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Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.

ABSTRACT: Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu, complex intracellular signaling networks and numerous transcriptional regulators. We combined experimental approaches and computational modeling to investigate the mechanisms controlling differentiation and plasticity of CD4+ T cells in the gut of mice. Our computational model encompasses the major intracellular pathways involved in CD4+ T cell differentiation into T helper 1 (Th1), Th2, Th17 and induced regulatory T cells (iTreg). Our modeling efforts predicted a critical role for peroxisome proliferator-activated receptor gamma (PPAR?) in modulating plasticity between Th17 and iTreg cells. PPAR? regulates differentiation, activation and cytokine production, thereby controlling the induction of effector and regulatory responses, and is a promising therapeutic target for dysregulated immune responses and inflammation. Our modeling efforts predict that following PPAR? activation, Th17 cells undergo phenotype switch and become iTreg cells. This prediction was validated by results of adoptive transfer studies showing an increase of colonic iTreg and a decrease of Th17 cells in the gut mucosa of mice with colitis following pharmacological activation of PPAR?. Deletion of PPAR? in CD4+ T cells impaired mucosal iTreg and enhanced colitogenic Th17 responses in mice with CD4+ T cell-induced colitis. Thus, for the first time we provide novel molecular evidence in vivo demonstrating that PPAR? in addition to regulating CD4+ T cell differentiation also plays a major role controlling Th17 and iTreg plasticity in the gut mucosa.

SUBMITTER: Carbo A

PROVIDER: S-EPMC3617204 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.

Carbo Adria A Hontecillas Raquel R Kronsteiner Barbara B Viladomiu Monica M Pedragosa Mireia M Lu Pinyi P Philipson Casandra W CW Hoops Stefan S Marathe Madhav M Eubank Stephen S Bisset Keith K Wendelsdorf Katherine K Jarrah Abdul A Mei Yongguo Y Bassaganya-Riera Josep J

PLoS computational biology 20130404 4

Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu, complex intracellular signaling networks and numerous transcriptional regulators. We combined experimental approaches and computational modeling to investigate the mechanisms controlling differentiation and plasticity of CD4+ T cells in the gut of mice. Our computational model encompasses the major intracellular pathways involved in CD4+ T cell differentiation into T helper 1 (Th1 ...[more]

PMID: 23592971

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Project description:Carbo2013 - Cytokine driven CD4+ T Cell differentiation and phenotype plasticity CD4+ T cells can differentiate into different phenotypes depending on the cytokine milieu. Here a computational and mathematical model with sixty ordinary differential equations representing a CD4+ T cell differentiating into either Th1, Th2, Th17 or iTreg cells, has been constructed. The model includes cytokines, nuclear receptors and transcription factors that define fate and function of CD4+ T cells. Computational simulations illustrate how a proinflammatory Th17 cell can undergo reprogramming into an anti-inflammatory iTreg phenotype following PPARc activation. This model is described in the article: Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity. Carbo A, Hontecillas R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe M, Eubank S, Bisset K, Wendelsdorf K, Jarrah A, Mei Y, Bassaganya-Riera J PLoS Computational Biology [2013, 9(4):e1003027] Abstract: Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu, complex intracellular signaling networks and numerous transcriptional regulators. We combined experimental approaches and computational modeling to investigate the mechanisms controlling differentiation and plasticity of CD4+ T cells in the gut of mice. Our computational model encompasses the major intracellular pathways involved in CD4+ T cell differentiation into T helper 1 (Th1), Th2, Th17 and induced regulatory T cells (iTreg). Our modeling efforts predicted a critical role for peroxisome proliferator-activated receptor gamma (PPARγ) in modulating plasticity between Th17 and iTreg cells. PPARγ regulates differentiation, activation and cytokine production, thereby controlling the induction of effector and regulatory responses, and is a promising therapeutic target for dysregulated immune responses and inflammation. Our modeling efforts predict that following PPARγ activation, Th17 cells undergo phenotype switch and become iTreg cells. This prediction was validated by results of adoptive transfer studies showing an increase of colonic iTreg and a decrease of Th17 cells in the gut mucosa of mice with colitis following pharmacological activation of PPARγ. Deletion of PPARγ in CD4+ T cells impaired mucosal iTreg and enhanced colitogenic Th17 responses in mice with CD4+ T cell-induced colitis. Thus, for the first time we provide novel molecular evidence in vivo demonstrating that PPARγ in addition to regulating CD4+ T cell differentiation also plays a major role controlling Th17 and iTreg plasticity in the gut mucosa. Author's comment: CD4+ T cell computational model (Version 1.4) Steady state corrected. There was a problem in the internalization of IL-17 in its mathematical function. This model is hosted on BioModels Database and identified by: MODEL1304230001 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:To navigate complex acoustic environments, listeners adapt neural processes to focus on behaviorally relevant sounds in the acoustic foreground while minimizing the impact of distractors in the background, an ability referred to as top-down selective attention. Particularly striking examples of attention-driven plasticity have been reported in primary auditory cortex via dynamic reshaping of spectro-temporal receptive fields (STRFs). By enhancing the neural response to features of the foreground while suppressing those to the background, STRFs can act as adaptive contrast matched filters that directly contribute to an improved cognitive segregation between behaviorally relevant and irrelevant sounds. In this study, we propose a novel discriminative framework for modeling attention-driven plasticity of STRFs in primary auditory cortex. The model describes a general strategy for cortical plasticity via an optimization that maximizes discriminability between the foreground and distractors while maintaining a degree of stability in the cortical representation. The first instantiation of the model describes a form of feature-based attention and yields STRF adaptation patterns consistent with a contrast matched filter previously reported in neurophysiological studies. An extension of the model captures a form of object-based attention, where top-down signals act on an abstracted representation of the sensory input characterized in the modulation domain. The object-based model makes explicit predictions in line with limited neurophysiological data currently available but can be readily evaluated experimentally. Finally, we draw parallels between the model and anatomical circuits reported to be engaged during active attention. The proposed model strongly suggests an interpretation of attention-driven plasticity as a discriminative adaptation operating at the level of sensory cortex, in line with similar strategies previously described across different sensory modalities.

Project description:BackgroundColorectal cancer is one of the most prevalent causes of cancer death. It has been studied extensively for a long time, and numerous genetic and epigenetic events have been associated with the disease. However, its molecular mechanisms are still unclear. High-throughput metabolomics data, combined with customized computational systems modeling, can assist our understanding of some of these mechanisms by revealing connections between alterations in enzymatic activities and their consequences for a person's metabolic profile. Of particular importance in this context is purine metabolism, as it provides the nucleotides needed for cell proliferation.Methods and findingsWe employ a computational systems approach to infer molecular mechanisms associated with purine metabolism in colorectal carcinoma. The approach uses a dynamic model of purine metabolism as the simulation system and metabolomics data as input. The execution of large-scale Monte Carlo simulations and optimization with the model permits a step-wise reduction in possibly affected enzyme mechanisms, from which likely targets emerge.ConclusionsAccording to our results, some enzymes in the purine pathway system are very unlikely the targets of colorectal carcinoma. In fact, only three enzymatic steps emerge with statistical confidence as most likely being affected, namely: amidophosphoribosyltransferase (ATASE), 5'-nucleotidase (5NUC), and the xanthine oxidase/dehydrogenase (XD) reactions. The first of these enzymes catalyzes the first committed step of de novo purine biosynthesis, while the other two enzymes are associated with critical purine salvage pathways. The identification of these enzymes is statistically significant and robust. In addition, the results suggest potential secondary targets. The computational method cannot discern whether the inferred mechanisms constitute symptoms of colorectal carcinoma, or whether they might be causative and critical components of the uncontrolled cellular growth in cancer. The inferred molecular mechanisms present testable hypotheses that suggest targeted experiments for future studies of colorectal carcinoma and might eventually lead to improved diagnosis and treatment.

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Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.

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Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.

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