1
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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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2
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Marcinkiewicz J, Witkowski JM, Olszanecki R. The dual role of the immune system in the course of COVID-19. The fatal impact of the aging immune system. Cent Eur J Immunol 2021; 46:1-9. [PMID: 33897278 PMCID: PMC8056340 DOI: 10.5114/ceji.2021.105240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
COVID-19 is a highly contagious respiratory disease caused by the novel coronavirus SARS-CoV-2. Since October 2020 the second wave of the pandemic has been observed around the world, as pathogen specific herd immunity has not been built yet. Moreover, the current, more contagious pathogen carrying the D614G mutation has become the globally dominant form of SARS-CoV-2. In this article we present the current state of knowledge on the impact of ACE2 and the reninangiotensin system (RAS) and the innate immune system on different outcomes of COVID-19. Especially, we point out the dual role of the immune system and ACE2 in pathogenesis of the disease. Namely, at the initial stage of the infection anti-viral activity of innate immunity is responsible for inhibition of SARS-CoV-2 replication. On the other hand, a dysregulated immune response may cause the detrimental hyperinflammation ("cytokine storm") responsible for the severe course of the disease. Concomitantly, we analyse the roles of ACE2 in both facilitation of infection and abrogation of its effects, as the major cellular entry receptor for SARS-CoV-2 and an important enzyme responsible for tissue protection, respectively. Finally, we discuss the dominant impact of aging on the fatal outcome of COVID-19.
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Affiliation(s)
- Janusz Marcinkiewicz
- Chair of Immunology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | | | - Rafał Olszanecki
- Chair of Pharmacology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
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3
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Cowan JE, Takahama Y, Bhandoola A, Ohigashi I. Postnatal Involution and Counter-Involution of the Thymus. Front Immunol 2020; 11:897. [PMID: 32477366 PMCID: PMC7235445 DOI: 10.3389/fimmu.2020.00897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/17/2020] [Indexed: 11/15/2022] Open
Abstract
Thymus involution occurs in all vertebrates. It is thought to impact on immune responses in the aged, and in other clinical circumstances such as bone marrow transplantation. Determinants of thymus growth and size are beginning to be identified. Ectopic expression of factors like cyclin D1 and Myc in thymic epithelial cells (TEC)s results in considerable increase in thymus size. These models provide useful experimental tools that allow thymus function to be understood. In future, understanding TEC-specific controllers of growth will provide new approaches to thymus regeneration.
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Affiliation(s)
- Jennifer E Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
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4
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Costa Del Amo P, Debebe B, Razavi-Mohseni M, Nakaoka S, Worth A, Wallace D, Beverley P, Macallan D, Asquith B. The Rules of Human T Cell Fate in vivo. Front Immunol 2020; 11:573. [PMID: 32322253 PMCID: PMC7156550 DOI: 10.3389/fimmu.2020.00573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/12/2020] [Indexed: 12/05/2022] Open
Abstract
The processes governing lymphocyte fate (division, differentiation, and death), are typically assumed to be independent of cell age. This assumption has been challenged by a series of elegant studies which clearly show that, for murine cells in vitro, lymphocyte fate is age-dependent and that younger cells (i.e., cells which have recently divided) are less likely to divide or die. Here we investigate whether the same rules determine human T cell fate in vivo. We combined data from in vivo stable isotope labeling in healthy humans with stochastic, agent-based mathematical modeling. We show firstly that the choice of model paradigm has a large impact on parameter estimates obtained using stable isotope labeling i.e., different models fitted to the same data can yield very different estimates of T cell lifespan. Secondly, we found no evidence in humans in vivo to support the model in which younger T cells are less likely to divide or die. This age-dependent model never provided the best description of isotope labeling; this was true for naïve and memory, CD4+ and CD8+ T cells. Furthermore, this age-dependent model also failed to predict an independent data set in which the link between division and death was explored using Annexin V and deuterated glucose. In contrast, the age-independent model provided the best description of both naïve and memory T cell dynamics and was also able to predict the independent dataset.
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Affiliation(s)
- Pedro Costa Del Amo
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Bisrat Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Shinji Nakaoka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Andrew Worth
- The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom
| | - Diana Wallace
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Peter Beverley
- TB Research Centre, National Heart and Lung Research Institute, Imperial College London, London, United Kingdom
| | - Derek Macallan
- Institute for Infection and Immunity, St. George's Hospital, University of London, London, United Kingdom
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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5
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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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6
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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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7
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Rane S, Hogan T, Seddon B, Yates AJ. Age is not just a number: Naive T cells increase their ability to persist in the circulation over time. PLoS Biol 2018; 16:e2003949. [PMID: 29641514 PMCID: PMC5894957 DOI: 10.1371/journal.pbio.2003949] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
The processes regulating peripheral naive T-cell numbers and clonal diversity remain poorly understood. Conceptually, homeostatic mechanisms must fall into the broad categories of neutral (simple random birth–death models), competition (regulation of cell numbers through quorum-sensing, perhaps via limiting shared resources), adaptation (involving cell-intrinsic changes in homeostatic fitness, defined as net growth rate over time), or selection (involving the loss or outgrowth of cell populations deriving from intercellular variation in fitness). There may also be stably maintained heterogeneity within the naive T-cell pool. To distinguish between these mechanisms, we confront very general models of these processes with an array of experimental data, both new and published. While reduced competition for homeostatic stimuli may impact cell survival or proliferation in neonates or under moderate to severe lymphopenia, we show that the only mechanism capable of explaining multiple, independent experimental studies of naive CD4+ and CD8+ T-cell homeostasis in mice from young adulthood into old age is one of adaptation, in which cells act independently and accrue a survival or proliferative advantage continuously with their post-thymic age. However, aged naive T cells may also be functionally impaired, and so the accumulation of older cells via ‘conditioning through experience’ may contribute to reduced immune responsiveness in the elderly. The body maintains large populations of naive T cells, a type of white blood cell that is able to respond specifically to pathogens. This arsenal is essential for our capacity to fight novel infections throughout our lifespan, and their numbers remain quite stable despite a gradual decline in the production of new naive T cells as we age. However, the mechanisms that underlie this stability are not well understood. In this study, we address this problem by testing a variety of potential mechanisms, each framed as a mathematical model, against multiple datasets obtained from experiments performed in mice. Our analysis supports a mechanism by which naïve T cells gradually increase their ability to survive the longer they reside in the circulation. Paradoxically, however, naïve T cells may also lose their ability to respond effectively to infections as they age. Together, these processes may drive the accumulation of older, functionally impaired T cells, potentially at the expense of younger and more immunologically potent cells, as we age.
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Affiliation(s)
- Sanket Rane
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Thea Hogan
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, London, United Kingdom
| | - 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 Medical Center, New York, New York, United States of America
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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8
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Holmes TH, He XS. Human immunophenotyping via low-variance, low-bias, interpretive regression modeling of small, wide data sets: Application to aging and immune response to influenza vaccination. J Immunol Methods 2016; 437:1-12. [PMID: 27196789 PMCID: PMC5242332 DOI: 10.1016/j.jim.2016.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022]
Abstract
Small, wide data sets are commonplace in human immunophenotyping research. As defined here, a small, wide data set is constructed by sampling a small to modest quantity n,1
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Affiliation(s)
- Tyson H Holmes
- Stanford University Human Immune Monitoring Center, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Xiao-Song He
- Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA; VA Palo Alto Healthcare System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA.
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9
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Silva SL, Sousa AE. Establishment and Maintenance of the Human Naïve CD4 + T-Cell Compartment. Front Pediatr 2016; 4:119. [PMID: 27843891 PMCID: PMC5086629 DOI: 10.3389/fped.2016.00119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022] Open
Abstract
The naïve CD4+ T-cell compartment is considered essential to guarantee immune competence throughout life. Its replenishment with naïve cells with broad diverse receptor repertoire, albeit with reduced self-reactivity, is ensured by the thymus. Nevertheless, cumulative data support a major requirement of post-thymic proliferation both for the establishment of the human peripheral naïve compartment during the accelerated somatic growth of childhood, as well as for its lifelong maintenance. Additionally, a dynamic equilibrium is operating at the cell level to fine-tune the T-cell receptor threshold to activation and survival cues, in order to counteract the continuous naïve cell loss by death or conversion into memory/effector cells. The main players in these processes are low-affinity self-peptide/MHC and cytokines, particularly IL-7. Moreover, although naïve CD4+ T-cells are usually seen as a homogeneous population regarding stage of maturation and cell differentiation, increasing evidence points to a variety of phenotypic and functional subsets with distinct homeostatic requirements. The paradigm of cells committed to a distinct lineage in the thymus are the naïve regulatory T-cells, but other functional subpopulations have been identified based on their time span after thymic egress, phenotypic markers, such as CD31, or cytokine production, namely IL-8. Understanding the regulation of these processes is of utmost importance to promote immune reconstitution in several clinical settings, namely transplantation, persistent infections, and aging. In this mini review, we provide an overview of the mechanisms underlying human naïve CD4+ T-cell homeostasis, combining clinical data, experimental studies, and modeling approaches.
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Affiliation(s)
- Susana L Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Centro de Imunodeficiências Primárias, Lisboa, Portugal; Clinica Universitária de Imunoalergologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisboa, Portugal
| | - Ana E Sousa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Centro de Imunodeficiências Primárias, Lisboa, Portugal
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10
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Milanez-Almeida P, Meyer-Hermann M, Toker A, Khailaie S, Huehn J. Foxp3+ regulatory T-cell homeostasis quantitatively differs in murine peripheral lymph nodes and spleen. Eur J Immunol 2014; 45:153-66. [PMID: 25330759 DOI: 10.1002/eji.201444480] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 09/29/2014] [Accepted: 10/17/2014] [Indexed: 11/05/2022]
Abstract
Regulatory T (Treg) cells are essential for maintaining self-tolerance and modulating inflammatory immune responses. Treg cells either develop within the thymus or are converted from CD4(+) naive T (Tnaive) cells in the periphery. The Treg-cell population size is tightly controlled and Treg-cell development and homeostasis have been intensively studied; however, quantitative information about mechanisms of peripheral Treg-cell homeostasis is lacking. Here we developed the first mathematical model of peripheral Treg-cell homeostasis, incorporating secondary lymphoid organs as separate entities and encompassing factors determining the size of the Treg-cell population, namely thymic output, homeostatic proliferation, peripheral conversion, transorgan migration, apoptosis, and the Tnaive-cell population. Quantitative data were collected by monitoring Tnaive-cell homeostasis and Treg-cell rebound after selective in vivo depletion of Treg cells. Our model predicted the previously unanticipated possibility that Treg cells regulate migration of Tnaive cells between spleen and peripheral lymph nodes (LNs), whereas migration of Treg cells between these organs can largely be neglected. Furthermore, our simulations suggested that peripheral conversion significantly contributed to the maintenance of the Treg-cell population, especially in LNs. Hence, we provide the first estimation of the peripheral Treg-cell conversion rate and propose additional facets of Treg-cell-mediated immune regulation that may previously have escaped attention.
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Affiliation(s)
- Pedro Milanez-Almeida
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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11
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Bayesian immunological model development from the literature: example investigation of recent thymic emigrants. J Immunol Methods 2014; 414:32-50. [PMID: 25179832 DOI: 10.1016/j.jim.2014.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 06/16/2014] [Accepted: 08/21/2014] [Indexed: 11/21/2022]
Abstract
Bayesian estimation techniques offer a systematic and quantitative approach for synthesizing data drawn from the literature to model immunological systems. As detailed here, the practitioner begins with a theoretical model and then sequentially draws information from source data sets and/or published findings to inform estimation of model parameters. Options are available to weigh these various sources of information differentially per objective measures of their corresponding scientific strengths. This approach is illustrated in depth through a carefully worked example for a model of decline in T-cell receptor excision circle content of peripheral T cells during development and aging. Estimates from this model indicate that 21 years of age is plausible for the developmental timing of mean age of onset of decline in T-cell receptor excision circle content of peripheral T cells.
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12
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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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13
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Kinetic model of HIV infection including hematopoietic progenitor cells. Math Biosci 2012; 236:36-43. [DOI: 10.1016/j.mbs.2012.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 01/10/2012] [Accepted: 01/13/2012] [Indexed: 12/16/2022]
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14
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Le Saux S, Weyand CM, Goronzy JJ. Mechanisms of immunosenescence: lessons from models of accelerated immune aging. Ann N Y Acad Sci 2012; 1247:69-82. [PMID: 22224726 DOI: 10.1111/j.1749-6632.2011.06297.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
With increasing age, the ability of the adaptive immune system to respond to vaccines and to protect from infection declines. In parallel, the production of inflammatory mediators increases. While cross-sectional studies have been successful in defining age-dependent immunological phenotypes, studies of accelerated immune aging in human subpopulations have been instrumental in obtaining mechanistic insights. The immune system depends on its regenerative capacity; however, the T cell repertoire, once established, is relatively robust to aging and only decompensates when additionally stressed. Such stressors include chronic infections such as CMV and HIV, even when viral replication is controlled, and autoimmune diseases. Reduced regenerative capacity, chronic immune activation in the absence of cell exhaustion, T cell memory inflation, and accumulation of highly potent effector T cells in these patients synergize to develop an immune phenotype that is characteristic of the elderly. Studies of accelerated immune aging in autoimmune diseases have identified an unexpected link to chronic DNA damage responses that are known to be important in aging, but so far had not been implicated in immune aging.
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Affiliation(s)
- Sabine Le Saux
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA
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15
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Germain RN, Meier-Schellersheim M, Nita-Lazar A, Fraser IDC. Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol 2011; 29:527-85. [PMID: 21219182 DOI: 10.1146/annurev-immunol-030409-101317] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and to conduct simulations of immune function. We provide descriptions of the key data-gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and the reasons why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease.
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Affiliation(s)
- Ronald N Germain
- Program in Systems Immunology and Infectious Disease Modeling, National Institute of Allergy and Infectious Disease, Laboratory of Immunology, National Institutes of Health, Bethesda, Maryland 20892, USA.
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16
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Naumov YN, Naumova EN, Yassai MB, Gorski J. Selective T cell expansion during aging of CD8 memory repertoires to influenza revealed by modeling. THE JOURNAL OF IMMUNOLOGY 2011; 186:6617-24. [PMID: 21515795 DOI: 10.4049/jimmunol.1100091] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aging of T cell memory is often considered in terms of senescence, a process viewed as decay and loss of memory T cells. How senescence would affect memory is a function of the initial structure of the memory repertoire and whether the clonotypes that make up the repertoire decay at random. We examine this issue using the T cell memory generated to the conserved influenza A epitope M1(58-66), which induces a strong, focused, but polyclonal CD8 T cell response in HLA-A2 individuals. We analyzed the CD8 T cell memory repertoires in eight healthy middle-aged and eight healthy older blood donors representing an average age difference of ∼ 27 y. Although the repertoires show broadly similar clonotype distributions, the number of observable clonotypes decreases significantly. This decrease disproportionally affects low-frequency clonotypes. Rank frequency analysis shows the same two-component clonotype distribution described earlier for these repertoires. The first component includes lower frequency clonotypes for which distribution can be described by a power law. The slope of this first component is significantly steeper in the older cohort. Generating a representative repertoire for each healthy cohort allowed agent-based modeling of the aging process. Interestingly, simple senescence of middle-aged repertoires is insufficient to describe the older clonotype distribution. Rather, a selective clonotype expansion must be included to achieve the best fit. We propose that responses to periodic virus exposure may drive such expansion, ensuring that the remaining clonotypes are optimized for continued protection.
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Affiliation(s)
- Yuri N Naumov
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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17
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Signaling thresholds govern heterogeneity in IL-7-receptor-mediated responses of naïve CD8(+) T cells. Immunol Cell Biol 2011; 89:581-94. [PMID: 21339767 PMCID: PMC3342499 DOI: 10.1038/icb.2011.5] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Variable sensitivity to T-cell-receptor (TCR)- and IL-7-receptor (IL-7R)-mediated homeostatic signals among naïve T cells has thus far been largely attributed to differences in TCR specificity. We show here that even when withdrawn from self-peptide-induced TCR stimulation, CD8+ T cells exhibit heterogeneous responses to interleukin-7 (IL-7) that are mechanistically associated with IL-7R expression differences that correlate with relative CD5 expression. Whereas CD5hi and CD5lo T cells survive equivalently in the presence of saturating IL-7 levels in vitro, CD5hi T cells proliferate more robustly. Conversely, CD5lo T cells exhibit prolonged survival when withdrawn from homeostatic stimuli. Through quantitative experimental analysis of signaling downstream of IL-7R, we find that the enhanced IL-7 responsiveness of CD5hi T cells is directly related to their greater surface IL-7R expression. Further, we identify a quantitative threshold in IL-7R-mediated signaling capacity required for proliferation that lies well above an analogous threshold requirement for survival. These distinct thresholds allow subtle differences in IL-7R expression between CD5lo and CD5hi T cells to give rise to significant variations in their respective IL-7-induced proliferation, without altering survival. Heterogeneous IL-7 responsiveness is observed similarly in vivo, with CD5hi naïve T cells proliferating preferentially in lymphopenic mice or lymphoreplete mice administered with exogenous IL-7. However, IL-7 in lymphoreplete mice appears to be maintained at an effective level for preserving homeostasis, such that neither CD5hi IL-7Rhi nor CD5lo IL-7Rlo T cells proliferate or survive preferentially. Our findings indicate that IL-7R-mediated signaling not only maintains the size but also impacts the diversity of the naïve T-cell repertoire.
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Allen S, Turner SJ, Bourges D, Gleeson PA, Driel IR. Shaping the T‐cell repertoire in the periphery. Immunol Cell Biol 2010; 89:60-9. [DOI: 10.1038/icb.2010.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Stacey Allen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Stephen J Turner
- Department of Microbiology and Immunology, The University of Melbourne Parkville Victoria Australia
| | - Dorothée Bourges
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Paul A Gleeson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Ian R Driel
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
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Downey JS, Imami N. T-cell dysfunction in HIV-1 infection: targeting the inhibitors. ACTA ACUST UNITED AC 2010. [DOI: 10.2217/hiv.09.51] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since AIDS emerged almost three decades ago, there have been considerable advances in the field of antiretroviral chemotherapy for those chronically infected with HIV-1. However, this therapy is noncurative and as our understanding of HIV-1 immunopathogenesis increases, it is becoming apparent that further therapeutic interventions are required to reverse the devastating effects of HIV-1 infection worldwide. While viral clearance remains the principle goal of HIV-1 treatment, this article describes immunotherapeutic options that target the immunological effects of the virus, to reduce its presence in the body and counteract viral-induced T-cell dysfunction and inhibition. Such approaches may augment existing antiretroviral therapy to overturn virus-induced T-cell anergy in the infected host, improving levels of immune control that reduce viremia and decrease the rate of transmission.
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Affiliation(s)
- Jocelyn S Downey
- Department of Immunology, Imperial College London, Chelsea & Westminster Hospital, 369 Fulham Road, London, SW10 9NH, UK
| | - Nesrina Imami
- Department of Immunology, Imperial College London, Chelsea & Westminster Hospital, 369 Fulham Road, London, SW10 9NH, UK
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