1
|
Dreiwi H, Feliciangeli F, Castro M, Lythe G, Molina-París C, López-García M. Stochastic journeys of cell progenies through compartments and the role of self-renewal, symmetric and asymmetric division. Sci Rep 2024; 14:16287. [PMID: 39009631 PMCID: PMC11251179 DOI: 10.1038/s41598-024-63500-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 05/29/2024] [Indexed: 07/17/2024] Open
Abstract
Division and differentiation events by which cell populations with specific functions are generated often take place as part of a developmental programme, which can be represented by a sequence of compartments. A compartment is the set of cells with common characteristics; sharing, for instance, a spatial location or a phenotype. Differentiation events are transitions from one compartment to the next. Cells may also die or divide. We consider three different types of division events: (i) where both daughter cells inherit the mother's phenotype (self-renewal), (ii) where only one of the daughters changes phenotype (asymmetric division), and (iii) where both daughters change phenotype (symmetric division). The self-renewal probability in each compartment determines whether the progeny of a single cell, moving through the sequence of compartments, is finite or grows without bound. We analyse the progeny stochastic dynamics with probability generating functions. In the case of self-renewal, by following one of the daughters after any division event, we may construct lifelines containing only one cell at any time. We analyse the number of divisions along such lines, and the compartment where lines terminate with a death event. Analysis and numerical simulations are applied to a five-compartment model of the gradual differentiation of hematopoietic stem cells and to a model of thymocyte development: from pre-double positive to single positive (SP) cells with a bifurcation to either SP4 or SP8 in the last compartment of the sequence.
Collapse
Affiliation(s)
- Hanan Dreiwi
- School of Mathematics, University of Leeds, Leeds, UK
| | - Flavia Feliciangeli
- School of Mathematics, University of Leeds, Leeds, UK
- Systems Pharmacology and Medicine, Bayer AG, Leverkusen, Germany
| | - Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Instituto de Investigación Tecnológica (IIT), Universidad Pontificia Comillas, Madrid, Spain
| | - Grant Lythe
- School of Mathematics, University of Leeds, Leeds, UK
| | - Carmen Molina-París
- School of Mathematics, University of Leeds, Leeds, UK
- Los Alamos National Laboratory, Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos, NM, USA
| | | |
Collapse
|
2
|
Kulesh V, Peskov K, Helmlinger G, Bocharov G. An integrative mechanistic model of thymocyte dynamics. Front Immunol 2024; 15:1321309. [PMID: 38469297 PMCID: PMC10925769 DOI: 10.3389/fimmu.2024.1321309] [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: 11/06/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024] Open
Abstract
Background The thymus plays a central role in shaping human immune function. A mechanistic, quantitative description of immune cell dynamics and thymic output under homeostatic conditions and various patho-physiological scenarios are of particular interest in drug development applications, e.g., in the identification of potential therapeutic targets and selection of lead drug candidates against infectious diseases. Methods We here developed an integrative mathematical model of thymocyte dynamics in human. It incorporates mechanistic features of thymocyte homeostasis as well as spatial constraints of the thymus and considerations of age-dependent involution. All model parameter estimates were obtained based on published physiological data of thymocyte dynamics and thymus properties in mouse and human. We performed model sensitivity analyses to reveal potential therapeutic targets through an identification of processes critically affecting thymic function; we further explored differences in thymic function across healthy subjects, multiple sclerosis patients, and patients on fingolimod treatment. Results We found thymic function to be most impacted by the egress, proliferation, differentiation and death rates of those thymocytes which are most differentiated. Model predictions also showed that the clinically observed decrease in relapse risk with age, in multiple sclerosis patients who would have discontinued fingolimod therapy, can be explained mechanistically by decreased thymic output with age. Moreover, we quantified the effects of fingolimod treatment duration on thymic output. Conclusions In summary, the proposed model accurately describes, in mechanistic terms, thymic output as a function of age. It may be further used to perform predictive simulations of clinically relevant scenarios which combine specific patho-physiological conditions and pharmacological interventions of interest.
Collapse
Affiliation(s)
- Victoria Kulesh
- Research Center of Model-Informed Drug Development, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
| | - Kirill Peskov
- Research Center of Model-Informed Drug Development, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
- Modeling & Simulation Decisions FZ - LLC, Dubai, United Arab Emirates
- Sirius University of Science and Technology, Sirius, Russia
| | | | - Gennady Bocharov
- Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences (RAS), Moscow, Russia
- Institute for Computer Science and Mathematical Modelling, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics at INM Russian Academy of Sciences (RAS), Moscow, Russia
| |
Collapse
|
3
|
Furuya T, Ishihara S, Ogi H, Masuda K, Shibata S, Nakazono C, Okada S, Shimomura M, Tando S, Yaoi T, Maeda Y, Yamagishi M, Kawamoto H, Itoh K, Inoue M. Characteristic differences in the abundance of tumor-infiltrating lymphocytes and intratumoral developing T cells in thymoma, with special reference to PD-1 expression. Cancer Immunol Immunother 2023; 72:2585-2596. [PMID: 37060363 DOI: 10.1007/s00262-023-03431-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/19/2023] [Indexed: 04/16/2023]
Abstract
PURPOSE Though programmed cell death-1 (PD-1) inhibitors mainly target tumor-infiltrating lymphocytes (TILs) expressing PD-1, developing T cells in thymus also express PD-1 in their process of maturation. To predict the therapeutic effect of PD-1 inhibitors for thymoma, it is necessary to clarify the proportions of TILs and intratumoral developing T cells. METHODS The expressions of CD4, CD8, and PD-1 on T cells were analyzed by flow cytometry in 31 thymomas. The amount of T cell receptor excision circles (TRECs), which can be detected in newly formed naïve T cells in the thymus, was evaluated using sorted lymphocytes from thymomas by quantitative PCR. The expressions of granzyme B (GZMB) and lymphocyte activation gene-3 (LAG-3) in PD-1 + CD8 T cells were analyzed by image cytometry using multiplex immunohistochemistry. RESULTS The PD-1 + rate in both CD4 and CD8 T cells was significantly higher in type AB/B1/B2 than in type A/B3 thymomas. The amounts of TRECs in CD4 and CD8 T cells were significantly higher in type AB/B1/B2 than in type A/B3 thymomas and comparable to normal thymus. PD-1 expression at each stage of T cell development of type AB/B1/B2 thymomas was comparable to that of normal thymus. Both the percentages and cell densities of PD-1 + CD8 T cells expressing GZMB or LAG-3, which are known to contain tumor-reactive T cells, were significantly lower in type AB/B1/B2 thymomas. CONCLUSION Most PD-1 + T cells in type AB/B1/B2 thymomas are intratumoral developing T cells and are not TILs.
Collapse
Affiliation(s)
- Tatsuo Furuya
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
- Lab of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shunta Ishihara
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hiroshi Ogi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- SCREEN Holdings Co., Ltd, Kyoto, Japan
| | - Kyoko Masuda
- Lab of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | | | - Chiaki Nakazono
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Satoru Okada
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Masanori Shimomura
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - So Tando
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takeshi Yaoi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshinobu Maeda
- Department of Pediatric Cardiovascular Surgery, Children's Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masaaki Yamagishi
- Department of Pediatric Cardiovascular Surgery, Children's Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Kawamoto
- Lab of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masayoshi Inoue
- Division of Thoracic Surgery, Department of Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.
| |
Collapse
|
4
|
Weng NP. Transcriptome-based measurement of CD8 + T cell age and its applications. Trends Immunol 2023; 44:542-550. [PMID: 37248098 PMCID: PMC10330598 DOI: 10.1016/j.it.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/31/2023]
Abstract
The ability of T cells to undergo robust cell division in response to antigenic stimulation is essential for competent T cell function. However, this ability is reduced with aging and contributes to increased susceptibility to infectious diseases, cancers, and other diseases among older adults. To better understand T cell aging, improved measurements of age-related cellular changes in T cells are necessary. The recent development of machine learning (ML)-assisted transcriptome-based quantification of individual CD8+ T cell age represents a significant step forward in this regard. It reveals both prominent and subtle changes in gene expression and points to potential functional alterations of CD8+ T cells with aging. I argue that single-cell transcriptome-based age prediction in the immune system may have promising future applications.
Collapse
Affiliation(s)
- Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
5
|
Gavish A, Chain B, Salame TM, Antebi YE, Nevo S, Reich-Zeliger S, Friedman N. From pseudo to real-time dynamics of T cell thymic differentiation. iScience 2022; 26:105826. [PMID: 36624839 PMCID: PMC9823121 DOI: 10.1016/j.isci.2022.105826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/14/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Numerous methods have recently emerged for ordering single cells along developmental trajectories. However, accurate depiction of developmental dynamics can only be achieved after rescaling the trajectory according to the relative time spent at each developmental point. We formulate a model which estimates local cell densities and fluxes, and incorporates cell division and apoptosis rates, to infer the real-time dimension of the developmental trajectory. We validate the model using mathematical simulations and apply it to experimental high dimensional cytometry data obtained from the mouse thymus to construct the true time profile of the thymocyte developmental process. Our method can easily be implemented in any of the existing tools for trajectory inference.
Collapse
Affiliation(s)
- Avishai Gavish
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel,Corresponding author
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Tomer M. Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yaron E. Antebi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shir Nevo
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomit Reich-Zeliger
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel,Corresponding author
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
6
|
Feliciangeli F, Dreiwi H, López-García M, Castro Ponce M, Molina-París C, Lythe G. Why are cell populations maintained via multiple compartments? J R Soc Interface 2022; 19:20220629. [PMID: 36349449 PMCID: PMC9653237 DOI: 10.1098/rsif.2022.0629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/12/2022] [Indexed: 10/02/2023] Open
Abstract
We consider the maintenance of 'product' cell populations from 'progenitor' cells via a sequence of one or more cell types, or compartments, where each cell's fate is chosen stochastically. If there is only one compartment then large amplification, that is, a large ratio of product cells to progenitors comes with disadvantages. The product cell population is dominated by large families (cells descended from the same progenitor) and many generations separate, on average, product cells from progenitors. These disadvantages are avoided using suitably constructed sequences of compartments: the amplification factor of a sequence is the product of the amplification factors of each compartment, while the average number of generations is a sum over contributions from each compartment. Passing through multiple compartments is, in fact, an efficient way to maintain a product cell population from a small flux of progenitors, avoiding excessive clonality and minimizing the number of rounds of division en route. We use division, exit and death rates, estimated from measurements of single-positive thymocytes, to choose illustrative parameter values in the single-compartment case. We also consider a five-compartment model of thymocyte differentiation, from double-negative precursors to single-positive product cells.
Collapse
Affiliation(s)
- Flavia Feliciangeli
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- Systems Pharmacology and Medicine, Bayer AG, Leverkusen 51368, Germany
| | - Hanan Dreiwi
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | | | - Mario Castro Ponce
- Instituto de Investigación Tecnológica (ITT), Universidad Pontificia Comillas, Madrid, Spain
| | - Carmen Molina-París
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Grant Lythe
- School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| |
Collapse
|
7
|
Ratiu JJ, Barclay WE, Lin E, Wang Q, Wellford S, Mehta N, Harnois MJ, DiPalma D, Roy S, Contreras AV, Shinohara ML, Wiest D, Zhuang Y. Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes. Nat Commun 2022; 13:5901. [PMID: 36202870 PMCID: PMC9537144 DOI: 10.1038/s41467-022-33610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Production of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.
Collapse
Affiliation(s)
- Jeremy J Ratiu
- Duke University, Department of Immunology, Durham, NC, 27710, USA.
| | | | - Elliot Lin
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Qun Wang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Naren Mehta
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Devon DiPalma
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Sumedha Roy
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Alejandra V Contreras
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Mari L Shinohara
- Duke University, Department of Immunology, Durham, NC, 27710, USA
- Duke University, Department of Molecular Genetics and Microbiology, Durham, NC, 27710, USA
| | - David Wiest
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Yuan Zhuang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| |
Collapse
|
8
|
Stefanski HE, Xing Y, Nicholls J, Jonart L, Goren E, Taylor PA, Mills AA, Riddle M, McGrath J, Tolar J, Hollander GA, Blazar BR. P63 targeted deletion under the FOXN1 promoter disrupts pre-and post-natal thymus development, function and maintenance as well as induces severe hair loss. PLoS One 2022; 17:e0261770. [PMID: 35077450 PMCID: PMC8789144 DOI: 10.1371/journal.pone.0261770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Progressive immune deficiency of aging is characterized by severe thymic atrophy, contracted T cell repertoire, and poor immune function. p63 is critical for the proliferative potential of embryonic and adult stem cells, as well as thymic epithelial cells (TECs). Because p63 null mice experience rapid post-natal lethality due to epidermal and limb morphogenesis defects, studies to define a role for p63 expression in TEC biology focused on embryonic thymus development and in vitro experiments. Since post-natal thymic stromal development and function differs from that of the embryo, we assessed the impact of lineage-restricted p63 loss on pre- and post-natal murine TEC function by generating mice with a loss of p63 function targeted to TEC, termed p63TECko mice. In adult p63TECko mice, severe thymic hypoplasia was observed with a lack in a discernable segregation into medullary and cortical compartments and peripheral T cell lymphopenia. This profound thymic defect was seen in both neonatal as well as embryonic p63TECko mice. In addition to TECs, p63 also plays in important role in the development of stratified epithelium of the skin; lack of p63 results in defects in skin epidermal stratification and differentiation. Interestingly, all adult p63TECko mice lacked hair follicles despite having normal p63 expression in the skin. Together our results show a critical role of TEC p63 in thymic development and maintenance and show that p63 expression is critical for hair follicle formation.
Collapse
Affiliation(s)
- Heather E. Stefanski
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Yan Xing
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Jemma Nicholls
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Leslie Jonart
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Emily Goren
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Patricia A. Taylor
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Alea A. Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, New York, United States of America
| | - Megan Riddle
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - John McGrath
- Molecular Dermatology, St John’s Institute of Dermatology, King’s College, London, England
| | - Jakub Tolar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| | - Georg A. Hollander
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- Department of Biomedicine, Basel University Children’s Hospital, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Bruce R. Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States of America
| |
Collapse
|
9
|
Modeling the Dynamics of T-Cell Development in the Thymus. ENTROPY 2021; 23:e23040437. [PMID: 33918050 PMCID: PMC8069328 DOI: 10.3390/e23040437] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 12/24/2022]
Abstract
The thymus hosts the development of a specific type of adaptive immune cells called T cells. T cells orchestrate the adaptive immune response through recognition of antigen by the highly variable T-cell receptor (TCR). T-cell development is a tightly coordinated process comprising lineage commitment, somatic recombination of Tcr gene loci and selection for functional, but non-self-reactive TCRs, all interspersed with massive proliferation and cell death. Thus, the thymus produces a pool of T cells throughout life capable of responding to virtually any exogenous attack while preserving the body through self-tolerance. The thymus has been of considerable interest to both immunologists and theoretical biologists due to its multi-scale quantitative properties, bridging molecular binding, population dynamics and polyclonal repertoire specificity. Here, we review experimental strategies aimed at revealing quantitative and dynamic properties of T-cell development and how they have been implemented in mathematical modeling strategies that were reported to help understand the flexible dynamics of the highly dividing and dying thymic cell populations. Furthermore, we summarize the current challenges to estimating in vivo cellular dynamics and to reaching a next-generation multi-scale picture of T-cell development.
Collapse
|
10
|
Chan CT, Fenn AM, Harder NK, Mindur JE, McAlpine CS, Patel J, Valet C, Rattik S, Iwamoto Y, He S, Anzai A, Kahles F, Poller WC, Janssen H, Wong LP, Fernandez-Hernando C, Koolbergen DR, van der Laan AM, Yvan-Charvet L, Sadreyev RI, Nahrendorf M, Westerterp M, Tall AR, Gustafsson JA, Swirski FK. Liver X receptors are required for thymic resilience and T cell output. J Exp Med 2021; 217:151978. [PMID: 32716519 PMCID: PMC7537384 DOI: 10.1084/jem.20200318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
The thymus is a primary lymphoid organ necessary for optimal T cell development. Here, we show that liver X receptors (LXRs)—a class of nuclear receptors and transcription factors with diverse functions in metabolism and immunity—critically contribute to thymic integrity and function. LXRαβ-deficient mice develop a fatty, rapidly involuting thymus and acquire a shrunken and prematurely immunoinhibitory peripheral T cell repertoire. LXRαβ’s functions are cell specific, and the resulting phenotypes are mutually independent. Although thymic macrophages require LXRαβ for cholesterol efflux, thymic epithelial cells (TECs) use LXRαβ for self-renewal and thymocytes for negative selection. Consequently, TEC-derived LXRαβ protects against homeostatic premature involution and orchestrates thymic regeneration following stress, while thymocyte-derived LXRαβ limits cell disposal during negative selection and confers heightened sensitivity to experimental autoimmune encephalomyelitis. These results identify three distinct but complementary mechanisms by which LXRαβ governs T lymphocyte education and illuminate LXRαβ’s indispensable roles in adaptive immunity.
Collapse
Affiliation(s)
- Christopher T Chan
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Ashley M Fenn
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Nina K Harder
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - John E Mindur
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Cameron S McAlpine
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jyoti Patel
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Colin Valet
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Sara Rattik
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Yoshiko Iwamoto
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Shun He
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Atsushi Anzai
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Florian Kahles
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Wolfram C Poller
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Henrike Janssen
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA
| | - Carlos Fernandez-Hernando
- Vascular Biology and Therapeutics Program, Department of Comparative Medicine and Pathology, Yale University School of Medicine, New Haven, CT
| | - David R Koolbergen
- Heart Center, Department of Cardiothoracic Surgery, Amsterdam Universitair Medische Centra, University of Amsterdam, Amsterdam, Netherlands
| | - Anja M van der Laan
- Heart Center, Department of Cardiology, Amsterdam Universitair Medische Centra, University of Amsterdam, Amsterdam, Netherlands
| | - Laurent Yvan-Charvet
- Institut National de la Santé et de la Recherche Médicale, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire, Atip-Avenir, Fédération Hospitalo-Universitaire Oncoage, Nice, France.,Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY
| | - Ruslan I Sadreyev
- Department of Molecular Biology and Department of Pathology, Massachusetts General Hospital, and Harvard Medical School, Boston, MA
| | - Matthias Nahrendorf
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Marit Westerterp
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY.,Department of Pediatrics, Section Molecular Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alan R Tall
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY
| | - Jan-Ake Gustafsson
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX
| | - Filip K Swirski
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
11
|
Webb LM, Sengupta S, Edell C, Piedra-Quintero ZL, Amici SA, Miranda JN, Bevins M, Kennemer A, Laliotis G, Tsichlis PN, Guerau-de-Arellano M. Protein arginine methyltransferase 5 promotes cholesterol biosynthesis-mediated Th17 responses and autoimmunity. J Clin Invest 2020; 130:1683-1698. [PMID: 32091410 PMCID: PMC7108896 DOI: 10.1172/jci131254] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) catalyzes symmetric dimethylation (SDM) of arginine, a posttranslational modification involved in oncogenesis and embryonic development. However, the role and mechanisms by which PRMT5 modulates Th cell polarization and autoimmune disease have not yet been elucidated. Here, we found that PRMT5 promoted SREBP1 SDM and the induction of cholesterol biosynthetic pathway enzymes that produce retinoid-related orphan receptor (ROR) agonists that activate RORγt. Specific loss of PRMT5 in the CD4+ Th cell compartment suppressed Th17 differentiation and protected mice from developing experimental autoimmune encephalomyelitis (EAE). We also found that PRMT5 controlled thymic and peripheral homeostasis in the CD4+ Th cell life cycle and invariant NK (iNK) T cell development and CD8+ T cell maintenance. This work demonstrates that PRMT5 expression in recently activated T cells is necessary for the cholesterol biosynthesis metabolic gene expression program that generates RORγt agonistic activity and promotes Th17 differentiation and EAE. These results point to Th PRMT5 and its downstream cholesterol biosynthesis pathway as promising therapeutic targets in Th17-mediated diseases.
Collapse
MESH Headings
- Animals
- Autoimmunity
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/pathology
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cholesterol/genetics
- Cholesterol/immunology
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Mice
- Mice, Transgenic
- Natural Killer T-Cells/immunology
- Natural Killer T-Cells/pathology
- Nuclear Receptor Subfamily 1, Group F, Member 3/genetics
- Nuclear Receptor Subfamily 1, Group F, Member 3/immunology
- Protein-Arginine N-Methyltransferases/genetics
- Protein-Arginine N-Methyltransferases/immunology
- Sterol Regulatory Element Binding Protein 1/genetics
- Sterol Regulatory Element Binding Protein 1/immunology
- Th17 Cells/immunology
- Th17 Cells/pathology
Collapse
Affiliation(s)
- Lindsay M Webb
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Biomedical Sciences Graduate Program, and
| | - Shouvonik Sengupta
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Biomedical Sciences Graduate Program, and
| | - Claudia Edell
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Zayda L Piedra-Quintero
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Stephanie A Amici
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Janiret Narvaez Miranda
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | | | - Austin Kennemer
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
| | - Georgios Laliotis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University Comprehensive Cancer Center
| | - Philip N Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
- The Ohio State University Comprehensive Cancer Center
| | - Mireia Guerau-de-Arellano
- School of Health and Rehabilitation Sciences, Division of Medical Laboratory Science, College of Medicine, Wexner Medical Center
- Institute for Behavioral Medicine Research
- Department of Microbial Infection and Immunity, and
- Department of Neuroscience, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
12
|
Kaneko KB, Tateishi R, Miyao T, Takakura Y, Akiyama N, Yokota R, Akiyama T, Kobayashi TJ. Quantitative analysis reveals reciprocal regulations underlying recovery dynamics of thymocytes and thymic environment in mice. Commun Biol 2019; 2:444. [PMID: 31815199 PMCID: PMC6884561 DOI: 10.1038/s42003-019-0688-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 11/10/2019] [Indexed: 01/17/2023] Open
Abstract
Thymic crosstalk, a set of reciprocal regulations between thymocytes and the thymic environment, is relevant for orchestrating appropriate thymocyte development as well as thymic recovery from various exogenous insults. In this work, interactions shaping thymic crosstalk and the resultant dynamics of thymocytes and thymic epithelial cells are inferred based on quantitative analysis and modeling of the recovery dynamics induced by irradiation. The analysis identifies regulatory interactions consistent with known molecular evidence and reveals their dynamic roles in the recovery process. Moreover, the analysis also predicts, and a subsequent experiment verifies, a previously unrecognized regulation of CD4+CD8+ double positive thymocytes which temporarily increases their proliferation rate upon the decrease in their population size. Our model establishes a pivotal step towards the dynamic understanding of thymic crosstalk as a regulatory network system.
Collapse
Affiliation(s)
- Kazumasa B. Kaneko
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku Tokyo, 113-8656 Japan
| | - Ryosuke Tateishi
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Takahisa Miyao
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yuki Takakura
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Nobuko Akiyama
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Ryo Yokota
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505 Japan
| | - Taishin Akiyama
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku Tokyo, 113-8656 Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505 Japan
- PREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012 Japan
| |
Collapse
|
13
|
Li H, Wetchapinant C, Zhang L, Wu K. High-Fat Diet from Weaning until Early Adulthood Impairs T Cell Development in the Thymus. Lipids 2019; 55:35-44. [PMID: 31608450 DOI: 10.1002/lipd.12193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/27/2022]
Abstract
The growing prevalence of childhood obesity has become a serious health problem over the past few decades. Although the immune system is greatly affected by childhood obesity, whether obesity influences the T cell development in the thymus is poorly understood. In this study, we used a high-fat diet (HFD)-induced obesity mice model to study the influence of HFD from weaning on the thymus. C57BL/6 mice (male, 3 weeks old) were fed a HFD or standard diet (lean controls) for 6 weeks. The bodyweight of mice fed with an HFD was 28% higher than that in the control group, while the thymus weight of HFD mice decreased by 15% compared with controls. As expected, thymic triacylglycerol content of the HFD mice increased by 37% compared to the control mice. Importantly, the frequencies of CD4+ and CD8+ single-positive (SP) thymocytes decreased by 38% and 44%, respectively. The apoptotic analysis revealed that thymic tissue of HFD mice had a higher level of Annexin-V positive thymocytes than control animals. Furthermore, the immunoblotting analysis showed that survival signal pathways in the thymus were impaired in the HFD mice, including the AKT/mTOR and ERK pathways. With the analysis of T-cell receptor excision circles (TREC), we found that HFD-induced obesity decreased recent thymic emigrants in spleen tissue. Our findings indicate that HFD from the weaning period impairs T cell development in the thymus, possibly by induction of apoptosis of thymocytes, involving disruption of survival signal pathways.
Collapse
Affiliation(s)
- Hao Li
- Department of Pathophysiology, Navy Medical University, 800 Xiangyin road, Shanghai, 200433, China
| | | | - Liya Zhang
- Baodi Clinical College of Tianjin Medical University, 8 Guangchuan road, Tianjin, 301800, China
| | - Kunpeng Wu
- Fudan University, 220 Handan road, Shanghai, 200433, China.,Department of Hematology, Huashan Hospital, Fudan University, 12 middle urumqi road, Shanghai, 200040, China
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
de la Higuera L, López-García M, Castro M, Abourashchi N, Lythe G, Molina-París C. Fate of a Naive T Cell: A Stochastic Journey. Front Immunol 2019; 10:194. [PMID: 30894850 PMCID: PMC6415700 DOI: 10.3389/fimmu.2019.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
The homeostasis of T cell populations depends on migration, division and death of individual cells (1). T cells migrate between spatial compartments (spleen, lymph nodes, lung, liver, etc.), where they may divide or differentiate, and eventually die (2). The kinetics of recirculation influences the speed at which local infections are detected and controlled (3). New experimental techniques have been developed to measure the lifespan of cells, and their migration dynamics; for example, fluorescence-activated cell sorting (4), in vitro time-lapse microscopy (5), or in vivo stable isotope labeling (e.g., deuterium) (6). When combined with mathematical and computational models, they allow estimation of rates of migration, division, differentiation and death (6, 7). In this work, we develop a stochastic model of a single cell migrating between spatial compartments, dividing and eventually dying. We calculate the number of division events during a T cell's journey, its lifespan, the probability of dying in each compartment and the number of progeny cells. A fast-migration approximation allows us to compute these quantities when migration rates are larger than division and death rates. Making use of published rates: (i) we analyse how perturbations in a given spatial compartment impact the dynamics of a T cell, (ii) we study the accuracy of the fast-migration approximation, and (iii) we quantify the role played by direct migration (not via the blood) between some compartments.
Collapse
Affiliation(s)
- Luis de la Higuera
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Mario Castro
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
- Grupo Interdisciplinar de Sistemas Complejos and DNL, Universidad Pontificia Comillas, Madrid, Spain
| | - Niloufar Abourashchi
- Department of Statistical Science, University College London, London, United Kingdom
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
16
|
Majumdar S, Adiga V, Raghavan A, Rananaware SR, Nandi D. Comparative analysis of thymic subpopulations during different modes of atrophy identifies the reactive oxygen species scavenger, N-acetyl cysteine, to increase the survival of thymocytes during infection-induced and lipopolysaccharide-induced thymic atrophy. Immunology 2019; 157:21-36. [PMID: 30659606 DOI: 10.1111/imm.13043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/07/2018] [Accepted: 01/10/2019] [Indexed: 12/17/2022] Open
Abstract
The development of immunocompetent T cells entails a complex pathway of differentiation in the thymus. Thymic atrophy occurs with ageing and during conditions such as malnutrition, infections and cancer chemotherapy. The comparative changes in thymic subsets under different modes of thymic atrophy and the mechanisms involved are not well characterized. These aspects were investigated, using mice infected with Salmonella Typhimurium, injection with lipopolysaccharide (LPS), an inflammatory but non-infectious stimulus, etoposide (Eto), a drug used to treat some cancers, and dexamethasone (Dex), a steroid used in some inflammatory diseases. The effects on the major subpopulations of thymocytes based on multicolour flow cytometry studies were, first, the CD4- CD8- double-negative (DN) cells, mainly DN2-4, were reduced with infection, LPS and Eto treatment, but not with Dex. Second, the CD8+ CD3lo immature single-positive cells (ISPs) were highly sensitive to infection, LPS and Eto, but not Dex. Third, treatment with LPS, Eto and Dex reduced all three subpopulations of CD4+ CD8+ double-positive (DP) thymocytes, i.e. DP1, DP2 and DP3, but the DP3 subset was relatively more resistant during infection. Fourth, both CD4+ and CD8+ single-positive (SP) thymocytes were lowered by Eto and Dex, but not during infection. Notably, LPS lowered CD4+ SP subsets, whereas the CD8+ SP subsets were relatively more resistant. Interestingly, the reactive oxygen species quencher, N-acetyl cysteine, greatly improved the survival of thymocytes, especially DNs, ISPs and DPs, during infection and LPS treatment. The implications of these observations for the development of potential thymopoietic drugs are discussed.
Collapse
Affiliation(s)
- Shamik Majumdar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vasista Adiga
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Abinaya Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| |
Collapse
|
17
|
Abstract
Higher organisms are all born with general immunity as well as with, increasingly, more specific immune systems. All immune mechanisms function with the intent of aiding the body in defense against infection. Internal and external factors alike have varying effects on the immune system, and the immune response is tailored specifically to each one. Accompanying the components of the human innate and adaptive immune systems are the other intermingling systems of the human body. Increasing understanding of the body's immune interactions with other systems has opened new avenues of study, including that of the microbiome. The microbiome has become a highly active area of research over the last 10 to 20 years since the NIH began funding the Human Microbiome Project (HMP), which was established in 2007. Several publications have focused on the characterization, functions, and complex interplay of the microbiome as it relates to the rest of the body. A dysfunction between the microbiome and the host has been linked to various diseases including cancers, metabolic deficiencies, autoimmune disorders, and infectious diseases. Further understanding of the microbiome and its interaction with the host in relation to diseases is needed in order to understand the implications of microbiome dysfunction and the possible use of microbiota in the prevention of disease. In this review, we have summarized information on the immune system, the microbiome, the microbiome's interplay with other systems, and the association of the immune system and the microbiome in diseases such as diabetes and colorectal cancer.
Collapse
Affiliation(s)
| | - Sohail Siraj
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Krishna Patel
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Umesh T. Sankpal
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| | - Stephen Mathew
- Graduate School of Biomedical Sciences, UNT Health Science Center, Fort Worth, TX
| | - Riyaz Basha
- Graduate School of Biomedical Sciences, UNT Health Science Center, Fort Worth, TX
- Texas College of Osteopathic Medicine, UNT Health Science Center, Fort Worth, TX
| |
Collapse
|
18
|
Wu K, Zhao M, Ma C, Zhang H, Liu X, Zhou L, Zhao J, Gao L, Wang D. Thyrotropin Alters T Cell Development in the Thymus in Subclinical Hypothyroidism Mouse Model. Scand J Immunol 2017; 85:35-42. [PMID: 27864993 DOI: 10.1111/sji.12507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/11/2016] [Indexed: 02/06/2023]
Abstract
Subclinical hypothyroidism (SCH) is highly prevalent in the general population and is associated with potential deleterious effects. Although developing T cells express thyroid-stimulating hormone receptor (TSH-R), the changes of T cell development in thymus in SCH have not been fully clarified. SCH mouse model, which is characterized by elevated serum TSH but similar thyroid hormone levels, was used to study the role of TSH in T cell development. Thymus weight of SCH mice increased 18% compared with controls. Importantly, the frequencies of CD4+ and CD8+ single-positive (SP) thymocytes increased 38% and 44%, respectively. We demonstrated that TSH protected thymocytes from apoptosis as evidenced by a significant decrease of Annexin V-positive thymocytes in SCH mice. Further analysis showed that extracellular-regulated kinases (ERK) 1/2 in thymus were activated in SCH mice. With analysis of T cell receptor excision circles (TREC), we found that TSH increased recent thymic emigrants (RTE) in spleen tissue in SCH mice. Thus, these results suggest that TSH promoted T cell development and enhanced the thymic recent output in SCH mice, possibly by suppression of apoptosis of thymocytes, indicating that modification of the ERK signalling pathways.
Collapse
Affiliation(s)
- K Wu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - M Zhao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - C Ma
- Scientific Center, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - H Zhang
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - X Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - L Zhou
- Department of Endocrinology and Metabolism, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - J Zhao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, Shandong, China
| | - L Gao
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, Shandong, China.,Scientific Center, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - D Wang
- Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| |
Collapse
|
19
|
Artalejo JR, Gómez-Corral A, López-García M, Molina-París C. Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery. J Math Biol 2017; 74:673-708. [PMID: 27350044 PMCID: PMC5258823 DOI: 10.1007/s00285-016-1020-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/20/2016] [Indexed: 12/11/2022]
Abstract
The population of naive T cells in the periphery is best described by determining both its T cell receptor diversity, or number of clonotypes, and the sizes of its clonal subsets. In this paper, we make use of a previously introduced mathematical model of naive T cell homeostasis, to study the fate and potential of naive T cell clonotypes in the periphery. This is achieved by the introduction of several new stochastic descriptors for a given naive T cell clonotype, such as its maximum clonal size, the time to reach this maximum, the number of proliferation events required to reach this maximum, the rate of contraction of the clonotype during its way to extinction, as well as the time to a given number of proliferation events. Our results show that two fates can be identified for the dynamics of the clonotype: extinction in the short-term if the clonotype experiences too hostile a peripheral environment, or establishment in the periphery in the long-term. In this second case the probability mass function for the maximum clonal size is bimodal, with one mode near one and the other mode far away from it. Our model also indicates that the fate of a recent thymic emigrant (RTE) during its journey in the periphery has a clear stochastic component, where the probability of extinction cannot be neglected, even in a friendly but competitive environment. On the other hand, a greater deterministic behaviour can be expected in the potential size of the clonotype seeded by the RTE in the long-term, once it escapes extinction.
Collapse
Affiliation(s)
- J R Artalejo
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, 28040, Madrid, Spain
| | - A Gómez-Corral
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, 28040, Madrid, Spain
- Instituto de Ciencias Matemáticas, CSIC-UAM-UC3M-UCM, Calle Nicolás Cabrera 13-15, Campus de Cantoblanco UAM, 28049, Madrid, Spain
| | - M López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - C Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
20
|
Krueger A, Ziętara N, Łyszkiewicz M. T Cell Development by the Numbers. Trends Immunol 2016; 38:128-139. [PMID: 27842955 DOI: 10.1016/j.it.2016.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023]
Abstract
T cells are continually generated in the thymus in a highly dynamic process comprising discrete steps of lineage commitment, T cell receptor (TCR) gene rearrangement, and selection. These steps are linked to distinct rates of proliferation, survival, and cell death, but a quantitative picture of T cell development is only beginning to emerge. Here we summarize recent technical advances, including genetic fate mapping, barcoding, and molecular timers, that have allowed the implementation of computational models to quantify developmental dynamics in the thymus. Coupling new techniques with mathematical models has recently resulted in the emergence of new paradigms in early hematopoiesis and might similarly open new perspectives on T cell development.
Collapse
Affiliation(s)
- Andreas Krueger
- Institute of Molecular Medicine, Goethe University Frankfurt am Main, 60590 Frankfurt am Main, Germany.
| | - Natalia Ziętara
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
| | - Marcin Łyszkiewicz
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
| |
Collapse
|
21
|
Modeling the development of the post-natal mouse thymus in the absence of bone marrow progenitors. Sci Rep 2016; 6:36159. [PMID: 27824070 PMCID: PMC5099910 DOI: 10.1038/srep36159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023] Open
Abstract
Many mathematical models have been published with the purpose of explaining aspects of T-cell development in the thymus. In this manuscript we adapted a four-compartment model of the thymus and used a range of mathematical approaches with the aim of explaining the dynamics of the four main thymocyte populations in the mouse thymus, from the emergence of the first fetal thymocyte until the death of the animal. At various pre-natal and post-natal stages we investigated experimentally the number and composition of thymocytes populations, their apoptosis and proliferation, along with data from literature, to create and validate the model. In our model the proliferation processes are characterized by decreasing proliferation rates, which allows us to model the natural involution of the thymus. The best results were obtained when different sets of parameters were used for the fetal and post-natal periods, suggesting that birth may induce a discontinuity in the modeled processes. Our model is able to model the development of both pre-natal and post-natal thymocyte populations. Also, our findings showed that the post-natal thymus is able to develop in the absence of the daily input of bone marrow progenitors, providing more evidence to support the autonomous development of the post-natal thymus.
Collapse
|
22
|
Hu Z, Lancaster JN, Ehrlich LIR. The Contribution of Chemokines and Migration to the Induction of Central Tolerance in the Thymus. Front Immunol 2015; 6:398. [PMID: 26300884 PMCID: PMC4528182 DOI: 10.3389/fimmu.2015.00398] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/20/2015] [Indexed: 02/01/2023] Open
Abstract
As T cells develop, they migrate throughout the thymus where they undergo essential bi-directional signaling with stromal cells in distinct thymic microenvironments. Immature thymocyte progenitors are located in the thymic cortex. Following T cell receptor expression and positive selection, thymocytes undergo a dramatic transition: they become rapidly motile and relocate to the thymic medulla. Antigen-presenting cells (APCs) within the cortex and medulla display peptides derived from a wide array of self-proteins, which promote thymocyte self-tolerance. If a thymocyte is auto-reactive against such antigens, it undergoes either negative selection, via apoptosis, or differentiation into the regulatory T cell lineage. This induction of central tolerance is critical for prevention of autoimmunity. Chemokines and adhesion molecules play an essential role in tolerance induction, as they promote migration of developing thymocytes through the different thymic microenvironments and enhance interactions with APCs displaying self-antigens. Herein, we review the contribution of chemokines and other regulators of thymocyte localization and motility to T cell development, with a focus on their contribution to the induction of central tolerance.
Collapse
Affiliation(s)
- Zicheng Hu
- Ehrlich Laboratory, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, TX , USA
| | - Jessica Naomi Lancaster
- Ehrlich Laboratory, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, TX , USA
| | - Lauren I R Ehrlich
- Ehrlich Laboratory, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, TX , USA
| |
Collapse
|
23
|
Starskaya IS, Kudryavtsev IV, Guselnikova VV, Serebriakova MK, Polevshchikov AV. Apoptosis level in developing T cells in the thymus. DOKL BIOCHEM BIOPHYS 2015; 462:163-5. [DOI: 10.1134/s1607672915030060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 11/23/2022]
|
24
|
Abstract
During blood cell development, hematopoietic stem cells generate diverse mature populations via several rounds of binary fate decisions. At each bifurcation, precursors adopt one fate and inactivate the alternative fate either stochastically or in response to extrinsic stimuli and stably maintain the selected fates. Studying of these processes would contribute to better understanding of etiology of immunodeficiency and leukemia, which are caused by abnormal gene regulation during the development of hematopoietic cells. The CD4(+) helper versus CD8(+) cytotoxic T-cell fate decision serves as an excellent model to study binary fate decision processes. These two cell types are derived from common precursors in the thymus. Positive selection of their TCRs by self-peptide presented on either MHC class I or class II triggers their fate decisions along with mutually exclusive retention and silencing of two coreceptors, CD4 and CD8. In the past few decades, extensive effort has been made to understand the T-cell fate decision processes by studying regulation of genes encoding the coreceptors and selection processes. These studies have identified several key transcription factors and gene regulatory networks. In this chapter, I will discuss recent advances in our understanding of the binary cell fate decision processes of T cells.
Collapse
Affiliation(s)
- Takeshi Egawa
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA.
| |
Collapse
|
25
|
Khailaie S, Robert PA, Toker A, Huehn J, Meyer-Hermann M. A signal integration model of thymic selection and natural regulatory T cell commitment. THE JOURNAL OF IMMUNOLOGY 2014; 193:5983-96. [PMID: 25392533 DOI: 10.4049/jimmunol.1400889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The extent of TCR self-reactivity is the basis for selection of a functional and self-tolerant T cell repertoire and is quantified by repeated engagement of TCRs with a diverse pool of self-peptides complexed with self-MHC molecules. The strength of a TCR signal depends on the binding properties of a TCR to the peptide and the MHC, but it is not clear how the specificity to both components drives fate decisions. In this study, we propose a TCR signal-integration model of thymic selection that describes how thymocytes decide among distinct fates, not only based on a single TCR-ligand interaction, but taking into account the TCR stimulation history. These fates are separated based on sustained accumulated signals for positive selection and transient peak signals for negative selection. This spans up the cells into a two-dimensional space where they are either neglected, positively selected, negatively selected, or selected as natural regulatory T cells (nTregs). We show that the dynamics of the integrated signal can serve as a successful basis for extracting specificity of thymocytes to MHC and detecting the existence of cognate self-peptide-MHC. It allows to select a self-MHC-biased and self-peptide-tolerant T cell repertoire. Furthermore, nTregs in the model are enriched with MHC-specific TCRs. This allows nTregs to be more sensitive to activation and more cross-reactive than conventional T cells. This study provides a mechanistic model showing that time integration of TCR-mediated signals, as opposed to single-cell interaction events, is needed to gain a full view on the properties emerging from thymic selection.
Collapse
Affiliation(s)
- Sahamoddin Khailaie
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Philippe A Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Aras Toker
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; and
| | - Jochen Huehn
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; and
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Institute for Biochemistry, Biotechnology, and Bioinformatics, University of Technology Braunschweig, 38106 Braunschweig, Germany
| |
Collapse
|
26
|
Morel PA, Faeder JR, Hawse WF, Miskov-Zivanov N. Modeling the T cell immune response: a fascinating challenge. J Pharmacokinet Pharmacodyn 2014; 41:401-13. [PMID: 25155903 PMCID: PMC4210366 DOI: 10.1007/s10928-014-9376-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/13/2014] [Indexed: 12/11/2022]
Abstract
The immune system is designed to protect the organism from infection and to repair damaged tissue. An effective response requires recognition of the threat, the appropriate effector mechanism to clear the pathogen and a return to homeostasis with minimal damage to self-tissues. T cells play a central role in orchestrating the immune response at all stages of the response and have been the subject of intense study by both experimental immunologists and modelers. This review examines some of the more critical questions in T cell biology and describes the latest attempts to address those questions using approaches that combine mathematical modeling and experiments.
Collapse
Affiliation(s)
- Penelope A Morel
- Departments of Immunology, University of Pittsburgh, 200 Lothrop Street, BST E1055, Pittsburgh, PA, 15261, USA,
| | | | | | | |
Collapse
|
27
|
Perry JSA, Lio CWJ, Kau AL, Nutsch K, Yang Z, Gordon JI, Murphy KM, Hsieh CS. Distinct contributions of Aire and antigen-presenting-cell subsets to the generation of self-tolerance in the thymus. Immunity 2014; 41:414-426. [PMID: 25220213 PMCID: PMC4175925 DOI: 10.1016/j.immuni.2014.08.007] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/18/2014] [Indexed: 02/07/2023]
Abstract
The contribution of thymic antigen-presenting-cell (APC) subsets in selecting a self-tolerant T cell population remains unclear. We show that bone marrow (BM) APCs and medullary thymic epithelial cells (mTECs) played nonoverlapping roles in shaping the T cell receptor (TCR) repertoire by deletion and regulatory T (Treg) cell selection of distinct TCRs. Aire, which induces tissue-specific antigen expression in mTECs, affected the TCR repertoire in a manner distinct from mTEC presentation. Approximately half of Aire-dependent deletion or Treg cell selection utilized a pathway dependent on antigen presentation by BM APCs. Batf3-dependent CD8α⁺ dendritic cells (DCs) were the crucial BM APCs for Treg cell selection via this pathway, showing enhanced ability to present antigens from stromal cells. These results demonstrate the division of function between thymic APCs in shaping the self-tolerant TCR repertoire and reveal an unappreciated cooperation between mTECs and CD8α⁺ DCs for presentation of Aire-induced self-antigens to developing thymocytes.
Collapse
Affiliation(s)
- Justin S A Perry
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chan-Wang J Lio
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L Kau
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Katherine Nutsch
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhuo Yang
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Kenneth M Murphy
- Howard Hughes Medical Institute and Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Division of Rheumatology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|