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Geiß C, Salas E, Guevara-Coto J, Régnier-Vigouroux A, Mora-Rodríguez RA. Multistability in Macrophage Activation Pathways and Metabolic Implications. Cells 2022; 11:404. [PMID: 35159214 PMCID: PMC8834178 DOI: 10.3390/cells11030404] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/22/2022] Open
Abstract
Macrophages are innate immune cells with a dynamic range of reversible activation states including the classical pro-inflammatory (M1) and alternative anti-inflammatory (M2) states. Deciphering how macrophages regulate their transition from one state to the other is key for a deeper understanding of inflammatory diseases and relevant therapies. Common regulatory motifs reported for macrophage transitions, such as positive or double-negative feedback loops, exhibit a switchlike behavior, suggesting the bistability of the system. In this review, we explore the evidence for multistability (including bistability) in macrophage activation pathways at four molecular levels. First, a decision-making module in signal transduction includes mutual inhibitory interactions between M1 (STAT1, NF-KB/p50-p65) and M2 (STAT3, NF-KB/p50-p50) signaling pathways. Second, a switchlike behavior at the gene expression level includes complex network motifs of transcription factors and miRNAs. Third, these changes impact metabolic gene expression, leading to switches in energy production, NADPH and ROS production, TCA cycle functionality, biosynthesis, and nitrogen metabolism. Fourth, metabolic changes are monitored by metabolic sensors coupled to AMPK and mTOR activity to provide stability by maintaining signals promoting M1 or M2 activation. In conclusion, we identify bistability hubs as promising therapeutic targets for reverting or blocking macrophage transitions through modulation of the metabolic environment.
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Affiliation(s)
- Carsten Geiß
- Institute for Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, 55128 Mainz, Germany;
| | - Elvira Salas
- Department of Biochemistry, Faculty of Medicine, Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
| | - Jose Guevara-Coto
- Department of Computer Sciences and Informatics (ECCI), Faculty of Engineering, Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica;
- Research Center for Information and Communication Technologies (CITIC), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Anne Régnier-Vigouroux
- Institute for Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, 55128 Mainz, Germany;
| | - Rodrigo A. Mora-Rodríguez
- Institute for Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, 55128 Mainz, Germany;
- Research Center on Surgery and Cancer (CICICA), Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica
- Research Center for Tropical Diseases (CIET), Lab of Tumor Chemosensitivity (LQT), Faculty of Microbiology, Campus Rodrigo Facio, University of Costa Rica, San José 11501-2060, Costa Rica
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Frank AS, Larripa K, Ryu H, Snodgrass RG, Röblitz S. Bifurcation and sensitivity analysis reveal key drivers of multistability in a model of macrophage polarization. J Theor Biol 2020; 509:110511. [PMID: 33045246 DOI: 10.1016/j.jtbi.2020.110511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022]
Abstract
In this paper, we present and analyze a mathematical model for polarization of a single macrophage which, despite its simplicity, exhibits complex dynamics in terms of multistability. In particular, we demonstrate that an asymmetry in the regulatory mechanisms and parameter values is important for observing multiple phenotypes. Bifurcation and sensitivity analyses show that external signaling cues are necessary for macrophage commitment and emergence to a phenotype, but that the intrinsic macrophage pathways are equally important. Based on our numerical results, we formulate hypotheses that could be further investigated by laboratory experiments to deepen our understanding of macrophage polarization.
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Affiliation(s)
- Anna S Frank
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Kamila Larripa
- Department of Mathematics, Humboldt State University, Arcata, CA, USA.
| | - Hwayeon Ryu
- Department of Mathematics and Statistics, Elon University, Elon, NC, USA.
| | - Ryan G Snodgrass
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany.
| | - Susanna Röblitz
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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3
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Amelio P, Portevin D, Reither K, Mhimbira F, Mpina M, Tumbo A, Nickel B, Marti H, Knopp S, Ding S, Penn-Nicholson A, Darboe F, Ohmiti K, Scriba TJ, Pantaleo G, Daubenberger C, Perreau M. Mixed Th1 and Th2 Mycobacterium tuberculosis-specific CD4 T cell responses in patients with active pulmonary tuberculosis from Tanzania. PLoS Negl Trop Dis 2017; 11:e0005817. [PMID: 28759590 PMCID: PMC5552332 DOI: 10.1371/journal.pntd.0005817] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/10/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) and helminth infections elicit antagonistic immune effector functions and are co-endemic in several regions of the world. We therefore hypothesized that helminth infection may influence Mtb-specific T-cell immune responses. We evaluated the cytokine profile of Mtb-specific T cells in 72 individuals with pulmonary TB disease recruited from two Sub-Saharan regions with high and moderate helminth burden i.e. 55 from Tanzania (TZ) and 17 from South Africa (SA), respectively. We showed that Mtb-specific CD4 T-cell functional profile of TB patients from Tanzania are primarily composed of polyfunctional Th1 and Th2 cells, associated with increased expression of Gata-3 and reduced expression of T-bet in memory CD4 T cells. In contrast, the cytokine profile of Mtb-specific CD4 T cells of TB patients from SA was dominated by single IFN-γ and dual IFN-γ/TNF-α and associated with TB-induced systemic inflammation and elevated serum levels of type I IFNs. Of note, the proportion of patients with Mtb-specific CD8 T cells was significantly reduced in Mtb/helminth co-infected patients from TZ. It is likely that the underlying helminth infection and possibly genetic and other unknown environmental factors may have caused the induction of mixed Th1/Th2 Mtb-specific CD4 T cell responses in patients from TZ. Taken together, these results indicate that the generation of Mtb-specific CD4 and CD8 T cell responses may be substantially influenced by environmental factors in vivo. These observations may have major impact in the identification of immune biomarkers of disease status and correlates of protection. Mycobacterium tuberculosis (Mtb) and helminth infections are co-endemic in several regions of the world and their immune responses may be mutually antagonistic. We therefore hypothesized that helminth infection would impact and potentially shape Mtb-specific T-cell responses and systemic inflammation in patients suffering from active pulmonary tuberculosis (TB) enrolled from two helminth endemic regions i.e. Tanzania (TZ) and South Africa (SA). In this study, we demonstrate for the first time that TB patients from SA and TZ harbor distinct immune responses to Mtb antigens. Indeed, we showed that Mtb-specific CD4 T-cell responses of TB patients from TZ were composed by a mixed T helper type 1 (Th1) and Th2 responses. In contrast, the cytokine profile of Mtb-specific CD4 T cells of TB patients from SA was dominated by Th1 cells and associated with TB-induced systemic inflammation and elevated serum levels of type I IFN. Taken together, these data indicate that Mtb-specific T-cell responses are diverse in human populations and can be strongly influenced by host and pathogen genetic background, co-infections and yet unknown environmental factors. Identification of correlates of risk and protection from TB disease will help in the rational development of protective T-cell based vaccines against TB, early monitoring TB treatment outcomes and focused follow up of high risk populations.
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Affiliation(s)
- Patrizia Amelio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Beatrice Nickel
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Hanspeter Marti
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Stefanie Knopp
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Song Ding
- EuroVacc Foundation, Lausanne, Switzerland
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Fatoumatta Darboe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Khalid Ohmiti
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- SVRI, Lausanne, Switzerland
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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4
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Li X, Levine H. Bistability of the cytokine-immune cell network in a cancer microenvironment. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa6c07] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biol 2016; 14:e2000640. [PMID: 28027308 PMCID: PMC5189937 DOI: 10.1371/journal.pbio.2000640] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/22/2016] [Indexed: 01/09/2023] Open
Abstract
Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. But how progenitor cells overcome the stability of their gene expression configuration (attractor) to exit the attractor in one direction remains elusive. Here we show that commitment of blood progenitor cells to the erythroid or myeloid lineage is preceded by the destabilization of their high-dimensional attractor state, such that differentiating cells undergo a critical state transition. Single-cell resolution analysis of gene expression in populations of differentiating cells affords a new quantitative index for predicting critical transitions in a high-dimensional state space based on decrease of correlation between cells and concomitant increase of correlation between genes as cells approach a tipping point. The detection of “rebellious cells” that enter the fate opposite to the one intended corroborates the model of preceding destabilization of a progenitor attractor. Thus, early warning signals associated with critical transitions can be detected in statistical ensembles of high-dimensional systems, offering a formal theory-based approach for analyzing single-cell molecular profiles that goes beyond current computational pattern recognition, does not require knowledge of specific pathways, and could be used to predict impending major shifts in development and disease. A certain type of multipotent progenitor cell of the blood can commit to either the white (myeloid) or the red (erythroid) blood cell lineage, thus making a discrete binary cell fate decision. To test a theory on fundamental principles of cell fate dynamics (as opposed to the usually studied molecular mechanisms), we monitored such a fate decision in vitro using single-cell resolution gene expression analysis. We found that blood progenitor cells undergoing a fate decision to commit to either lineage after treatment with fate-determining cytokines, according to theory, first destabilized their original state. Cell states hereby diversified, manifesting the predicted flattening of an attractor’s potential well, which allows the increasingly vacillating progenitor cells to “spill” into adjacent potential wells corresponding to either lineage—myeloid or erythroid. This destabilization of an old stable state until suddenly opening access to new stable states is consistent with a critical transition (tipping point). We propose and demonstrate a new type of early warning signal that precedes critical transitions: an index IC based on a change in the high-dimensional cell population structure obtained from single-cell resolution measurements. This index may be used to predict imminent tipping point–like transitions in multicell systems, e.g., before pathological changes in tissues.
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6
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Morel PA, Lee REC, Faeder JR. Demystifying the cytokine network: Mathematical models point the way. Cytokine 2016; 98:115-123. [PMID: 27919524 DOI: 10.1016/j.cyto.2016.11.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022]
Abstract
Cytokines provide the means by which immune cells communicate with each other and with parenchymal cells. There are over one hundred cytokines and many exist in families that share receptor components and signal transduction pathways, creating complex networks. Reductionist approaches to understanding the role of specific cytokines, through the use of gene-targeted mice, have revealed further complexity in the form of redundancy and pleiotropy in cytokine function. Creating an understanding of the complex interactions between cytokines and their target cells is challenging experimentally. Mathematical and computational modeling provides a robust set of tools by which complex interactions between cytokines can be studied and analyzed, in the process creating novel insights that can be further tested experimentally. This review will discuss and provide examples of the different modeling approaches that have been used to increase our understanding of cytokine networks. This includes discussion of knowledge-based and data-driven modeling approaches and the recent advance in single-cell analysis. The use of modeling to optimize cytokine-based therapies will also be discussed.
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Affiliation(s)
- Penelope A Morel
- Department of Immunology, University of Pittsburgh, Pittsburgh, USA.
| | - Robin E C Lee
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - James R Faeder
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
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7
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Wu B, Wang Y, Wang C, Wang GG, Wu J, Wan YY. BPTF Is Essential for T Cell Homeostasis and Function. THE JOURNAL OF IMMUNOLOGY 2016; 197:4325-4333. [PMID: 27799308 DOI: 10.4049/jimmunol.1600642] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a ubiquitously expressed ATP-dependent chromatin-remodeling factor, is critical for epigenetically regulating DNA accessibility and gene expression. Although BPTF is important for the development of thymocytes, its function in mature T cells remains largely unknown. By specifically deleting BPTF from late double-negative 3/double-negative 4 stage of developing T cells, we found that BPTF was critical for the homeostasis of T cells via a cell-intrinsic manner. In addition, BPTF was essential for the maintenance and function of regulatory T (Treg) cells. Treg cell-specific BPTF deletion led to reduced Foxp3 expression, increased lymphocyte infiltration in the nonlymphoid organs, and a systemic autoimmune syndrome. These findings therefore reveal a vital role for BPTF in T and Treg cell function and immune homeostasis.
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Affiliation(s)
- Bing Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yunqi Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Chaojun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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Anandamide attenuates Th-17 cell-mediated delayed-type hypersensitivity response by triggering IL-10 production and consequent microRNA induction. PLoS One 2014; 9:e93954. [PMID: 24699635 PMCID: PMC3974854 DOI: 10.1371/journal.pone.0093954] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 03/12/2014] [Indexed: 11/19/2022] Open
Abstract
Endogenous cannabinoids [endocannabinoids] are lipid signaling molecules that have been shown to modulate immune functions. However, their role in the regulation of Th17 cells has not been studied previously. In the current study, we used methylated Bovine Serum Albumin [mBSA]-induced delayed type hypersensitivity [DTH] response in C57BL/6 mice, mediated by Th17 cells, as a model to test the anti-inflammatory effects of endocannabinoids. Administration of anandamide [AEA], a member of the endocannabinoid family, into mice resulted in significant mitigation of mBSA-induced inflammation, including foot pad swelling, cell infiltration, and cell proliferation in the draining lymph nodes [LN]. AEA treatment significantly reduced IL-17 and IFN-γ production, as well as decreased RORγt expression while causing significant induction of IL-10 in the draining LNs. IL-10 was critical for the AEA-induced mitigation of DTH response inasmuch as neutralization of IL-10 reversed the effects of AEA. We next analyzed miRNA from the LN cells and found that 100 out of 609 miRNA species were differentially regulated in AEA-treated mice when compared to controls. Several of these miRNAs targeted proinflammatory mediators. Interestingly, many of these miRNA were also upregulated upon in vitro treatment of LN cells with IL-10. Together, the current study demonstrates that AEA may suppress Th-17 cell–mediated DTH response by inducing IL-10 which in turn triggers miRNA that target proinflammatory pathways.
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Magombedze G, Eda S, Ganusov VV. Competition for antigen between Th1 and Th2 responses determines the timing of the immune response switch during Mycobaterium avium subspecies paratuberulosis infection in ruminants. PLoS Comput Biol 2014; 10:e1003414. [PMID: 24415928 PMCID: PMC3886887 DOI: 10.1371/journal.pcbi.1003414] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/11/2013] [Indexed: 12/15/2022] Open
Abstract
Johne's disease (JD), a persistent and slow progressing infection of ruminants such as cows and sheep, is caused by slow replicating bacilli Mycobacterium avium subspecies paratuberculosis (MAP) infecting macrophages in the gut. Infected animals initially mount a cell-mediated CD4 T cell response against MAP which is characterized by the production of interferon (Th1 response). Over time, Th1 response diminishes in most animals and antibody response to MAP antigens becomes dominant (Th2 response). The switch from Th1 to Th2 response occurs concomitantly with disease progression and shedding of the bacteria in feces. Mechanisms controlling this Th1/Th2 switch remain poorly understood. Because Th1 and Th2 responses are known to cross-inhibit each other, it is unclear why initially strong Th1 response is lost over time. Using a novel mathematical model of the immune response to MAP infection we show that the ability of extracellular bacteria to persist outside of macrophages naturally leads to switch of the cellular response to antibody production. Several additional mechanisms may also contribute to the timing of the Th1/Th2 switch including the rate of proliferation of Th1/Th2 responses at the site of infection, efficiency at which immune responses cross-inhibit each other, and the rate at which Th1 response becomes exhausted over time. Our basic model reasonably well explains four different kinetic patterns of the Th1/Th2 responses in MAP-infected sheep by variability in the initial bacterial dose and the efficiency of the MAP-specific T cell responses. Taken together, our novel mathematical model identifies factors of bacterial and host origin that drive kinetics of the immune response to MAP and provides the basis for testing the impact of vaccination or early treatment on the duration of infection. Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic enteric disease of ruminants such as sheep and cows. Due to early culling and reduction in milk production of affected animals, MAP inflicts high economic cost to diary farms. MAP infection has a long incubation period of several years, and during the asymptomatic stage a strong cellular (T helper 1) immune response is thought to control MAP replication. Over time, Th1 response is lost and ineffective antibody response driven by Th2 cells becomes predominant. We develop the first mathematical model of helper T cell response to MAP infection to understand impact of various mechanisms on the dynamics of the switch from Th1 to Th2 response. Our results suggest that in contrast to the generally held belief, Th1/Th2 switch may be driven by the accumulation of long-lived extracellular bacteria, and therefore, may be the consequence of the disease progression of MAP-infected animals and not its cause. Our model highlights limitations of our current understanding of regulation of helper T cell responses during MAP infection and identifies areas for future experimental research.
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Affiliation(s)
- Gesham Magombedze
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennesse, United States of America
- * E-mail: ;
| | - Shigetoshi Eda
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, Tennesse, United States of America
| | - Vitaly V. Ganusov
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennesse, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennesse, United States of America
- Department of Mathematics, University of Tennessee, Knoxville, Tennesse, United States of America
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Magombedze G, Reddy PBJ, Eda S, Ganusov VV. Cellular and population plasticity of helper CD4(+) T cell responses. Front Physiol 2013; 4:206. [PMID: 23966946 PMCID: PMC3744810 DOI: 10.3389/fphys.2013.00206] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 07/21/2013] [Indexed: 12/29/2022] Open
Abstract
Vertebrates are constantly exposed to pathogens, and the adaptive immunity has most likely evolved to control and clear such infectious agents. CD4+ T cells are the major players in the adaptive immune response to pathogens. Following recognition of pathogen-derived antigens naïve CD4+ T cells differentiate into effectors which then control pathogen replication either directly by killing pathogen-infected cells or by assisting with generation of cytotoxic T lymphocytes (CTLs) or pathogen-specific antibodies. Pathogen-specific effector CD4+ T cells are highly heterogeneous in terms of cytokines they produce. Three major subtypes of effector CD4+ T cells have been identified: T-helper 1 (Th1) cells producing IFN-γ and TNF-α, Th2 cells producing IL-4 and IL-10, and Th17 cells producing IL-17. How this heterogeneity is maintained and what regulates changes in effector T cell composition during chronic infections remains poorly understood. In this review we discuss recent advances in our understanding of CD4+ T cell differentiation in response to microbial infections. We propose that a change in the phenotype of pathogen-specific effector CD4+ T cells during chronic infections, for example, from Th1 to Th2 response as observed in Mycobactrium avium ssp. paratuberculosis (MAP) infection of ruminants, can be achieved by conversion of T cells from one effector subset to another (cellular plasticity) or due to differences in kinetics (differentiation, proliferation, death) of different effector T cell subsets (population plasticity). We also shortly review mathematical models aimed at describing CD4+ T cell differentiation and outline areas for future experimental and theoretical research.
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Affiliation(s)
- Gesham Magombedze
- National Institute for Mathematical and Biological Synthesis, University of Tennessee Knoxville, TN, USA
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11
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Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. PLoS Biol 2013; 11:e1001616. [PMID: 23935451 PMCID: PMC3728017 DOI: 10.1371/journal.pbio.1001616] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 06/14/2013] [Indexed: 12/17/2022] Open
Abstract
An experimental and theoretical study of T cell differentiation in response to mixed-input conditions reveals that cells can tune between Th1 and Th2 states through a continuum of mixed phenotypes. Cell differentiation is typically directed by external signals that drive opposing regulatory pathways. Studying differentiation under polarizing conditions, with only one input signal provided, is limited in its ability to resolve the logic of interactions between opposing pathways. Dissection of this logic can be facilitated by mapping the system's response to mixtures of input signals, which are expected to occur in vivo, where cells are simultaneously exposed to various signals with potentially opposing effects. Here, we systematically map the response of naïve T cells to mixtures of signals driving differentiation into the Th1 and Th2 lineages. We characterize cell state at the single cell level by measuring levels of the two lineage-specific transcription factors (T-bet and GATA3) and two lineage characteristic cytokines (IFN-γ and IL-4) that are driven by these transcription regulators. We find a continuum of mixed phenotypes in which individual cells co-express the two lineage-specific master regulators at levels that gradually depend on levels of the two input signals. Using mathematical modeling we show that such tunable mixed phenotype arises if autoregulatory positive feedback loops in the gene network regulating this process are gradual and dominant over cross-pathway inhibition. We also find that expression of the lineage-specific cytokines follows two independent stochastic processes that are biased by expression levels of the master regulators. Thus, cytokine expression is highly heterogeneous under mixed conditions, with subpopulations of cells expressing only IFN-γ, only IL-4, both cytokines, or neither. The fraction of cells in each of these subpopulations changes gradually with input conditions, reproducing the continuous internal state at the cell population level. These results suggest a differentiation scheme in which cells reflect uncertainty through a continuously tuneable mixed phenotype combined with a biased stochastic decision rather than a binary phenotype with a deterministic decision. During cell differentiation, progenitor cells respond to external signals that drive the expression of genes that are characteristic of the differentiated cell states. This process is controlled by gene regulatory networks that typically involve positive autoregulation and cross-inhibition between master regulators of the two differentiated states. Mapping the system's response to mixtures of external signals can help us to understand the operational logic of these binary cell fate decisions. Here, we study differentiation of CD4+ T cells into Th1 and Th2 lineages under mixed-input conditions, at the single cell level. We reveal that cell state is not restricted to a small number of well-defined phenotypes, but rather tunes through a continuum of mixed-phenotype states in which levels of lineage-specifying transcription factors gradually change with the levels of the two inputs. Using mathematical modeling we establish the conditions under which the system has one stable steady state that continuously tunes in response to changes in levels of the inputs. Results of this model qualitatively explain our experimental observations. We further characterize expression patterns of downstream lineage-specific genes—cytokines that are driven by the two master regulators upon cell re-stimulation. We find a highly heterogeneous population with cells expressing either one of the cytokines, both cytokines, or neither. Of note, the fraction of cells in these subpopulations continuously tunes with input levels, thus reproducing a tunable state at the cell population level. Our results can be explained by a two-stage scheme in which the gene regulatory network is responsible for a continuously tunable cell state, which is translated into a heterogeneous cytokine expression pattern through uncorrelated and biased stochastic processes.
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Affiliation(s)
- Yaron E. Antebi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yuval Hart
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inbal Eizenberg
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Rimer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Prabhakar Putheti
- Transplantation Institute and Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dana Pe'er
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Polonsky M, Zaretsky I, Friedman N. Dynamic single-cell measurements of gene expression in primary lymphocytes: challenges, tools and prospects. Brief Funct Genomics 2013; 12:99-108. [DOI: 10.1093/bfgp/els061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Kogan Y, Agur Z, Elishmereni M. A mathematical model for the immunotherapeutic control of the Th1/Th2 imbalance in melanoma. ACTA ACUST UNITED AC 2013. [DOI: 10.3934/dcdsb.2013.18.1017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Hong T, Xing J, Li L, Tyson JJ. A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comput Biol 2011; 7:e1002122. [PMID: 21829337 PMCID: PMC3145653 DOI: 10.1371/journal.pcbi.1002122] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 05/27/2011] [Indexed: 11/18/2022] Open
Abstract
The reciprocal differentiation of T helper 17 (TH17) cells and induced regulatory T (iTreg) cells plays a critical role in both the pathogenesis and resolution of diverse human inflammatory diseases. Although initial studies suggested a stable commitment to either the TH17 or the iTreg lineage, recent results reveal remarkable plasticity and heterogeneity, reflected in the capacity of differentiated effectors cells to be reprogrammed among TH17 and iTreg lineages and the intriguing phenomenon that a group of naïve precursor CD4+ T cells can be programmed into phenotypically diverse populations by the same differentiation signal, transforming growth factor beta. To reconcile these observations, we have built a mathematical model of TH17/iTreg differentiation that exhibits four different stable steady states, governed by pitchfork bifurcations with certain degrees of broken symmetry. According to the model, a group of precursor cells with some small cell-to-cell variability can differentiate into phenotypically distinct subsets of cells, which exhibit distinct levels of the master transcription-factor regulators for the two T cell lineages. A dynamical control system with these properties is flexible enough to be steered down alternative pathways by polarizing signals, such as interleukin-6 and retinoic acid and it may be used by the immune system to generate functionally distinct effector cells in desired fractions in response to a range of differentiation signals. Additionally, the model suggests a quantitative explanation for the phenotype with high expression levels of both master regulators. This phenotype corresponds to a re-stabilized co-expressing state, appearing at a late stage of differentiation, rather than a bipotent precursor state observed under some other circumstances. Our simulations reconcile most published experimental observations and predict novel differentiation states as well as transitions among different phenotypes that have not yet been observed experimentally. In order to perform complex functions upon pathogenic challenges, the immune system needs to efficiently deploy a repertoire of specialized cells by inducing the differentiation of precursor cells into effector cells. In a critical process of the adaptive immune system, one common type of precursor cell can give rise to both T helper 17 cells and regulatory T cells, which have distinct phenotypes and functions. Recent discoveries have revealed a certain heterogeneity in this reciprocal differentiation system. In particular, treating precursor cells with a single differentiation signal can result in a remarkably diverse population. An understanding of such variable responses is limited by a lack of quantitative models. Our mathematical model of this cell differentiation system reveals how the control system generates phenotypic diversity and how its final state can be regulated by various signals. The model suggests a new quantitative explanation for the scenario in which the master regulators of two different T cell lineages can be highly expressed in a single cell. The model provides a new framework for understanding the dynamic properties of this type of regulatory network and the mechanisms that help to maintain a balance of effector cells during the inflammatory response to infection.
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Affiliation(s)
- Tian Hong
- Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Jianhua Xing
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Liwu Li
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - John J. Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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Homs S, Mansour H, Desvaux D, Diet C, Hazan M, Buchler M, Lebranchu Y, Buob D, Badoual C, Matignon M, Audard V, Lang P, Grimbert P. Predominant Th1 and cytotoxic phenotype in biopsies from renal transplant recipients with transplant glomerulopathy. Am J Transplant 2009; 9:1230-6. [PMID: 19422348 DOI: 10.1111/j.1600-6143.2009.02596.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transplant glomerulopathy (TGP) appears to be a pathogenic feature of chronic antibody-mediated rejection, but the pathogenesis of this histologic entity is still poorly understood. Previous studies suggest the involvement of lymphocytes but the phenotypes of these cells have never been analyzed. Here, we report the first study of mRNAs for specific markers of CD4+ T cells including Th1 (T-bet and INFgamma), Th2 (IL4 and GATA3), Treg (Foxp3) and Th17 (IL-17 and RORgammat) subsets, cytotoxic CD8 T cells (Granzyme B) and B-cell markers (CD20) in renal biopsies from renal transplant recipients suffering interstitial fibrosis and tubular atrophy (IF/TA) with or without TGP but with a similar inflammatory score and controls including transplant recipients with normal renal function. Only INFgamma, T-bet (both functionally defined markers of Th1 CD4 T cells) and granzyme B (a CD8 cytotoxic marker) were significantly more strongly expressed in patients with TGP than in patients without TGP and normal controls. These results indicate a role of an active T-mediated inflammatory and cytotoxic process in the pathogenesis of TGP.
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Affiliation(s)
- S Homs
- Nephrology and Transplantation Unit, Henri Mondor Hospital and Centre de Recherche, INSERM 841, AP-HP, Institut Francilien de Recherche en Néphrologie et Transplantation, Paris XII University, Créteil, France
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Zhdanov VP. Bistability in gene transcription: Interplay of messenger RNA, protein, and nonprotein coding RNA. Biosystems 2009; 95:75-81. [DOI: 10.1016/j.biosystems.2008.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/04/2008] [Accepted: 07/09/2008] [Indexed: 11/26/2022]
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17
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van den Ham HJ, de Boer RJ. From the two-dimensional Th1 and Th2 phenotypes to high-dimensional models for gene regulation. Int Immunol 2008; 20:1269-77. [DOI: 10.1093/intimm/dxn093] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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