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Open Access Highly Accessed Research article

An integrative modeling framework reveals plasticity of TGF-β signaling

Geoffroy Andrieux1, Michel Le Borgne2 and Nathalie Théret1*

Author Affiliations

1 INSERM U1085, IRSET, Université de Rennes 1, 2 avenue Pr Léon Bernard, 35043 Rennes, France

2 Université de Rennes 1, IRISA, 263 avenue du général Leclerc, 35042 Rennes, France

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BMC Systems Biology 2014, 8:30  doi:10.1186/1752-0509-8-30

Published: 12 March 2014

Abstract

Background

The TGF-β transforming growth factor is the most pleiotropic cytokine controlling a broad range of cellular responses that include proliferation, differentiation and apoptosis. The context-dependent multifunctional nature of TGF-β is associated with complex signaling pathways. Differential models describe the dynamics of the TGF-β canonical pathway, but modeling the non-canonical networks constitutes a major challenge. Here, we propose a qualitative approach to explore all TGF-β-dependent signaling pathways.

Results

Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating the 137 human signaling maps from the Pathway Interaction Database into a single unified dynamic model. Temporal property-checking analyses of 15934 trajectories that regulate 145 TGF-β target genes reveal the association of specific pathways with distinct biological processes. We identify 31 different combinations of TGF-β with other extracellular stimuli involved in non-canonical TGF-β pathways that regulate specific gene networks. Extensive analysis of gene expression data further demonstrates that genes sharing CADBIOM trajectories tend to be co-regulated.

Conclusions

As applied here to TGF-β signaling, CADBIOM allows, for the first time, a full integration of highly complex signaling pathways into dynamic models that permit to explore cell responses to complex microenvironment stimuli.

Keywords:
TGF-β; Discrete dynamic model; Signaling pathways; Guarded transition