Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis

PLoS Comput Biol. 2022 Aug 22;18(8):e1010383. doi: 10.1371/journal.pcbi.1010383. eCollection 2022 Aug.

Abstract

The paper describes a mathematical model of the molecular switches of cell survival, apoptosis, and necroptosis in cellular signaling pathways initiated by tumor necrosis factor 1. Based on experimental findings in the literature, we constructed a Petri net model based on detailed molecular reactions of the molecular players, protein complexes, post-translational modifications, and cross talk. The model comprises 118 biochemical entities, 130 reactions, and 299 edges. We verified the model by evaluating invariant properties of the system at steady state and by in silico knockout analysis. Applying Petri net analysis techniques, we found 279 pathways, which describe signal flows from receptor activation to cellular response, representing the combinatorial diversity of functional pathways.120 pathways steered the cell to survival, whereas 58 and 35 pathways led to apoptosis and necroptosis, respectively. For 65 pathways, the triggered response was not deterministic and led to multiple possible outcomes. We investigated the in silico knockout behavior and identified important checkpoints of the TNFR1 signaling pathway in terms of ubiquitination within complex I and the gene expression dependent on NF-κB, which controls the caspase activity in complex II and apoptosis induction. Despite not knowing enough kinetic data of sufficient quality, we estimated system's dynamics using a discrete, semi-quantitative Petri net model.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis / genetics
  • Models, Biological*
  • Models, Theoretical
  • NF-kappa B / genetics
  • NF-kappa B / metabolism
  • Receptors, Tumor Necrosis Factor, Type I* / genetics
  • Receptors, Tumor Necrosis Factor, Type I* / metabolism
  • Signal Transduction / genetics
  • Tumor Necrosis Factor-alpha / metabolism

Substances

  • NF-kappa B
  • Receptors, Tumor Necrosis Factor, Type I
  • Tumor Necrosis Factor-alpha

Grants and funding

This work was supported by the Cluster of Excellence ’Macromolecular Complexes’ of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, 3212070002/TP2, LA,IK,ID), by the Collaborative Research Centre ‘Molecular and Functional Characterization of Selective Autophagy’ of the DFG (Project-ID 259130777-SFB 1177, ID), by the LOEWE program Ubiquitin Networks (Ub-Net) of the State of Hesse (Germany, 20120712/B4, JH,ID), by the Hessian Ministry of the Arts and Sciences (HMWK) within the LOEWE Research Initiative ACLF-I (ID, IK), and by the Clusterproject ENABLE funded by the HMWK (2995/1502/11 IK, ID). We acknowledge and thank the Goethe University Frankfurt and Hessian Ministry of Higher Education, Research and the Arts for providing financial and infrastructural support. The founders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.