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Zhou CY, Yang YL, Han ZY, Chen YX, Liu HL, Fan K, Li MC, Tu SH, Wen Q, Zhou XY, Ma L. Peripheral blood MR1 tetramer-positive mucosal-associated invariant T-cell function is modulated by mammalian target of rapamycin complex 1 in patients with active tuberculosis. Immunology 2024. [PMID: 39022997 DOI: 10.1111/imm.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Tuberculosis (TB) is still an urgent global public health problem. Notably, mucosal-associated invariant T (MAIT) cells play an important role in early anti-TB immune response. Targeted control of them may be an effective method to improve vaccine efficacy and TB treatment. However, the biology and signal regulation mechanisms of MAIT cells in TB patients are still poorly understood. Previous studies have been limited by the lack of reagents to specifically identify MAIT cells. In addition, the use of alternative markers may subsume non-MAIT cell into MAIT cell populations. In this study, the human MR1 tetramer which can specifically identify MAIT cells was used to further explore the effect and mechanism of MAIT cells in anti-TB immune response. Our results showed that the tetramer+ MAIT cells in peripheral blood of TB patients were mainly CD8+ or CD4-CD8- cells, and very few were CD4+ cells. After BCG infecting autologous antigen-presenting cells, MAIT cells in patients produced significantly higher levels of cytokines, lysis and proliferation compared with healthy controls. After suppression of mTORC1 by the mTORC1-specific inhibitor rapamycin, the immune response of MAIT cells in patients was significantly reduced. This study demonstrates that peripheral blood tetramer+ MAIT cells from TB patients have significant anti-TB immune effect, which is regulated by mTORC1. This could provide ideas and potential therapeutic targets for the development of novel anti-TB immunotherapy.
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Affiliation(s)
- Chao-Ying Zhou
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Ya-Long Yang
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Zhen-Yu Han
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Yao-Xin Chen
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Hong-Lin Liu
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Ke Fan
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Ming-Chong Li
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Si-Hang Tu
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Qian Wen
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Xin-Ying Zhou
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
| | - Li Ma
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, China
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Hudson D, Fernandes RA, Basham M, Ogg G, Koohy H. Can we predict T cell specificity with digital biology and machine learning? Nat Rev Immunol 2023; 23:511-521. [PMID: 36755161 PMCID: PMC9908307 DOI: 10.1038/s41577-023-00835-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 02/10/2023]
Abstract
Recent advances in machine learning and experimental biology have offered breakthrough solutions to problems such as protein structure prediction that were long thought to be intractable. However, despite the pivotal role of the T cell receptor (TCR) in orchestrating cellular immunity in health and disease, computational reconstruction of a reliable map from a TCR to its cognate antigens remains a holy grail of systems immunology. Current data sets are limited to a negligible fraction of the universe of possible TCR-ligand pairs, and performance of state-of-the-art predictive models wanes when applied beyond these known binders. In this Perspective article, we make the case for renewed and coordinated interdisciplinary effort to tackle the problem of predicting TCR-antigen specificity. We set out the general requirements of predictive models of antigen binding, highlight critical challenges and discuss how recent advances in digital biology such as single-cell technology and machine learning may provide possible solutions. Finally, we describe how predicting TCR specificity might contribute to our understanding of the broader puzzle of antigen immunogenicity.
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Affiliation(s)
- Dan Hudson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Didcot, UK
| | - Ricardo A Fernandes
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | | | - Graham Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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Kim J, Lee J, Nam K, Lee S. Investigation of genetic variants and causal biomarkers associated with brain aging. Sci Rep 2023; 13:1526. [PMID: 36707530 PMCID: PMC9883521 DOI: 10.1038/s41598-023-27903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
Delta age is a biomarker of brain aging that captures differences between the chronological age and the predicted biological brain age. Using multimodal data of brain MRI, genomics, and blood-based biomarkers and metabolomics in UK Biobank, this study investigates an explainable and causal basis of high delta age. A visual saliency map of brain regions showed that lower volumes in the fornix and the lower part of the thalamus are key predictors of high delta age. Genome-wide association analysis of the delta age using the SNP array data identified associated variants in gene regions such as KLF3-AS1 and STX1. GWAS was also performed on the volumes in the fornix and the lower part of the thalamus, showing a high genetic correlation with delta age, indicating that they share a genetic basis. Mendelian randomization (MR) for all metabolomic biomarkers and blood-related phenotypes showed that immune-related phenotypes have a causal impact on increasing delta age. Our analysis revealed regions in the brain that are susceptible to the aging process and provided evidence of the causal and genetic connections between immune responses and brain aging.
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Affiliation(s)
- Jangho Kim
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Junhyeong Lee
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Kisung Nam
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea.
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Gargano F, Guerrera G, Piras E, Serafini B, Di Paola M, Rizzetto L, Buscarinu MC, Annibali V, Vuotto C, De Bardi M, D’Orso S, Ruggieri S, Gasperini C, Pavarini L, Ristori G, Picozza M, Rosicarelli B, Ballerini C, Mechelli R, Vitali F, Cavalieri D, Salvetti M, Angelini DF, Borsellino G, De Filippo C, Battistini L. Proinflammatory mucosal-associated invariant CD8+ T cells react to gut flora yeasts and infiltrate multiple sclerosis brain. Front Immunol 2022; 13:890298. [PMID: 35979352 PMCID: PMC9376942 DOI: 10.3389/fimmu.2022.890298] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
The composition of the intestinal microbiota plays a critical role in shaping the immune system. Modern lifestyle, the inappropriate use of antibiotics, and exposure to pollution have significantly affected the composition of commensal microorganisms. The intestinal microbiota has been shown to sustain inappropriate autoimmune responses at distant sites in animal models of disease, and may also have a role in immune-mediated central nervous system (CNS) diseases such as multiple sclerosis (MS). We studied the composition of the gut mycobiota in fecal samples from 27 persons with MS (pwMS) and in 18 healthy donors (HD), including 5 pairs of homozygous twins discordant for MS. We found a tendency towards higher fungal abundance and richness in the MS group, and we observed that MS twins showed a higher rate of food-associated strains, such as Saccharomyces cerevisiae. We then found that in pwMS, a distinct population of cells with antibacterial and antifungal activity is expanded during the remitting phase and markedly decreases during clinically and/or radiologically active disease. These cells, named MAIT (mucosal-associated invariant T cells) lymphocytes, were significantly more activated in pwMS compared to HD in response to S. cerevisiae and Candida albicans strains isolated from fecal samples. This activation was also mediated by fungal-induced IL-23 secretion by innate immune cells. Finally, immunofluorescent stainings of MS post-mortem brain tissues from persons with the secondary progressive form of the disease showed that MAIT cells cross the blood–brain barrier (BBB) and produce pro-inflammatory cytokines in the brain. These results were in agreement with the hypothesis that dysbiosis of the gut microbiota might determine the inappropriate response of a subset of pathogenic mucosal T cells and favor the development of systemic inflammatory and autoimmune diseases.
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Affiliation(s)
- Francesca Gargano
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Gisella Guerrera
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Eleonora Piras
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Barbara Serafini
- Istituto Superiore di Sanità, Department of Neuroscience, Rome, Italy
| | - Monica Di Paola
- University of Florence, Department of Biology, Florence, Italy
| | - Lisa Rizzetto
- Research and Innovation Centre – Fondazione Edmund Mach, S. Michele all’Adige (TN), Italy
| | - Maria Chiara Buscarinu
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Viviana Annibali
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Claudia Vuotto
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Marco De Bardi
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Silvia D’Orso
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Serena Ruggieri
- Department of Neuroscience “Lancisi”, S. Camillo Hospital, Rome, Italy
| | - Claudio Gasperini
- Department of Neuroscience “Lancisi”, S. Camillo Hospital, Rome, Italy
| | - Lorenzo Pavarini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- University of Florence, Department of Biology, Florence, Italy
| | - Giovanni Ristori
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Mario Picozza
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | | | - Clara Ballerini
- University of Florence, Clinical and Experimental Medicine, Florence, Italy
| | - Rosella Mechelli
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Francesco Vitali
- National Research Council, Institute of Agricultural Biology and Biotechnology, Pisa, Italy
| | | | - Marco Salvetti
- Neurology and Centre for Experimental Neurological therapies (CENTERS), S. Andrea Hospital, Sapienza University, Rome, Italy
| | - Daniela F. Angelini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
| | - Giovanna Borsellino
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- *Correspondence: Giovanna Borsellino, ; Luca Battistini,
| | - Carlotta De Filippo
- National Research Council, Institute of Agricultural Biology and Biotechnology, Pisa, Italy
| | - Luca Battistini
- Neuroimmunology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia Foundation, Rome, Italy
- *Correspondence: Giovanna Borsellino, ; Luca Battistini,
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Oh SF, Jung DJ, Choi E. Gut Microbiota-Derived Unconventional T Cell Ligands: Contribution to Host Immune Modulation. Immunohorizons 2022; 6:476-487. [PMID: 35868838 PMCID: PMC9924074 DOI: 10.4049/immunohorizons.2200006] [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: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 01/26/2023] Open
Abstract
Besides the prototypic innate and adaptive pathways, immune responses by innate-like lymphocytes have gained significant attention due to their unique roles. Among innate-like lymphocytes, unconventional T cells such as NKT cells and mucosal-associated invariant T (MAIT) cells recognize small nonpeptide molecules of specific chemical classes. Endogenous or microbial ligands are loaded to MHC class I-like molecule CD1d or MR1, and inducing immediate effector T cell and ligand structure is one of the key determinants of NKT/MAIT cell functions. Unconventional T cells are in close, constant contact with symbiotic microbes at the mucosal layer, and CD1d/MR1 can accommodate diverse metabolites produced by gut microbiota. There is a strong interest to identify novel immunoactive molecules of endobiotic (symbiont-produced) origin as new NKT/MAIT cell ligands, as well as new cognate Ags for previously uncharacterized unconventional T cell subsets. Further studies will open an possibility to explore basic biology as well as therapeutic potential.
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Affiliation(s)
- Sungwhan F. Oh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Da-Jung Jung
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Eungyo Choi
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Boston, MA
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James CA, Yu KKQ, Mayer-Blackwell K, Fiore-Gartland A, Smith MT, Layton ED, Johnson JL, Hanekom WA, Scriba TJ, Seshadri C. Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans. Front Immunol 2022; 13:834757. [PMID: 35432299 PMCID: PMC9005636 DOI: 10.3389/fimmu.2022.834757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG) has been used for 100 years and prevents disseminated tuberculosis and death in young children. However, it shows only partial efficacy against pulmonary tuberculosis (TB) in adults, so new vaccines are urgently needed. The protective efficacy of BCG depends on T cells, which are typically activated by pathogen-derived protein antigens that bind to highly polymorphic major histocompatibility complex (MHC) molecules. Some T cells recognize non-protein antigens via antigen presenting systems that are independent of genetic background, leading to their designation as donor-unrestricted T (DURT) cells. Whether live whole cell vaccines, like BCG, can induce durable expansions of DURT cells in humans is not known. We used combinatorial tetramer staining, multi-parameter flow cytometry, and immunosequencing to comprehensively characterize the effect of BCG on activation and expansion of DURT cell subsets. We examined peripheral blood mononuclear cells (PBMC) derived from a Phase I study of South African adults in which samples were archived at baseline, 3 weeks, and 52 weeks post-BCG revaccination. We did not observe a change in the frequency of total mucosal-associated invariant T (MAIT) cells, invariant natural killer T (iNKT) cells, germline encoded mycolyl-reactive (GEM) T cells, or γδ T cells at 52 weeks post-BCG. However, immunosequencing revealed a set of TCR-δ clonotypes that were expanded at 52 weeks post-BCG revaccination. These expanded clones expressed the Vδ2 gene segment and could be further defined on the basis of biochemical similarity into several 'meta-clonotypes' that likely recognize similar epitopes. Our data reveal that BCG vaccination leads to durable expansion of DURT cell clonotypes despite a limited effect on total circulating frequencies in the blood and have implications for defining the immunogenicity of candidate whole cell TB vaccines.
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Affiliation(s)
- Charlotte A. James
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Krystle K. Q. Yu
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Koshlan Mayer-Blackwell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Malisa T. Smith
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Erik D. Layton
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - John L. Johnson
- Tuberculosis Research Unit, Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA, United States
- Tuberculosis Research and Training Center, University of Washington, Seattle, WA, United States
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