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Tzfadia O, Gijsbers A, Vujkovic A, Snobre J, Vargas R, Dewaele K, Meehan CJ, Farhat M, Hakke S, Peters PJ, de Jong BC, Siroy A, Ravelli RBG. Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiol Spectr 2024:e0381623. [PMID: 38874407 DOI: 10.1128/spectrum.03816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/15/2024] Open
Abstract
Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens. IMPORTANCE We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.
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Affiliation(s)
- Oren Tzfadia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Abril Gijsbers
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alexandra Vujkovic
- Clinical Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- ADReM Data Lab, University of Antwerp, Antwerp, Belgium
| | - Jihad Snobre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaas Dewaele
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Axel Siroy
- Unité de soutien à l'Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM, IECB, US1, Université de Bordeaux, Pessac, France
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
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Imbratta C, Reid T, Toefy A, Scriba TJ, Nemes E. OMIP-101: 27-color flow cytometry panel for immunophenotyping of major leukocyte populations in fixed whole blood. Cytometry A 2024; 105:165-170. [PMID: 38343094 PMCID: PMC10958279 DOI: 10.1002/cyto.a.24827] [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: 07/27/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/16/2024]
Abstract
This 27-color flow cytometry antibody panel allows broad immune-profiling of major leukocyte subsets in human whole blood (WB). It includes lineage markers to identify myeloid and lymphoid cell populations including granulocytes, monocytes, myeloid dendritic cells (mDCs), natural killer (NK) cells, NKT-like cells, B cells, conventional CD4 and CD8 T cells, γδ T cells, mucosa-associated invariant T (MAIT) cells and innate lymphoid cells (ILC). To further characterize each of these populations, markers defining stages of cell differentiation (CCR7, CD27, CD45RA, CD127, CD57), cytotoxic potential (perforin, granzyme B) and cell activation/proliferation (HLA-DR, CD38, Ki-67) were included. This panel was developed for quantifying absolute counts and phenotyping major leukocyte populations in cryopreserved, fixed WB collected from participants enrolled in large multi-site tuberculosis (TB) vaccine clinical trials. This antibody panel can be applied to profile major leukocyte subsets in other sample types such as fresh WB or peripheral blood mononuclear cells (PBMCs) with only minor additional optimization.
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Affiliation(s)
- Claire Imbratta
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tim Reid
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Asma Toefy
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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A spotlight on the tuberculosis epidemic in South Africa. Nat Commun 2024; 15:1290. [PMID: 38346962 PMCID: PMC10861440 DOI: 10.1038/s41467-024-45491-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
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Imbratta C, Gela A, Bilek N, Mabwe S, Cloete Y, Mortensen R, Borges ÁH, Maenetje P, Mlotshwa M, Churchyard G, Sudi L, Sabi I, Meewes P, Wallis CL, Hatherill M, Scriba TJ, Nemes E. Qualification of the differential leukocyte count and immunophenotyping in cryopreserved ex vivo whole blood assay. Cytometry A 2023; 103:992-1003. [PMID: 37675607 DOI: 10.1002/cyto.a.24793] [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: 02/07/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/08/2023]
Abstract
We developed a flow cytometry-based assay, termed Differential Leukocyte Counting and Immunophenotyping in Cryopreserved Ex vivo whole blood (DLC-ICE), that allows quantification of absolute counts and frequencies of leukocyte subsets and measures expression of activation, phenotypic and functional markers. We evaluated the performance of the DLC-ICE assay by determining inter-operator variability for processing fresh whole blood (WB) from healthy donors collected at multiple clinical sites. In addition, we assessed inter-operator variability for staining of fixed cells and robustness across different anticoagulants. Accuracy was evaluated by comparing DLC-ICE measurements to real-time cell enumeration using an accredited hematology analyzer. Finally, we developed and tested the performance of a 27-colour immunophenotyping panel on cryopreserved fixed WB and compared results to matched fresh WB. Overall, we observed <20% variability in absolute counts and frequencies of granulocytes, monocytes and lymphocytes (T, B and NK cells) when fresh WB was collected in different anti-coagulant tubes, processed or stained by independent operators. Absolute cell counts measured across operators and anti-coagulants using the DLC-ICE method exhibited excellent correlation with the reference method, complete blood count (CBC) with differential, measured using a hematology analyzer (r2 > 0.9 for majority of measurements). A comparison of leukocyte immunophenotyping on fresh WB versus DLC-ICE processed blood yielded equivalent and linear results over a wide dynamic range (r2 = 0.94 over 10-104 cells/μL). These results demonstrate low variability across trained operators, high robustness, linearity and accuracy, supporting utility of the DLC-ICE assay for large cohort studies involving multiple clinical research sites.
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Affiliation(s)
- Claire Imbratta
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anele Gela
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicole Bilek
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Simbarashe Mabwe
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Yolundi Cloete
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rasmus Mortensen
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Álvaro H Borges
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Pholo Maenetje
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Mandla Mlotshwa
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Gavin Churchyard
- Aurum Institute, Parktown, South Africa
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Lwitiho Sudi
- Mbeya Medical Research Centre, National Institute for Medical Research (NIMR), Mbeya, Tanzania
| | - Issa Sabi
- Mbeya Medical Research Centre, National Institute for Medical Research (NIMR), Mbeya, Tanzania
| | | | - Carole L Wallis
- BARC, South Africa
- Lancet Laboratories, Johannesburg, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Looney MM, Hatherill M, Musvosvi M, Flynn J, Kagina BM, Frick M, Kafuko Z, Schmidt A, Southern J, Wilder-Smith A, Tippoo P, Paradkar V, Popadić D, Scriba TJ, Hanekom W, Giersing B. Conference report: WHO meeting summary on mRNA-based tuberculosis vaccine development. Vaccine 2023; 41:7060-7066. [PMID: 37872013 DOI: 10.1016/j.vaccine.2023.10.026] [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: 09/05/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Tuberculosis (TB) is a global health emergency. Across the globe, approximately 2 billion people are currently infected with Mycobacterium tuberculosis (Mtb), and of those, 5-10% may progress to become ill and potentially transmit the bacterium. In 2021, nearly 10.6 million people developed TB disease and 1.6 million died. There is an urgent need for accelerated development of new TB-focused interventions, in particular, improved TB vaccines. However, progress in developing highly effective TB vaccines has been slow and is chronically under-resourced. The mRNA vaccine platform may offer an opportunity to accelerate development of new TB vaccines. In April 2023, the World Health Organization convened global experts to discuss the feasibility and potential value of mRNA-based vaccines for TB. Here we report on meeting deliberations related to the current TB vaccine pipeline and potential novel antigens, the status of efforts to identify correlates of protection, potential clinical development strategies and considerations for community acceptance of new TB vaccines based on this relatively new platform. The role of industry collaborations, ethics, social science, and responsibility to the global community regarding transparency and manufacturing capacity building were discussed through expert presentations and panel sessions. The overall conclusion of the meeting is that mRNA-based vaccines constitute a potentially powerful new tool for reducing the global burden of TB.
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Affiliation(s)
- Monika M Looney
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Munyaradzi Musvosvi
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - JoAnne Flynn
- Department of Microbiology and Molecular Genetics and the Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Benjamin M Kagina
- Vaccines for Africa (VACFA), School of Public Health and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Mike Frick
- Treatment Action Group, New York City, NY, USA
| | | | - Alex Schmidt
- Bill & Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - James Southern
- South African Health Products Regulatory Authority (SAPHRA), Gauteng, South Africa
| | | | | | | | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Willem Hanekom
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
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Kaufmann SHE. Vaccine development against tuberculosis before and after Covid-19. Front Immunol 2023; 14:1273938. [PMID: 38035095 PMCID: PMC10684952 DOI: 10.3389/fimmu.2023.1273938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease (Covid-19) has not only shaped awareness of the impact of infectious diseases on global health. It has also provided instructive lessons for better prevention strategies against new and current infectious diseases of major importance. Tuberculosis (TB) is a major current health threat caused by Mycobacterium tuberculosis (Mtb) which has claimed more lives than any other pathogen over the last few centuries. Hence, better intervention measures, notably novel vaccines, are urgently needed to accomplish the goal of the World Health Organization to end TB by 2030. This article describes how the research and development of TB vaccines can benefit from recent developments in the Covid-19 vaccine pipeline from research to clinical development and outlines how the field of TB research can pursue its own approaches. It begins with a brief discussion of major vaccine platforms in general terms followed by a short description of the most widely applied Covid-19 vaccines. Next, different vaccination regimes and particular hurdles for TB vaccine research and development are described. This specifically considers the complex immune mechanisms underlying protection and pathology in TB which involve innate as well as acquired immune mechanisms and strongly depend on fine tuning the response. A brief description of the TB vaccine candidates that have entered clinical trials follows. Finally, it discusses how experiences from Covid-19 vaccine research, development, and rollout can and have been applied to the TB vaccine pipeline, emphasizing similarities and dissimilarities.
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Affiliation(s)
- Stefan H. E. Kaufmann
- Max Planck Institute for Infection Biology, Berlin, Germany
- Systems Immunology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
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Immune cell interactions in tuberculosis. Cell 2022; 185:4682-4702. [PMID: 36493751 DOI: 10.1016/j.cell.2022.10.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Despite having been identified as the organism that causes tuberculosis in 1882, Mycobacterium tuberculosis has managed to still evade our understanding of the protective immune response against it, defying the development of an effective vaccine. Technology and novel experimental models have revealed much new knowledge, particularly with respect to the heterogeneity of the bacillus and the host response. This review focuses on certain immunological elements that have recently yielded exciting data and highlights the importance of taking a holistic approach to understanding the interaction of M. tuberculosis with the many host cells that contribute to the development of protective immunity.
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Abstract
Tuberculosis (TB) is an infectious disease bedeviled by complexity. This poses myriad challenges for a research ecosystem organized around specialist host- and/or pathogen-focused thrusts. Here, we highlight the key challenges and their implications for developing new tools to control TB.
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Affiliation(s)
- Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ryan Dinkele
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
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