1
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Ullas S, Sinclair C. Applications of Flow Cytometry in Drug Discovery and Translational Research. Int J Mol Sci 2024; 25:3851. [PMID: 38612661 PMCID: PMC11011675 DOI: 10.3390/ijms25073851] [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: 02/21/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Flow cytometry is a mainstay technique in cell biology research, where it is used for phenotypic analysis of mixed cell populations. Quantitative approaches have unlocked a deeper value of flow cytometry in drug discovery research. As the number of drug modalities and druggable mechanisms increases, there is an increasing drive to identify meaningful biomarkers, evaluate the relationship between pharmacokinetics and pharmacodynamics (PK/PD), and translate these insights into the evaluation of patients enrolled in early clinical trials. In this review, we discuss emerging roles for flow cytometry in the translational setting that supports the transition and evaluation of novel compounds in the clinic.
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Affiliation(s)
| | - Charles Sinclair
- Flagship Pioneering, 140 First Street, Cambridge, MA 02141, USA;
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2
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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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3
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Derksen LY, Tesselaar K, Borghans JAM. Memories that last: Dynamics of memory T cells throughout the body. Immunol Rev 2023. [PMID: 37114435 DOI: 10.1111/imr.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Memory T cells form an essential part of immunological memory, which can last for years or even a lifetime. Much experimental work has shown that the individual cells that make up the memory T-cell pool are in fact relatively short-lived. Memory T cells isolated from the blood of humans, or the lymph nodes and spleen of mice, live about 5-10 fold shorter than naive T cells, and much shorter than the immunological memory they convey. The commonly accepted view is, therefore, that long-term T-cell memory is maintained dynamically rather than by long-lived cells. This view is largely based on memory T cells in the circulation, identified using rather broad phenotypic markers, and on research in mice living in overly clean conditions. We wondered to what extent there may be heterogeneity in the dynamics and lifespans of memory T cells. We here review what is currently known about the dynamics of memory T cells in different memory subsets, locations in the body and conditions of microbial exposure, and discuss how this may be related to immunometabolism and how this knowledge can be used in various clinical settings.
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Affiliation(s)
- Lyanne Y Derksen
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kiki Tesselaar
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - José A M Borghans
- Leukocyte Dynamics Group, Center for Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
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4
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Kuczynski EA, Carnevalli L, Sinclair C. Longitudinal tracking of T cell lymphomas in mice using flow cytometry. STAR Protoc 2023; 4:102144. [PMID: 36905629 PMCID: PMC10024047 DOI: 10.1016/j.xpro.2023.102144] [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: 01/09/2023] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 03/12/2023] Open
Abstract
T cell hematological cancer has a complex interplay with host immune cells, but the ability to experimentally discriminate transferred cancer cells from host cells by flow cytometry is technically challenging. Here, we present a flow cytometry protocol to evaluate cancer cell and host immune phenotypes following transplant of a T cell lymphoma bearing a congenic marker (CD45.2) into a syngeneic host (CD45.1). We describe steps for isolation of primary immune cells from mice, staining preparation with flow cytometry antibody cocktails, and analysis by flow cytometry. For complete details on the use and execution of this protocol, please refer to Kuczynski et al.1.
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Affiliation(s)
| | | | - Charles Sinclair
- Flagship Pioneering, Suite 500E, 55 Cambridge Parkway, Cambridge, MA 02142, USA.
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5
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Unique roles of co-receptor-bound LCK in helper and cytotoxic T cells. Nat Immunol 2023; 24:174-185. [PMID: 36564464 PMCID: PMC9810533 DOI: 10.1038/s41590-022-01366-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/20/2022] [Indexed: 12/24/2022]
Abstract
The kinase LCK and CD4/CD8 co-receptors are crucial components of the T cell antigen receptor (TCR) signaling machinery, leading to key T cell fate decisions. Despite decades of research, the roles of CD4-LCK and CD8-LCK interactions in TCR triggering in vivo remain unknown. In this study, we created animal models expressing endogenous levels of modified LCK to resolve whether and how co-receptor-bound LCK drives TCR signaling. We demonstrated that the role of LCK depends on the co-receptor to which it is bound. The CD8-bound LCK is largely dispensable for antiviral and antitumor activity of cytotoxic T cells in mice; however, it facilitates CD8+ T cell responses to suboptimal antigens in a kinase-dependent manner. By contrast, the CD4-bound LCK is required for efficient development and function of helper T cells via a kinase-independent stabilization of surface CD4. Overall, our findings reveal the role of co-receptor-bound LCK in T cell biology, show that CD4- and CD8-bound LCK drive T cell development and effector immune responses using qualitatively different mechanisms and identify the co-receptor-LCK interactions as promising targets for immunomodulation.
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6
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This S, Rogers D, Mallet Gauthier È, Mandl JN, Melichar HJ. What's self got to do with it: Sources of heterogeneity among naive T cells. Semin Immunol 2023; 65:101702. [PMID: 36463711 DOI: 10.1016/j.smim.2022.101702] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022]
Abstract
There is a long-standing assumption that naive CD4+ and CD8+ T cells are largely homogeneous populations despite the extraordinary diversity of their T cell receptors (TCR). The self-immunopeptidome plays a key role in the selection of the naive T cell repertoire in the thymus, and self-peptides are also an important driver of differences between individual naive T cells with regard to their subsequent functional contributions to an immune response. Accumulating evidence suggests that as early as the β-selection stage of T cell development, when only one of the recombined chains of the mature TCR is expressed, signaling thresholds may be established for positive selection of immature thymocytes. Stochastic encounters subsequently made with self-ligands during positive selection in the thymus imprint functional biases that a T cell will carry with it throughout its lifetime, although ongoing interactions with self in the periphery ensure a level of plasticity in the gene expression wiring of naive T cells. Identifying the sources of heterogeneity in the naive T cell population and which functional attributes of T cells can be modulated through post-thymic interventions versus those that are fixed during T cell development, could enable us to better select or generate T cells with particular traits to improve the efficacy of T cell therapies.
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Affiliation(s)
- Sébastien This
- Department of Microbiology, Infectious Disease, and Immunology, Université de Montréal, Montreal, Canada; Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Canada
| | - Dakota Rogers
- Department of Physiology and McGill Research Centre on Complex Traits, McGill University, Montreal, Canada
| | - Ève Mallet Gauthier
- Department of Microbiology, Infectious Disease, and Immunology, Université de Montréal, Montreal, Canada; Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Canada
| | - Judith N Mandl
- Department of Physiology and McGill Research Centre on Complex Traits, McGill University, Montreal, Canada.
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Canada; Department of Medicine, Université de Montréal, Montreal, Canada.
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7
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Baliu-Piqué M, Tesselaar K, Borghans JAM. Are homeostatic mechanisms aiding the reconstitution of the T-cell pool during lymphopenia in humans? Front Immunol 2022; 13:1059481. [PMID: 36483556 PMCID: PMC9723355 DOI: 10.3389/fimmu.2022.1059481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
A timely recovery of T-cell numbers following haematopoietic stem-cell transplantation (HSCT) is essential for preventing complications, such as increased risk of infection and disease relapse. In analogy to the occurrence of lymphopenia-induced proliferation in mice, T-cell dynamics in humans are thought to be homeostatically regulated in a cell density-dependent manner. The idea is that T cells divide faster and/or live longer when T-cell numbers are low, thereby helping the reconstitution of the T-cell pool. T-cell reconstitution after HSCT is, however, known to occur notoriously slowly. In fact, the evidence for the existence of homeostatic mechanisms in humans is quite ambiguous, since lymphopenia is often associated with infectious complications and immune activation, which confound the study of homeostatic regulation. This calls into question whether homeostatic mechanisms aid the reconstitution of the T-cell pool during lymphopenia in humans. Here we review the changes in T-cell dynamics in different situations of T-cell deficiency in humans, including the early development of the immune system after birth, healthy ageing, HIV infection, thymectomy and hematopoietic stem cell transplantation (HSCT). We discuss to what extent these changes in T-cell dynamics are a side-effect of increased immune activation during lymphopenia, and to what extent they truly reflect homeostatic mechanisms.
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Affiliation(s)
| | | | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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8
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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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9
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Belluccini G, López-García M, Lythe G, Molina-París C. Counting generations in birth and death processes with competing Erlang and exponential waiting times. Sci Rep 2022; 12:11289. [PMID: 35789162 PMCID: PMC9253354 DOI: 10.1038/s41598-022-14202-0] [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: 11/25/2021] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not divide at all. If individual cells behave independently, then each cell can be imagined as sampling from a probability density of times to division and death. The exponential density is the most mathematically and computationally convenient choice. It has the advantage of satisfying the memoryless property, consistent with a Markov process, but it overestimates the probability of short division times. With the aim of preserving the advantages of a Markovian framework while improving the representation of experimentally-observed division times, we consider a multi-stage model of cellular division and death. We use Erlang-distributed (or, more generally, phase-type distributed) times to division, and exponentially distributed times to death. We classify cells into generations, using the rule that the daughters of cells in generation n are in generation \documentclass[12pt]{minimal}
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\begin{document}$$n+1$$\end{document}n+1. In some circumstances, our representation is equivalent to established models of lymphocyte dynamics. We find the growth rate of the cell population by calculating the proportions of cells by stage and generation. The exponent describing the late-time cell population growth, and the criterion for extinction of the population, differs from what would be expected if N steps with rate \documentclass[12pt]{minimal}
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\begin{document}$$\lambda$$\end{document}λ were equivalent to a single step of rate \documentclass[12pt]{minimal}
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\begin{document}$$\lambda /N$$\end{document}λ/N. We link with a published experimental dataset, where cell counts were reported after T cells were transferred to lymphopenic mice, using Approximate Bayesian Computation. In the comparison, the death rate is assumed to be proportional to the generation and the Erlang time to division for generation 0 is allowed to differ from that of subsequent generations. The multi-stage representation is preferred to a simple exponential in posterior distributions, and the mean time to first division is estimated to be longer than the mean time to subsequent divisions.
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Affiliation(s)
| | | | - Grant Lythe
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Carmen Molina-París
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK. .,T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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10
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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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11
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Di Rosa F, Cossarizza A, Hayday AC. To Ki or Not to Ki: Re-Evaluating the Use and Potentials of Ki-67 for T Cell Analysis. Front Immunol 2021; 12:653974. [PMID: 33897702 PMCID: PMC8062736 DOI: 10.3389/fimmu.2021.653974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
This study discusses substantive advances in T cell proliferation analysis, with the aim to provoke a re-evaluation of the generally-held view that Ki-67 is a reliable proliferation marker per se, and to offer a more sensitive and effective method for T cell cycle analysis, with informative examples in mouse and human settings. We summarize recent experimental work from our labs showing that, by Ki-67/DNA dual staining and refined flow cytometric methods, we were able to identify T cells in the S-G2/M phases of the cell-cycle in the peripheral blood (collectively termed “T Double S” for T cells in S-phase in Sanguine: in short “TDS” cells). Without our refinement, such cells may be excluded from conventional lymphocyte analyses. Specifically, we analyzed clonal expansion of antigen-specific CD8 T cells in vaccinated mice, and demonstrated the potential of TDS cells to reflect immune dynamics in human blood samples from healthy donors, and patients with type 1 diabetes, infectious mononucleosis, and COVID-19. The Ki-67/DNA dual staining, or TDS assay, provides a reliable approach by which human peripheral blood can be used to reflect the dynamics of human lymphocytes, rather than providing mere steady-state phenotypic snapshots. The method does not require highly sophisticated “-omics” capabilities, so it should be widely-applicable to health care in diverse settings. Furthermore, our results argue that the TDS assay can provide a window on immune dynamics in extra-lymphoid tissues, a long-sought potential of peripheral blood monitoring, for example in relation to organ-specific autoimmune diseases and infections, and cancer immunotherapy.
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Affiliation(s)
- Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy.,National Institute for Cardiovascular Research, Bologna, Italy
| | - Adrian C Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom.,Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
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12
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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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13
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Paprckova D, Stepanek O. Narcissistic T cells: reactivity to self makes a difference. FEBS J 2020; 288:1778-1788. [PMID: 32738029 DOI: 10.1111/febs.15498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/22/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
It has been appreciated for more than three decades that the interactions between the T-cell antigen receptor and self-antigens are the major determinants of the cell fates of developing thymocytes and the establishment of central tolerance. However, recent evidence shows that the level of self-reactivity substantially contributes to fate choices of positively selected mature T cells in homeostasis, as well as during immune responses. This implies that individual clones of peripheral T cells are predisposed to specific functional properties based on the self-reactivity of their antigen receptors. Overall, the relative difference in the self-reactivity among peripheral T cells is an important factor contributing to the diversity of T-cell responses to foreign antigens.
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Affiliation(s)
- Darina Paprckova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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14
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Kurd NS, Lutes LK, Yoon J, Chan SW, Dzhagalov IL, Hoover AR, Robey EA. A role for phagocytosis in inducing cell death during thymocyte negative selection. eLife 2019; 8:48097. [PMID: 31868579 PMCID: PMC6957271 DOI: 10.7554/elife.48097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022] Open
Abstract
Autoreactive thymocytes are eliminated during negative selection in the thymus, a process important for establishing self-tolerance. Thymic phagocytes serve to remove dead thymocytes, but whether they play additional roles during negative selection remains unclear. Here, using a murine thymic slice model in which thymocytes undergo negative selection in situ, we demonstrate that phagocytosis promotes negative selection, and provide evidence for the escape of autoreactive CD8 T cells to the periphery when phagocytosis in the thymus is impaired. We also show that negative selection is more efficient when the phagocyte also presents the negative selecting peptide. Our findings support a model for negative selection in which the death process initiated following strong TCR signaling is facilitated by phagocytosis. Thus, the phagocytic capability of cells that present self-peptides is a key determinant of thymocyte fate.
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Affiliation(s)
- Nadia S Kurd
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Lydia K Lutes
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jaewon Yoon
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Shiao Wei Chan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ivan L Dzhagalov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ashley R Hoover
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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15
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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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16
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Payne H, Chain G, Adams S, Hunter P, Luckhurst N, Gilmour K, Lewis J, Babiker A, Cotton M, Violari A, Gibb D, Callard R, Klein N. Naive B Cell Output in HIV-Infected and HIV-Uninfected Children. AIDS Res Hum Retroviruses 2019; 35:33-39. [PMID: 30298747 PMCID: PMC6863188 DOI: 10.1089/aid.2018.0170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In this study, we aimed to quantify KREC (kappa-deleting recombination excision circle) levels and naive B cell output in healthy HIV-uninfected children, compared with HIV-infected South African children, before and after starting ART (antiretroviral therapy). Samples were acquired from a Child Wellness Clinic (n = 288 HIV-uninfected South African children, 2 weeks-12 years) and the Children with HIV Early Antiretroviral Therapy (CHER) trial (n = 153 HIV-infected South African children, 7 weeks-8 years). Naive B cell output was estimated using a mathematical model combining KREC levels to reflect B cell emigration into the circulation, flow cytometry measures of naive unswitched B cells to quantify total body naive B cells, and their rates of proliferation using the intracellular marker Ki67. Naive B cell output increases from birth to 1 year, followed by a decline and plateau into late childhood. HIV-infected children on or off ART had higher naive B cell outputs than their uninfected counterparts (p = .01 and p = .04). This is the first study to present reference ranges for measurements of KRECs and naive B cell output in healthy and HIV-infected children. Comparison between HIV-uninfected healthy children and HIV-infected children suggests that HIV may increase naive B cell output. Further work is required to fully understand the mechanisms involved and clinical value of measuring naive B cell output in children.
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Affiliation(s)
- Helen Payne
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Clinical Trials Unit, Medical Research Council, London, United Kingdom
| | - Gabriel Chain
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Stuart Adams
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Patricia Hunter
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Natasha Luckhurst
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Immunology, Kingston University, London, United Kingdom
| | - Kimberly Gilmour
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Joanna Lewis
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- CoMPLEX, UCL, London, United Kingdom
| | - Abdel Babiker
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Mark Cotton
- Children's Infectious Diseases Clinical Research Unit, Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Avy Violari
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Diana Gibb
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Robin Callard
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Nigel Klein
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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17
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Pribikova M, Moudra A, Stepanek O. Opinion: Virtual memory CD8 T cells and lymphopenia-induced memory CD8 T cells represent a single subset: Homeostatic memory T cells. Immunol Lett 2018; 203:57-61. [PMID: 30243945 DOI: 10.1016/j.imlet.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/25/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
It is well established that lymphopenia induces the formation of the memory-phenotype T cells without the exposure to foreign antigens. More recently, the memory-phenotype antigen-inexperienced memory T cells were described in lymphoreplete mice and called virtual memory T cells. In this review, we compare multiple aspects of the biology of lymphopenia-induced memory T cells and virtual memory T cells, including cytokine requirements, the role of T-cell receptor specificity in the differentiation process, gene expression signature, and the immune response. Based on this comparison, we conclude that lymphopenia-induced memory T cells and virtual memory T cells most likely represent a single T-cell subset, for which we propose a term 'homeostatic memory T cells'.
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Affiliation(s)
- Michaela Pribikova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Moudra
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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18
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Baliu-Piqué M, Verheij MW, Drylewicz J, Ravesloot L, de Boer RJ, Koets A, Tesselaar K, Borghans JAM. Short Lifespans of Memory T-cells in Bone Marrow, Blood, and Lymph Nodes Suggest That T-cell Memory Is Maintained by Continuous Self-Renewal of Recirculating Cells. Front Immunol 2018; 9:2054. [PMID: 30254637 PMCID: PMC6141715 DOI: 10.3389/fimmu.2018.02054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Memory T-cells are essential to maintain long-term immunological memory. It is widely thought that the bone marrow (BM) plays an important role in the long-term maintenance of memory T-cells. There is controversy however on the longevity and recirculating kinetics of BM memory T-cells. While some have proposed that the BM is a reservoir for long-lived, non-circulating memory T-cells, it has also been suggested to be the preferential site for memory T-cell self-renewal. In this study, we used in vivo deuterium labeling in goats to simultaneously quantify the average turnover rates—and thereby expected lifespans—of memory T-cells from BM, blood and lymph nodes (LN). While the fraction of Ki-67 positive cells, a snapshot marker for recent cell division, was higher in memory T-cells from blood compared to BM and LN, in vivo deuterium labeling revealed no substantial differences in the expected lifespans of memory T-cells between these compartments. Our results support the view that the majority of memory T-cells in the BM are self-renewing as fast as those in the periphery, and are continuously recirculating between the blood, BM, and LN.
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Affiliation(s)
- Mariona Baliu-Piqué
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Myrddin W Verheij
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Lars Ravesloot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Ad Koets
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - José A M Borghans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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19
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Drobek A, Moudra A, Mueller D, Huranova M, Horkova V, Pribikova M, Ivanek R, Oberle S, Zehn D, McCoy KD, Draber P, Stepanek O. Strong homeostatic TCR signals induce formation of self-tolerant virtual memory CD8 T cells. EMBO J 2018; 37:embj.201798518. [PMID: 29752423 PMCID: PMC6043851 DOI: 10.15252/embj.201798518] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/11/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022] Open
Abstract
Virtual memory T cells are foreign antigen‐inexperienced T cells that have acquired memory‐like phenotype and constitute 10–20% of all peripheral CD8+ T cells in mice. Their origin, biological roles, and relationship to naïve and foreign antigen‐experienced memory T cells are incompletely understood. By analyzing T‐cell receptor repertoires and using retrogenic monoclonal T‐cell populations, we demonstrate that the virtual memory T‐cell formation is a so far unappreciated cell fate decision checkpoint. We describe two molecular mechanisms driving the formation of virtual memory T cells. First, virtual memory T cells originate exclusively from strongly self‐reactive T cells. Second, the stoichiometry of the CD8 interaction with Lck regulates the size of the virtual memory T‐cell compartment via modulating the self‐reactivity of individual T cells. Although virtual memory T cells descend from the highly self‐reactive clones and acquire a partial memory program, they are not more potent in inducing experimental autoimmune diabetes than naïve T cells. These data underline the importance of the variable level of self‐reactivity in polyclonal T cells for the generation of functional T‐cell diversity.
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Affiliation(s)
- Ales Drobek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Moudra
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Mueller
- Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Veronika Horkova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Pribikova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Robert Ivanek
- Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Susanne Oberle
- Swiss Vaccine Research Institute, Epalinges, Switzerland
| | - Dietmar Zehn
- Swiss Vaccine Research Institute, Epalinges, Switzerland.,Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kathy D McCoy
- Department of Clinical Research (DKF), Inselspital, University of Bern, Bern, Switzerland
| | - Peter Draber
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic .,Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland
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20
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Ramesh M, Hamm D, Simchoni N, Cunningham-Rundles C. Clonal and constricted T cell repertoire in Common Variable Immune Deficiency. Clin Immunol 2017; 178:1-9. [PMID: 25596453 PMCID: PMC4501913 DOI: 10.1016/j.clim.2015.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/22/2014] [Accepted: 01/04/2015] [Indexed: 01/08/2023]
Abstract
We used high throughput sequencing to examine the structure and composition of the T cell receptor β chain in Common Variable Immune Deficiency (CVID). TCRβ CDR3 regions were amplified and sequenced from genomic DNA of 44 adult CVID subjects and 22 healthy adults, using a high-throughput multiplex PCR. CVID TCRs had significantly less junctional diversity, fewer n-nucleotide insertions and deletions, and completely lacked a population of highly modified TCRs, with 13 or more V-gene nucleotide deletions, seen in healthy controls. The CVID CDR3 sequences were significantly more clonal than control DNA, and displayed unique V gene usage. Despite reduced junctional diversity, increased clonality and similar infectious exposures, DNA of CVID subjects shared fewer TCR sequences as compared to controls. These abnormalities are pervasive, found in out-of-frame sequences and thus independent of selection and were not associated with specific clinical complications. These data support an inherent T cell defect in CVID.
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Affiliation(s)
| | | | - Noa Simchoni
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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21
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Gossel G, Hogan T, Cownden D, Seddon B, Yates AJ. Memory CD4 T cell subsets are kinetically heterogeneous and replenished from naive T cells at high levels. eLife 2017; 6:23013. [PMID: 28282024 PMCID: PMC5426903 DOI: 10.7554/elife.23013] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 03/04/2017] [Indexed: 01/27/2023] Open
Abstract
Characterising the longevity of immunological memory requires establishing the rules underlying the renewal and death of peripheral T cells. However, we lack knowledge of the population structure and how self-renewal and de novo influx contribute to the maintenance of memory compartments. Here, we characterise the kinetics and structure of murine CD4 T cell memory subsets by measuring the rates of influx of new cells and using detailed timecourses of DNA labelling that also distinguish the behaviour of recently divided and quiescent cells. We find that both effector and central memory CD4 T cells comprise subpopulations with highly divergent rates of turnover, and show that inflows of new cells sourced from the naive pool strongly impact estimates of memory cell lifetimes and division rates. We also demonstrate that the maintenance of CD4 T cell memory subsets in healthy mice is unexpectedly and strikingly reliant on this replenishment.
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Affiliation(s)
- Graeme Gossel
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary & Life Sciences University of Glasgow, Glasgow, United Kingdom,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Thea Hogan
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Daniel Cownden
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary & Life Sciences University of Glasgow, Glasgow, United Kingdom
| | - Benedict Seddon
- Institute of Immunity and Transplantation, University College London, London, United Kingdom, (BS)
| | - Andrew J Yates
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary & Life Sciences University of Glasgow, Glasgow, United Kingdom, (AJY)
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22
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Donovan GM, Lythe G. T cell and reticular network co-dependence in HIV infection. J Theor Biol 2016; 395:211-220. [PMID: 26874227 DOI: 10.1016/j.jtbi.2016.01.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 11/29/2022]
Abstract
Fibroblastic reticular cells (FRC) are arranged on a network in the T cell zone of lymph nodes, forming a scaffold for T cell migration, and providing survival factors, especially interleukin-7 (IL-7). Conversely, CD4(+) T cells are the major producers of lymphotoxin-β (LT-β), necessary for the construction and maintenance of the FRC network. This interdependence creates the possibility of a vicious cycle, perpetuating loss of both FRC and T cells. Furthermore, evidence that HIV infection is responsible for collagenation of the network suggests that long term loss of network function might be responsible for the attenuated recovery in T cell count seen in HIV patients undergoing antiretroviral therapy (ART). We present computational and mathematical models of this interaction mechanism and subsequent naive CD4(+) T-cell depletion in which (1) collagen deposition impedes access of naive T cells to IL-7 on the FRC and loss of IL-7 production by loss of FRC network itself, leading to the depletion of naive T cells through increased apoptosis; and (2) depletion of naive T cells as the source of LT-β on which the FRC depend for survival leads to loss of the network, thereby amplifying and perpetuating the cycle of depletion of both naive T cells and stromal cells. Our computational model explicitly includes an FRC network and its cytokine exchange with a heterogeneous T-cell population. We also derive lumped models, in terms of partial differential equations and reduced to ordinary differential equations, that provide additional insight into the mechanisms at work. The central conclusions are that (1) damage to the reticular network, caused by HIV infection is a plausible mechanism for attenuated recovery post-ART; (2) within this, the production of T cell survival factors by FRCs may be the key rate-limiting step; and (3) the methods of model reduction and analysis presented are useful for both immunological studies and other contexts in which agent-based models are severely limited by computational cost.
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Affiliation(s)
- Graham M Donovan
- Department of Mathematics, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Grant Lythe
- Department of Mathematics, University of Leeds, LS29JT, UK
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23
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Diebner HH, Kirberg J, Roeder I. An evolutionary stability perspective on oncogenesis control in mature T-cell populations. J Theor Biol 2016; 389:88-100. [PMID: 26549469 DOI: 10.1016/j.jtbi.2015.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/05/2015] [Accepted: 10/19/2015] [Indexed: 01/29/2023]
Abstract
Here we present a mathematical model for the dynamics of oncogenesis control in mature T-cell populations within the blood and lymphatic system. T-cell homeostasis is maintained by clonal competition for trophic niches (survival signals stimulated through interactions with self-antigens bound to major histocompatibility molecules), where a clone is defined as the set of T cells carrying the same antigen specific T-cell receptor (TCR). We analytically derive fitness functions of healthy and leukemic clone variants, respectively, that capture the dependency of the stability of the healthy T-cell pool against leukemic invaders on clonal diversity and kinetic parameters. Similar to the stability of ecosystems with high biodiversity, leukemic mutants are suppressed within polyclonal T-cell populations, i.e., in the presence of a huge number of different TCRs. To the contrary, for a low clonal diversity the leukemic clone variants are able to invade the healthy T-cell pool. The model, therefore, describes the experimentally observed phenomenon that preleukemic clone variants prevail in quasi-monoclonal experimental settings (in mice), whereas in polyclonal settings the healthy TCR variants are able to suppress the outgrowth of tumours. Between the two extremal situations of mono- and polyclonality there exists a range of coexistence of healthy and oncogenic clone variants with moderate fitness (stability) each. A variation of cell cycle times considerably changes the dynamics within this coexistence region. Faster proliferating variants increase their chance to dominate. Finally, a simplified niche variation scheme illustrates a possible mechanism to increase clonal T-cell diversity given a small niche diversity.
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Affiliation(s)
- Hans H Diebner
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany.
| | - Jörg Kirberg
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Ingo Roeder
- Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstrasse 74, D-01307 Dresden, Germany
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24
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Lythe G, Callard RE, Hoare RL, Molina-París C. How many TCR clonotypes does a body maintain? J Theor Biol 2015; 389:214-24. [PMID: 26546971 PMCID: PMC4678146 DOI: 10.1016/j.jtbi.2015.10.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/13/2015] [Accepted: 10/07/2015] [Indexed: 01/08/2023]
Abstract
We consider the lifetime of a T cell clonotype, the set of T cells with the same T cell receptor, from its thymic origin to its extinction in a multiclonal repertoire. Using published estimates of total cell numbers and thymic production rates, we calculate the mean number of cells per TCR clonotype, and the total number of clonotypes, in mice and humans. When there is little peripheral division, as in a mouse, the number of cells per clonotype is small and governed by the number of cells with identical TCR that exit the thymus. In humans, peripheral division is important and a clonotype may survive for decades, during which it expands to comprise many cells. We therefore devise and analyse a computational model of homeostasis of a multiclonal population. Each T cell in the model competes for self pMHC stimuli, cells of any one clonotype only recognising a small fraction of the many subsets of stimuli. A constant mean total number of cells is maintained by a balance between cell division and death, and a stable number of clonotypes by a balance between thymic production of new clonotypes and extinction of existing ones. The number of distinct clonotypes in a human body may be smaller than the total number of naive T cells by only one order of magnitude. The number of T cells of one clonotype is an integer. The history of a clonotype starts with release from the thymus, and ends with extinction. Competition and cross-reactivity are included in a natural way. The average number of cells per clonotype, in a human body, is only of order 10.
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Affiliation(s)
- Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK.
| | - Robin E Callard
- Institute for Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London WC1N 1EH, UK
| | - Rollo L Hoare
- Institute for Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, Gower Street, London WC1N 1EH, UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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25
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Ayoub H, Ainseba B, Langlais M, Thiébaut R. Parameters identification for a model of T cell homeostasis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2015; 12:917-936. [PMID: 26280181 DOI: 10.3934/mbe.2015.12.917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this study, we consider a model of T cell homeostasis based on the Smith-Martin model. This nonlinear model is structured by age and CD44 expression. First, we establish the mathematical well-posedness of the model system. Next, we prove the theoretical identifiability regarding the up-regulation of CD44, the proliferation time phase and the rate of entry into division, by using the experimental data. Finally, we compare two versions of the Smith-Martin model and we identify which model fits the experimental data best.
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Affiliation(s)
- Houssein Ayoub
- IMB UMR CNRS 5251, Bordeaux University, 3 Place de la Victoire, 33076 Bordeaux Cedex, France.
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26
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Westera L, van Hoeven V, Drylewicz J, Spierenburg G, van Velzen JF, de Boer RJ, Tesselaar K, Borghans JAM. Lymphocyte maintenance during healthy aging requires no substantial alterations in cellular turnover. Aging Cell 2015; 14:219-27. [PMID: 25627171 PMCID: PMC4364834 DOI: 10.1111/acel.12311] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 12/19/2022] Open
Abstract
In healthy humans, lymphocyte populations are maintained at a relatively constant size throughout life, reflecting a balance between lymphocyte production and loss. Given the profound immunological changes that occur during healthy aging, including a significant decline in T-cell production by the thymus, lymphocyte maintenance in the elderly is generally thought to require homeostatic alterations in lymphocyte dynamics. Surprisingly, using in vivo2H2O labeling, we find similar dynamics of most lymphocyte subsets between young adult and elderly healthy individuals. As the contribution of thymic output to T-cell production is only minor from young adulthood onward, compensatory increases in peripheral T-cell division rates are not required to maintain the T-cell pool, despite a tenfold decline in thymic output. These fundamental insights will aid the interpretation of further research into aging and clinical conditions related to disturbed lymphocyte dynamics.
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Affiliation(s)
- Liset Westera
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Vera van Hoeven
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Julia Drylewicz
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
- Theoretical Biology and Bioinformatics; Department of Biology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Gerrit Spierenburg
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Jeroen F. van Velzen
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics; Department of Biology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Kiki Tesselaar
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
| | - José A. M. Borghans
- Laboratory of Translational Immunology; Department of Immunology; University Medical Center Utrecht; Lundlaan 6 3584 EA Utrecht The Netherlands
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27
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Schim van der Loeff I, Hsu LY, Saini M, Weiss A, Seddon B. Zap70 is essential for long-term survival of naive CD8 T cells. THE JOURNAL OF IMMUNOLOGY 2014; 193:2873-80. [PMID: 25092893 DOI: 10.4049/jimmunol.1400858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Survival of naive T cells requires engagement of TCR with self-peptide major histocompatibility Ags. The signaling pathways required to transmit this survival signal are poorly understood. In this study, we asked whether the tyrosine kinase Zap70 is required to transmit survival signals in naive CD8 T cells. In the absence of Zap70 expression, thymic development is completely blocked. Using a tetracycline-inducible Zap70 transgene (TetZap70), thymic development of Zap70-deficient TCR transgenic F5 mice was restored. Feeding mice doxycycline to induce Zap70 expression resulted in repopulation of the peripheral naive compartment. Zap70 transgene expression was then ablated by withdrawal of doxycycline. Survival of Zap70-deficient naive CD8 T cells depended on host environment. In hosts with a replete T cell compartment, naive T cells died rapidly in the absence of Zap70 expression. In lymphopenic hosts, Zap70-deficient T cells survived far longer, in an IL-7-dependent manner, but failed to undergo lymphopenia-induced proliferation. Analyzing mixed bone marrow chimeras revealed that intact Zap70-dependent signaling was important for integration of recent thymic emigrants into the mature naive compartment. Finally, we asked whether adaptor function conferred by Zap70 tyrosines 315 and 319 was necessary for transmission of homeostatic TCR signals. This was done by analyzing F5 mice expressing mutant Zap70 in which these residues had been mutated to alanines (Zap70(YYAA)). Inducible Zap70 expression rescued thymic development in F5 TetZap70 Zap70(YYAA) mice. However, in the absence of wild-type Zap70 expression, the Zap70(YYAA) mutant failed to transmit either survival or proliferative homeostatic signals.
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Affiliation(s)
- Ina Schim van der Loeff
- Division of Immune Cell Biology, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Lih-Yun Hsu
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Manoj Saini
- Division of Immune Cell Biology, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; and
| | - Art Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143
| | - Benedict Seddon
- Division of Immune Cell Biology, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; and
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Parameter identification for model of T cell proliferation in lymphopenia conditions. Math Biosci 2014; 251:63-71. [PMID: 24631178 DOI: 10.1016/j.mbs.2014.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 02/19/2014] [Accepted: 03/01/2014] [Indexed: 11/22/2022]
Abstract
The number of T Lymphocytes (T cells) in the body is under homeostatic control. At equilibrium, the majority of naive T cells are non-dividing and express low levels of the surface protein CD44. In conditions of T cell deficiency (lymphopenia), naive T cells enter into a proliferative phase, undergoing cell division accompanied by a subtle change in their surface expression of CD44. In this study, we use a mathematical modelling approach to analyse the proliferative response of transgenic T cells in lymphopenic conditions. Our nonlinear model is composed of ordinary differential equations and partial differential equations structured by age (maturity of cell) and CD44 expression. To better understand the evolution of CD44 expression on the surface of T cells during cell division, we present a numerical analysis to solve a parameter identification problem. Finally, we show the parameters and the simulations that we obtain from the model and compare them to experimental data.
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Hapuarachchi T, Lewis J, Callard RE. A mechanistic model for naive CD4 T cell homeostasis in healthy adults and children. Front Immunol 2013; 4:366. [PMID: 24273540 PMCID: PMC3822783 DOI: 10.3389/fimmu.2013.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/27/2013] [Indexed: 12/16/2022] Open
Abstract
The size and composition of the T lymphocyte compartment is subject to strict homeostatic regulation and is remarkably stable throughout life in spite of variable dynamics in cell production and death during T cell development and immune responses. Homeostasis is achieved by careful orchestration of lymphocyte survival and cell division. New T cells are generated from the thymus and the number of peripheral T cells is regulated by controlling survival and proliferation. How these processes combine is however very complex. Thymic output increases in the first year of life and then decreases but is crucial for establishing repertoire diversity. Proliferation of new naive T cells plays a crucial role for maintaining numbers but at a potential cost to TCR repertoire diversity. A mechanistic two-compartment model of T cell homeostasis is described here that includes specific terms for thymic output, cell proliferation, and cell death of both resting and dividing cells. The model successfully predicts the homeostatic set point for T cells in adults and identifies variables that determine the total number of T cells. It also accurately predicts T cell numbers in children in early life despite rapid changes in thymic output and growth over this period.
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