An Algorithm for Cellular Reprogramming

Computational Methods in Systems Biology

Haar

et al. 2019

We address the sequential reprogramming of gene regulatory networks modelled as Boolean networks. We develop an attractor-based sequential reprogramming method to compute all sequential reprogramming paths from a source attractor to a target attractor, where only attractors of the network are used as intermediates. Our method is more practical than existing reprogramming methods as it incorporates several practical constraints: (1) only biologically observable states, viz. attractors, can act as intermediates; (2) certain attractors, such as apoptosis, can be avoided as intermediates; (3) certain nodes can be avoided to perturb as they may be essential for cell survival or difficult to perturb with biomolecular techniques; and (4) given a threshold k, all sequential reprogramming paths with no more than k perturbations are computed. We compare our method with the minimal one-step reprogramming and the minimal sequential reprogramming on a variety of biological networks. The results show that our method can greatly reduce the number of perturbations compared to the one-step reprogramming, while having comparable results with the minimal sequential reprogramming. Moreover, our implementation is scalable for networks of more than 60 nodes.

Section: Discussionmentioning

confidence: 99%

Section: Motivationmentioning

confidence: 99%

Sequential Reprogramming of Boolean Networks Made Practical

Computational Methods in Systems Biology

Haar

et al. 2019

“…In other works [1], [18], the model allows for sequential reprogramming, making them sequential existential reprogramming. In [1], the existence of solutions is checked through a model checker, and specific perturbation paths can be tested.…”

Section: Discussionmentioning

confidence: 99%

“…In [1], the existence of solutions is checked through a model checker, and specific perturbation paths can be tested. In [18], the model is probabilistic and use timeseries data, thus allowing to make perturbations at different times in the series.…”

Section: Discussionmentioning

confidence: 99%

“…Current experimental settings and computational models mainly consider cell reprogramming by applying the set of perturbations simultaneously in the initial state. However, as suggested in [18] and as we will demonstrate formally in this paper, one finds novel reprogramming strategies, potentially requiring fewer interventions and / or achieving more objectives, by using sequential reprogram-ming, i.e., where perturbations are applied at particular points in time, and in a particular ordering.…”

Section: Introductionmentioning

confidence: 89%

See 1 more Smart Citation

Algorithms for the Sequential Reprogramming of Boolean Networks

IEEE/ACM Trans. Comput. Biol. and Bioinf.

Pang

et al. 2019

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. !

Temporal Reprogramming of Boolean Networks

Computational Methods in Systems Biology

Haar

Paulevé

2017

Cellular reprogramming, a technique that opens huge opportunities in modern and regenerative medicine, heavily relies on identifying key genes to perturb. Most of computational methods focus on finding mutations to apply to the initial state in order to control which attractor the cell will reach. However, it has been shown, and is proved in this article, that waiting between the perturbations and using the transient dynamics of the system allow new reprogramming strategies. To identify these temporal perturbations, we consider a qualitative model of regulatory networks, and rely on Petri nets to model their dynamics and the putative perturbations. Our method establishes a complete characterization of temporal perturbations, whether permanent (mutations) or only temporary, to achieve the existential or inevitable reachability of an arbitrary state of the system. We apply a prototype implementation on small models from the literature and show that we are able to derive temporal perturbations to achieve trans-differentiation.