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2020 | OriginalPaper | Chapter

Control Strategy Identification via Trap Spaces in Boolean Networks

Authors : Laura Cifuentes Fontanals, Elisa Tonello, Heike Siebert

Published in: Computational Methods in Systems Biology

Publisher: Springer International Publishing

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Abstract

The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables, force the system to evolve to a desired state. This work presents a new approach for finding control strategies in biological systems modeled by Boolean networks. In this context, we explore the properties of trap spaces, subspaces of the state space which the dynamics cannot leave. Trap spaces for biological networks can often be efficiently computed, and provide useful approximations of attraction basins. Our approach provides control strategies for a target phenotype that are based on interventions that allow the control to be eventually released. Moreover, our method can incorporate information about the attractors to find new control strategies that would escape usual percolation-based methods. We show the applicability of our approach to two cell fate decision models.

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previous chapter Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model

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Baig, S., Seevasant, I., Mohamad, J., Mukheem, A., Huri, H.Z., Kamarul, T.: Potential of apoptotic pathway-targeted cancer therapeutic research: where do we stand? Cell Death Dis. 7(1), e2850 (2016). https://doi.org/10.1038/cddis.2015.275CrossRef

Biane, C., Delaplace, F.: Causal reasoning on boolean control networks based on abduction: theory and application to cancer drug discovery. IEEE/ACM Trans. Comput. Biol. Bioinform. 16(5), 1574–1585 (2019). https://doi.org/10.1109/TCBB.2018.2889102CrossRef

Calzone, L., et al.: Mathematical modelling of cell-fate decision in response to death receptor engagement. PLOS Comput. Biol. 6(3), 1–15 (2010). https://doi.org/10.1371/journal.pcbi.1000702MathSciNetCrossRef

Chaouiya, C., Naldi, A., Thieffry, D.: Logical modelling of gene regulatory networks with GINsim. Bacterial Mol. Netw. 804, 463–479 (2012)CrossRef

Csermely, P., Korcsmáros, T., Kiss, H.J., London, G., Nussinov, R.: Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol. Therapeutics 138(3), 333–408 (2013). https://doi.org/10.1016/j.pharmthera.2013.01.016CrossRef

Flobak, Å., et al.: Discovery of drug synergies in gastric cancer cells predicted by logical modeling. PLOS Comput. Biol. 11(8), 1–20 (2015). https://doi.org/10.1371/journal.pcbi.1004426CrossRef

Grieco, L., Calzone, L., Bernard-Pierrot, I., Radvanyi, F., Kahn-Perlès, B., Thieffry, D.: Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLOS Comput. Biol. 9(10), 1–15 (2013). https://doi.org/10.1371/journal.pcbi.1003286

Kaminski, R., Schaub, T., Siegel, A., Videla, S.: Minimal intervention strategies in logical signaling networks with asp. Theor. Pract. Logic Program. 13, 675–690 (2013). https://doi.org/10.1017/S1471068413000422MathSciNetCrossRefMATH

Kim, J., Park, S.M., Cho, K.H.: Discovery of a kernel for controlling biomolecular regulatory networks. Sci. Rep. 3, 2223 (2013). https://doi.org/10.1038/srep02223CrossRef

10.

Klarner, H., Bockmayr, A., Siebert, H.: Computing maximal and minimal trap spaces of Boolean networks. Natural Comput. 14(4), 535–544 (2015). https://doi.org/10.1007/s11047-015-9520-7MathSciNetCrossRefMATH

11.

Klarner, H., Siebert, H.: Approximating attractors of Boolean networks by iterative ctl model checking. Front. Bioeng. Biotechnol. 3, 130 (2015). https://doi.org/10.3389/fbioe.2015.00130CrossRef

12.

Klarner, H., Streck, A., Siebert, H.: PyBoolNet: a python package for the generation, analysis and visualization of Boolean networks. Bioinformatics 33(5), 770–772 (2016). https://doi.org/10.1093/bioinformatics/btw682CrossRef

13.

Liu, Y.Y., Slotine, J.J., Barabási, A.L.: Controllability of complex networks. Nature 473, 167–173 (2011). https://doi.org/10.1038/nature10011CrossRef

14.

Mandon, H., Su, C., Haar, S., Pang, J., Paulevé, L.: Sequential reprogramming of boolean networks made practical. In: Bortolussi, L., Sanguinetti, G. (eds.) Computational Methods in Systems Biology. vol. 11773, pp. 3–19. Springer International Publishing, Cham (2019). https://doi.org/10.1007/978-3-030-31304-3_1

15.

Murrugarra, D., Veliz-Cuba, A., Aguilar, B., Laubenbacher, R.: Identification of control targets in boolean molecular network models via computational algebra. BMC Syst. Biol. 10(1), 94 (2016). https://doi.org/10.1186/s12918-016-0332-xCrossRef

16.

Samaga, R., Kamp, A.V., Klamt, S.: Computing combinatorial intervention strategies and failure modes in signaling networks. J. Comput. Biol. 17(1), 39–53 (2010). https://doi.org/10.1089/cmb.2009.0121MathSciNetCrossRef

17.

Takahashi, K., Yamanaka, S.: A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17(3), 183–193 (2016). https://doi.org/10.1038/nrm.2016.8CrossRef

18.

Yang, G., Gómez Tejeda Zañudo, J., Albert, R.: Target control in logical models using the domain of influence of nodes. Front. Physiol. 9, 454 (2018). DOI: https://doi.org/10.3389/fphys.2018.00454

19.

Zañudo, J.G.T., Yang, G., Albert, R.: Structure-based control of complex networks with nonlinear dynamics. Proc. Natl. Acad. Sci. 114(28), 7234–7239 (2017). https://doi.org/10.1073/pnas.1617387114CrossRef

20.

Zañudo, J.G.T., Albert, R.: Cell fate reprogramming by control of intracellular network dynamics. PLOS Comput. Biol. 11(4), 1–24 (2015). https://doi.org/10.1371/journal.pcbi.1004193CrossRef

21.

Zhang, R., et al.: Network model of survival signaling in large granular lymphocyte leukemia. Proc. Natl. Acad. Sci. 105(42), 16308–16313 (2008). https://doi.org/10.1073/pnas.0806447105CrossRef

Title: Control Strategy Identification via Trap Spaces in Boolean Networks
Authors: Laura Cifuentes Fontanals
Elisa Tonello
Heike Siebert
Publisher: Springer International Publishing
Book: Computational Methods in Systems Biology
Print ISBN: 978-3-030-60326-7

Electronic ISBN: 978-3-030-60327-4

Copyright Year: 2020
DOI: https://doi.org/10.1007/978-3-030-60327-4_9

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