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Mueller S, Huard J, Waldow K, Huang X, D'Alessandro LA, Bohl S, Börner K, Grimm D, Klamt S, Klingmüller U, Schilling M. T160‐phosphorylated CDK2 defines threshold for HGF dependent proliferation in primary hepatocytes. Mol Syst Biol 2016; 11:795. [PMID: 26148348 PMCID: PMC4380929 DOI: 10.15252/msb.20156032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Liver regeneration is a tightly controlled process mainly achieved by proliferation of usually quiescent hepatocytes. The specific molecular mechanisms ensuring cell division only in response to proliferative signals such as hepatocyte growth factor (HGF) are not fully understood. Here, we combined quantitative time-resolved analysis of primary mouse hepatocyte proliferation at the single cell and at the population level with mathematical modeling. We showed that numerous G1/S transition components are activated upon hepatocyte isolation whereas DNA replication only occurs upon additional HGF stimulation. In response to HGF, Cyclin:CDK complex formation was increased, p21 rather than p27 was regulated, and Rb expression was enhanced. Quantification of protein levels at the restriction point showed an excess of CDK2 over CDK4 and limiting amounts of the transcription factor E2F-1. Analysis with our mathematical model revealed that T160 phosphorylation of CDK2 correlated best with growth factor-dependent proliferation, which we validated experimentally on both the population and the single cell level. In conclusion, we identified CDK2 phosphorylation as a gate-keeping mechanism to maintain hepatocyte quiescence in the absence of HGF.
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Affiliation(s)
- Stephanie Mueller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Jérémy Huard
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburg, Germany
| | - Katharina Waldow
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Xiaoyun Huang
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL)Heidelberg, Germany
| | - Lorenza A D'Alessandro
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Sebastian Bohl
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - Kathleen Börner
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworksHeidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site HeidelbergHeidelberg, Germany
| | - Dirk Grimm
- Centre for Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworksHeidelberg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburg, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL)Heidelberg, Germany
- ** Corresponding author. Tel: +49 6221 42 4481; Fax: +49 6221 42 4488; E-mail:
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ)Heidelberg, Germany
- * Corresponding author. Tel: +49 6221 42 4485; Fax: +49 6221 42 4488; E-mail:
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D’Alessandro LA, Samaga R, Maiwald T, Rho SH, Bonefas S, Raue A, Iwamoto N, Kienast A, Waldow K, Meyer R, Schilling M, Timmer J, Klamt S, Klingmüller U. Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Comput Biol 2015; 11:e1004192. [PMID: 25905717 PMCID: PMC4427303 DOI: 10.1371/journal.pcbi.1004192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/12/2015] [Indexed: 01/25/2023] Open
Abstract
Signaling pathways are characterized by crosstalk, feedback and feedforward mechanisms giving rise to highly complex and cell-context specific signaling networks. Dissecting the underlying relations is crucial to predict the impact of targeted perturbations. However, a major challenge in identifying cell-context specific signaling networks is the enormous number of potentially possible interactions. Here, we report a novel hybrid mathematical modeling strategy to systematically unravel hepatocyte growth factor (HGF) stimulated phosphoinositide-3-kinase (PI3K) and mitogen activated protein kinase (MAPK) signaling, which critically contribute to liver regeneration. By combining time-resolved quantitative experimental data generated in primary mouse hepatocytes with interaction graph and ordinary differential equation modeling, we identify and experimentally validate a network structure that represents the experimental data best and indicates specific crosstalk mechanisms. Whereas the identified network is robust against single perturbations, combinatorial inhibition strategies are predicted that result in strong reduction of Akt and ERK activation. Thus, by capitalizing on the advantages of the two modeling approaches, we reduce the high combinatorial complexity and identify cell-context specific signaling networks.
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Affiliation(s)
- Lorenza A. D’Alessandro
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Regina Samaga
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Tim Maiwald
- Institute of Physics, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Seong-Hwan Rho
- Institute of Physics, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sandra Bonefas
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Andreas Raue
- Institute of Physics, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Merrimack Pharmaceuticals, Inc., Cambridge, Massachusetts, United States of America
| | - Nao Iwamoto
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Alexandra Kienast
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Katharina Waldow
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Rene Meyer
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- * E-mail: (JT); (SK); (UK)
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- * E-mail: (JT); (SK); (UK)
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- * E-mail: (JT); (SK); (UK)
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Hahn B, D'Alessandro LA, Depner S, Waldow K, Boehm ME, Bachmann J, Schilling M, Klingmüller U, Lehmann WD. Cellular ERK phospho-form profiles with conserved preference for a switch-like pattern. J Proteome Res 2012; 12:637-46. [PMID: 23210697 DOI: 10.1021/pr3007232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ERK is a member of the MAPK pathway with essential functions in cell proliferation, differentiation, and survival. Complete ERK activation by the kinase MEK requires dual phosphorylation at T and Y within the activation motif TEY. We show that exposure of primary mouse hepatocytes to hepatocyte growth factor (HGF) results in phosphorylation at the activation motif, but not of other residues nearby. To determine the relative abundances of unphosphorylated ERK and the three ERK phospho-forms pT, pY, and pTpY, we employed an extended one-source peptide/phosphopeptide standard method in combination with nanoUPLC-MS. This method enabled us to determine the abundances of phospho-forms with a relative variability of ≤5% (SD). We observed a switch-like preference of ERK phospho-form abundances toward the active, doubly phosphorylated and the inactive, unphosphorylated form. Interestingly, ERK phospho-form profiles were similar upon growth factor and cytokine stimulation. A screening of several murine and human cell systems revealed that the balance between TY- and pTpY-ERK is conserved while the abundances of pT- and pY-ERK are more variable within cell types. We show that the phospho-form profiles do not change by blocking MEK activity suggesting that cellular phosphatases determine the ERK phospho-form distribution. This study provides novel quantitative insights into multisite phosphorylation.
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Affiliation(s)
- Bettina Hahn
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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