title: Boolean Modeling Reveals the Necessity of Transcriptional Regulation for Bistability in PC12 Cell Differentiation.
abstract: The nerve growth factor NGF has been shown to cause cell fate decisions toward either differentiation or proliferation depending on the relative activity of downstream pERK, pAKT, or pJNK signaling. However, how these protein signals are translated into and fed back from transcriptional activity to complete cellular differentiation over a time span of hours to days is still an open question. Comparing the time-resolved transcriptome response of NGF- or EGF-stimulated PC12 cells over 24 h in combination with protein and phenotype data we inferred a dynamic Boolean model capturing the temporal sequence of protein signaling, transcriptional response and subsequent autocrine feedback. Network topology was optimized by fitting the model to time-resolved transcriptome data under MEK, PI3K, or JNK inhibition. The integrated model confirmed the parallel use of MAPK/ERK, PI3K/AKT, and JNK/JUN for PC12 cell differentiation. Redundancy of cell signaling is demonstrated from the inhibition of the different MAPK pathways. As suggested in silico and confirmed in vitro, differentiation was substantially suppressed under JNK inhibition, yet delayed only under MEK/ERK inhibition. Most importantly, we found that positive transcriptional feedback induces bistability in the cell fate switch. De novo gene expression was necessary to activate autocrine feedback that caused Urokinase-Type Plasminogen Activator (uPA) Receptor signaling to perpetuate the MAPK activity, finally resulting in the expression of late, differentiation related genes. Thus, the cellular decision toward differentiation depends on the establishment of a transcriptome-induced positive feedback between protein signaling and gene expression thereby constituting a robust control between proliferation and differentiation.
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Offermann
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Knauer
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: Amit
authors.initials: A
authors.lastname: Singh
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: María L
authors.initials: ML
authors.lastname: Fernández-Cachón
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Klose
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg Freiburg, Germany.
authors.forename: Silke
authors.initials: S
authors.lastname: Kowar
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University FreiburgFreiburg, Germany; German Cancer ConsortiumFreiburg, Germany; German Cancer Research CenterHeidelberg, Germany.
authors.forename: Hauke
authors.initials: H
authors.lastname: Busch
authors.affiliation: Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University FreiburgFreiburg, Germany; German Cancer ConsortiumFreiburg, Germany; German Cancer Research CenterHeidelberg, Germany.
authors.forename: Melanie
authors.initials: M
authors.lastname: Boerries
keywords: Boolean modeling; EGF signaling; NGF signaling; PC12 cells; bistability