility in immunocompetent individuals, we developed a genetically defined sst1-susceptible mouse model that uniquely reproduces a defining feature of human TB: development of necrotic lung lesions after infection with virulent Mtb. In this study, we explored the connectivity of the sst1-regulated pathways during prolonged macrophage activation with TNF. We determined that the aberrant response of the sst1-susceptible macrophages to TNF was primarily driven by conflicting Myc and antioxidant response pathways that resulted in a coordinated failure to properly sequester intracellular iron and activate ferroptosis inhibitor enzymes. Consequently, iron-mediated lipid peroxidation fueled IFNβ superinduction and sustained the Type I Interferon (IFN-I) pathway hyperactivity that locked the sst1-susceptible macrophages in a state of unresolving stress and compromised their resistance to Mtb. The accumulation of the aberrantly activated, stressed, macrophages within granuloma microenvironment led to the local failure of anti-tuberculosis immunity and tissue necrosis. Our findings suggest a novel link between metabolic dysregulation in macrophages and susceptibility to TB, offering insights into potential therapeutic targets aimed at modulating macrophage function and improving TB control.
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Affiliation(s)
- Shivraj M. Yabaji
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | | | - Suruchi Lata
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Salam Al Abdullatif
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Yuriy Alekseev
- The Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118
| | - Qicheng Ma
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - Gargi Dayama
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - Nelson C. Lau
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- Department of Biochemistry, and Cell Biology and Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine
| | - William R. Bishai
- Center for TB Research, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Nicholas A. Crossland
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- The Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118
| | - Joshua D. Campbell
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven CT, USA
| | | | | | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA
- Pulmonary Center, The Department of Medicine, Boston University Chobanian & Avedisian School of Medicine
- Dept. of Microbiology, Boston University Chobanian & Avedisian School of Medicine
- Lead contact
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O’Farrell HE, Kok HC, Goel S, Chang AB, Yerkovich ST. Endotypes of Paediatric Cough-Do They Exist and Finding New Techniques to Improve Clinical Outcomes. J Clin Med 2024; 13:756. [PMID: 38337450 PMCID: PMC10856076 DOI: 10.3390/jcm13030756] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Chronic cough is a common symptom of many childhood lung conditions. Given the phenotypic heterogeneity of chronic cough, better characterization through endotyping is required to provide diagnostic certainty, precision therapies and to identify pathobiological mechanisms. This review summarizes recent endotype discoveries in airway diseases, particularly in relation to children, and describes the multi-omic approaches that are required to define endotypes. Potential biospecimens that may contribute to endotype and biomarker discoveries are also discussed. Identifying endotypes of chronic cough can likely provide personalized medicine and contribute to improved clinical outcomes for children.
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Affiliation(s)
- Hannah E. O’Farrell
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Hing Cheong Kok
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Department of Paediatrics, Sabah Women and Children’s Hospital, Kota Kinabalu 88996, Sabah, Malaysia
| | - Suhani Goel
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Anne B. Chang
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Department of Respiratory and Sleep Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
| | - Stephanie T. Yerkovich
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
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Ashenafi S, Loreti MG, Bekele A, Aseffa G, Amogne W, Kassa E, Aderaye G, Brighenti S. Inflammatory immune profiles associated with disease severity in pulmonary tuberculosis patients with moderate to severe clinical TB or anemia. Front Immunol 2023; 14:1296501. [PMID: 38162636 PMCID: PMC10756900 DOI: 10.3389/fimmu.2023.1296501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Background Immune control of Mycobacterium tuberculosis (Mtb) infection is largely influenced by the extensive disease heterogeneity that is typical for tuberculosis (TB). In this study, the peripheral inflammatory immune profile of different sub-groups of pulmonary TB patients was explored based on clinical disease severity, anemia of chronic disease, or the radiological extent of lung disease. Methods Plasma samples were obtained from n=107 patients with active pulmonary TB at the time of diagnosis and after start of standard chemotherapy. A composite clinical TB symptoms score, blood hemoglobin status and chest X-ray imaging were used to sub-group TB patients into 1.) mild and moderate-severe clinical TB, 2.) anemic and non-anemic TB, or 3.) limited and extensive lung involvement. Plasma levels of biomarkers associated with inflammation pathways were assessed using a Bio-Plex Magpix 37-multiplex assay. In parallel, Th1/Th2 cytokines were quantified with a 27-multiplex in matched plasma and cell culture supernatants from whole blood stimulated with M. tuberculosis-antigens using the QuantiFERON-TB Gold assay. Results Clinical TB disease severity correlated with low blood hemoglobin levels and anemia but not with radiological findings in this study cohort. Multiplex protein analyses revealed that distinct clusters of inflammation markers and cytokines separated the different TB disease sub-groups with variable efficacy. Several top-ranked markers overlapped, while other markers were unique with regards to their importance to differentiate the TB disease severity groups. A distinct immune response profile defined by elevated levels of BAFF, LIGHT, sTNF-R1 and 2, IP-10, osteopontin, chitinase-3-like protein 1, and IFNα2 and IL-8, were most effective in separating TB patients with different clinical disease severity and were also promising candidates for treatment monitoring. TB patients with mild disease displayed immune polarization towards mixed Th1/Th2 responses, while pro-inflammatory and B cell stimulating cytokines as well as immunomodulatory mediators predominated in moderate-severe TB disease and anemia of TB. Conclusions Our data demonstrated that clinical disease severity in TB is associated with anemia and distinct inflammatory immune profiles. These results contribute to the understanding of immunopathology in pulmonary TB and define top-ranked inflammatory mediators as biomarkers of disease severity and treatment prognosis.
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Affiliation(s)
- Senait Ashenafi
- Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Marco Giulio Loreti
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Amsalu Bekele
- Department of Internal Medicine, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Getachew Aseffa
- Department of Radiology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Wondwossen Amogne
- Department of Internal Medicine, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Endale Kassa
- Department of Internal Medicine, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Getachew Aderaye
- Department of Internal Medicine, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Susanna Brighenti
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
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Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko BN, Gimelbrant AA, Kramnik I. Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages. SCIENCE ADVANCES 2023; 9:eadh4119. [PMID: 37756395 PMCID: PMC10530096 DOI: 10.1126/sciadv.adh4119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Understanding cell state transitions and purposefully controlling them to improve therapies is a longstanding challenge in biological research and medicine. Here, we identify a transcriptional signature that distinguishes activated macrophages from the tuberculosis (TB) susceptible and resistant mice. We then apply the cSTAR (cell state transition assessment and regulation) approach to data from screening-by-RNA sequencing to identify chemical perturbations that shift the transcriptional state of tumor necrosis factor (TNF)-activated TB-susceptible macrophages toward that of TB-resistant cells, i.e., prevents their aberrant activation without suppressing beneficial TNF responses. Last, we demonstrate that the compounds identified with this approach enhance the resistance of the TB-susceptible mouse macrophages to virulent Mycobacterium tuberculosis.
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Affiliation(s)
- Shivraj M. Yabaji
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Oleksii S. Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - Sujoy Chatterjee
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Bidisha Bhattacharya
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Emily Wood
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
| | - Marina Kasaikina
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
- Pulmonary Center, The Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
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6
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Suliman S, Jaganath D, DiNardo A. Predicting Pediatric Tuberculosis: The Need for Age-Specific Host Biosignatures. Clin Infect Dis 2023; 77:450-452. [PMID: 37144361 PMCID: PMC10425193 DOI: 10.1093/cid/ciad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/03/2023] [Indexed: 05/06/2023] Open
Affiliation(s)
- Sara Suliman
- Department of Medicine, Division of Experimental Medicine, Zuckerberg San Francisco General Hospital, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Devan Jaganath
- Division of Pediatric Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Andrew DiNardo
- Global TB Program, Center for Human Immunbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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7
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Motta I, Boeree M, Chesov D, Dheda K, Günther G, Horsburgh CR, Kherabi Y, Lange C, Lienhardt C, McIlleron HM, Paton NI, Stagg HR, Thwaites G, Udwadia Z, Van Crevel R, Velásquez GE, Wilkinson RJ, Guglielmetti L. Recent advances in the treatment of tuberculosis. Clin Microbiol Infect 2023:S1198-743X(23)00339-7. [PMID: 37482332 DOI: 10.1016/j.cmi.2023.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Tuberculosis (TB) is a global health challenge and one of the leading causes of death worldwide. In the last decade, the TB treatment landscape has dramatically changed. After long years of stagnation, new compounds entered the market (bedaquiline, delamanid, and pretomanid) and phase III clinical trials have shown promising results towards shortening duration of treatment for both drug-susceptible (Study 31/A5349, TRUNCATE-TB, and SHINE) and drug-resistant TB (STREAM, NiX-TB, ZeNix, and TB-PRACTECAL). Dose optimization of rifamycins and repurposed drugs has also brought hopes of further development of safe and effective regimens. Consequently, international and WHO clinical guidelines have been updated multiple times in the last years to keep pace with these advances. OBJECTIVES This narrative review aims to summarize the state-of-the-art on treatment of drug-susceptible and drug-resistant TB, as well as recent trial results and an overview of ongoing clinical trials. SOURCES A non-systematic literature review was conducted in PubMed and MEDLINE, focusing on the treatment of TB. Ongoing clinical trials were listed according to the authors' knowledge and completed consulting clinicaltrials.gov and other publicly available websites (www.resisttb.org/clinical-trials-progress-report, www.newtbdrugs.org/pipeline/trials). CONTENT This review summarizes the recent, major changes in the landscape for drug-susceptible and drug-resistant treatment, with a specific focus on their potential impact on patient outcomes and programmatic TB management. Moreover, insights in host-directed therapies, and advances in pharmacokinetics and pharmacogenomics are discussed. A thorough outline of ongoing therapeutic clinical trials is presented, highlighting different approaches and goals in current TB clinical research. IMPLICATIONS Future research should be directed to individualize regimens and protect these recent breakthroughs by preventing and identifying the selection of drug resistance and providing widespread, affordable, patient-centred access to new treatment options for all people affected by TB.
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Affiliation(s)
- Ilaria Motta
- Médecins Sans Frontières, Manson Unit, London, United Kingdom
| | - Martin Boeree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dumitru Chesov
- Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Moldova; Department of Pulmonology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Moldova; Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute and South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gunar Günther
- Department of Pulmonology and Allergology, Inselspital, Bern University Hospital, Bern, Switzerland; Department of Medical Sciences, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
| | - Charles Robert Horsburgh
- Departments of Epidemiology, Biostatistics, Global Health and Medicine, Boston University, Boston, MA, United States
| | - Yousra Kherabi
- Infectious, and Tropical Diseases Department, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany; German Center for Infection Research (DZIF), Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Department of International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany; Department of Pediatrics-Global Immigrant, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, United States
| | - Christian Lienhardt
- Department of Translational Research Applied to HIV and Infectious Diseases, Institut de Recherche pour le Développement, Montpellier, France; Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Helen M McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicholas I Paton
- Department of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Helen R Stagg
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Zarir Udwadia
- Department of Internal Medicine and Pulmonology, Hinduja Hospital & Research Centre, Mumbai, India
| | - Reinout Van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Gustavo E Velásquez
- UCSF Center for Tuberculosis, University of California, San Francisco, San Francisco, CA, United States; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Robert J Wilkinson
- Francis Crick Institute, London, United Kingdom; Department of Infectious Diseases, Imperial College London, United Kingdom
| | - Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France; AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France.
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Tateosian NL, Morelli MP, Pellegrini JM, García VE. Beyond the Clinic: The Activation of Diverse Cellular and Humoral Factors Shapes the Immunological Status of Patients with Active Tuberculosis. Int J Mol Sci 2023; 24:5033. [PMID: 36902461 PMCID: PMC10002939 DOI: 10.3390/ijms24055033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis (TB), has killed nearly one billion people in the last two centuries. Nowadays, TB remains a major global health problem, ranking among the thirteen leading causes of death worldwide. Human TB infection spans different levels of stages: incipient, subclinical, latent and active TB, all of them with varying symptoms, microbiological characteristics, immune responses and pathologies profiles. After infection, Mtb interacts with diverse cells of both innate and adaptive immune compartments, playing a crucial role in the modulation and development of the pathology. Underlying TB clinical manifestations, individual immunological profiles can be identified in patients with active TB according to the strength of their immune responses to Mtb infection, defining diverse endotypes. Those different endotypes are regulated by a complex interaction of the patient's cellular metabolism, genetic background, epigenetics, and gene transcriptional regulation. Here, we review immunological categorizations of TB patients based on the activation of different cellular populations (both myeloid and lymphocytic subsets) and humoral mediators (such as cytokines and lipid mediators). The analysis of the participating factors that operate during active Mtb infection shaping the immunological status or immune endotypes of TB patients could contribute to the development of Host Directed Therapy.
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Affiliation(s)
- Nancy Liliana Tateosian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - María Paula Morelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Joaquín Miguel Pellegrini
- Centre d’Immunologie de Marseille Luminy, INSERM, CNRS, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, Case 906, CEDEX 09, 13288 Marseille, France
| | - Verónica Edith García
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Intendente Güiraldes 2160, Pabellón II, 4°piso, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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9
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Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko B, Gimelbrant AA, Kramnik I. Cell state transition analysis identifies interventions that improve control of M. tuberculosis infection by susceptible macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527908. [PMID: 36798271 PMCID: PMC9934610 DOI: 10.1101/2023.02.09.527908] [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: 02/12/2023]
Abstract
Understanding cell state transitions and purposefully controlling them to improve therapies is a longstanding challenge in biological research and medicine. Here, we identify a transcriptional signature that distinguishes activated macrophages from TB-susceptible and TB-resistant mice. We then apply the cSTAR (cell State Transition Assessment and Regulation) approach to data from screening-by-RNA sequencing to identify chemical perturbations that shift the. transcriptional state of the TB-susceptible macrophages towards that of TB-resistant cells. Finally, we demonstrate that the compounds identified with this approach enhance resistance of the TB-susceptible mouse macrophages to virulent M. tuberculosis .
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Affiliation(s)
- Shivraj M Yabaji
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sujoy Chatterjee
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University
| | - Bidisha Bhattacharya
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University
| | - Emily Wood
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Marina Kasaikina
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University
| | - Boris Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, USA
| | | | - Igor Kramnik
- The National Emerging Infectious Diseases Laboratories (NEIDL), Boston University
- Pulmonary Center, The Department of Medicine, Boston University School of Medicine
- Department of Microbiology, Boston University School of Medicine
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10
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Wallis RS, O'Garra A, Sher A, Wack A. Host-directed immunotherapy of viral and bacterial infections: past, present and future. Nat Rev Immunol 2023; 23:121-133. [PMID: 35672482 PMCID: PMC9171745 DOI: 10.1038/s41577-022-00734-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 02/06/2023]
Abstract
The advent of COVID-19 and the persistent threat of infectious diseases such as tuberculosis, malaria, influenza and HIV/AIDS remind us of the marked impact that infections continue to have on public health. Some of the most effective protective measures are vaccines but these have been difficult to develop for some of these infectious diseases even after decades of research. The development of drugs and immunotherapies acting directly against the pathogen can be equally challenging, and such pathogen-directed therapeutics have the potential disadvantage of selecting for resistance. An alternative approach is provided by host-directed therapies, which interfere with host cellular processes required for pathogen survival or replication, or target the host immune response to infection (immunotherapies) to either augment immunity or ameliorate immunopathology. Here, we provide a historical perspective of host-directed immunotherapeutic interventions for viral and bacterial infections and then focus on SARS-CoV-2 and Mycobacterium tuberculosis, two major human pathogens of the current era, to indicate the key lessons learned and discuss candidate immunotherapeutic approaches, with a focus on drugs currently in clinical trials.
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Affiliation(s)
- Robert S Wallis
- The Aurum Institute, Johannesburg, South Africa.
- Vanderbilt University, Nashville, TN, USA.
- Rutgers University, Newark, NJ, USA.
- Case Western Reserve University, Cleveland, OH, USA.
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, UK.
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11
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Inflammation-mediated tissue damage in pulmonary tuberculosis and host-directed therapeutic strategies. Semin Immunol 2023; 65:101672. [PMID: 36469987 DOI: 10.1016/j.smim.2022.101672] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 12/04/2022]
Abstract
Treatment of tuberculosis (TB) involves the administration of anti-mycobacterial drugs for several months. The emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb, the causative agent) together with increased disease severity in people with co-morbidities such as diabetes mellitus and HIV have hampered efforts to reduce case fatality. In severe disease, TB pathology is largely attributable to over-exuberant host immune responses targeted at controlling bacterial replication. Non-resolving inflammation driven by host pro-inflammatory mediators in response to high bacterial load leads to pulmonary pathology including cavitation and fibrosis. The need to improve clinical outcomes and reduce treatment times has led to a two-pronged approach involving the development of novel antimicrobials as well as host-directed therapies (HDT) that favourably modulate immune responses to Mtb. HDT strategies incorporate aspects of immune modulation aimed at downregulating non-productive inflammatory responses and augmenting antimicrobial effector mechanisms to minimise pulmonary pathology and accelerate symptom resolution. HDT in combination with existing antimycobacterial agents offers a potentially promising strategy to improve the long-term outcome for TB patients. In this review, we describe components of the host immune response that contribute to inflammation and tissue damage in pulmonary TB, including cytokines, matrix metalloproteinases, lipid mediators, and neutrophil extracellular traps. We then proceed to review HDT directed at these pathways.
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12
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Ashenafi S, Brighenti S. Reinventing the human tuberculosis (TB) granuloma: Learning from the cancer field. Front Immunol 2022; 13:1059725. [PMID: 36591229 PMCID: PMC9797505 DOI: 10.3389/fimmu.2022.1059725] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in the world and every 20 seconds a person dies from TB. An important attribute of human TB is induction of a granulomatous inflammation that creates a dynamic range of local microenvironments in infected organs, where the immune responses may be considerably different compared to the systemic circulation. New and improved technologies for in situ quantification and multimodal imaging of mRNA transcripts and protein expression at the single-cell level have enabled significantly improved insights into the local TB granuloma microenvironment. Here, we review the most recent data on regulation of immunity in the TB granuloma with an enhanced focus on selected in situ studies that enable spatial mapping of immune cell phenotypes and functions. We take advantage of the conceptual framework of the cancer-immunity cycle to speculate how local T cell responses may be enhanced in the granuloma microenvironment at the site of Mycobacterium tuberculosis infection. This includes an exploratory definition of "hot", immune-inflamed, and "cold", immune-excluded TB granulomas that does not refer to the level of bacterial replication or metabolic activity, but to the relative infiltration of T cells into the infected lesions. Finally, we reflect on the current knowledge and controversy related to reactivation of active TB in cancer patients treated with immune checkpoint inhibitors such as PD-1/PD-L1 and CTLA-4. An understanding of the underlying mechanisms involved in the induction and maintenance or disruption of immunoregulation in the TB granuloma microenvironment may provide new avenues for host-directed therapies that can support standard antibiotic treatment of persistent TB disease.
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Affiliation(s)
- Senait Ashenafi
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, ANA Futura, Huddinge, Sweden,Department of Pathology, School of Medicine, College of Health Sciences, Tikur Anbessa Specialized Hospital and Addis Ababa University, Addis Ababa, Ethiopia
| | - Susanna Brighenti
- Department of Medicine Huddinge, Center for Infectious Medicine (CIM), Karolinska Institutet, ANA Futura, Huddinge, Sweden,*Correspondence: Susanna Brighenti,
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13
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Jeong EK, Lee HJ, Jung YJ. Host-Directed Therapies for Tuberculosis. Pathogens 2022; 11:1291. [PMID: 36365041 PMCID: PMC9697779 DOI: 10.3390/pathogens11111291] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 02/04/2024] Open
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, consistently threatening public health. Conventional tuberculosis treatment requires a long-term treatment regimen and is associated with side effects. The efficacy of antitubercular drugs has decreased with the emergence of drug-resistant TB; therefore, the development of new TB treatment strategies is urgently needed. In this context, we present host-directed therapy (HDT) as an alternative to current tuberculosis therapy. Unlike antitubercular drugs that directly target Mycobacterium tuberculosis (Mtb), the causative agent of TB, HDT is an approach for treating TB that appropriately modulates host immune responses. HDT primarily aims to enhance the antimicrobial activity of the host in order to control Mtb infection and attenuate excessive inflammation in order to minimize tissue damage. Recently, research based on the repositioning of drugs for use in HDT has been in progress. Based on the overall immune responses against Mtb infection and the immune-evasion mechanisms of Mtb, this review examines the repositioned drugs available for HDT and their mechanisms of action.
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Affiliation(s)
- Eui-Kwon Jeong
- BIT Medical Convergence Graduate Program, Kangwon National University, Chuncheon 24341, Korea
| | - Hyo-Ji Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
| | - Yu-Jin Jung
- BIT Medical Convergence Graduate Program, Kangwon National University, Chuncheon 24341, Korea
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
- Kangwon Radiation Convergence Research Support Center, Kangwon National University, Chuncheon 24341, Korea
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14
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Bahlool AZ, Fattah S, O’Sullivan A, Cavanagh B, MacLoughlin R, Keane J, O’Sullivan MP, Cryan SA. Development of Inhalable ATRA-Loaded PLGA Nanoparticles as Host-Directed Immunotherapy against Tuberculosis. Pharmaceutics 2022; 14:pharmaceutics14081745. [PMID: 36015371 PMCID: PMC9415714 DOI: 10.3390/pharmaceutics14081745] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Developing new effective treatment strategies to overcome the rise in multi-drug resistant tuberculosis cases (MDR-TB) represents a global challenge. A host-directed therapy (HDT), acting on the host immune response rather than Mtb directly, could address these resistance issues. We developed an HDT for targeted TB treatment, using All Trans Retinoic Acid (ATRA)-loaded nanoparticles (NPs) that are suitable for nebulization. Efficacy studies conducted on THP-1 differentiated cells infected with the H37Ra avirulent Mycobacterium tuberculosis (Mtb) strain, have shown a dose-dependent reduction in H37Ra growth as determined by the BACT/ALERT® system. Confocal microscopy images showed efficient and extensive cellular delivery of ATRA-PLGA NPs into THP-1-derived macrophages. A commercially available vibrating mesh nebulizer was used to generate nanoparticle-loaded droplets with a mass median aerodynamic diameter of 2.13 μm as measured by cascade impaction, and a volumetric median diameter of 4.09 μm as measured by laser diffraction. In an adult breathing simulation experiment, 65.1% of the ATRA PLGA-NP dose was inhaled. This targeted inhaled HDT could offer a new adjunctive TB treatment option that could enhance current dosage regimens leading to better patient prognosis and a decreasing incidence of MDR-TB.
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Affiliation(s)
- Ahmad Z. Bahlool
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Tissue Engineering Research Group, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, Trinity College Dublin, The University of Dublin, D08 9WRT Dublin, Ireland
| | - Sarinj Fattah
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Tissue Engineering Research Group, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
| | - Andrew O’Sullivan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Research and Development, Science and Emerging Technologies, Aerogen Ltd., Galway Business Park, Dangan, H91 HE94 Galway, Ireland
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland RCSI, D02 YN77 Dublin, Ireland
| | - Ronan MacLoughlin
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Research and Development, Science and Emerging Technologies, Aerogen Ltd., Galway Business Park, Dangan, H91 HE94 Galway, Ireland
- School of Pharmacy and Pharmaceutical Sciences, Trinity College, D02 PN40 Dublin, Ireland
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, Trinity College Dublin, The University of Dublin, D08 9WRT Dublin, Ireland
| | - Mary P. O’Sullivan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, Trinity College Dublin, The University of Dublin, D08 9WRT Dublin, Ireland
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- Tissue Engineering Research Group, Royal College of Surgeons in Ireland (RCSI), 123 St. Stephens Green, D02 YN77 Dublin, Ireland
- SFI Advanced Materials and Bioengineering Research (AMBER) Centre, RCSI and Trinity College Dublin, D02 PN40 Dublin, Ireland
- SFI Centre for Research in Medical Devices (CÚRAM), NUIG & RCSI, H91 W2TY Galway, Ireland
- Correspondence:
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15
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Pellegrini JM, Gorvel JP, Mémet S. Immunosuppressive Mechanisms in Brucellosis in Light of Chronic Bacterial Diseases. Microorganisms 2022; 10:microorganisms10071260. [PMID: 35888979 PMCID: PMC9324529 DOI: 10.3390/microorganisms10071260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 01/27/2023] Open
Abstract
Brucellosis is considered one of the major zoonoses worldwide, constituting a critical livestock and human health concern with a huge socio-economic burden. Brucella genus, its etiologic agent, is composed of intracellular bacteria that have evolved a prodigious ability to elude and shape host immunity to establish chronic infection. Brucella’s intracellular lifestyle and pathogen-associated molecular patterns, such as its specific lipopolysaccharide (LPS), are key factors for hiding and hampering recognition by the immune system. Here, we will review the current knowledge of evading and immunosuppressive mechanisms elicited by Brucella species to persist stealthily in their hosts, such as those triggered by their LPS and cyclic β-1,2-d-glucan or involved in neutrophil and monocyte avoidance, antigen presentation impairment, the modulation of T cell responses and immunometabolism. Attractive strategies exploited by other successful chronic pathogenic bacteria, including Mycobacteria, Salmonella, and Chlamydia, will be also discussed, with a special emphasis on the mechanisms operating in brucellosis, such as granuloma formation, pyroptosis, and manipulation of type I and III IFNs, B cells, innate lymphoid cells, and host lipids. A better understanding of these stratagems is essential to fighting bacterial chronic infections and designing innovative treatments and vaccines.
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16
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Azad TD, Shah PP, Kim HB, Stevens RD. Endotypes and the Path to Precision in Moderate and Severe Traumatic Brain Injury. Neurocrit Care 2022; 37:259-266. [PMID: 35314969 DOI: 10.1007/s12028-022-01475-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/19/2022]
Abstract
Heterogeneity is recognized as a major barrier in efforts to improve the care and outcomes of patients with traumatic brain injury (TBI). Even within the narrower stratum of moderate and severe TBI, current management approaches do not capture the complexity of this condition characterized by manifold clinical, anatomical, and pathophysiologic features. One approach to heterogeneity may be to resolve undifferentiated TBI populations into endotypes, subclasses that are distinguished by shared biological characteristics. The endotype paradigm has been explored in a range of medical domains, including psychiatry, oncology, immunology, and pulmonology. In intensive care, endotypes are being investigated for syndromes such as sepsis and acute respiratory distress syndrome. This review provides an overview of the endotype paradigm as well as some of its methods and use cases. A conceptual framework is proposed for endotype research in moderate and severe TBI, together with a scientific road map for endotype discovery and validation in this population.
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Affiliation(s)
- Tej D Azad
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pavan P Shah
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Han B Kim
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Phipps Suite 455, Baltimore, MD, 21287, USA
| | - Robert D Stevens
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Phipps Suite 455, Baltimore, MD, 21287, USA.
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17
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DiNardo AR, Gandhi T, Heyckendorf J, Grimm SL, Rajapakshe K, Nishiguchi T, Reimann M, Kirchner HL, Kahari J, Dlamini Q, Lange C, Goldmann T, Marwitz S, Abhimanyu, Cirillo JD, Kaufmann SH, Netea MG, van Crevel R, Mandalakas AM, Coarfa C. Gene expression signatures identify biologically and clinically distinct tuberculosis endotypes. Eur Respir J 2022; 60:13993003.02263-2021. [PMID: 35169026 PMCID: PMC9474892 DOI: 10.1183/13993003.02263-2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/27/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND In vitro, animal model, and clinical evidence suggests that tuberculosis is not a monomorphic disease, and that host response to tuberculosis is protean with multiple distinct molecular pathways and pathologies (endotypes). We applied unbiased clustering to identify separate tuberculosis endotypes with classifiable gene expression patterns and clinical outcomes. METHODS A cohort comprised of microarray gene expression data from microbiologically confirmed tuberculosis patients were used to identify putative endotypes. One microarray cohort with longitudinal clinical outcomes was reserved for validation, as was two RNA-seq cohorts. Finally, a separate cohort of tuberculosis patients with functional immune responses was evaluated to clarify stimulated from unstimulated immune responses. RESULTS A discovery cohort, including 435 tuberculosis patients and 533 asymptomatic controls, identified two tuberculosis endotypes. Endotype A is characterised by increased expression of genes related to inflammation and immunity and decreased metabolism and proliferation; in contrast, endotype B has increased activity of metabolism and proliferation pathways. An independent RNA-seq validation cohort, including 118 tuberculosis patients and 179 controls, validated the discovery results. Gene expression signatures for treatment failure were elevated in endotype A in the discovery cohort, and a separate validation cohort confirmed that endotype A patients had slower time to culture conversion, and a reduced cure rate. These observations suggest that endotypes reflect functional immunity, supported by the observation that tuberculosis patients with a hyperinflammatory endotype have less responsive cytokine production upon stimulation. CONCLUSION These findings provide evidence that metabolic and immune profiling could inform optimisation of endotype-specific host-directed therapies for tuberculosis.
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Affiliation(s)
- Andrew R DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA .,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Co-first authors contributing equally
| | - Tanmay Gandhi
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, USA.,Co-first authors contributing equally
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Co-first authors contributing equally
| | - Sandra L Grimm
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, USA.,Co-first authors contributing equally
| | - Kimal Rajapakshe
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, USA
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany
| | - H Lester Kirchner
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Jaqueline Kahari
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Qiniso Dlamini
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Christoph Lange
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA.,Division of Clinical Infectious Diseases, Research Center Borstel; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Torsten Goldmann
- Division of Clinical Infectious Diseases, Research Center Borstel; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany
| | - Sebastian Marwitz
- Division of Clinical Infectious Diseases, Research Center Borstel; German Center for Infection Research (DZIF) Clinical Tuberculosis Unit, Borstel, Germany
| | | | - Abhimanyu
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, USA
| | - Stefan He Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany.,Hagler Institute for Advanced Study at Texas A&M University, College Station, TX, USA.,Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Genomics and Immunoregulation, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, WTS Center for Human Immunobiology, Department of Pediatrics, Baylor College of Medicine, Houston, USA.,Co-senior authors contributing equally
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, USA.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, USA.,Co-senior authors contributing equally
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18
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Bahlool AZ, Grant C, Cryan SA, Keane J, O'Sullivan MP. All trans retinoic acid as a host-directed immunotherapy for tuberculosis. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:54-72. [PMID: 35496824 PMCID: PMC9040133 DOI: 10.1016/j.crimmu.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis (TB) is the top bacterial infectious disease killer and one of the top ten causes of death worldwide. The emergence of strains of multiple drug-resistant tuberculosis (MDR-TB) has pushed our available stock of anti-TB agents to the limit of effectiveness. This has increased the urgent need to develop novel treatment strategies using currently available resources. An adjunctive, host-directed therapy (HDT) designed to act on the host, instead of the bacteria, by boosting the host immune response through activation of intracellular pathways could be the answer. The integration of multidisciplinary approaches of repurposing currently FDA-approved drugs, with a targeted drug-delivery platform is a very promising option to reduce the long timeline associated with the approval of new drugs - time that cannot be afforded given the current levels of morbidity and mortality associated with TB infection. The deficiency of vitamin A has been reported to be highly associated with the increased susceptibility of TB. All trans retinoic acid (ATRA), the active metabolite of vitamin A, has proven to be very efficacious against TB both in vitro and in vivo. In this review, we discuss and summarise the importance of vitamin A metabolites in the fight against TB and what is known regarding the molecular mechanisms of ATRA as a host-directed therapy for TB including its effect on macrophages cytokine profile and cellular pathways. Furthermore, we focus on the issues behind why previous clinical trials with vitamin A supplementation have failed, and how these issues might be overcome. Tuberculosis deaths and resistance are increasing – novel therapies are needed. Vitamin A deficiency is a strong risk factor for active tuberculosis in contacts. All Trans Retinoic Acid is a promising host-directed therapy for tuberculosis. It has pleiotropic effects on macrophages & other immune cells in vitro and in vivo. Inhaled rather than systemic All Trans Retinoic Acid therapy may be most effective.
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Affiliation(s)
- Ahmad Z. Bahlool
- School of Pharmacy and Biomolecular Sciences (PBS), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Conor Grant
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences (PBS), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- SFI Advanced Materials and Bioengineering Research (AMBER) Centre, RCSI & TCD, Dublin, Ireland
- SFI Centre for Research in Medical Devices (CURAM), RCSI, Dublin and National University of Ireland, Galway, Ireland
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Mary P. O'Sullivan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
- Corresponding author.
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19
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Mehta K, Spaink HP, Ottenhoff THM, van der Graaf PH, van Hasselt JGC. Host-directed therapies for tuberculosis: quantitative systems pharmacology approaches. Trends Pharmacol Sci 2021; 43:293-304. [PMID: 34916092 DOI: 10.1016/j.tips.2021.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/26/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
Host-directed therapies (HDTs) that modulate host-pathogen interactions offer an innovative strategy to combat Mycobacterium tuberculosis (Mtb) infections. When combined with tuberculosis (TB) antibiotics, HDTs could contribute to improving treatment outcomes, reducing treatment duration, and preventing resistance development. Translation of the interplay of host-pathogen interactions leveraged by HDTs towards therapeutic outcomes in patients is challenging. Quantitative understanding of the multifaceted nature of the host-pathogen interactions is vital to rationally design HDT strategies. Here, we (i) provide an overview of key Mtb host-pathogen interactions as basis for HDT strategies; and (ii) discuss the components and utility of quantitative systems pharmacology (QSP) models to inform HDT strategies. QSP models can be used to identify and optimize treatment targets, to facilitate preclinical to human translation, and to design combination treatment strategies.
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Affiliation(s)
| | | | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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20
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Domaszewska T, Zyla J, Otto R, Kaufmann SHE, Weiner J. Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients. Front Immunol 2021; 12:694680. [PMID: 34421903 PMCID: PMC8375662 DOI: 10.3389/fimmu.2021.694680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/19/2021] [Indexed: 11/22/2022] Open
Abstract
Group-aggregated responses to tuberculosis (TB) have been well characterized on a molecular level. However, human beings differ and individual responses to infection vary. We have combined a novel approach to individual gene set analysis (GSA) with the clustering of transcriptomic profiles of TB patients from seven datasets in order to identify individual molecular endotypes of transcriptomic responses to TB. We found that TB patients differ with respect to the intensity of their hallmark interferon (IFN) responses, but they also show variability in their complement system, metabolic responses and multiple other pathways. This variability cannot be sufficiently explained with covariates such as gender or age, and the molecular endotypes are found across studies and populations. Using datasets from a Cynomolgus macaque model of TB, we revealed that transcriptional signatures of different molecular TB endotypes did not depend on TB progression post-infection. Moreover, we provide evidence that patients with molecular endotypes characterized by high levels of IFN responses (IFN-rich), suffered from more severe lung pathology than those with lower levels of IFN responses (IFN-low). Harnessing machine learning (ML) models, we derived gene signatures classifying IFN-rich and IFN-low TB endotypes and revealed that the IFN-low signature allowed slightly more reliable overall classification of TB patients from non-TB patients than the IFN-rich one. Using the paradigm of molecular endotypes and the ML-based predictions allows more precisely tailored treatment regimens, predicting treatment-outcome with higher accuracy and therefore bridging the gap between conventional treatment and precision medicine.
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Affiliation(s)
- Teresa Domaszewska
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Joanna Zyla
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Raik Otto
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan H. E. Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
- Max Planck Institute for Biophysical Chemistry, Emeritus Group Systems Immunology, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
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Reichmann MT, Tezera LB, Vallejo AF, Vukmirovic M, Xiao R, Reynolds J, Jogai S, Wilson S, Marshall B, Jones MG, Leslie A, D’Armiento JM, Kaminski N, Polak ME, Elkington P. Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets. J Clin Invest 2021; 131:148136. [PMID: 34128839 PMCID: PMC8321576 DOI: 10.1172/jci148136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) is a persistent global pandemic, and standard treatment for it has not changed for 30 years. Mycobacterium tuberculosis (Mtb) has undergone prolonged coevolution with humans, and patients can control Mtb even after extensive infection, demonstrating the fine balance between protective and pathological host responses within infected granulomas. We hypothesized that whole transcriptome analysis of human TB granulomas isolated by laser capture microdissection could identify therapeutic targets, and that comparison with a noninfectious granulomatous disease, sarcoidosis, would identify disease-specific pathological mechanisms. Bioinformatic analysis of RNAseq data identified numerous shared pathways between TB and sarcoidosis lymph nodes, and also specific clusters demonstrating TB results from a dysregulated inflammatory immune response. To translate these insights, we compared 3 primary human cell culture models at the whole transcriptome level and demonstrated that the 3D collagen granuloma model most closely reflected human TB disease. We investigated shared signaling pathways with human disease and identified 12 intracellular enzymes as potential therapeutic targets. Sphingosine kinase 1 inhibition controlled Mtb growth, concurrently reducing intracellular pH in infected monocytes and suppressing inflammatory mediator secretion. Immunohistochemical staining confirmed that sphingosine kinase 1 is expressed in human lung TB granulomas, and therefore represents a host therapeutic target to improve TB outcomes.
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Affiliation(s)
- Michaela T. Reichmann
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Liku B. Tezera
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Department of Infection and Immunity, University College London, London, United Kingdom
| | - Andres F. Vallejo
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Milica Vukmirovic
- Firestone Institute for Respiratory Health-Division of Respirology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Rui Xiao
- Columbia University Medical Center, New York, New York, USA
| | | | - Sanjay Jogai
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Susan Wilson
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben Marshall
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Mark G. Jones
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Alasdair Leslie
- Department of Infection and Immunity, University College London, London, United Kingdom
- Africa Health Research Institute, KwaZulu Natal, South Africa
| | | | - Naftali Kaminski
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Marta E. Polak
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Paul Elkington
- NIHR Biomedical Research Center, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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