1
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Bullock ME, Hogan T, Williams C, Morris S, Nowicka M, Sharjeel M, van Dorp C, Yates AJ, Seddon B. The dynamics and longevity of circulating CD4 + memory T cells depend on cell age and not the chronological age of the host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562650. [PMID: 38948729 PMCID: PMC11212895 DOI: 10.1101/2023.10.16.562650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Quantifying the kinetics with which memory T cell populations are generated and maintained is essential for identifying the determinants of the duration of immunity. The quality and persistence of circulating CD4+ effector memory (TEM) and central memory (TCM) T cells in mice appear to shift with age, but it is unclear whether these changes are driven by the aging host environment, by cell age effects, or both. Here we address these issues by combining DNA labelling methods, established fate-mapping systems, a novel reporter mouse strain, and mathematical models. Together, these allow us to quantify the dynamics of both young and established circulating memory CD4+ T cell subsets, within both young and old mice. We show that that these cells and their descendents become more persistent the longer they reside within the TCM and TEM pools. This behaviour may limit memory CD4 T cell diversity by skewing TCR repertoires towards clones generated early in life, but may also compensate for functional defects in new memory cells generated in old age.
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Affiliation(s)
- M. Elise Bullock
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Cayman Williams
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Sinead Morris
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Maria Nowicka
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Minahil Sharjeel
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Christiaan van Dorp
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, United Kingdom
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2
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de Boer RJ, Tesselaar K, Borghans JAM. Better safe than sorry: Naive T-cell dynamics in healthy ageing. Semin Immunol 2023; 70:101839. [PMID: 37716048 DOI: 10.1016/j.smim.2023.101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/18/2023]
Abstract
It is well-known that the functioning of the immune system gradually deteriorates with age, and we are increasingly confronted with its consequences as the life expectancy of the human population increases. Changes in the T-cell pool are among the most prominent features of the changing immune system during healthy ageing, and changes in the naive T-cell pool in particular are generally held responsible for its gradual deterioration. These changes in the naive T-cell pool are thought to be due to involution of the thymus. It is commonly believed that the gradual loss of thymic output induces compensatory mechanisms to maintain the number of naive T cells at a relatively constant level, and induces a loss of diversity in the T-cell repertoire. Here we review the studies that support or challenge this widely-held view of immune ageing and discuss the implications for vaccination strategies.
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Affiliation(s)
- Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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3
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Lukas E, Hogan T, Williams C, Seddon B, Yates AJ. Quantifying cellular dynamics in mice using a novel fluorescent division reporter system. Front Immunol 2023; 14:1157705. [PMID: 37575229 PMCID: PMC10412932 DOI: 10.3389/fimmu.2023.1157705] [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: 02/02/2023] [Accepted: 06/20/2023] [Indexed: 08/15/2023] Open
Abstract
The dynamics of cell populations are frequently studied in vivo using pulse-chase DNA labeling techniques. When combined with mathematical models, the kinetic of label uptake and loss within a population of interest then allows one to estimate rates of cell production and turnover through death or onward differentiation. Here we explore an alternative method of quantifying cellular dynamics, using a cell fate-mapping mouse model in which dividing cells can be induced to constitutively express a fluorescent protein, using a Ki67 reporter construct. We use a pulse-chase approach with this reporter mouse system to measure the lifespans and division rates of naive CD4 and CD8 T cells using a variety of modeling approaches, and show that they are all consistent with estimates derived from other published methods. However we propose that to obtain unbiased parameter estimates and full measures of their uncertainty one should simultaneously model the timecourses of the frequencies of labeled cells within both the population of interest and its precursor. We conclude that Ki67 reporter mice provide a promising system for modeling cellular dynamics.
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Affiliation(s)
- Eva Lukas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Cayman Williams
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London (UCL), Royal Free Hospital, London, United Kingdom
| | - Andrew J. Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
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4
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Yu P, Lian Y, Zuleger CL, Albertini RJ, Albertini MR, Newton MA. SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548950. [PMID: 37503118 PMCID: PMC10369934 DOI: 10.1101/2023.07.13.548950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant T cell clones. Our specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.
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Affiliation(s)
- Peng Yu
- Department of Statistics, University of Wisconsin, Madison
| | - Yumin Lian
- Department of Chemistry, Laboratory of Genetics, University of Wisconsin, Madison
| | - Cindy L. Zuleger
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
| | | | - Mark R. Albertini
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
- Medical Service, William S. Middleton Memorial Veterans Hospital, Madison
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
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5
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De Boer RJ, Yates AJ. Modeling T Cell Fate. Annu Rev Immunol 2023; 41:513-532. [PMID: 37126420 PMCID: PMC11100019 DOI: 10.1146/annurev-immunol-101721-040924] [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] [Indexed: 05/02/2023]
Abstract
Many of the pathways that underlie the diversification of naive T cells into effector and memory subsets, and the maintenance of these populations, remain controversial. In recent years a variety of experimental tools have been developed that allow us to follow the fates of cells and their descendants. In this review we describe how mathematical models provide a natural language for describing the growth, loss, and differentiation of cell populations. By encoding mechanistic descriptions of cell behavior, models can help us interpret these new datasets and reveal the rules underpinning T cell fate decisions, both at steady state and during immune responses.
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Affiliation(s)
- Rob J De Boer
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands;
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA;
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6
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Swain AC, Borghans JA, de Boer RJ. Effect of cellular aging on memory T-cell homeostasis. Front Immunol 2022; 13:947242. [PMID: 36059495 PMCID: PMC9429809 DOI: 10.3389/fimmu.2022.947242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
Abstract
The fact that T-cell numbers remain relatively stable throughout life, and that T-cell proliferation rates increase during lymphopenia, has led to the consensus that T-cell numbers are regulated in a density-dependent manner. Competition for resources among memory T cells has been proposed to underlie this ‘homeostatic’ regulation. We first review how two classic models of resource competition affect the T-cell receptor (TCR) diversity of the memory T-cell pool. First, ‘global’ competition for cytokines leads to a skewed repertoire that tends to be dominated by the very first immune response. Second, additional ‘cognate’ competition for specific antigens results in a very diverse and stable memory T-cell pool, allowing every antigen to be remembered, which we therefore define as the ‘gold-standard’. Because there is limited evidence that memory T cells of the same specificity compete more strongly with each other than with memory T cells of different specificities, i.e., for ‘cognate’ competition, we investigate whether cellular aging could account for a similar level of TCR diversity. We define cellular aging as a declining cellular fitness due to reduced proliferation. We find that the gradual erosion of previous T-cell memories due to cellular aging allows for better establishment of novel memories and for a much higher level of TCR diversity compared to global competition. A small continual source (either from stem-cell-like memory T-cells or from naive T-cells due to repeated antigen exposure) improves the diversity of the memory T-cell pool, but remarkably, only in the cellular aging model. We further show that the presence of a source keeps the inflation of chronic memory responses in check by maintaining the immune memories to non-chronic antigens. We conclude that cellular aging along with a small source provides a novel and immunologically realistic mechanism to achieve and maintain the ‘gold-standard’ level of TCR diversity in the memory T-cell pool.
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Affiliation(s)
- Arpit C. Swain
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Arpit C. Swain,
| | - José A.M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rob J. de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
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7
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Rane S, Hogan T, Lee E, Seddon B, Yates AJ. Towards a unified model of naive T cell dynamics across the lifespan. eLife 2022; 11:78168. [PMID: 35678373 PMCID: PMC9348855 DOI: 10.7554/elife.78168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
Naive CD4 and CD8 T cells are cornerstones of adaptive immunity, but the dynamics of their establishment early in life and how their kinetics change as they mature following release from the thymus are poorly understood. Further, due to the diverse signals implicated in naive T cell survival, it has been a long-held and conceptually attractive view that they are sustained by active homeostatic control as thymic activity wanes. Here we use multiple modelling and experimental approaches to identify a unified model of naive CD4 and CD8 T cell population dynamics in mice, across their lifespan. We infer that both subsets divide rarely, and progressively increase their survival capacity with cell age. Strikingly, this simple model is able to describe naive CD4 T cell dynamics throughout life. In contrast, we find that newly generated naive CD8 T cells are lost more rapidly during the first 3-4 weeks of life, likely due to increased recruitment into memory. We find no evidence for elevated division rates in neonates, or for feedback regulation of naive T cell numbers at any age. We show how confronting mathematical models with diverse datasets can reveal a quantitative and remarkably simple picture of naive T cell dynamics in mice from birth into old age.
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Affiliation(s)
- Sanket Rane
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, United States.,Irving Institute for Cancer Dynamics, Columbia University, New York, United States
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - Edward Lee
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, United States
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, United States
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8
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Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation. Front Immunol 2022; 12:735135. [PMID: 35250963 PMCID: PMC8891377 DOI: 10.3389/fimmu.2021.735135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
The specificity of T cells is that each T cell has only one T cell receptor (TCR). A T cell clone represents a collection of T cells with the same TCR sequence. Thus, the number of different T cell clones in an organism reflects the number of different T cell receptors (TCRs) that arise from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution, are important factors in immune functions. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. We describe the heterogeneous steady-state population of naive T cells (those that have not yet been antigenically triggered) by using a mean-field model of a regulated birth-death-immigration process. After accounting for random sampling, we investigate how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or “clone counts”). By using reasonable physiological parameter values and fitting predicted clone counts to experimentally sampled clone abundances, we show that realistic levels of heterogeneity in immigration rates cause very little change to predicted clone-counts, but that modest heterogeneity in proliferation rates can generate the observed clone abundances. Our analysis provides constraints among physiological parameters that are necessary to yield predictions that qualitatively match the data. Assumptions of the model and potentially other important mechanistic factors are discussed.
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Affiliation(s)
- Renaud Dessalles
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Yunbei Pan
- Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Mingtao Xia
- Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Davide Maestrini
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Maria R D'Orsogna
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Tom Chou
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
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9
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Immunopathogenesis of patients with COVID-19: from the perspective of immune system 'evolution' and 'revolution'. Expert Rev Mol Med 2022; 24:e19. [PMID: 35535759 PMCID: PMC9884756 DOI: 10.1017/erm.2022.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 is sweeping the world, threatening millions of lives and drastically altering our ways of living. According to current studies, failure to either activate or eliminate inflammatory responses timely and properly at certain stages could result in the progression of the disease. In other words, robust immune responses to coronavirus disease 2019 (COVID-19) are critical. However, they do not theoretically present in some special groups of people, including the young, the aged, patients with autoimmunity or cancer. Differences also do occur between men and women. Our immune system evolves to ensure delicate coordination at different stages of life. The innate immune cells mainly consisted of myeloid lineage cells, including neutrophils, basophils, eosinophils, dendritic cells and mast cells; they possess phagocytic capacity to different degrees at different stages of life. They are firstly recruited upon infection and may activate the adaptive immunity when needed. The adaptive immune cells, on the other way, are comprised mainly of lymphoid lineages. As one grows up, the adaptive immunity matures and expands its memory repertoire, accompanied by an adjustment in quantity and quality. In this review, we would summarise and analyse the immunological characteristics of these groups from the perspective of the immune system 'evolution' as well as 'revolution' that has been studied and speculated so far, which would aid the comprehensive understanding of COVID-19 and personalised-treatment strategy.
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10
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Nauman G, Danzl NM, Lee J, Borsotti C, Madley R, Fu J, Hölzl MA, Dahmani A, Dorronsoro Gonzalez A, Chavez É, Campbell SR, Yang S, Satwani P, Liu K, Sykes M. Defects in Long-Term APC Repopulation Ability of Adult Human Bone Marrow Hematopoietic Stem Cells (HSCs) Compared with Fetal Liver HSCs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1652-1663. [PMID: 35315788 PMCID: PMC8976823 DOI: 10.4049/jimmunol.2100966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/25/2022] [Indexed: 04/28/2023]
Abstract
Immunodeficient mice reconstituted with immune systems from patients, or personalized immune (PI) mice, are powerful tools for understanding human disease. Compared with immunodeficient mice transplanted with human fetal thymus tissue and fetal liver-derived CD34+ cells administered i.v. (Hu/Hu mice), PI mice, which are transplanted with human fetal thymus and adult bone marrow (aBM) CD34+ cells, demonstrate reduced levels of human reconstitution. We characterized APC and APC progenitor repopulation in human immune system mice and detected significant reductions in blood, bone marrow (BM), and splenic APC populations in PI compared with Hu/Hu mice. APC progenitors and hematopoietic stem cells (HSCs) were less abundant in aBM CD34+ cells compared with fetal liver-derived CD34+ cell preparations, and this reduction in APC progenitors was reflected in the BM of PI compared with Hu/Hu mice 14-20 wk posttransplant. The number of HSCs increased in PI mice compared with the originally infused BM cells and maintained functional repopulation potential, because BM from some PI mice 28 wk posttransplant generated human myeloid and lymphoid cells in secondary recipients. Moreover, long-term PI mouse BM contained functional T cell progenitors, evidenced by thymopoiesis in thymic organ cultures. Injection of aBM cells directly into the BM cavity, transgenic expression of hematopoietic cytokines, and coinfusion of human BM-derived mesenchymal stem cells synergized to enhance long-term B cell and monocyte levels in PI mice. These improvements allow a sustained time frame of 18-22 wk where APCs and T cells are present and greater flexibility for modeling immune disease pathogenesis and immunotherapies in PI mice.
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Affiliation(s)
- Grace Nauman
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Nichole M Danzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jaeyop Lee
- Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Chiara Borsotti
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Rachel Madley
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Markus A Hölzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Alexander Dahmani
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Akaitz Dorronsoro Gonzalez
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Éstefania Chavez
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Sean R Campbell
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Suxiao Yang
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Prakash Satwani
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Pediatrics, Columbia University Medical Center, Columbia University, New York, NY
| | - Kang Liu
- Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT; and
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, NY;
- Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY
- Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Surgery, Columbia University Medical Center, Columbia University, New York, NY
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11
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Toma G, Lemnian IM, Karapetian E, Grosse I, Seliger B. Transcriptional Analysis of Total CD8 + T Cells and CD8 +CD45RA - Memory T Cells From Young and Old Healthy Blood Donors. Front Immunol 2022; 13:806906. [PMID: 35154123 PMCID: PMC8829550 DOI: 10.3389/fimmu.2022.806906] [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: 11/01/2021] [Accepted: 01/05/2022] [Indexed: 12/02/2022] Open
Abstract
Memory CD8+ T cells accumulate with aging, while the naïve T cell compartment decreases, leading to an increased susceptibility to infections and a decreased vaccine efficiency. To get deeper insights into the underlying mechanisms, this study aims to determine the age-dependent expression profile of total versus memory CD8+ T cells from young and old donors. Total CD8+ and CD8+CD45RA- memory T cells isolated from young (<30 years) and old (>60 years) donors were stimulated with anti-CD3 and anti-CD28 antibodies for 48h before analyzing the cytokine secretion and activation markers by flow cytometry and changes in the expression profiles using RNA sequencing. Gene ontology (GO) term enrichment analyses were performed for up-regulated and uniquely expressed transcripts identified in the T cell populations of both age groups. Total and memory CD8+ T cells from old donors expressed significantly higher CD25 levels and have an increased cytokine secretion. While approximately 1,500 up-regulated transcripts were identified in all groups, CD8+CD45RA- memory T cells of old donors had approximately 500 more uniquely expressed transcripts. Four GO terms related to the JAK-STAT pathway were identified for up-regulated transcripts in the total CD8+ T cells of old donors, whereas CD8+CD45RA- memory T cells GO terms related to adjacent pathways, like JNK and MAPK/ERK, were found. Additionally, the unique transcripts of CD8+CD45RA- memory T cells of old donors were related to the JNK, MAPK and IL-12 pathways. For both T cell populations of the old donors, cytokine and JAK-STAT pathway transcripts were up-regulated. Thus, an age-dependent effect was observed on the transcriptomes of total and memory CD8+ T cells. The CD8+ CD45RA- memory T cells from old donors maintained the increased cytokine secretion of the total CD8+ T cell population and the increased JAK-STAT pathway transcripts, which have an impact on inflammation and senescence.
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Affiliation(s)
- Georgiana Toma
- Institute for Medical Immunology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Ioana Maria Lemnian
- Institute for Computer Science, Martin-Luther University Halle-Wittenberg, Halle, Germany.,Institute for Human Genetics, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Eliza Karapetian
- Institute for Medical Immunology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Ivo Grosse
- Institute for Computer Science, Martin-Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Barbara Seliger
- Institute for Medical Immunology, Martin-Luther University Halle-Wittenberg, Halle, Germany.,Department for Therapeutics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
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12
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Quan Y, Li L, Yin Z, Chen S, Yi J, Lang J, Zhang L, Yue Q, Zhao J. Bulbus Fritillariae Cirrhosae as a Respiratory Medicine: Is There a Potential Drug in the Treatment of COVID-19? Front Pharmacol 2022; 12:784335. [PMID: 35126123 PMCID: PMC8811224 DOI: 10.3389/fphar.2021.784335] [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: 09/27/2021] [Accepted: 12/03/2021] [Indexed: 01/08/2023] Open
Abstract
Bulbus fritillariae cirrhosae (BFC) is one of the most used Chinese medicines for lung disease, and exerts antitussive, expectorant, anti-inflammatory, anti-asthmatic, and antioxidant effects, which is an ideal therapeutic drug for respiratory diseases such as ARDS, COPD, asthma, lung cancer, and pulmonary tuberculosis. Through this review, it is found that the therapeutic mechanism of BFC on respiratory diseases exhibits the characteristics of multi-components, multi-targets, and multi-signaling pathways. In particular, the therapeutic potential of BFC in terms of intervention of “cytokine storm”, STAT, NF-κB, and MAPK signaling pathways, as well as the renin-angiotensin system (RAS) that ACE is involved in. In the “cytokine storm” of SARS-CoV-2 infection there is an intense inflammatory response. ACE2 regulates the RAS by degradation of Ang II produced by ACE, which is associated with SARS-CoV-2. For COVID-19, may it be a potential drug? This review summarized the research progress of BFC in the respiratory diseases, discussed the development potentiality of BFC for the treatment of COVID-19, explained the chemical diversity and biological significance of the alkaloids in BFC, and clarified the material basis, molecular targets, and signaling pathways of BFC for the respiratory diseases. We hope this review can provide insights on the drug discovery of anti-COVID-19.
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Affiliation(s)
- Yunyun Quan
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
- Department of Pharmacognosy, West China School of Pharmacy Sichuan University, Chengdu, China
| | - Li Li
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Zhujun Yin
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Shilong Chen
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Jing Yi
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Jirui Lang
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Lu Zhang
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Qianhua Yue
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
| | - Junning Zhao
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, China
- Department of Pharmacognosy, West China School of Pharmacy Sichuan University, Chengdu, China
- *Correspondence: Junning Zhao,
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13
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Abstract
Naïve T cells are critical for protection against emerging viral and bacterial infections. However, the ability of these cells to elicit effective long-term immune responses declines with age and contributes to increased disease susceptibility in older individuals. This decline has been linked with the breakdown of cellular quiescence that causes partial differentiation of naïve T cells with age, but the underlying mediators of this breakdown are unclear. Comparisons to stem cell quiescence in mice and man offer insight into naïve T cells and aging. However, the utilization of single cell technologies in combination with advances in the biology of human tissue aging is needed to provide further understanding of naïve T cell complexity and quiescence breakdown with age.
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14
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Gustafson CE, Kim C, Weyand CM, Goronzy JJ. Influence of immune aging on vaccine responses. J Allergy Clin Immunol 2021; 145:1309-1321. [PMID: 32386655 PMCID: PMC7198995 DOI: 10.1016/j.jaci.2020.03.017] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Impaired vaccine responses in older individuals are associated with alterations in both the quantity and quality of the T-cell compartment with age. As reviewed herein, the T-cell response to vaccination requires a fine balance between the generation of inflammatory effector T cells versus follicular helper T (TFH) cells that mediate high-affinity antibody production in tandem with the induction of long-lived memory cells for effective recall immunity. During aging, we find that this balance is tipped where T cells favor short-lived effector but not memory or TFH responses. Consistently, vaccine-induced antibodies commonly display a lower protective capacity. Mechanistically, multiple, potentially targetable, changes in T cells have been identified that contribute to these age-related defects, including posttranscription regulation, T-cell receptor signaling, and metabolic function. Although research into the induction of tissue-specific immunity by vaccines and with age is still limited, current mechanistic insights provide a framework for improved design of age-specific vaccination strategies that require further evaluation in a clinical setting.
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Affiliation(s)
- Claire E Gustafson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Department of Medicine, Veterans Administration Healthcare System, Palo Alto, Calif
| | - Chulwoo Kim
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Department of Medicine, Veterans Administration Healthcare System, Palo Alto, Calif
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Department of Medicine, Veterans Administration Healthcare System, Palo Alto, Calif
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, Calif; Department of Medicine, Veterans Administration Healthcare System, Palo Alto, Calif.
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15
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Baliu-Piqué M, van Hoeven V, Drylewicz J, van der Wagen LE, Janssen A, Otto SA, van Zelm MC, de Boer RJ, Kuball J, Borghans JA, Tesselaar K. Cell-density independent increased lymphocyte production and loss rates post-autologous HSCT. eLife 2021; 10:59775. [PMID: 33538246 PMCID: PMC7886352 DOI: 10.7554/elife.59775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Lymphocyte numbers need to be quite tightly regulated. It is generally assumed that lymphocyte production and lifespan increase homeostatically when lymphocyte numbers are low and, vice versa, return to normal once cell numbers have normalized. This widely accepted concept is largely based on experiments in mice, but is hardly investigated in vivo in humans. Here we quantified lymphocyte production and loss rates in vivo in patients 0.5–1 year after their autologous hematopoietic stem cell transplantation (autoHSCT). We indeed found that the production rates of most T- and B-cell subsets in autoHSCT-patients were two to eight times higher than in healthy controls, but went hand in hand with a threefold to ninefold increase in cell loss rates. Both rates also did not normalize when cell numbers did. This shows that increased lymphocyte production and loss rates occur even long after autoHSCT and can persist in the face of apparently normal cell numbers.
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Affiliation(s)
- Mariona Baliu-Piqué
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Vera van Hoeven
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Julia Drylewicz
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Anke Janssen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Sigrid A Otto
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Menno C van Zelm
- Department of Immunology and Pathology, Monash University and Alfred Hospital, Melbourne, Australia
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Jürgen Kuball
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Hematology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jose Am Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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16
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Yiu HH, Schoettle LN, Garcia-Neuer M, Blattman JN, Johnson PLF. Selection influences naive CD8+ TCR-β repertoire sharing. Immunology 2021; 162:464-475. [PMID: 33345304 DOI: 10.1111/imm.13299] [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: 01/16/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 11/28/2022] Open
Abstract
Within each individual, the adaptive immune system generates a repertoire of cells expressing receptors capable of recognizing diverse potential pathogens. The theoretical diversity of the T-cell receptor (TCR) repertoire exceeds the actual size of the T-cell population in an individual by several orders of magnitude - making the observation of identical TCRs in different individuals extremely improbable if all receptors were equally likely. Despite this disparity between the theoretical and the realized diversity of the repertoire, these 'public' receptor sequences have been identified in autoimmune, cancer and pathogen interaction contexts. Biased generation processes explain the presence of public TCRs in the naive repertoire, but do not adequately explain the different abundances of these public TCRs. We investigate and characterize the distribution of genomic TCR-β sequences of naive CD8+ T cells from three genetically identical mice, comparing non-productive (non-functional sequences) and productive sequences. We find public TCR-β sequences at higher abundances compared with unshared sequences in the productive, but not in the non-productive, repertoire. We show that neutral processes such as recombination biases, codon degeneracy and generation probability do not fully account for these differences, and conclude that thymic or peripheral selection plays an important role in increasing the abundances of public TCR-β sequences.
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Affiliation(s)
- Hao H Yiu
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Louis N Schoettle
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Marlene Garcia-Neuer
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joseph N Blattman
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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17
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Zöphel D, Hof C, Lis A. Altered Ca 2+ Homeostasis in Immune Cells during Aging: Role of Ion Channels. Int J Mol Sci 2020; 22:ijms22010110. [PMID: 33374304 PMCID: PMC7794837 DOI: 10.3390/ijms22010110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/29/2022] Open
Abstract
Aging is an unstoppable process and begins shortly after birth. Each cell of the organism is affected by the irreversible process, not only with equal density but also at varying ages and with different speed. Therefore, aging can also be understood as an adaptation to a continually changing cellular environment. One of these very prominent changes in age affects Ca2+ signaling. Especially immune cells highly rely on Ca2+-dependent processes and a strictly regulated Ca2+ homeostasis. The intricate patterns of impaired immune cell function may represent a deficit or compensatory mechanisms. Besides, altered immune function through Ca2+ signaling can profoundly affect the development of age-related disease. This review attempts to summarize changes in Ca2+ signaling due to channels and receptors in T cells and beyond in the context of aging.
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Affiliation(s)
| | | | - Annette Lis
- Correspondence: ; Tel.: +49-(0)-06841-1616318; Fax: +49-(0)-6841-1616302
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18
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D’Ippolito E, Wagner KI, Busch DH. Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells. Int J Mol Sci 2020; 21:E8324. [PMID: 33171940 PMCID: PMC7664211 DOI: 10.3390/ijms21218324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.
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MESH Headings
- Antigens, Neoplasm/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Neoplasms/genetics
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
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Affiliation(s)
- Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Focus Group ‘‘Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München (TUM), 81675 Munich, Germany
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19
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Verheijen M, Rane S, Pearson C, Yates AJ, Seddon B. Fate Mapping Quantifies the Dynamics of B Cell Development and Activation throughout Life. Cell Rep 2020; 33:108376. [PMID: 33207189 PMCID: PMC8622872 DOI: 10.1016/j.celrep.2020.108376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 01/10/2023] Open
Abstract
Follicular mature (FM) and germinal center (GC) B cells underpin humoral immunity, but the dynamics of their generation and maintenance are not clearly defined. Here, we exploited a fate-mapping system in mice that tracks B cells as they develop into peripheral subsets, together with a cell division fate reporter mouse and mathematical models. We find that FM cells are kinetically homogeneous, recirculate freely, are continually replenished from transitional populations, and self-renew rarely. In contrast, GC B cell lineages persist for weeks with rapid turnover and site-specific dynamics. Those in the spleen derive from transitional cells and are kinetically homogeneous, while those in lymph nodes derive from FM B cells and comprise both transient and persistent clones. These differences likely derive from the nature of antigen exposure at the different sites. Our integrative approach also reveals how the host environment drives cell-extrinsic, age- related changes in B cell homeostasis. Verheijen and Rane et al. combine fate mapping and mathematical models to quantify the development and dynamics of follicular mature B cells and germinal center B cells in spleen and lymph nodes, and show how these processes vary across the mouse lifespan.
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Affiliation(s)
- Melissa Verheijen
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK
| | - Sanket Rane
- Department of Pathology and Cell Biology, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA
| | - Claire Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA.
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK.
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20
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Lung innervation in the eye of a cytokine storm: neuroimmune interactions and COVID-19. Nat Rev Neurol 2020; 16:645-652. [PMID: 32843733 PMCID: PMC7446605 DOI: 10.1038/s41582-020-0402-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
COVID-19 is an infectious disease caused by the coronavirus SARS-CoV-2, which was first reported in Wuhan, China, in December 2019 and has caused a global pandemic. Acute respiratory distress syndrome (ARDS) is a common feature of severe forms of COVID-19 and can lead to respiratory failure, especially in older individuals. The increasing recognition of the neurotropic potential of SARS-CoV-2 has sparked interest in the role of the nervous system in respiratory failure in people with COVID-19. However, the neuroimmune interactions in the lung in the context of ARDS are poorly understood. In this Perspectives article, we propose the concept of the neuroimmune unit as a critical determinant of lung function in the context of COVID-19, inflammatory conditions and ageing, focusing particularly on the involvement of the vagus nerve. We discuss approaches such as neurostimulation and pharmacological neuromodulation to reduce tissue inflammation with the aim of preventing respiratory failure. Acute respiratory distress syndrome is a common occurrence in COVID-19, an infectious disease caused by the coronavirus SARS-CoV-2. In this article, the authors consider how lung innervation might crosstalk with the immune system to modulate lung function and influence outcomes in COVID-19.
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21
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Morris SE, Farber DL, Yates AJ. Tissue-Resident Memory T Cells in Mice and Humans: Towards a Quantitative Ecology. THE JOURNAL OF IMMUNOLOGY 2020; 203:2561-2569. [PMID: 31685700 DOI: 10.4049/jimmunol.1900767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
In recent years, tissue-resident memory T cells (TRM) have emerged as essential components of immunological memory. Following antigenic challenge, TRM remain in nonlymphoid tissues and defend against re-exposure. Although accumulating evidence suggests important roles for TRM in mediating protective immunity, fundamental aspects of the population biology of TRM remain poorly understood. In this article, we discuss how results from different systems shed light on the ecological dynamics of TRM in mice and humans. We highlight the importance of dissecting processes contributing to TRM maintenance, and how these might vary across phenotypically and spatially heterogeneous subsets. We also discuss how the diversity of TRM communities within specific tissues may evolve under competition and in response to antigenic perturbation. Throughout, we illustrate how mathematical models can clarify inferences obtained from experimental data and help elucidate the homeostatic mechanisms underpinning the ecology of TRM populations.
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Affiliation(s)
- Sinead E Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032; and.,Department of Surgery, Columbia University Medical Center, New York, NY 10032
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032;
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22
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Abstract
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depends on the context and application, and whether a predictive mechanistic model exists. In this topical review, we first summarize the relevant mathematical principles underlying heterogeneity in a large population, before outlining the various definitions of 'diversity' and providing examples of scientific topics in which its quantification plays an important role. We then review how diversity has been a ubiquitous concept across multiple fields, including ecology, immunology, cellular barcoding experiments, and socioeconomic studies. Since many of these applications involve sampling of populations, we also review how diversity in small samples is related to the diversity in the entire population. Features that arise in each of these applications are highlighted.
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Affiliation(s)
- Song Xu
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, United States of America
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23
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de Greef PC, Oakes T, Gerritsen B, Ismail M, Heather JM, Hermsen R, Chain B, de Boer RJ. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes. eLife 2020; 9:e49900. [PMID: 32187010 PMCID: PMC7080410 DOI: 10.7554/elife.49900] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
The clone size distribution of the human naive T-cell receptor (TCR) repertoire is an important determinant of adaptive immunity. We estimated the abundance of TCR sequences in samples of naive T cells from blood using an accurate quantitative sequencing protocol. We observe most TCR sequences only once, consistent with the enormous diversity of the repertoire. However, a substantial number of sequences were observed multiple times. We detect abundant TCR sequences even after exclusion of methodological confounders such as sort contamination, and multiple mRNA sampling from the same cell. By combining experimental data with predictions from models we describe two mechanisms contributing to TCR sequence abundance. TCRα abundant sequences can be primarily attributed to many identical recombination events in different cells, while abundant TCRβ sequences are primarily derived from large clones, which make up a small percentage of the naive repertoire, and could be established early in the development of the T-cell repertoire.
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MESH Headings
- Adaptive Immunity
- Algorithms
- Antigens/immunology
- Clonal Evolution/genetics
- Computational Biology/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunologic Memory
- Models, Biological
- Organ Specificity/genetics
- Organ Specificity/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- V(D)J Recombination
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Affiliation(s)
- Peter C de Greef
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Theres Oakes
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
- Department of Pathology, Yale School of MedicineNew HavenUnited States
| | - Mazlina Ismail
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - James M Heather
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Benjamin Chain
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
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24
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Hogan T, Nowicka M, Cownden D, Pearson CF, Yates AJ, Seddon B. Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4 + T cell memory. eLife 2019; 8:e48901. [PMID: 31742553 PMCID: PMC6905650 DOI: 10.7554/elife.48901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/17/2019] [Indexed: 11/13/2022] Open
Abstract
Laboratory mice develop populations of circulating memory CD4+ T cells in the absence of overt infection. We have previously shown that these populations are replenished from naive precursors at high levels throughout life (Gossel et al., 2017). However, the nature, relative importance and timing of the forces generating these cells remain unclear. Here, we tracked the generation of memory CD4+ T cell subsets in mice housed in facilities differing in their 'dirtiness'. We found evidence for sequential naive to central memory to effector memory development, and confirmed that both memory subsets are heterogeneous in their rates of turnover. We also inferred that early exposure to self and environmental antigens establishes persistent memory populations at levels determined largely, although not exclusively, by the dirtiness of the environment. After the first few weeks of life, however, these populations are continuously supplemented by new memory cells at rates that are independent of environment.
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Affiliation(s)
- Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and ImmunityUniversity College LondonLondonUnited Kingdom
| | - Maria Nowicka
- Department of Pathology and Cell BiologyColumbia University Medical CenterNew YorkUnited States
| | - Daniel Cownden
- Institute of Infection, Immunity and InflammationUniversity of GlasgowGlasgowUnited Kingdom
| | - Claire F Pearson
- Kennedy Institute of RheumatologyUniversity of OxfordOxfordUnited Kingdom
| | - Andrew J Yates
- Department of Pathology and Cell BiologyColumbia University Medical CenterNew YorkUnited States
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and ImmunityUniversity College LondonLondonUnited Kingdom
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25
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Mold JE, Réu P, Olin A, Bernard S, Michaëlsson J, Rane S, Yates A, Khosravi A, Salehpour M, Possnert G, Brodin P, Frisén J. Cell generation dynamics underlying naive T-cell homeostasis in adult humans. PLoS Biol 2019; 17:e3000383. [PMID: 31661488 PMCID: PMC6818757 DOI: 10.1371/journal.pbio.3000383] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/23/2019] [Indexed: 01/07/2023] Open
Abstract
Thymic involution and proliferation of naive T cells both contribute to shaping the naive T-cell repertoire as humans age, but a clear understanding of the roles of each throughout a human life span has been difficult to determine. By measuring nuclear bomb test–derived 14C in genomic DNA, we determined the turnover rates of CD4+ and CD8+ naive T-cell populations and defined their dynamics in healthy individuals ranging from 20 to 65 years of age. We demonstrate that naive T-cell generation decreases with age because of a combination of declining peripheral division and thymic production during adulthood. Concomitant decline in T-cell loss compensates for decreased generation rates. We investigated putative mechanisms underlying age-related changes in homeostatic regulation of CD4+ naive T-cell turnover, using mass cytometry to profile candidate signaling pathways involved in T-cell activation and proliferation relative to CD31 expression, a marker of thymic proximity for the CD4+ naive T-cell population. We show that basal nuclear factor κB (NF-κB) phosphorylation positively correlated with CD31 expression and thus is decreased in peripherally expanded naive T-cell clones. Functionally, we found that NF-κB signaling was essential for naive T-cell proliferation to the homeostatic growth factor interleukin (IL)-7, and reduced NF-κB phosphorylation in CD4+CD31− naive T cells is linked to reduced homeostatic proliferation potential. Our results reveal an age-related decline in naive T-cell turnover as a putative regulator of naive T-cell diversity and identify a molecular pathway that restricts proliferation of peripherally expanded naive T-cell clones that accumulate with age. Our pool of naive T cells is critical for protection against new infections and cancers. By measuring remnant 14C from 1960s nuclear bomb blasts that has been incorporated into cellular DNA, this study defines the average age of the naive T-cell pool in healthy adults, revealing the slow, regulated turnover of the naive T-cell pool, supporting its maintenance for a human lifetime.
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Affiliation(s)
- Jeff E. Mold
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Pedro Réu
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Axel Olin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - Samuel Bernard
- Institut Camille Jordan, CNRS UMR 5208, University of Lyon, Villeurbanne, France
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Sanket Rane
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Andrew Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- Institute of Infection, Immunity & Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Azadeh Khosravi
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Mehran Salehpour
- Department of Physics and Astronomy, Ion Physics, Uppsala University, Uppsala, Sweden
| | - Göran Possnert
- Department of Physics and Astronomy, Ion Physics, Uppsala University, Uppsala, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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26
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Abstract
Generating and maintaining a diverse repertoire of naive T cells is essential for protection against pathogens, and developing a mechanistic and quantitative description of the processes involved lies at the heart of our understanding of vertebrate immunity. Here, we review the biology of naive T cells from birth to maturity and outline how the integration of mathematical models and experiments has helped us to develop a full picture of their life histories.
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Affiliation(s)
- Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, UK
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
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27
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Fate mapping reveals the age structure of the peripheral T cell compartment. Proc Natl Acad Sci U S A 2019; 116:3974-3981. [PMID: 30765525 DOI: 10.1073/pnas.1811634116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Accumulating evidence indicates that the immune system does not develop in a linear fashion, but rather as distinct developmental layers formed from sequential waves of hematopoietic stem cells, each giving rise to unique populations of immune cells at different stages of development. Although recent studies have indicated that conventional CD8+ T cells produced in early life persist into adulthood and exhibit distinct roles during infection, the developmental architecture of the peripheral T cell compartment remains undefined. In this study, we used a mouse model to permanently label CD8+ T cells produced during distinct windows of development and traced their history to generate fate maps of CD8+ T cells produced during different stages of life. We then used mathematical modeling to understand the age structure of the CD8+ T cell compartment across the lifespan. Interestingly, we found that survival rate of CD8+ T cells depends on both the age and developmental origin of the cells. Recently produced cells show an initial rapid decay rate, which slows with age of the animal at which the cells were produced. For cells produced at any age, the rate of decay also slows with the age of the cell. We derive a function to describe this and predict the "age distribution" of the CD8+ T cell pool for animals of any given age. These data provide a quantitative framework for understanding the ontogeny of the CD8+ T cell compartment and help to contextualize age-related changes in the CD8+ T cell response to infection.
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28
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Lythe G, Molina-París C. Some deterministic and stochastic mathematical models of naïve T-cell homeostasis. Immunol Rev 2018; 285:206-217. [DOI: 10.1111/imr.12696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Grant Lythe
- School of Mathematics; University of Leeds; Leeds UK
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