1
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Rook GAW. Evolution and the critical role of the microbiota in the reduced mental and physical health associated with low socioeconomic status (SES). Neurosci Biobehav Rev 2024; 161:105653. [PMID: 38582194 DOI: 10.1016/j.neubiorev.2024.105653] [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: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The evolution of the gut-microbiota-brain axis in animals reveals that microbial inputs influence metabolism, the regulation of inflammation and the development of organs, including the brain. Inflammatory, neurodegenerative and psychiatric disorders are more prevalent in people of low socioeconomic status (SES). Many aspects of low SES reduce exposure to the microbial inputs on which we are in a state of evolved dependence, whereas the lifestyle of wealthy citizens maintains these exposures. This partially explains the health deficit of low SES, so focussing on our evolutionary history and on environmental and lifestyle factors that distort microbial exposures might help to mitigate that deficit. But the human microbiota is complex and we have poor understanding of its functions at the microbial and mechanistic levels, and in the brain. Perhaps its composition is more flexible than the microbiota of animals that have restricted habitats and less diverse diets? These uncertainties are discussed in relation to the encouraging but frustrating results of attempts to treat psychiatric disorders by modulating the microbiota.
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Affiliation(s)
- Graham A W Rook
- Centre for Clinical Microbiology, Department of infection, UCL (University College London), London, UK.
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2
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Bharadwaj NS, Zumwalde NA, Kapur A, Patankar M, Gumperz JE. Human CD4 + memory phenotype T cells use mitochondrial metabolism to generate sensitive IFN-γ responses. iScience 2024; 27:109775. [PMID: 38726371 PMCID: PMC11079467 DOI: 10.1016/j.isci.2024.109775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The transition of naive T lymphocytes into antigenically activated effector cells is associated with a metabolic shift from oxidative phosphorylation to aerobic glycolysis. This shift facilitates production of the key anti-tumor cytokine interferon (IFN)-γ; however, an associated loss of mitochondrial efficiency in effector T cells ultimately limits anti-tumor immunity. Memory phenotype (MP) T cells are a newly recognized subset that arises through homeostatic activation signals following hematopoietic transplantation. We show here that human CD4+ MP cell differentiation is associated with increased glycolytic and oxidative metabolic activity, but MP cells retain less compromised mitochondria compared to effector CD4+ T cells, and their IFN-γ response is less dependent on glucose and more reliant on glutamine. MP cells also produced IFN-γ more efficiently in response to weak T cell receptor (TCR) agonism than effectors and mediated stronger responses to transformed B cells. MP cells may thus be particularly well suited to carry out sustained immunosurveillance against neoplastic cells.
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Affiliation(s)
- Nikhila S. Bharadwaj
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Nicholas A. Zumwalde
- Department of Genetics, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Arvinder Kapur
- QIAGEN Sciences Inc., 19300 Germantown Road, Germantown, MD 20874, USA
| | - Manish Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
| | - Jenny E. Gumperz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health; Madison, WI 53706, USA
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3
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De Boer RJ, Kesmir C, Perelson AS, Borghans JAM. Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution? Front Immunol 2024; 15:1266349. [PMID: 38605941 PMCID: PMC11008227 DOI: 10.3389/fimmu.2024.1266349] [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: 07/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
We have previously argued that the antigen receptors of T and B lymphocytes evolved to be sufficiently specific to avoid massive deletion of clonotypes by negative selection. Their optimal 'specificity' level, i.e., probability of binding any particular epitope, was shown to be inversely related to the number of self-antigens that the cells have to be tolerant to. Experiments have demonstrated that T lymphocytes also become more specific during negative selection in the thymus, because cells expressing the most crossreactive receptors have the highest likelihood of binding a self-antigen, and hence to be tolerized (i.e., deleted, anergized, or diverted into a regulatory T cell phenotype). Thus, there are two -not mutually exclusive- explanations for the exquisite specificity of T cells, one involving evolution and the other thymic selection. To better understand the impact of both, we extend a previously developed mathematical model by allowing for T cells with very different binding probabilities in the pre-selection repertoire. We confirm that negative selection tends to tolerize the most crossreactive clonotypes. As a result, the average level of specificity in the functional post-selection repertoire depends on the number of self-antigens, even if there is no evolutionary optimization of binding probabilities. However, the evolutionary optimal range of binding probabilities in the pre-selection repertoire also depends on the number of self-antigens. Species with more self antigens need more specific pre-selection repertoires to avoid excessive loss of T cells during thymic selection, and hence mount protective immune responses. We conclude that both evolution and negative selection are responsible for the high level of specificity of lymphocytes.
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Affiliation(s)
- Rob J. De Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Alan S. Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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4
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Li X, Zhang Y, Guo S, Wu Z, Wang H, Huang Y, Wang Y, Qiu M, Lang J, Xiao Y, Zhu Y, Jin G, Hu L, Kong X. Global analysis of T-cell groups reveals immunological features and common antigen targets of digestive tract tumors. J Cancer Res Clin Oncol 2024; 150:129. [PMID: 38488909 PMCID: PMC10943170 DOI: 10.1007/s00432-024-05645-1] [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: 12/26/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND T cells are key players in the tumor immune microenvironment (TIME), as they can recognize and eliminate cancer cells that express neoantigens derived from somatic mutations. However, the diversity and specificity of T-cell receptors (TCRs) that recognize neoantigens are largely unknown, due to the high variability of TCR sequences among individuals. METHODS To address this challenge, we applied GLIPH2, a novel algorithm that groups TCRs based on their predicted antigen specificity and HLA restriction, to cluster the TCR repertoire of 1,702 patients with digestive tract cancer. The patients were divided into five groups based on whether they carried tumor-infiltrating or clonal-expanded TCRs and calculated their TCR diversity. The prognosis, tumor subtype, gene mutation, gene expression, and immune microenvironment of these groups were compared. Viral specificity inference and immunotherapy relevance analysis performed for the TCR groups. RESULTS This approach reduced the complexity of TCR sequences to 249 clonally expanded and 150 tumor-infiltrating TCR groups, which revealed distinct patterns of TRBV usage, HLA association, and TCR diversity. In gastric adenocarcinoma (STAD), patients with tumor-infiltrating TCRs (Patients-TI) had significantly worse prognosis than other patients (Patients-nonTI). Patients-TI had richer CD8+ T cells in the immune microenvironment, and their gene expression features were positively correlated with immunotherapy response. We also found that tumor-infiltrating TCR groups were associated with four distinct tumor subtypes, 26 common gene mutations, and 39 gene expression signatures. We discovered that tumor-infiltrating TCRs had cross-reactivity with viral antigens, indicating a possible link between viral infections and tumor immunity. CONCLUSION By applying GLIPH2 to TCR sequences from digestive tract tumors, we uncovered novel insights into the tumor immune landscape and identified potential candidates for shared TCRs and neoantigens.
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Affiliation(s)
- Xiaoxue Li
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuchao Zhang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Shanghai, China
| | - Zhenchuan Wu
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China
| | - Hailong Wang
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yi Huang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yue Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mengni Qiu
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jingyu Lang
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Yichuan Xiao
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Yufei Zhu
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Shanghai, China.
| | - Landian Hu
- Anda Biology Medicine Development (Shenzhen) Co., Ltd., Shenzhen, China.
| | - Xiangyin Kong
- Shanghai Institute of Nutrition and Health, CAS Key Laboratory of Tissue Microenvironment and Tumor, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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5
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Pan YG, Bartolo L, Xu R, Patel B, Zarnitsyna V, Su L. Differentiation marker-negative CD4 + T cells persist after yellow fever virus vaccination and contribute to durable memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584523. [PMID: 38559113 PMCID: PMC10979963 DOI: 10.1101/2024.03.11.584523] [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: 04/04/2024]
Abstract
Factors that contribute to durable immunological memory remain incompletely understood. In our longitudinal analyses of CD4+ T cell responses to the yellow fever virus (YFV) vaccine by peptide-MHC tetramers, we unexpectedly found naïve phenotype virus-specific CD4+ T cells that persisted months to years after immunization. These Marker negative T cells (TMN) lacked CD95, CXCR3, CD11a, and CD49d surface protein expression, distinguishing them from previously discovered stem-cell memory T cells. Functionally, they resembled genuine naïve T cells upon in vitro stimulation. Single-cell TCR sequencing detected expanded clonotypes within the TMN subset and identified a shared repertoire with memory and effector T cells. T cells expressing TMN-associated TCRs were rare before vaccination, suggesting their expansion following vaccination. Longitudinal tracking of YFV-specific responses over the subsequent years revealed superior stability of the TMN subset and their association with the longevity of the overall population. The identification of these long-lived, antigen-experienced T cells may inform the design of durable T cell-based vaccines and engineered T cell therapies.
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Affiliation(s)
- Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruozhang Xu
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Bijal Patel
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Laura Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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6
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Yin R, Melton S, Huseby ES, Kardar M, Chakraborty AK. How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease. Proc Natl Acad Sci U S A 2024; 121:e2318599121. [PMID: 38446856 PMCID: PMC10945823 DOI: 10.1073/pnas.2318599121] [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: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
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Affiliation(s)
- Rose Yin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Melton
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eric S. Huseby
- Basic Pathology, Department of Pathology, University of Massachusetts Medical School, Worcester, MA01655
| | - Mehran Kardar
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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7
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Tran KA, Pernet E, Sadeghi M, Downey J, Chronopoulos J, Lapshina E, Tsai O, Kaufmann E, Ding J, Divangahi M. BCG immunization induces CX3CR1 hi effector memory T cells to provide cross-protection via IFN-γ-mediated trained immunity. Nat Immunol 2024; 25:418-431. [PMID: 38225437 DOI: 10.1038/s41590-023-01739-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024]
Abstract
After a century of using the Bacillus Calmette-Guérin (BCG) vaccine, our understanding of its ability to provide protection against homologous (Mycobacterium tuberculosis) or heterologous (for example, influenza virus) infections remains limited. Here we show that systemic (intravenous) BCG vaccination provides significant protection against subsequent influenza A virus infection in mice. We further demonstrate that the BCG-mediated cross-protection against influenza A virus is largely due to the enrichment of conventional CD4+ effector CX3CR1hi memory αβ T cells in the circulation and lung parenchyma. Importantly, pulmonary CX3CR1hi T cells limit early viral infection in an antigen-independent manner via potent interferon-γ production, which subsequently enhances long-term antimicrobial activity of alveolar macrophages. These results offer insight into the unknown mechanism by which BCG has persistently displayed broad protection against non-tuberculosis infections via cross-talk between adaptive and innate memory responses.
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Affiliation(s)
- Kim A Tran
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Erwan Pernet
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
- Department of Medical Biology, Université du Québec à Trois-Rivières, Quebec, Quebec, Canada
| | - Mina Sadeghi
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Jeffrey Downey
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Julia Chronopoulos
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Elizabeth Lapshina
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Oscar Tsai
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Eva Kaufmann
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Jun Ding
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada
| | - Maziar Divangahi
- Department of Medicine, Department of Pathology, Department of Microbiology & Immunology, Research Institute of the McGill University Health Centre, McGill International TB Centre, Meakins-Christie Laboratories, McGill University, Montreal, Quebec, Canada.
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8
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Akama-Garren EH, Yin X, Prestwood TR, Ma M, Utz PJ, Carroll MC. T cell help shapes B cell tolerance. Sci Immunol 2024; 9:eadj7029. [PMID: 38363829 DOI: 10.1126/sciimmunol.adj7029] [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: 07/11/2023] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Abstract
T cell help is a crucial component of the normal humoral immune response, yet whether it promotes or restrains autoreactive B cell responses remains unclear. Here, we observe that autoreactive germinal centers require T cell help for their formation and persistence. Using retrogenic chimeras transduced with candidate TCRs, we demonstrate that a follicular T cell repertoire restricted to a single autoreactive TCR, but not a foreign antigen-specific TCR, is sufficient to initiate autoreactive germinal centers. Follicular T cell specificity influences the breadth of epitope spreading by regulating wild-type B cell entry into autoreactive germinal centers. These results demonstrate that TCR-dependent T cell help can promote loss of B cell tolerance and that epitope spreading is determined by TCR specificity.
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Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Xihui Yin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tyler R Prestwood
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minghe Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Utz
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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9
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Beurel E. Stress in the microbiome-immune crosstalk. Gut Microbes 2024; 16:2327409. [PMID: 38488630 PMCID: PMC10950285 DOI: 10.1080/19490976.2024.2327409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
The gut microbiota exerts a mutualistic interaction with the host in a fragile ecosystem and the host intestinal, neural, and immune cells. Perturbations of the gastrointestinal track composition after stress have profound consequences on the central nervous system and the immune system. Reciprocally, brain signals after stress affect the gut microbiota highlighting the bidirectional communication between the brain and the gut. Here, we focus on the potential role of inflammation in mediating stress-induced gut-brain changes and discuss the impact of several immune cells and inflammatory molecules of the gut-brain dialogue after stress. Understanding the impact of microbial changes on the immune system after stress might provide new avenues for therapy.
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Affiliation(s)
- Eléonore Beurel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
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10
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Bela-Ong DB, Thompson KD, Kim HJ, Park SB, Jung TS. CD4 + T lymphocyte responses to viruses and virus-relevant stimuli in teleost fish. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109007. [PMID: 37625734 DOI: 10.1016/j.fsi.2023.109007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Fish diseases caused by viruses are a major threat to aquaculture. Development of disease protection strategies for sustainable fish aquaculture requires a better understanding of the immune mechanisms involved in antiviral defence. The innate and adaptive arms of the vertebrate immune system collaborate to mount an effective defence against viral pathogens. The T lymphocyte components of the adaptive immune system, comprising two major classes (helper T, Th or CD4+ and cytotoxic T lymphocytes, CTLs or CD8+ T cells), are responsible for cell-mediated immune responses. In particular, CD4+ T cells and their different subsets orchestrate the actions of various other immune cells during immune responses, making CD4+ T cells central drivers of responses to pathogens and vaccines. CD4+ T cells are also present in teleost fish. Here we review the literature that reported the use of antibodies against CD4 in a few teleost fish species and transcription profiling of Th cell-relevant genes in the context of viral infections and virus-relevant immunomodulation. Studies reveal massive CD4+ T cell proliferation and expression of key cytokines, transcription factors, and effector molecules that evoke mammalian Th cell responses. We also discuss gaps in the current understanding and evaluation of teleost CD4+ T cell responses and how development and application of novel tools and approaches to interrogate such responses could bridge these gaps. A greater understanding of fish Th cell responses will further illuminate the evolution of vertebrate adaptive immunity, inform strategies to address viral infections in aquaculture, and could further foster fish as model organisms.
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Affiliation(s)
- Dennis Berbulla Bela-Ong
- Laboratory of Aquatic Animal Diseases, Research Institute of Natural Science, College of Veterinary Medicine, Gyeongsang National University, 501-201, 501 Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
| | - Kim D Thompson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, Scotland, United Kingdom
| | - Hyoung Jun Kim
- WOAH Reference Laboratory for VHS, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Seong Bin Park
- Coastal Research and Extension Center, Mississippi State University, Pascagula, MS, 39567, USA
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Research Institute of Natural Science, College of Veterinary Medicine, Gyeongsang National University, 501-201, 501 Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
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11
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Malyshkina A, Brüggemann A, Paschen A, Dittmer U. Cytotoxic CD4 + T cells in chronic viral infections and cancer. Front Immunol 2023; 14:1271236. [PMID: 37965314 PMCID: PMC10642198 DOI: 10.3389/fimmu.2023.1271236] [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: 08/02/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
CD4+ T cells play an important role in immune responses against pathogens and cancer cells. Although their main task is to provide help to other effector immune cells, a growing number of infections and cancer entities have been described in which CD4+ T cells exhibit direct effector functions against infected or transformed cells. The most important cell type in this context are cytotoxic CD4+ T cells (CD4+ CTL). In infectious diseases anti-viral CD4+ CTL are mainly found in chronic viral infections. Here, they often compensate for incomplete or exhausted CD8+ CTL responses. The induction of CD4+ CTL is counter-regulated by Tregs, most likely because they can be dangerous inducers of immunopathology. In viral infections, CD4+ CTL often kill via the Fas/FasL pathway, but they can also facilitate the exocytosis pathway of killing. Thus, they are very important effectors to keep persistent virus in check and guarantee host survival. In contrast to viral infections CD4+ CTL attracted attention as direct anti-tumor effectors in solid cancers only recently. Anti-tumor CD4+ CTL are defined by the expression of cytolytic markers and have been detected within the lymphocyte infiltrates of different human cancers. They kill tumor cells in an antigen-specific MHC class II-restricted manner not only by cytolysis but also by release of IFNγ. Thus, CD4+ CTL are interesting tools for cure approaches in chronic viral infections and cancer, but their potential to induce immunopathology has to be carefully taken into consideration.
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Affiliation(s)
- Anna Malyshkina
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alicia Brüggemann
- Department of Dermatology, Venereology, and Allergology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Annette Paschen
- Department of Dermatology, Venereology, and Allergology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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12
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Ponziani FR, Coppola G, Rio P, Caldarelli M, Borriello R, Gambassi G, Gasbarrini A, Cianci R. Factors Influencing Microbiota in Modulating Vaccine Immune Response: A Long Way to Go. Vaccines (Basel) 2023; 11:1609. [PMID: 37897011 PMCID: PMC10611107 DOI: 10.3390/vaccines11101609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Vaccine immunogenicity still represents an unmet need in specific populations, such as people from developing countries and "edge populations". Both intrinsic and extrinsic factors, such as the environment, age, and dietary habits, influence cellular and humoral immune responses. The human microbiota represents a potential key to understanding how these factors impact the immune response to vaccination, with its modulation being a potential step to address vaccine immunogenicity. The aim of this narrative review is to explore the intricate interactions between the microbiota and the immune system in response to vaccines, highlighting the state of the art in gut microbiota modulation as a novel therapeutic approach to enhancing vaccine immunogenicity and laying the foundation for future, more solid data for its translation to the clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | - Rossella Cianci
- Department of Translational Medicine and Surgery, Catholic University, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy (G.C.); (P.R.); (M.C.); (R.B.); (G.G.); (A.G.)
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13
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Rook GAW. The old friends hypothesis: evolution, immunoregulation and essential microbial inputs. FRONTIERS IN ALLERGY 2023; 4:1220481. [PMID: 37772259 PMCID: PMC10524266 DOI: 10.3389/falgy.2023.1220481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023] Open
Abstract
In wealthy urbanised societies there have been striking increases in chronic inflammatory disorders such as allergies, autoimmunity and inflammatory bowel diseases. There has also been an increase in the prevalence of individuals with systemically raised levels of inflammatory biomarkers correlating with increased risk of metabolic, cardiovascular and psychiatric problems. These changing disease patterns indicate a broad failure of the mechanisms that should stop the immune system from attacking harmless allergens, components of self or gut contents, and that should terminate inappropriate inflammation. The Old Friends Hypothesis postulates that this broad failure of immunoregulation is due to inadequate exposures to the microorganisms that drive development of the immune system, and drive the expansion of components such as regulatory T cells (Treg) that mediate immunoregulatory mechanisms. An evolutionary approach helps us to identify the organisms on which we are in a state of evolved dependence for this function (Old Friends). The bottom line is that most of the organisms that drive the regulatory arm of the immune system come from our mothers and family and from the natural environment (including animals) and many of these organisms are symbiotic components of a healthy microbiota. Lifestyle changes that are interrupting our exposure to these organisms can now be identified, and many are closely associated with low socioeconomic status (SES) in wealthy countries. These insights will facilitate the development of education, diets and urban planning that can correct the immunoregulatory deficit, while simultaneously reducing other contributory factors such as epithelial damage.
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Affiliation(s)
- Graham A. W. Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, United Kingdom
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14
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Cho E, Han S, Eom HS, Lee SJ, Han C, Singh R, Kim SH, Park BM, Kim BG, Kim YH, Kwon BS, Nam KT, Choi BK. Cross-Activation of Regulatory T Cells by Self Antigens Limits Self-Reactive and Activated CD8 + T Cell Responses. Int J Mol Sci 2023; 24:13672. [PMID: 37761976 PMCID: PMC10530955 DOI: 10.3390/ijms241813672] [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: 08/03/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The interaction between regulatory T (Treg) cells and self-reactive T cells is a crucial mechanism for maintaining immune tolerance. In this study, we investigated the cross-activation of Treg cells by self-antigens and its impact on self-reactive CD8+ T cell responses, with a focus on the P53 signaling pathway. We discovered that major histocompatibility complex (MHC) I-restricted self-peptides not only activated CD8+ T cells but also induced the delayed proliferation of Treg cells. Following HLA-A*0201-restricted Melan-A-specific (pMelan) CD8+ T cells, we observed the direct expansion of Treg cells and concurrent suppression of pMelan+CD8+ T cell proliferation upon stimulation with Melan-A peptide. Transcriptome analysis revealed no significant alterations in specific signaling pathways in pMelan+CD8+ T cells that were co-cultured with activated Treg cells. However, there was a noticeable upregulation of genes involved in P53 accumulation, a critical regulator of cell survival and apoptosis. Consistent with such observation, the blockade of P53 induced a continuous proliferation of pMelan+CD8+ T cells. The concurrent stimulation of Treg cells through self-reactive TCRs by self-antigens provides insights into the immune system's ability to control activated self-reactive CD8+ T cells as part of peripheral tolerance, highlighting the intricate interplay between Treg cells and CD8+ T cells and implicating therapeutic interventions in autoimmune diseases and cancer immunotherapy.
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Affiliation(s)
- Eunjung Cho
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Seongeun Han
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Hyeon Seok Eom
- Hematological Malignancy Center of the Hospital, National Cancer Center, Goyang 10408, Republic of Korea
| | - Sang-Jin Lee
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Chungyong Han
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
| | - Rohit Singh
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
| | - Seon-Hee Kim
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Department of Biomedical Laboratory Science, Catholic Kwandong University, Gangneung 25601, Republic of Korea
| | - Bo-Mi Park
- Biomedicine Production Branch, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Young H. Kim
- Eutilex, Co., Ltd., Geumcheon-gu, Seoul 08594, Republic of Korea
| | - Byoung S. Kwon
- Eutilex, Co., Ltd., Geumcheon-gu, Seoul 08594, Republic of Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Beom K. Choi
- Immuno-Oncology Branch, Division of Rare and Refractory Cancer, National Cancer Center, Goyang 10408, Republic of Korea (S.-J.L.)
- Innobationbio, Co., Ltd., Mapo-gu, Seoul 03929, Republic of Korea
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15
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Pircher H, Pinschewer DD, Boehm T. MHC I tetramer staining tends to overestimate the number of functionally relevant self-reactive CD8 T cells in the preimmune repertoire. Eur J Immunol 2023; 53:e2350402. [PMID: 37179469 DOI: 10.1002/eji.202350402] [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: 01/23/2023] [Revised: 04/19/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Previous studies that used peptide-MHC (pMHC) tetramers (tet) to identify self-specific T cells have questioned the effectiveness of thymic-negative selection. Here, we used pMHCI tet to enumerate CD8 T cells specific for the immunodominant gp33 epitope of lymphocytic choriomeningitis virus glycoprotein (GP) in mice transgenically engineered to express high levels of GP as a self-antigen in the thymus. In GP-transgenic mice (GP+ ), monoclonal P14 TCR+ CD8 T cells that express a GP-specific TCR could not be detected by gp33/Db -tet staining, indicative of their complete intrathymic deletion. By contrast, in the same GP+ mice, substantial numbers of polyclonal CD8 T cells identifiable by gp33/Db -tet were present. The gp33-tet staining profiles of polyclonal T cells from GP+ and GP-negative (GP- ) mice were overlapping, but mean fluorescence intensities were ∼15% lower in cells from GP+ mice. Remarkably, the gp33-tet+ T cells in GP+ mice failed to clonally expand after lymphocytic choriomeningitis virus infection, whereas those of GP- mice did so. In Nur77GFP -reporter mice, dose-dependent responses to gp33 peptide-induced TCR stimulation revealed that gp33-tet+ T cells with high ligand sensitivity are lacking in GP+ mice. Hence, pMHCI tet staining identifies self-specific CD8 T cells but tends to overestimate the number of truly self-reactive cells.
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Affiliation(s)
- Hanspeter Pircher
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Daniel D Pinschewer
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
- Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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16
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Sengupta S, Zhang J, Reed MC, Yu J, Kim A, Boronina TN, Board NL, Wrabl JO, Shenderov K, Welsh RA, Yang W, Timmons AE, Hoh R, Cole RN, Deeks SG, Siliciano JD, Siliciano RF, Sadegh-Nasseri S. A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design. J Exp Med 2023; 220:e20221654. [PMID: 37058141 PMCID: PMC10114365 DOI: 10.1084/jem.20221654] [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: 09/26/2022] [Revised: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josephine Zhang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madison C. Reed
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanna Yu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aeryon Kim
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Tatiana N. Boronina
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan L. Board
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James O. Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Shenderov
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robin A. Welsh
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E. Timmons
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Robert N. Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Janet D. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert F. Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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17
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Afroz S, Bartolo L, Su LF. Pre-existing T Cell Memory to Novel Pathogens. Immunohorizons 2023; 7:543-553. [PMID: 37436166 PMCID: PMC10587503 DOI: 10.4049/immunohorizons.2200003] [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: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
Immunological experiences lead to the development of specific T and B cell memory, which readies the host for a later pathogen rechallenge. Currently, immunological memory is best understood as a linear process whereby memory responses are generated by and directed against the same pathogen. However, numerous studies have identified memory cells that target pathogens in unexposed individuals. How "pre-existing memory" forms and impacts the outcome of infection remains unclear. In this review, we discuss differences in the composition of baseline T cell repertoire in mice and humans, factors that influence pre-existing immune states, and recent literature on their functional significance. We summarize current knowledge on the roles of pre-existing T cells in homeostasis and perturbation and their impacts on health and disease.
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Affiliation(s)
- Sumbul Afroz
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laurent Bartolo
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
| | - Laura F. Su
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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18
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Jiang N, Malone M, Chizari S. Antigen-specific and cross-reactive T cells in protection and disease. Immunol Rev 2023; 316:120-135. [PMID: 37209375 PMCID: PMC10524458 DOI: 10.1111/imr.13217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Human T cells have a diverse T-cell receptor (TCR) repertoire that endows them with the ability to identify and defend against a broad spectrum of antigens. The universe of possible antigens that T cells may encounter, however, is even larger. To effectively surveil such a vast universe, the T-cell repertoire must adopt a high degree of cross-reactivity. Likewise, antigen-specific and cross-reactive T-cell responses play pivotal roles in both protective and pathological immune responses in numerous diseases. In this review, we explore the implications of these antigen-driven T-cell responses, with a particular focus on CD8+ T cells, using infection, neurodegeneration, and cancer as examples. We also summarize recent technological advances that facilitate high-throughput profiling of antigen-specific and cross-reactive T-cell responses experimentally, as well as computational biology approaches that predict these interactions.
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Affiliation(s)
- Ning Jiang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, 19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Shahab Chizari
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
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19
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Gouttefangeas C, Klein R, Maia A. The good and the bad of T cell cross-reactivity: challenges and opportunities for novel therapeutics in autoimmunity and cancer. Front Immunol 2023; 14:1212546. [PMID: 37409132 PMCID: PMC10319254 DOI: 10.3389/fimmu.2023.1212546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/24/2023] [Indexed: 07/07/2023] Open
Abstract
T cells are main actors of the immune system with an essential role in protection against pathogens and cancer. The molecular key event involved in this absolutely central task is the interaction of membrane-bound specific T cell receptors with peptide-MHC complexes which initiates T cell priming, activation and recall, and thus controls a range of downstream functions. While textbooks teach us that the repertoire of mature T cells is highly diverse, it is clear that this diversity cannot possibly cover all potential foreign peptides that might be encountered during life. TCR cross-reactivity, i.e. the ability of a single TCR to recognise different peptides, offers the best solution to this biological challenge. Reports have shown that indeed, TCR cross-reactivity is surprisingly high. Hence, the T cell dilemma is the following: be as specific as possible to target foreign danger and spare self, while being able to react to a large spectrum of body-threatening situations. This has major consequences for both autoimmune diseases and cancer, and significant implications for the development of T cell-based therapies. In this review, we will present essential experimental evidence of T cell cross-reactivity, implications for two opposite immune conditions, i.e. autoimmunity vs cancer, and how this can be differently exploited for immunotherapy approaches. Finally, we will discuss the tools available for predicting cross-reactivity and how improvements in this field might boost translational approaches.
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Affiliation(s)
- Cécile Gouttefangeas
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ana Maia
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
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20
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Mayassi T, Xavier RJ. Untangling the CD4 T cell response to the microbiota. Proc Natl Acad Sci U S A 2023; 120:e2303351120. [PMID: 37036966 PMCID: PMC10120056 DOI: 10.1073/pnas.2303351120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
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21
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Hong SH. Influence of Microbiota on Vaccine Effectiveness: "Is the Microbiota the Key to Vaccine-induced Responses?". J Microbiol 2023:10.1007/s12275-023-00044-6. [PMID: 37052795 PMCID: PMC10098251 DOI: 10.1007/s12275-023-00044-6] [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: 01/17/2023] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Vaccines are one of the most powerful tools for preventing infectious diseases. To effectively fight pathogens, vaccines should induce potent and long-lasting immune responses that are specific to the pathogens. However, not all vaccines can induce effective immune responses, and the responses vary greatly among individuals and populations. Although several factors, such as age, host genetics, nutritional status, and region, affect the effectiveness of vaccines, increasing data have suggested that the gut microbiota is critically associated with vaccine-induced immune responses. In this review, I discuss how gut microbiota affects vaccine effectiveness based on the clinical and preclinical data, and summarize possible underlying mechanisms related to the adjuvant effects of microbiota. A better understanding of the link between vaccine-induced immune responses and the gut microbiota using high-throughput technology and sophisticated system vaccinology approaches could provide crucial insights for designing effective personalized preventive and therapeutic vaccination strategies.
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Affiliation(s)
- So-Hee Hong
- Department of Microbiology, College of Medicine, Ewha Womans University, Seoul, 07084, Republic of Korea.
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22
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Gao F, Mallajosyula V, Arunachalam PS, van der Ploeg K, Manohar M, Röltgen K, Yang F, Wirz O, Hoh R, Haraguchi E, Lee JY, Willis R, Ramachandiran V, Li J, Kathuria KR, Li C, Lee AS, Shah MM, Sindher SB, Gonzalez J, Altman JD, Wang TT, Boyd SD, Pulendran B, Jagannathan P, Nadeau KC, Davis MM. Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8 + T cell responses post SARS-CoV-2 infection. Immunity 2023; 56:864-878.e4. [PMID: 36996809 PMCID: PMC10017386 DOI: 10.1016/j.immuni.2023.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/05/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
T cells are a critical component of the response to SARS-CoV-2, but their kinetics after infection and vaccination are insufficiently understood. Using "spheromer" peptide-MHC multimer reagents, we analyzed healthy subjects receiving two doses of the Pfizer/BioNTech BNT162b2 vaccine. Vaccination resulted in robust spike-specific T cell responses for the dominant CD4+ (HLA-DRB1∗15:01/S191) and CD8+ (HLA-A∗02/S691) T cell epitopes. Antigen-specific CD4+ and CD8+ T cell responses were asynchronous, with the peak CD4+ T cell responses occurring 1 week post the second vaccination (boost), whereas CD8+ T cells peaked 2 weeks later. These peripheral T cell responses were elevated compared with COVID-19 patients. We also found that previous SARS-CoV-2 infection resulted in decreased CD8+ T cell activation and expansion, suggesting that previous infection can influence the T cell response to vaccination.
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Affiliation(s)
- Fei Gao
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Kattria van der Ploeg
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ramona Hoh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily Haraguchi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard Willis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Jiefu Li
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Karan Raj Kathuria
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra S Lee
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mihir M Shah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Gonzalez
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John D Altman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Kari C Nadeau
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard, MA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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23
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Lozenov S, Krastev B, Nikolaev G, Peshevska-Sekulovska M, Peruhova M, Velikova T. Gut Microbiome Composition and Its Metabolites Are a Key Regulating Factor for Malignant Transformation, Metastasis and Antitumor Immunity. Int J Mol Sci 2023; 24:ijms24065978. [PMID: 36983053 PMCID: PMC10054493 DOI: 10.3390/ijms24065978] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The genetic and metabolomic abundance of the microbiome exemplifies that the microbiome comprises a more extensive set of genes than the entire human genome, which justifies the numerous metabolic and immunological interactions between the gut microbiota, macroorganisms and immune processes. These interactions have local and systemic impacts that can influence the pathological process of carcinogenesis. The latter can be promoted, enhanced or inhibited by the interactions between the microbiota and the host. This review aimed to present evidence that interactions between the host and the gut microbiota might be a significant exogenic factor for cancer predisposition. It is beyond doubt that the cross-talk between microbiota and the host cells in terms of epigenetic modifications can regulate gene expression patterns and influence cell fate in both beneficial and adverse directions for the host's health. Furthermore, bacterial metabolites could shift pro- and anti-tumor processes in one direction or another. However, the exact mechanisms behind these interactions are elusive and require large-scale omics studies to better understand and possibly discover new therapeutic approaches for cancer.
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Affiliation(s)
- Stefan Lozenov
- Laboratory for Control and Monitoring of the Antibiotic Resistance, National Centre for Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd, 1504 Sofia, Bulgaria
| | - Boris Krastev
- Nadezhda Paradise Medical Center, 1330 Sofia, Bulgaria
| | - Georgi Nikolaev
- Department of Cell and Developmental Biology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 1504 Sofia, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, Sofia, Medical Faculty, Sofia University "St. Kliment Ohridski", 1407 Sofia, Bulgaria
| | - Milena Peruhova
- Department of Gastroenterology, University Hospital Heart and Brain, 5804 Pleven, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, Kozyak 1 str., 1407 Sofia, Bulgaria
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24
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Curran AM, Girgis AA, Jang Y, Crawford JD, Thomas MA, Kawalerski R, Coller J, Bingham CO, Na CH, Darrah E. Citrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis. Nat Commun 2023; 14:1061. [PMID: 36828807 PMCID: PMC9958131 DOI: 10.1038/s41467-023-36620-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Cryptic peptides, hidden from the immune system under physiologic conditions, are revealed by changes to MHC class II processing and hypothesized to drive the loss of immune tolerance to self-antigens in autoimmunity. Rheumatoid arthritis (RA) is an autoimmune disease characterized by immune responses to citrullinated self-antigens, in which arginine residues are converted to citrullines. Here, we investigate the hypothesis that citrullination exposes cryptic peptides by modifying protein structure and proteolytic cleavage. We show that citrullination alters processing and presentation of autoantigens, resulting in the generation of a unique citrullination-dependent repertoire composed primarily of native sequences. This repertoire stimulates T cells from RA patients with anti-citrullinated protein antibodies more robustly than controls. The generation of this unique repertoire is achieved through altered protease cleavage and protein destabilization, rather than direct presentation of citrulline-containing epitopes, suggesting a novel paradigm for the role of protein citrullination in the breach of immune tolerance in RA.
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Affiliation(s)
- Ashley M Curran
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander A Girgis
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yura Jang
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunology, Office of Biotechnology Products, Center for Drugs Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan D Crawford
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mekha A Thomas
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan Kawalerski
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeff Coller
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Clifton O Bingham
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chan Hyun Na
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erika Darrah
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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25
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Eshleman EM, Shao TY, Woo V, Rice T, Engleman L, Didriksen BJ, Whitt J, Haslam DB, Way SS, Alenghat T. Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity. J Clin Invest 2023; 133:e162190. [PMID: 36602872 PMCID: PMC9927950 DOI: 10.1172/jci162190] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Aberrant immune responses to resident microbes promote inflammatory bowel disease and other chronic inflammatory conditions. However, how microbiota-specific immunity is controlled in mucosal tissues remains poorly understood. Here, we found that mice lacking epithelial expression of microbiota-sensitive histone deacetylase 3 (HDAC3) exhibited increased accumulation of commensal-specific CD4+ T cells in the intestine, provoking the hypothesis that epithelial HDAC3 may instruct local microbiota-specific immunity. Consistent with this, microbiota-specific CD4+ T cells and epithelial HDAC3 expression were concurrently induced following early-life microbiota colonization. Further, epithelium-intrinsic ablation of HDAC3 decreased commensal-specific Tregs, increased commensal-specific Th17 cells, and promoted T cell-driven colitis. Mechanistically, HDAC3 was essential for NF-κB-dependent regulation of epithelial MHC class II (MHCII). Epithelium-intrinsic MHCII dampened local accumulation of commensal-specific Th17 cells in adult mice and protected against microbiota-triggered inflammation. Remarkably, HDAC3 enabled the microbiota to induce MHCII expression on epithelial cells and limit the number of commensal-specific T cells in the intestine. Collectively, these data reveal a central role for an epithelial histone deacetylase in directing the dynamic balance of tissue-intrinsic CD4+ T cell subsets that recognize commensal microbes and control inflammation.
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Affiliation(s)
| | - Tzu-Yu Shao
- Center for Inflammation and Tolerance
- Division of Infectious Disease, and
- Immunology Graduate Program, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Vivienne Woo
- Division of Immunobiology
- Center for Inflammation and Tolerance
| | - Taylor Rice
- Division of Immunobiology
- Center for Inflammation and Tolerance
| | - Laura Engleman
- Division of Immunobiology
- Center for Inflammation and Tolerance
| | - Bailey J. Didriksen
- Division of Immunobiology
- Center for Inflammation and Tolerance
- Immunology Graduate Program, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jordan Whitt
- Division of Immunobiology
- Center for Inflammation and Tolerance
| | | | - Sing Sing Way
- Center for Inflammation and Tolerance
- Division of Infectious Disease, and
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26
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Abdulla ZA, Al-Bashir SM, Alzoubi H, Al-Salih NS, Aldamen AA, Abdulazeez AZ. The Role of Immunity in the Pathogenesis of SARS-CoV-2 Infection and in the Protection Generated by COVID-19 Vaccines in Different Age Groups. Pathogens 2023; 12:329. [PMID: 36839601 PMCID: PMC9967364 DOI: 10.3390/pathogens12020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
This study aims to review the available data regarding the central role of immunity in combating SARS-CoV-2 infection and in the generation of protection by vaccination against COVID-19 in different age groups. Physiologically, the immune response and the components involved in it are variable, both functionally and quantitatively, in neonates, infants, children, adolescents, and adults. These immunological differences are mirrored during COVID-19 infection and in the post-vaccination period. The outcome of SARS-CoV-2 infection is greatly dependent on the reaction orchestrated by the immune system. This is clearly obvious in relation to the clinical status of COVID-19 infection, which can be symptomless, mild, moderate, or severe. Even the complications of the disease show a proportional pattern in relation to the immune response. On the contrary, the commonly used anti-COVID-19 vaccines generate protective humoral and cellular immunity. The magnitude of this immunity and the components involved in it are discussed in detail. Furthermore, many of the adverse effects of these vaccines can be explained on the basis of immune reactions against the different components of the vaccines. Regarding the appropriate choice of vaccine for different age groups, many factors have to be considered. This is a cornerstone, particularly in the following age groups: 1 day to 5 years, 6 to 11 years, and 12 to 17 years. Many factors are involved in deciding the route, doses, and schedule of vaccination for children. Another important issue in this dilemma is the hesitancy of families in making the decision about whether to vaccinate their children. Added to these difficulties is the choice by health authorities and governments concerning whether to make children's vaccination compulsory. In this respect, although rare and limited, adverse effects of vaccines in children have been detected, some of which, unfortunately, have been serious or even fatal. However, to achieve comprehensive control over COVID-19 in communities, both children and adults have to be vaccinated, as the former group represents a reservoir for viral transmission. The understanding of the various immunological mechanisms involved in SARS-CoV-2 infection and in the preparation and application of its vaccines has given the sciences a great opportunity to further deepen and expand immunological knowledge. This will hopefully be reflected positively on other diseases through gaining an immunological background that may aid in diagnosis and therapy. Humanity is still in continuous conflict with SARS-CoV-2 infection and will be for a while, but the future is expected to be in favor of the prevention and control of this disease.
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Affiliation(s)
| | - Sharaf M. Al-Bashir
- Department of Clinical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Hiba Alzoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Noor S. Al-Salih
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
| | - Ala A. Aldamen
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 21163, Jordan
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27
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Miyauchi E, Shimokawa C, Steimle A, Desai MS, Ohno H. The impact of the gut microbiome on extra-intestinal autoimmune diseases. Nat Rev Immunol 2023; 23:9-23. [PMID: 35534624 DOI: 10.1038/s41577-022-00727-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 02/08/2023]
Abstract
The prevalence of autoimmune diseases (ADs) worldwide has rapidly increased over the past few decades. Thus, in addition to the classical risk factors for ADs, such as genetic polymorphisms, infections and smoking, environmental triggers have been considered. Recent sequencing-based approaches have revealed that patients with extra-intestinal ADs, such as multiple sclerosis, rheumatoid arthritis, type 1 diabetes and systemic lupus erythematosus, have distinct gut microbiota compositions compared to healthy controls. Faecal microbiota transplantation or inoculation with specific microbes in animal models of ADs support the hypothesis that alterations of gut microbiota influence autoimmune responses and disease outcome. Here, we describe the compositional and functional changes in the gut microbiota in patients with extra-intestinal AD and discuss how the gut microbiota affects immunity. Moreover, we examine how the gut microbiota might be modulated in patients with ADs as a potential preventive or therapeutic approach.
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Affiliation(s)
- Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Haebashi, Gunma, Japan
| | - Chikako Shimokawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Parasitology, National Institute of Infectious Disease, Tokyo, Japan
| | - Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
- Laboratory for Immune Regulation, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
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28
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Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Tanes C, Bittinger K, Friedman ES, Gimotty PA, Wu GD, Su LF. SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol 2022; 7:eabn3127. [PMID: 35857619 PMCID: PMC9348748 DOI: 10.1126/sciimmunol.abn3127] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
The baseline composition of T cells directly affects later response to pathogens, but the complexity of precursor states remains poorly defined. Here, we examined the baseline state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells in unexposed individuals. SARS-CoV-2-specific CD4+ T cells were identified in prepandemic blood samples by major histocompatibility complex (MHC) class II tetramer staining and enrichment. Our data revealed a substantial number of SARS-CoV-2-specific T cells that expressed memory phenotype markers. Integrated phenotypic analyses demonstrated diverse preexisting memory states that included cells with distinct polarization features and trafficking potential to barrier tissues. T cell clones generated from tetramer-labeled cells cross-reacted with antigens from commensal bacteria in the skin and gastrointestinal tract. Direct ex vivo tetramer staining for one spike-specific population showed a similar level of cross-reactivity to sequences from endemic coronavirus and commensal bacteria. These data highlight the complexity of precursor T cell repertoire and implicate noninfectious exposures to common microbes as a key factor that shapes human preexisting immunity to SARS-CoV-2.
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Affiliation(s)
- Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sumbul Afroz
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruozhang Xu
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Lea Williams
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Chin-Fang Lin
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura F. Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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29
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Abbas M, Hayirli Z, Drakesmith H, Andrews SC, Lewis MC. Effects of iron deficiency and iron supplementation at the host-microbiota interface: Could a piglet model unravel complexities of the underlying mechanisms? Front Nutr 2022; 9:927754. [PMID: 36267902 PMCID: PMC9577221 DOI: 10.3389/fnut.2022.927754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/05/2022] [Indexed: 01/14/2023] Open
Abstract
Iron deficiency is the most prevalent human micronutrient deficiency, disrupting the physiological development of millions of infants and children. Oral iron supplementation is used to address iron-deficiency anemia and reduce associated stunting but can promote infection risk since restriction of iron availability serves as an innate immune mechanism against invading pathogens. Raised iron availability is associated with an increase in enteric pathogens, especially Enterobacteriaceae species, accompanied by reductions in beneficial bacteria such as Bifidobacteria and lactobacilli and may skew the pattern of gut microbiota development. Since the gut microbiota is the primary driver of immune development, deviations from normal patterns of bacterial succession in early life can have long-term implications for immune functionality. There is a paucity of knowledge regarding how both iron deficiency and luminal iron availability affect gut microbiota development, or the subsequent impact on immunity, which are likely to be contributors to the increased risk of infection. Piglets are naturally iron deficient. This is largely due to their low iron endowments at birth (primarily due to large litter sizes), and their rapid growth combined with the low iron levels in sow milk. Thus, piglets consistently become iron deficient within days of birth which rapidly progresses to anemia in the absence of iron supplementation. Moreover, like humans, pigs are omnivorous and share many characteristics of human gut physiology, microbiota and immunity. In addition, their precocial nature permits early maternal separation, individual housing, and tight control of nutritional intake. Here, we highlight the advantages of piglets as valuable and highly relevant models for human infants in promoting understanding of how early iron status impacts physiological development. We also indicate how piglets offer potential to unravel the complexities of microbiota-immune responses during iron deficiency and in response to iron supplementation, and the link between these and increased risk of infectious disease.
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Affiliation(s)
- Munawar Abbas
- Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Zeynep Hayirli
- Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon C. Andrews
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Marie C. Lewis
- Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
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30
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Serum IL-1ra Is Associated with but Has No Genetic Link to Type 1 Diabetes. ENDOCRINES 2022. [DOI: 10.3390/endocrines3030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Interleukin-1 antagonism is a proposed biomarker and potential therapy for the delay and/or treatment of type 1 diabetes (T1D). We evaluated the role of circulating interleukin-1 receptor antagonist (IL-1ra) in a prospectively monitored cohort of T1D patients. In order to determine a mechanistic association between IL-1ra and T1D, we performed co-localization analyses between serum IL-1ra protein quantitative trait loci and T1D genome-wide analysis studies. Adjusting for human leukocyte antigen (HLA) genotypes, first degree relative status, gender, and age, serum levels of IL-1ra were lower in subjects who progressed to T1D compared to the controls (p = 0.023). Our results suggest that females have higher levels of IL-1ra compared to males (p = 0.005). The 2q14.1 region associated with serum IL-1ra levels is not associated with a risk of developing T1D. Our data suggest that IL-1 antagonism by IL-1ra is not an effective therapy in T1D, but IL-1ra may be a biomarker for progression to T1D.
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31
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Sharma J, Mudalagiriyappa S, Nanjappa SG. T cell responses to control fungal infection in an immunological memory lens. Front Immunol 2022; 13:905867. [PMID: 36177012 PMCID: PMC9513067 DOI: 10.3389/fimmu.2022.905867] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
In recent years, fungal vaccine research emanated significant findings in the field of antifungal T-cell immunity. The generation of effector T cells is essential to combat many mucosal and systemic fungal infections. The development of antifungal memory T cells is integral for controlling or preventing fungal infections, and understanding the factors, regulators, and modifiers that dictate the generation of such T cells is necessary. Despite the deficiency in the clear understanding of antifungal memory T-cell longevity and attributes, in this review, we will compile some of the existing literature on antifungal T-cell immunity in the context of memory T-cell development against fungal infections.
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32
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Singh S, Saavedra-Avila NA, Tiwari S, Porcelli SA. A century of BCG vaccination: Immune mechanisms, animal models, non-traditional routes and implications for COVID-19. Front Immunol 2022; 13:959656. [PMID: 36091032 PMCID: PMC9459386 DOI: 10.3389/fimmu.2022.959656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022] Open
Abstract
Bacillus Calmette-Guerin (BCG) has been used as a vaccine against tuberculosis since 1921 and remains the only currently approved vaccine for this infection. The recent discovery that BCG protects against initial infection, and not just against progression from latent to active disease, has significant implications for ongoing research into the immune mechanisms that are relevant to generate a solid host defense against Mycobacterium tuberculosis (Mtb). In this review, we first explore the different components of immunity that are augmented after BCG vaccination. Next, we summarize current efforts to improve the efficacy of BCG through the development of recombinant strains, heterologous prime-boost approaches and the deployment of non-traditional routes. These efforts have included the development of new recombinant BCG strains, and various strategies for expression of important antigens such as those deleted during the M. bovis attenuation process or antigens that are present only in Mtb. BCG is typically administered via the intradermal route, raising questions about whether this could account for its apparent failure to generate long-lasting immunological memory in the lungs and the inconsistent level of protection against pulmonary tuberculosis in adults. Recent years have seen a resurgence of interest in the mucosal and intravenous delivery routes as they have been shown to induce a better immune response both in the systemic and mucosal compartments. Finally, we discuss the potential benefits of the ability of BCG to confer trained immunity in a non-specific manner by broadly stimulating a host immunity resulting in a generalized survival benefit in neonates and the elderly, while potentially offering benefits for the control of new and emerging infectious diseases such as COVID-19. Given that BCG will likely continue to be widely used well into the future, it remains of critical importance to better understand the immune responses driven by it and how to leverage these for the design of improved vaccination strategies against tuberculosis.
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Affiliation(s)
- Shivani Singh
- Department of Medicine, New York University School of Medicine, New York, NY, United States
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, United States
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
- *Correspondence: Shivani Singh,
| | | | - Sangeeta Tiwari
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, Texas, United States
| | - Steven A. Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, United States
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States
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33
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De Souza MM, Koltes DA, Beiki H, Sales MA, Tsai T, Maxwell CV, Zhao J, Koltes JE. Early-Life Exposure of Pigs to Topsoil Alters miRNA and mRNA Expression in Peripheral Blood Mononuclear Cells. Front Genet 2022; 13:886875. [PMID: 36081988 PMCID: PMC9445269 DOI: 10.3389/fgene.2022.886875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Exposure to less-hygienic conditions during early childhood has been associated with stimulation and development of the immune system. A recent study indicated that exposure of piglets to soil-borne microbes during lactation was related with modulation of gut microbiota and immune function. To identify the potential molecular mechanisms and pathways impacted by early-life topsoil exposure, we analyzed the messenger RNA (mRNA) and micro-RNA (miRNA) expression in peripheral blood mononuclear cells (PBMCs) from these piglets. Total RNA was extracted from the PBMCs of piglets exposed to topsoil only from d 4–d 21 of life (mRNA n = 6; miRNA n = 5) or unexposed control pigs (mRNA n = 6; miRNA n = 8) at 11, 20, and 56 days of age. Small RNA and mRNA were sequenced with 50-bp single-end reads using Illumina chemistry. Sequence data were quality checked with FASTQC software and aligned to the Sscrofa 11.1 genome with the STAR aligner for mRNA and mirDeep2 for miRNA. Differential expression (DE) analysis was performed using PROC Glimmix of SAS to evaluate changes in expression due to topsoil exposure over time with genes declared DE at a false discovery rate (FDR) of q < 0.10. A total of 138 mRNA and 21 miRNAs were identified as DE for the treatment by age interaction. Ontology enrichment analysis of DE mRNA revealed Gene ontology (GO) terms directly involved in the connection between T-cell and antigen-presenting cells that are associated with T-cell activation. Key regulatory genes identified include PTPRJ, ITGB3, TRBV30, CD3D, mir-143, mir-29, and mir-148a. While these results require validation, this study provides data supporting the hypothesis that less-hygienic environments during early life may contribute to the development of the immune system.
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Affiliation(s)
- M. M. De Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - D. A. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - H. Beiki
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - M. A. Sales
- Department of Animal Science, University of Arkansas-Division of Agriculture, Fayetteville, AR, United States
| | - T. Tsai
- Department of Animal Science, University of Arkansas-Division of Agriculture, Fayetteville, AR, United States
| | - C. V. Maxwell
- Department of Animal Science, University of Arkansas-Division of Agriculture, Fayetteville, AR, United States
| | - J. Zhao
- Department of Animal Science, University of Arkansas-Division of Agriculture, Fayetteville, AR, United States
| | - J. E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
- *Correspondence: J. E. Koltes,
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34
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Li S, Zhou Y, Yan D, Wan Y. An Update on the Mutual Impact between SARS-CoV-2 Infection and Gut Microbiota. Viruses 2022; 14:1774. [PMID: 36016396 PMCID: PMC9415881 DOI: 10.3390/v14081774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota is essential for good health. It has also been demonstrated that the gut microbiota can regulate immune responses against respiratory tract infections. Since the outbreak of the COVID-19 pandemic, accumulating evidence suggests that there is a link between the severity of COVID-19 and the alteration of one's gut microbiota. The composition of gut microbiota can be profoundly affected by COVID-19 and vice versa. Here, we summarize the observations of the mutual impact between SARS-CoV-2 infection and gut microbiota composition. We discuss the consequences and mechanisms of the bi-directional interaction. Moreover, we also discuss the immune cross-reactivity between SARS-CoV-2 and commensal bacteria, which represents a previously overlooked connection between COVID-19 and commensal gut bacteria. Finally, we summarize the progress in managing COVID-19 by utilizing microbial interventions.
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Affiliation(s)
- Shaoshuai Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Shanghai Public Health Clinical Center, Department of Laboratory Medicine, Shanghai 201508, China
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Dongmei Yan
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Shanghai Public Health Clinical Center, Department of Radiology, Shanghai 201508, China
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35
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Saggau C, Martini GR, Rosati E, Meise S, Messner B, Kamps AK, Bekel N, Gigla J, Rose R, Voß M, Geisen UM, Reid HM, Sümbül M, Tran F, Berner DK, Khodamoradi Y, Vehreschild MJGT, Cornely O, Koehler P, Krumbholz A, Fickenscher H, Kreuzer O, Schreiber C, Franke A, Schreiber S, Hoyer B, Scheffold A, Bacher P. The pre-exposure SARS-CoV-2-specific T cell repertoire determines the quality of the immune response to vaccination. Immunity 2022; 55:1924-1939.e5. [PMID: 35985324 PMCID: PMC9372089 DOI: 10.1016/j.immuni.2022.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 infection and vaccination generates enormous host-response heterogeneity and an age-dependent loss of immune-response quality. How the pre-exposure T cell repertoire contributes to this heterogeneity is poorly understood. We combined analysis of SARS-CoV-2-specific CD4+ T cells pre- and post-vaccination with longitudinal T cell receptor tracking. We identified strong pre-exposure T cell variability that correlated with subsequent immune-response quality and age. High-quality responses, defined by strong expansion of high-avidity spike-specific T cells, high interleukin-21 production, and specific immunoglobulin G, depended on an intact naive repertoire and exclusion of pre-existing memory T cells. In the elderly, T cell expansion from both compartments was severely compromised. Our results reveal that an intrinsic defect of the CD4+ T cell repertoire causes the age-dependent decline of immune-response quality against SARS-CoV-2 and highlight the need for alternative strategies to induce high-quality T cell responses against newly arising pathogens in the elderly.
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Affiliation(s)
- Carina Saggau
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Gabriela Rios Martini
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Elisa Rosati
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Silja Meise
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Berith Messner
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Ann-Kristin Kamps
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Nicole Bekel
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Johannes Gigla
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ulf M Geisen
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Hayley M Reid
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Melike Sümbül
- Department of Dermatology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Dennis K Berner
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Oliver Cornely
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany; Labor Dr. Krause und Kollegen MVZ GmbH, Kiel, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Claudia Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Bimba Hoyer
- Medical Department I, Department for Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrecht-University of Kiel, Arnold-Heller-Str. 3, Kiel, Schleswig-Holstein 24105, Germany; Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Rosalind-Franklin-Str. 12, Kiel, Schleswig-Holstein 24105, Germany.
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36
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Medetgul-Ernar K, Davis MM. Standing on the shoulders of mice. Immunity 2022; 55:1343-1353. [PMID: 35947979 PMCID: PMC10035762 DOI: 10.1016/j.immuni.2022.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 01/13/2023]
Abstract
While inbred mice have informed most of what we know about the immune system in the modern era, they have clear limitations with respect to their ability to be informative regarding genetic heterogeneity or microbial influences. They have also not been very predictive as models of human disease or vaccination results. Although there are concerted attempts to compensate for these flaws, the rapid rise of human studies, driven by both technical and conceptual advances, promises to fill in these gaps, as well as provide direct information about human diseases and vaccination responses. Work on human immunity has already provided important additional perspectives on basic immunology such as the importance of clonal deletion to self-tolerance, and while many challenges remain, it seems inevitable that "the human model" will continue to inform us about the immune system and even allow for the discovery of new mechanisms.
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Affiliation(s)
- Kwat Medetgul-Ernar
- Immunology Program, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Mark M Davis
- Howard Hughes Medical Institute, Institute for Immunity, Transplantation and Infection, Department of Microbiology and Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
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37
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Liu M, Tayob N, Penter L, Sellars M, Tarren A, Chea V, Carulli I, Huang T, Li S, Cheng SC, Le P, Frackiewicz L, Fasse J, Qi C, Liu JF, Stover EH, Curtis J, Livak KJ, Neuberg D, Zhang G, Matulonis UA, Wu CJ, Keskin DB, Konstantinopoulos PA. Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer. Clin Cancer Res 2022; 28:3356-3366. [PMID: 35443043 PMCID: PMC9357177 DOI: 10.1158/1078-0432.ccr-21-2834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/20/2021] [Accepted: 04/13/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Although local tissue-based immune responses are critical for elucidating direct tumor-immune cell interactions, peripheral immune responses are increasingly recognized as occupying an important role in anticancer immunity. We evaluated serial blood samples from patients with advanced epithelial ovarian cancer (EOC) undergoing standard-of-care neoadjuvant carboplatin and paclitaxel chemotherapy (including dexamethasone for prophylaxis of paclitaxel-associated hypersensitivity reactions) to characterize the evolution of the peripheral immune cell function and composition across the course of therapy. EXPERIMENTAL DESIGN Serial blood samples from 10 patients with advanced high-grade serous ovarian cancer treated with neoadjuvant chemotherapy (NACT) were collected before the initiation of chemotherapy, after the third and sixth cycles, and approximately 2 months after completion of chemotherapy. T-cell function was evaluated using ex vivo IFNγ ELISpot assays, and the dynamics of T-cell repertoire and immune cell composition were assessed using bulk and single-cell RNA sequencing (RNAseq). RESULTS T cells exhibited an improved response to viral antigens after NACT, which paralleled the decrease in CA125 levels. Single-cell analysis revealed increased numbers of memory T-cell receptor (TCR) clonotypes and increased central memory CD8+ and regulatory T cells throughout chemotherapy. Finally, administration of NACT was associated with increased monocyte frequency and expression of HLA class II and antigen presentation genes; single-cell RNAseq analyses showed that although driven largely by classical monocytes, increased class II gene expression was a feature observed across monocyte subpopulations after chemotherapy. CONCLUSIONS NACT may alleviate tumor-associated immunosuppression by reducing tumor burden and may enhance antigen processing and presentation. These findings have implications for the successful combinatorial applications of immune checkpoint blockade and therapeutic vaccine approaches in EOC.
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Affiliation(s)
- Min Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Nabihah Tayob
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Hematology, Oncology, and Tumor Immunology, Campus Virchow Klinikum, Berlin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - MacLean Sellars
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anna Tarren
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vipheaviny Chea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Isabel Carulli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Su-Chun Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Phuong Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura Frackiewicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Julia Fasse
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Courtney Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce F. Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth H. Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Curtis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth J. Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guanglan Zhang
- Department of Computer Science, Metropolitan College, Boston University, Boston, Massachusetts
| | - Ursula A. Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Computer Science, Metropolitan College, Boston University, Boston, Massachusetts.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark.,Corresponding Authors: Panagiotis A. Konstantinopoulos, Dana-Farber Cancer Institute, 450 Brookline Avenue, YC-1424, Boston, MA 02215. E-mail: ; and Derin B. Keskin,
| | - Panagiotis A. Konstantinopoulos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Corresponding Authors: Panagiotis A. Konstantinopoulos, Dana-Farber Cancer Institute, 450 Brookline Avenue, YC-1424, Boston, MA 02215. E-mail: ; and Derin B. Keskin,
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38
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Jo N, Zhang R, Ueno H, Yamamoto T, Weiskopf D, Nagao M, Yamanaka S, Hamazaki Y. Aging and CMV Infection Affect Pre-existing SARS-CoV-2-Reactive CD8 + T Cells in Unexposed Individuals. FRONTIERS IN AGING 2022; 2:719342. [PMID: 35822004 PMCID: PMC9261342 DOI: 10.3389/fragi.2021.719342] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022]
Abstract
Age is a major risk factor for COVID-19 severity, and T cells play a central role in anti-SARS-CoV-2 immunity. Because SARS-CoV-2-cross-reactive T cells have been detected in unexposed individuals, we investigated the age-related differences in pre-existing SARS-CoV-2-reactive T cells. SARS-CoV-2-reactive CD4+ T cells from young and elderly individuals were mainly detected in the central memory fraction and exhibited similar functionalities and numbers. Naïve-phenotype SARS-CoV-2-reactive CD8+ T cell populations decreased markedly in the elderly, while those with terminally differentiated and senescent phenotypes increased. Furthermore, senescent SARS-CoV-2-reactive CD8+ T cell populations were higher in cytomegalovirus seropositive young individuals compared to seronegative ones. Our findings suggest that age-related differences in pre-existing SARS-CoV-2-reactive CD8+ T cells may explain the poor outcomes in elderly patients and that cytomegalovirus infection is a potential factor affecting CD8+ T cell immunity against SARS-CoV-2. Thus, this study provides insights for developing effective therapeutic and vaccination strategies for the elderly.
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Affiliation(s)
- Norihide Jo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Alliance Laboratory for Advanced Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rui Zhang
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Hideki Ueno
- Department of Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA, United States
| | - Yoko Hamazaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Laboratory of Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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39
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Akama-Garren EH, Carroll MC. T Cell Help in the Autoreactive Germinal Center. Scand J Immunol 2022; 95:e13192. [PMID: 35587582 DOI: 10.1111/sji.13192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
The germinal center serves as a site of B cell selection and affinity maturation, critical processes for productive adaptive immunity. In autoimmune disease tolerance is broken in the germinal center reaction, leading to production of autoreactive B cells that may propagate disease. Follicular T cells are crucial regulators of this process, providing signals necessary for B cell survival in the germinal center. Here we review the emerging roles of follicular T cells in the autoreactive germinal center. Recent advances in immunological techniques have allowed study of the gene expression profiles and repertoire of follicular T cells at unprecedented resolution. These studies provide insight into the potential role follicular T cells play in preventing or facilitating germinal center loss of tolerance. Improved understanding of the mechanisms of T cell help in autoreactive germinal centers provides novel therapeutic targets for diseases of germinal center dysfunction.
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Affiliation(s)
- Elliot H Akama-Garren
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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40
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Li J, Zaslavsky M, Su Y, Guo J, Sikora MJ, van Unen V, Christophersen A, Chiou SH, Chen L, Li J, Ji X, Wilhelmy J, McSween AM, Palanski BA, Mallajosyula VVA, Bracey NA, Dhondalay GKR, Bhamidipati K, Pai J, Kipp LB, Dunn JE, Hauser SL, Oksenberg JR, Satpathy AT, Robinson WH, Dekker CL, Steinmetz LM, Khosla C, Utz PJ, Sollid LM, Chien YH, Heath JR, Fernandez-Becker NQ, Nadeau KC, Saligrama N, Davis MM. KIR +CD8 + T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science 2022; 376:eabi9591. [PMID: 35258337 PMCID: PMC8995031 DOI: 10.1126/science.abi9591] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/12/2021] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
In this work, we find that CD8+ T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49+CD8+ regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8+ T cells efficiently eliminated pathogenic gliadin-specific CD4+ T cells from the leukocytes of celiac disease patients in vitro. We also find elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 patients, correlating with disease severity and vasculitis. Selective ablation of Ly49+CD8+ T cells in virus-infected mice led to autoimmunity after infection. Our results indicate that in both species, these regulatory CD8+ T cells act specifically to suppress pathogenic T cells in autoimmune and infectious diseases.
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Affiliation(s)
- Jing Li
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxim Zaslavsky
- Program in Computer Science, Stanford University, Stanford, CA, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Jing Guo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J. Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent van Unen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Asbjørn Christophersen
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Shin-Heng Chiou
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang Chen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Jiefu Li
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Xuhuai Ji
- Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Wilhelmy
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alana M. McSween
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Nathan A. Bracey
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Gopal Krishna R. Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Kartik Bhamidipati
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joy Pai
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucas B. Kipp
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey E. Dunn
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen L. Hauser
- Department of Neurology and UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Jorge R. Oksenberg
- Department of Neurology and UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William H. Robinson
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Cornelia L. Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ludvig M. Sollid
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Yueh-Hsiu Chien
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Kari C. Nadeau
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Naresha Saligrama
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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41
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Abstract
A subset of CD8+ T cells regulate chronic inflammation by killing pathogenic CD4+ T cells.
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Affiliation(s)
- Anaïs Levescot
- Université de Paris Cité, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
| | - Nadine Cerf-Bensussan
- Université de Paris Cité, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
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Molodtsov IA, Kegeles E, Mitin AN, Mityaeva O, Musatova OE, Panova AE, Pashenkov MV, Peshkova IO, Alsalloum A, Asaad W, Budikhina AS, Deryabin AS, Dolzhikova IV, Filimonova IN, Gracheva AN, Ivanova OI, Kizilova A, Komogorova VV, Komova A, Kompantseva NI, Kucheryavykh E, Lagutkin DA, Lomakin YA, Maleeva AV, Maryukhnich EV, Mohammad A, Murugin VV, Murugina NE, Navoikova A, Nikonova MF, Ovchinnikova LA, Panarina Y, Pinegina NV, Potashnikova DM, Romanova EV, Saidova AA, Sakr N, Samoilova AG, Serdyuk Y, Shakirova NT, Sharova NI, Sheetikov SA, Shemetova AF, Shevkova LV, Shpektor AV, Trufanova A, Tvorogova AV, Ukrainskaya VM, Vinokurov AS, Vorobyeva DA, Zornikova KV, Efimov GA, Khaitov MR, Kofiadi IA, Komissarov AA, Logunov DY, Naigovzina NB, Rubtsov YP, Vasilyeva IA, Volchkov P, Vasilieva E. SARS-CoV-2-specific T cells and antibodies in COVID-19 protection: a prospective study. Clin Infect Dis 2022; 75:e1-e9. [PMID: 35435222 PMCID: PMC9047235 DOI: 10.1093/cid/ciac278] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background During the ongoing coronavirus disease 2019 (COVID-19) pandemic, many individuals were infected with and have cleared the virus, developing virus-specific antibodies and effector/memory T cells. An important unanswered question is what levels of T-cell and antibody responses are sufficient to protect from the infection. Methods In 5340 Moscow residents, we evaluated anti–severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin M (IgM)/immunoglobulin G (IgG) titers and frequencies of the T cells specific to the membrane, nucleocapsid, and spike proteins of SARS-CoV-2, using interferon gamma (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) assay. Additionally, we evaluated the fractions of virus-specific CD4+ and CD8+ T cells using intracellular staining of IFN-γ and interleukin 2 followed by flow cytometry. We analyzed the COVID-19 rates as a function of the assessed antibody and T-cell responses, using the Kaplan–Meier estimator method, for up to 300 days postinclusion. Results We showed that T-cell and antibody responses are closely interconnected and are commonly induced concurrently. Magnitudes of both responses inversely correlated with infection probability. Individuals positive for both responses demonstrated the highest levels of protectivity against the SARS-CoV-2 infection. A comparable level of protection was found in individuals with antibody response only, whereas the T-cell response by itself granted only intermediate protection. Conclusions We found that the contribution of the virus-specific antibodies to protection against SARS-CoV-2 infection is more pronounced than that of the T cells. The data on the virus-specific IgG titers may be instructive for making decisions in personalized healthcare and public anti–COVID-19 policies. Clinical Trials Registration. NCT04898140.
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Affiliation(s)
- Ivan A Molodtsov
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia
| | - Evgenii Kegeles
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Alexander N Mitin
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Olga Mityaeva
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Oksana E Musatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Anna E Panova
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Mikhail V Pashenkov
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Iuliia O Peshkova
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Almaqdad Alsalloum
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Walaa Asaad
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Anna S Budikhina
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Alexander S Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Inna V Dolzhikova
- Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia
| | - Ioanna N Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Alexandra N Gracheva
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Oxana I Ivanova
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Anastasia Kizilova
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Viktoria V Komogorova
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Anastasia Komova
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia.,Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, The National Medical Research Center for Endocrinology, 117036, 11 Dmitry Ulyanov str., Moscow, Russia
| | - Natalia I Kompantseva
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | | | - Denis A Lagutkin
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Alexandra V Maleeva
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Elena V Maryukhnich
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Afraa Mohammad
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Vladimir V Murugin
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Nina E Murugina
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Anna Navoikova
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Margarita F Nikonova
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Leyla A Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Yana Panarina
- The Government of Moscow, 125032, 13 Tverskaya str., Moscow, Russia
| | - Natalia V Pinegina
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Daria M Potashnikova
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Elizaveta V Romanova
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia
| | - Aleena A Saidova
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia
| | - Nawar Sakr
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Anastasia G Samoilova
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Yana Serdyuk
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Naina T Shakirova
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Nina I Sharova
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia
| | - Saveliy A Sheetikov
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Anastasia F Shemetova
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Liudmila V Shevkova
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia.,Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, The National Medical Research Center for Endocrinology, 117036, 11 Dmitry Ulyanov str., Moscow, Russia
| | - Alexander V Shpektor
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Anna Trufanova
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia
| | - Anna V Tvorogova
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia
| | - Valeria M Ukrainskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Anatoliy S Vinokurov
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Daria A Vorobyeva
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Ksenia V Zornikova
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Grigory A Efimov
- National Medical Research Center for Hematology, 125167, 4a Novy Zykovsky proezd, Moscow, Russia
| | - Musa R Khaitov
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia.,Pirogov Russian National Research Medical University, 119997, 1 Ostrovityanov str., Moscow, Russia
| | - Ilya A Kofiadi
- National Research Center - Institute of Immunology Federal Medical-Biological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia.,Pirogov Russian National Research Medical University, 119997, 1 Ostrovityanov str., Moscow, Russia
| | - Alexey A Komissarov
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Denis Y Logunov
- Federal State Budget Institution "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya" of the Ministry of Health of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia
| | - Nelli B Naigovzina
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
| | - Yury P Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 Miklukho-Maklaya str., Moscow, Russia
| | - Irina A Vasilyeva
- National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str., Moscow, Russia
| | - Pavel Volchkov
- Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia.,Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, The National Medical Research Center for Endocrinology, 117036, 11 Dmitry Ulyanov str., Moscow, Russia
| | - Elena Vasilieva
- Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia.,A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia
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Bayram Z, Musharrafieh U, Bizri AR. Revisiting the potential role of BCG and MMR vaccines in COVID-19. Sci Prog 2022; 105:368504221105172. [PMID: 35848578 PMCID: PMC10450304 DOI: 10.1177/00368504221105172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Despite the development and deployment of effective COVID-19 vaccines, many regions remain poorly covered. Seeking alternative tools for achieving immunity against COVID-19 remains to be of high importance. "Trained immunity" is the nonspecific immune response usually established through administering live attenuated vaccines and is a potential preventive tool against unrelated infections. Evidence regarding a possible protective role for certain live attenuated vaccines against COVID-19 has emerged mainly for those administered as part of childhood vaccination protocols. This review summarizes the relevant literature about the potential impact of Bacille Calmette-Guérin (BCG) and measles, mumps and rubella (MMR) vaccines on COVID-19. Existing available data suggest a potential role for BCG and MMR in reducing COVID-19 casualties and burden. However, more investigation and comparative studies are required for a better understanding of their impact on COVID-19 outcomes.
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Affiliation(s)
| | - Umayya Musharrafieh
- Department of Internal Medicine, Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Family Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Abdul Rahman Bizri
- Department of Internal Medicine, Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, Lebanon
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Abstract
Healthy development and function of essentially all physiological systems and organs, including the brain, require exposure to the microbiota of our mothers and of the natural environment, especially in early life. We also know that some infections, if we survive them, modulate the immune system in relevant ways. If we study the evolution of the immune and metabolic systems, we can understand how these requirements developed and the nature of the organisms that we need to encounter. We can then begin to identify the mechanisms of the beneficial effects of these exposures. Against this evolutionary background, we can analyze the ways in which the modern urban lifestyle, particularly for individuals experiencing low socioeconomic status (SES), results in deficient or distorted microbial exposures and microbiomes. Thus, an evolutionary approach facilitates the identification of practical solutions to the growing scandal of health disparities linked to inequality.
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45
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Latif MB, Shukla S, Del Rio Estrada PM, Ribeiro SP, Sekaly RP, Sharma AA. Immune mechanisms in cancer patients that lead to poor outcomes of SARS-CoV-2 infection. Transl Res 2022; 241:83-95. [PMID: 34871809 PMCID: PMC8641406 DOI: 10.1016/j.trsl.2021.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/28/2021] [Accepted: 12/01/2021] [Indexed: 02/09/2023]
Abstract
Patients with cancers have been severely affected by the COVID-19 pandemic. This is highlighted by the adverse outcomes in cancer patients with COVID-19 as well as by the impact of the COVID-19 pandemic on cancer care. Patients with cancer constitute a heterogeneous population that exhibits distinct mechanisms of immune dysfunction, associated with distinct systemic features of hot (T-cell-inflamed/infiltrated) and cold (Non-T-cell-inflamed and/or infiltrated) tumors. The former show hyper immune activated cells and a highly inflammatory environment while, contrastingly, the latter show the profile of a senescent and/or quiescent immune system. Thus, the evolution of SARS-CoV-2 infection in different types of cancers can show distinct trajectories which could lead to a variety of clinical and pathophysiological outcomes. The altered immunological environment including cytokines that characterizes hot and cold tumors will lead to different mechanisms of immune dysfunction, which will result in downstream effects on the course of SARS-CoV-2 infection. This review will focus on defining the known contributions of soluble pro- and anti-inflammatory mediators on immune function including altered T-cells and B-cells responses and as well on how these factors modulate the expression of SARS-CoV-2 receptor ACE2, TMPRSS2 expression, and lymph node fibrosis in cancer patients. We will propose immune mechanisms that underlie the distinct courses of SARS-CoV-2 infection in cancer patients and impact on the success of immune based therapies that have significantly improved cancer outcomes. Better understanding of the immune mechanisms prevalent in cancer patients that are associated to the outcomes of SARS-CoV-2 infection will help to identify the high-risk cancer patients and develop immune-based approaches to prevent significant adverse outcomes by targeting these pathways.
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Affiliation(s)
- Muhammad Bilal Latif
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia
| | - Sudhanshu Shukla
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia
| | - Perla Mariana Del Rio Estrada
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia
| | - Susan Pereira Ribeiro
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia
| | - Rafick Pierre Sekaly
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia.
| | - Ashish Arunkumar Sharma
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia
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Curato C, Aparicio-Soto M, Riedel F, Wehl I, Basaran A, Abbas A, Thierse HJ, Luch A, Siewert K. Frequencies and TCR Repertoires of Human 2,4,6-Trinitrobenzenesulfonic Acid-specific T Cells. FRONTIERS IN TOXICOLOGY 2022; 4:827109. [PMID: 35295228 PMCID: PMC8915883 DOI: 10.3389/ftox.2022.827109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Allergic contact dermatitis is a widespread T cell-mediated inflammatory skin disease, but in vitro monitoring of chemical-specific T cells remains challenging. We here introduce short-term CD154/CD137 upregulation to monitor human T cell responses to the experimental sensitizer 2,4,6-trinitrobenzenesulfonic acid (TNBS). Peripheral blood mononuclear cells (PBMC) from healthy donor buffy coats were TNBS-modified and incubated with unmodified PBMC. After 5 and 16 h, we detected TNBS-specific activated CD154+CD4+ and CD137+CD8+ T cells by multi-parameter flow cytometry, respectively. Activated cells were sorted for restimulation and bulk T cell receptor (TCR) high-throughput sequencing (HTS). Stimulation with TNBS-modified cells (3 mM) induced CD154 expression on 0.04% of CD4+ and CD137 expression on 0.60% of CD8+ memory T cells, respectively (means, n = 11–17 donors). CD69 co-expression argued for TCR-mediated activation, which was further supported by TNBS-specific restimulation of 10/13 CD154+CD4+ and 11/15 CD137+CD8+ T cell clones and lines. Major histocompatibility complex (MHC) blocking antibodies prevented activation, illustrating MHC restriction. The high frequencies of TNBS-specific T cells were associated with distinct common changes in the TCR β-chain repertoire. We observed an overrepresentation of tryptophan and lysine in the complementarity determining regions 3 (CDR3) (n = 3–5 donors), indicating a preferential interaction of these amino acids with the TNBS-induced epitopes. In summary, the detection of TNBS-specific T cells by CD154/CD137 upregulation is a fast, comprehensive and quantitative method. Combined with TCR HTS, the mechanisms of chemical allergen recognition that underlie unusually frequent T cell activation can be assessed. In the future, this approach may be adapted to detect T cells activated by additional chemical sensitizers.
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Affiliation(s)
- Caterina Curato
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Marina Aparicio-Soto
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Franziska Riedel
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ingrun Wehl
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Alev Basaran
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Amro Abbas
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- German Rheumatism Research Center (DRFZ), Berlin, Germany
| | - Hermann-Josef Thierse
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Andreas Luch
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Katherina Siewert
- Dermatotoxicology Study Centre, Berlin, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- *Correspondence: Katherina Siewert,
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47
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Nicoli F, Clave E, Wanke K, von Braun A, Bondet V, Alanio C, Douay C, Baque M, Lependu C, Marconi P, Stiasny K, Heinz FX, Muetsch M, Duffy D, Boddaert J, Sauce D, Toubert A, Karrer U, Appay V. Primary immune responses are negatively impacted by persistent herpesvirus infections in older people: results from an observational study on healthy subjects and a vaccination trial on subjects aged more than 70 years old. EBioMedicine 2022; 76:103852. [PMID: 35114631 PMCID: PMC8818547 DOI: 10.1016/j.ebiom.2022.103852] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 01/08/2023] Open
Abstract
Background Advanced age is accompanied by a decline of immune functions, which may play a role in increased vulnerability to emerging pathogens and low efficacy of primary vaccinations in elderly people. The capacity to mount immune responses against new antigens is particularly affected in this population. However, its precise determinants are not fully understood. We aimed here at establishing the influence of persistent viral infections on the naive T-cell compartment and primary immune responsiveness in older adults. Methods We assessed immunological parameters, related to CD8+ and CD4+ T-cell responsiveness, according to the serological status for common latent herpesviruses in two independent cohorts: 1) healthy individuals aged 19y to 95y (n = 150) and 2) individuals above 70y old enrolled in a primo-vaccination clinical trial (n = 137). Findings We demonstrate a prevalent effect of age and CMV infection on CD8+ and CD4+ naive T cells, respectively. CMV seropositivity was associated with blunted CD4+ T-cell and antibody responses to primary vaccination. Interpretation These data provide insights on the changes in adaptive immunity over time and the associated decline in vaccine efficacy with ageing. This knowledge is important for the management of emerging infectious diseases in elderly populations.
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Affiliation(s)
- Francesco Nicoli
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France; Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Emmanuel Clave
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris F-75010, France
| | - Kerstin Wanke
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland
| | - Amrei von Braun
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Vincent Bondet
- Translational Immunology Lab, Institut Pasteur, Université de Paris, Paris, France
| | - Cécile Alanio
- INSERM U932, PSL University, Institut Curie, Paris 75005, France; Laboratoire D'immunologie Clinique, Institut Curie, Paris 75005, France
| | - Corinne Douay
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris F-75010, France
| | - Margaux Baque
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France
| | - Claire Lependu
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France
| | - Peggy Marconi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara 44121, Italy
| | - Karin Stiasny
- Center for Virology, Medical University of Vienna, Austria
| | - Franz X Heinz
- Center for Virology, Medical University of Vienna, Austria
| | - Margot Muetsch
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Université de Paris, Paris, France
| | - Jacques Boddaert
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France
| | - Delphine Sauce
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France
| | - Antoine Toubert
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris F-75010, France; Laboratoire d'Immunologie et d'Histocompatibilité, AP-HP, Hopital Saint-Louis, Paris F-75010, France
| | - Urs Karrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Zurich, Switzerland; Division of Infectious Diseases, Department of Medicine, Cantonal Hospital of Winterthur, Winterthur, Switzerland.
| | - Victor Appay
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM U1135, 75013 Paris, France; Université de Bordeaux, CNRS UMR5164, INSERM ERL1303, ImmunoConcEpT, Bordeaux, France; International Research Center of Medical Sciences, Kumamoto University, Kumamoto, Japan.
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48
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Patel S, Ramnoruth N, Wehr P, Rossjohn J, Reid HH, Campbell K, Nel HJ, Thomas R. Evaluation of a fit-for-purpose assay to monitor antigen-specific functional CD4+ T-cell subpopulations in rheumatoid arthritis using flow cytometry-based peptide-MHC class-II tetramer staining. Clin Exp Immunol 2022; 207:72-83. [PMID: 35020859 PMCID: PMC8802177 DOI: 10.1093/cei/uxab008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Antigen-specific T cells can serve as a response biomarker in non-clinical or clinical immunotherapy studies in autoimmune disease. There are protocols with optimized multimer staining methods to detect peptide (p)MHCII+ CD4+ T cells, and some qualified and validated protocols for pMHCI+ CD8+ T cells. However, no protocol is fully or partially qualified to enumerate and characterize antigen-specific pMHCII+ CD4+ T cells from patient samples. Implementing such an assay requires a desired level of specificity and precision, in terms of assay repeatability and reproducibility. In transgenic type II collagen (CII)-immunized HLA-DR1/DR4 humanized mouse models of collagen-induced arthritis (CIA), CII259-273-specific T cells dominantly expand. Therefore antigen-specific T cells recognizing this epitope presented by rheumatoid arthritis (RA)-associated risk HLA-DR allomorphs are of interest to understand disease progression and responses to immunotherapy in RA patients. Using HLA-DRB1∗04:01 or ∗01:01-collagen type II (CII)259–273 tetramers, we evaluated parameters influencing precision and reproducibility of an optimized flow cytometry–based method for antigen-specific CD4+ T cells and eight specific subpopulations with and without tetramer positivity. We evaluated specificity, precision, and reproducibility for research environments and non-regulated laboratories. The assay has excellent overall precision with %CV<25% for intra-assay repeatability, inter-analyst precision, and inter-assay reproducibility. The precision of the assay correlated negatively with the cell viability after thawing, indicating that post-thaw viability is a critical parameter for reproducibility. This assay is suitable for longitudinal analysis of treatment response and disease activity outcome in RA patients, and adaptable for translational or immunotherapy clinical trial settings.
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Affiliation(s)
- Swati Patel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Nishta Ramnoruth
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pascale Wehr
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugh H Reid
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Kim Campbell
- Janssen Research & Development, LLC, Spring House, PA, USA.,Janssen Research & Development, LLC, La Jolla, CA, USA
| | - Hendrik J Nel
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
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49
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Elias G, Meysman P, Bartholomeus E, De Neuter N, Keersmaekers N, Suls A, Jansens H, Souquette A, De Reu H, Emonds MP, Smits E, Lion E, Thomas PG, Mortier G, Van Damme P, Beutels P, Laukens K, Van Tendeloo V, Ogunjimi B. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination. eLife 2022; 11:68388. [PMID: 35074048 PMCID: PMC8824481 DOI: 10.7554/elife.68388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Antigen recognition through the T cell receptor (TCR) αβ heterodimer is one of the primary determinants of the adaptive immune response. Vaccines activate naïve T cells with high specificity to expand and differentiate into memory T cells. However, antigen-specific memory CD4 T cells exist in unexposed antigen-naïve hosts. In this study, we use high-throughput sequencing of memory CD4 TCRβ repertoire and machine learning to show that individuals with preexisting vaccine-reactive memory CD4 T cell clonotypes elicited earlier and higher antibody titers and mounted a more robust CD4 T cell response to hepatitis B vaccine. In addition, integration of TCRβ sequence patterns into a hepatitis B epitope-specific annotation model can predict which individuals will have an early and more vigorous vaccine-elicited immunity. Thus, the presence of preexisting memory T cell clonotypes has a significant impact on immunity and can be used to predict immune responses to vaccination. Immune cells called CD4 T cells help the body build immunity to infections caused by bacteria and viruses, or after vaccination. Receptor proteins on the outside of the cells recognize pathogens, foreign molecules called antigens, or vaccine antigens. Vaccine antigens are usually inactivated bacteria or viruses, or fragments of these pathogens. After recognizing an antigen, CD4 T cells develop into memory CD4 T cells ready to defend against future infections with the pathogen. People who have never been exposed to a pathogen, or have never been vaccinated against it, may nevertheless have preexisting memory cells ready to defend against it. This happens because CD4 T cells can recognize multiple targets, which enables the immune system to be ready to defend against both new and familiar pathogens. Elias, Meysman, Bartholomeus et al. wanted to find out whether having preexisting memory CD4 T cells confers an advantage for vaccine-induced immunity. Thirty-four people who were never exposed to hepatitis B or vaccinated against it participated in the study. These individuals provided blood samples before vaccination, with 2 doses of the hepatitis B vaccine, and at 3 time points afterward. Using next generation immune sequencing and machine learning techniques, Elias et al. analyzed the individuals’ memory CD4 T cells before and after vaccination. The experiments showed that preexisting memory CD4 T cells may determine vaccination outcomes, and people with more preexisting memory cells develop quicker and stronger immunity after vaccination against hepatitis B. This information may help scientists to better understand how people develop immunity to pathogens. It may guide them develop better vaccines or predict who will develop immunity after vaccination.
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Affiliation(s)
- George Elias
- Laboratory of Experimental Hematology (LEH), University of Antwerp
| | - Pieter Meysman
- Biomedical Informatics Research Network Antwerp, Department of Mathematics and Informatics, University of Antwerp
| | | | - Nicolas De Neuter
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Nina Keersmaekers
- Centre for Health Economics Research & Modeling Infectious Diseases, University of Antwerp
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital
| | - Hans De Reu
- Laboratory of Experimental Hematology, University of Antwerp
| | | | - Evelien Smits
- Laboratory of Experimental Hematology, University of Antwerp
| | - Eva Lion
- Laboratory of Experimental Hematology, University of Antwerp
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital
| | - Geert Mortier
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Viggo Van Tendeloo
- Janssen Research and Development, Immunosciences WWDA, Johnson and Johnson
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
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50
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Tarabini RF, Rigo MM, Faustino Fonseca A, Rubin F, Bellé R, Kavraki LE, Ferreto TC, Amaral Antunes D, de Souza APD. Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2. Front Immunol 2022; 12:812176. [PMID: 35095907 PMCID: PMC8793865 DOI: 10.3389/fimmu.2021.812176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
Although not being the first viral pandemic to affect humankind, we are now for the first time faced with a pandemic caused by a coronavirus. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been responsible for the COVID-19 pandemic, which caused more than 4.5 million deaths worldwide. Despite unprecedented efforts, with vaccines being developed in a record time, SARS-CoV-2 continues to spread worldwide with new variants arising in different countries. Such persistent spread is in part enabled by public resistance to vaccination in some countries, and limited access to vaccines in other countries. The limited vaccination coverage, the continued risk for resistant variants, and the existence of natural reservoirs for coronaviruses, highlight the importance of developing additional therapeutic strategies against SARS-CoV-2 and other coronaviruses. At the beginning of the pandemic it was suggested that countries with Bacillus Calmette-Guérin (BCG) vaccination programs could be associated with a reduced number and/or severity of COVID-19 cases. Preliminary studies have provided evidence for this relationship and further investigation is being conducted in ongoing clinical trials. The protection against SARS-CoV-2 induced by BCG vaccination may be mediated by cross-reactive T cell lymphocytes, which recognize peptides displayed by class I Human Leukocyte Antigens (HLA-I) on the surface of infected cells. In order to identify potential targets of T cell cross-reactivity, we implemented an in silico strategy combining sequence-based and structure-based methods to screen over 13,5 million possible cross-reactive peptide pairs from BCG and SARS-CoV-2. Our study produced (i) a list of immunogenic BCG-derived peptides that may prime T cell cross-reactivity against SARS-CoV-2, (ii) a large dataset of modeled peptide-HLA structures for the screened targets, and (iii) new computational methods for structure-based screenings that can be used by others in future studies. Our study expands the list of BCG peptides potentially involved in T cell cross-reactivity with SARS-CoV-2-derived peptides, and identifies multiple high-density "neighborhoods" of cross-reactive peptides which could be driving heterologous immunity induced by BCG vaccination, therefore providing insights for future vaccine development efforts.
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Affiliation(s)
- Renata Fioravanti Tarabini
- Laboratory of Clinical and Experimental Immunology, Infant Center, School of Health Science, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | | | - André Faustino Fonseca
- Antunes Lab, Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Felipe Rubin
- School of Technology - Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Rafael Bellé
- Laboratório de alto desempenho – Centro de Apoio ao desenvolvimento cientifico e tecnológico da (IDEIA), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Lydia E Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Tiago Coelho Ferreto
- School of Technology - Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil,Laboratório de alto desempenho – Centro de Apoio ao desenvolvimento cientifico e tecnológico da (IDEIA), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Dinler Amaral Antunes
- Antunes Lab, Department of Biology and Biochemistry, University of Houston, Houston, TX, United States,*Correspondence: Ana Paula Duarte de Souza, ; Dinler Amaral Antunes,
| | - Ana Paula Duarte de Souza
- Laboratory of Clinical and Experimental Immunology, Infant Center, School of Health Science, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil,*Correspondence: Ana Paula Duarte de Souza, ; Dinler Amaral Antunes,
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