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A quantitative network modeling approach to evaluate the role of cytokine combinations on CD4+ T cell differentiation, partial polarization, and plasticity

https://doi.org/10.1101/232884
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Flow cytometric determination of cytokines in activated murine T helper lymphocytes: Expression of interleukin‐10 in interferon‐γ and in interleukin‐4‐expressing cells
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Th17 and Regulatory T Cells in Mediating and Restraining Inflammation
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TGFβ in the Context of an Inflammatory Cytokine Milieu Supports De Novo Differentiation of IL-17-Producing T Cells
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Molecular Antagonism and Plasticity of Regulatory and Inflammatory T Cell Programs
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Late Developmental Plasticity in the T Helper 17 Lineage
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The Transcriptional Repressor Bcl-6 Directs T Follicular Helper Cell Lineage Commitment
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Interferons Direct Th2 Cell Reprogramming to Generate a Stable GATA-3+T-bet+ Cell Subset with Combined Th2 and Th1 Cell Functions
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T Follicular Helper Cell Differentiation, Function, and Roles in Disease
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Th9 cells, new players in adaptive immunity
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Dendritic cell recruitment and activation in autoimmunity
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XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions
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New insights into the roles of Stat5a/b and Stat3 in T cell development and differentiation
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The plasticity of human Treg and Th17 cells and its role in autoimmunity
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The Transcription Factor GATA-3 Is Necessary and Sufficient for Th2 Cytokine Gene Expression in CD4 T Cells
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A Novel Transcription Factor, T-bet, Directs Th1 Lineage Commitment
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Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells
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Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation
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Metabolic maintenance of cell asymmetry following division in activated T lymphocytes
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The transcription factor T-bet controls regulatory T cell homeostasis and function during type 1 inflammation
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IL-6 programs TH-17 cell differentiation by promoting sequential engagement of the IL-21 and IL-23 pathways
inferredcites →https://doi.org/10.1038/ni1536openalex-snapshot
CD4+CD25+Foxp3+ regulatory T cells induce cytokine deprivation–mediated apoptosis of effector CD4+ T cells
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A dominant function for interleukin 27 in generating interleukin 10–producing anti-inflammatory T cells
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Foxp3 programs the development and function of CD4+CD25+ regulatory T cells
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De novo fatty acid synthesis controls the fate between regulatory T and T helper 17 cells
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Harnessing the plasticity of CD4+ T cells to treat immune-mediated disease
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Interleukin 2 plays a central role in Th2 differentiation
inferredcites →https://doi.org/10.1073/pnas.1615590114openalex-snapshot
Diverse continuum of CD4 + T-cell states is determined by hierarchical additive integration of cytokine signals
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Generation of interleukin 4 (IL-4)-producing cells in vivo and in vitro: IL-2 and IL-4 are required for in vitro generation of IL-4-producing cells.
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Heterogeneity of single cell cytokine gene expression in clonal T cell populations.
inferredcites →https://doi.org/10.1084/jem.182.5.1357openalex-snapshot
Heterogeneity of intracellular cytokine synthesis at the single-cell level in polarized T helper 1 and T helper 2 populations.
inferredcites →https://doi.org/10.1084/jem.183.3.901openalex-snapshot
Reversibility of T helper 1 and 2 populations is lost after long-term stimulation.
inferredcites →https://doi.org/10.1084/jem.20030152openalex-snapshot
Conversion of Peripheral CD4+CD25− Naive T Cells to CD4+CD25+ Regulatory T Cells by TGF-β Induction of Transcription Factor Foxp3
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Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
inferredcites →https://doi.org/10.1093/bioinformatics/btv013openalex-snapshot
Cooperative development of logical modelling standards and tools with CoLoMoTo
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Systems Biology Approaches to Development beyond Bioinformatics: Nonlinear Mechanistic Models Using Plant Systems
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Single-cell analysis by RT-PCR reveals differential expression of multiple type 1 and 2 cytokine genes among cells within polarized CD4+ T cell populations
inferredcites →https://doi.org/10.1093/intimm/7.5.869openalex-snapshot
Stability of Th1 and Th2 populations
inferredcites →https://doi.org/10.1098/rsif.2008.0132.focusopenalex-snapshot
Boolean network models of cellular regulation: prospects and limitations
inferredcites →https://doi.org/10.1103/physrevlett.109.118102openalex-snapshot
General Theory of Genotype to Phenotype Mapping: Derivation of Epigenetic Landscapes from N-Node Complex Gene Regulatory Networks
inferredcites →https://doi.org/10.1111/imr.12028openalex-snapshot
Th9 cells: differentiation and disease
inferredcites →https://doi.org/10.1111/j.0105-2896.2006.00420.xopenalex-snapshot
Interleukin‐10‐secreting type 1 regulatory T cells in rodents and humans
inferredcites →https://doi.org/10.1126/science.1071809openalex-snapshot
Signal Transduction by the TGF-β Superfamily
inferredcites →https://doi.org/10.1126/science.1079490openalex-snapshot
Control of Regulatory T Cell Development by the Transcription Factor Foxp3
inferredcites →https://doi.org/10.1126/science.1139393openalex-snapshot
Asymmetric T Lymphocyte Division in the Initiation of Adaptive Immune Responses
inferredcites →https://doi.org/10.1126/science.1175870openalex-snapshot
Bcl6 and Blimp-1 Are Reciprocal and Antagonistic Regulators of T Follicular Helper Cell Differentiation
inferredcites →https://doi.org/10.1126/science.1176676openalex-snapshot
Bcl6 Mediates the Development of T Follicular Helper Cells
inferredcites →https://doi.org/10.1126/science.8097338openalex-snapshot
Development of T H 1 CD4 + T Cells Through IL-12 Produced by Listeria -Induced Macrophages
inferredcites →https://doi.org/10.1146/annurev-immunol-030409-101212openalex-snapshot
Differentiation of Effector CD4 T Cell Populations
inferredcites →https://doi.org/10.1146/annurev-immunol-032712-100027openalex-snapshot
Dynamic Tuning of Lymphocytes: Physiological Basis, Mechanisms, and Function
inferredcites →https://doi.org/10.1146/annurev-immunol-032713-120257openalex-snapshot
TGF-β Activation and Function in Immunity
inferredcites →https://doi.org/10.1146/annurev.immunol.021908.132710openalex-snapshot
IL-17 and Th17 Cells
inferredcites →https://doi.org/10.1146/annurev.immunol.19.1.683openalex-snapshot
Interleukin-10 and the Interleukin-10 Receptor
inferredcites →https://doi.org/10.1146/annurev.immunol.21.120601.140942openalex-snapshot
Molecular Mechanisms RegulatinG Th1 Immune Responses
inferredcites →https://doi.org/10.1146/annurev.immunol.23.021704.115821openalex-snapshot
REGULATION OF TH2 DIFFERENTIATION AND Il4 LOCUS ACCESSIBILITY
inferredcites →https://doi.org/10.1172/jci57456openalex-snapshot
GATA3 controls Foxp3+ regulatory T cell fate during inflammation in mice
inferredcites →https://doi.org/10.1172/jci65459openalex-snapshot
Th9 cells promote antitumor immune responses in vivo
inferredcites →https://doi.org/10.1186/s12918-015-0166-yopenalex-snapshot
Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates
inferredcites →https://doi.org/10.1371/journal.pcbi.1000912openalex-snapshot
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling
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Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity
inferredcites →https://doi.org/10.1371/journal.pcbi.1004324openalex-snapshot
A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity
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Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape
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Model Checking to Assess T-Helper Cell Plasticity
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Macrophage Cytokines: Involvement in Immunity and Infectious Diseases
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Cellular and population plasticity of helper CD4+ T cell responses
inferredcites →https://doi.org/10.4049/jimmunol.0900568openalex-snapshot
IL-27 Is a Key Regulator of IL-10 and IL-17 Production by Human CD4+ T Cells
inferredcites →https://doi.org/10.4049/jimmunol.0901233openalex-snapshot
Cutting Edge: IL-27 Induces the Transcription Factor c-Maf, Cytokine IL-21, and the Costimulatory Receptor ICOS that Coordinately Act Together to Promote Differentiation of IL-10-Producing Tr1 Cells
inferredcites →https://doi.org/10.4049/jimmunol.1003613openalex-snapshot
Cutting Edge: Distinct Glycolytic and Lipid Oxidative Metabolic Programs Are Essential for Effector and Regulatory CD4+ T Cell Subsets
inferredcites →https://doi.org/10.4049/jimmunol.1101164openalex-snapshot
Rapid In Vivo Conversion of Effector T Cells into Th2 Cells during Helminth Infection
inferredcites →https://doi.org/10.4049/jimmunol.145.11.3796openalex-snapshot
IL-4 directs the development of Th2-like helper effectors.
inferredcites →https://doi.org/10.4049/jimmunol.178.11.6725openalex-snapshot
Cutting Edge: Regulatory T Cells Induce CD4+CD25−Foxp3− T Cells or Are Self-Induced to Become Th17 Cells in the Absence of Exogenous TGF-β
inferredcites →https://doi.org/10.4049/jimmunol.178.7.4022openalex-snapshot
Cutting Edge: IL-2 Is Essential for TGF-β-Mediated Induction of Foxp3+ T Regulatory Cells
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