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Metastable Regimes and Tipping Points of Biochemical Networks with Potential Applications in Precision Medicine

  • Satya Swarup Samal
  • Jeyashree Krishnan
  • Ali Hadizadeh Esfahani
  • Christoph Lüders
  • Andreas Weber
  • Ovidiu RadulescuEmail author
Chapter
Part of the Computational Biology book series (COBO, volume 30)

Abstract

The concept of attractor of dynamic biochemical networks has been used to explain cell types and cell alterations in health and disease. We have recently proposed an extension of the notion of attractor to take into account metastable regimes, defined as long-lived dynamical states of the network. These regimes correspond to slow dynamics on low- dimensional invariant manifolds of the biochemical networks. Methods based on tropical geometry allow to compute the metastable regimes and represent them as polyhedra in the space of logarithms of the species concentrations. We are looking for sensitive parameters and tipping points of the networks by analyzing how these polyhedra depend on the model parameters. Using the coupled MAPK and PI3K/Akt signaling networks as an example, we test the idea that large changes of the metastable states can be associated with cancer-specific alterations of the network. In particular, we show that for model parameters representing protein concentrations, the protein differential level between tumors of different types is reasonably reflected in the sensitivity scores, with sensitive parameters corresponding to differential proteins.

Notes

Acknowledgements

This work was supported by the ANR/DFG grant ANR-17-CE40-0036 (project SYMBIONT) and CompSE profile area, RWTH Aachen University. We thank R. Larive and D. Santamaria for their critical reading of the manuscript and for useful discussions.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Satya Swarup Samal
    • 1
    • 2
  • Jeyashree Krishnan
    • 3
  • Ali Hadizadeh Esfahani
    • 1
    • 2
  • Christoph Lüders
    • 4
  • Andreas Weber
    • 4
  • Ovidiu Radulescu
    • 5
    Email author
  1. 1.Joint Research Center for Computational BiomedicineRWTH Aachen UniversityAachenGermany
  2. 2.BASF SELudwigshafenGermany
  3. 3.AICES Graduate SchoolRWTH Aachen UniversityAachenGermany
  4. 4.Department of Computer Science IIUniversity of BonnBonnGermany
  5. 5.DIMNP UMR CNRS 5235University of MontpellierMontpellierFrance

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