Algorithms for the Sequential Reprogramming of Boolean Networks

Hugues Mandon (1, 2) , Cui Su (3) , Jun Pang (3, 4) , Soumya Paul (4) , Stefan Haar (5, 1) , Loïc Paulevé (6, 2)

1 LSV - Laboratoire Spécification et Vérification [Cachan]
2 BioInfo - LRI - Bioinformatique (LRI)
3 SnT - Interdisciplinary Centre for Security, Reliability and Trust [Luxembourg]
4 FSTC - Faculty of Science, Technology and Communication [Luxembourg]
5 MEXICO - Modeling and Exploitation of Interaction and Concurrency
6 LaBRI - Laboratoire Bordelais de Recherche en Informatique

Cellular reprogramming, a technique that opens huge opportunities in modern and regenerative medicine, heavily relies on identifying key genes to perturb. Most of the existing computational methods for controlling which attractor (steady state) the cell will reach focus on finding mutations to apply to the initial state. However, it has been shown, and is proved in this article, that waiting between perturbations so that the update dynamics of the system prepares the ground, allows for new reprogramming strategies. To identify such sequential perturbations, we consider a qualitative model of regulatory networks, and rely on Binary Decision Diagrams to model their dynamics and the putative perturbations. Our method establishes a set identification of sequential perturbations, whether permanent (mutations) or only temporary, to achieve the existential or inevitable reachability of an arbitrary state of the system. We apply an implementation for temporary perturbations on models from the literature, illustrating that we are able to derive sequential perturbations to achieve trans-differentiation.

Domaines: Modélisation et simulation; Systèmes et contrôle [cs.SY]; Algorithme et structure de données [cs.DS]; Bio-informatique [q-bio.QM]

Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, et al.. Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, 16 (5), pp.1610-1619. ⟨10.1109/TCBB.2019.2914383⟩. ⟨hal-02113864⟩