Modeling Signaling-dependent Pluripotency with Boolean Logic to Predict Cell Fate Transitions

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2018 Jan 31

PMID 29378814

Citations 27

Authors

Ayako Yachie-Kinoshita

Kento Onishi

Joel Ostblom

Matthew A Langley

Eszter Posfai

Janet Rossant

Peter W Zandstra

Affiliations

Soon will be listed here.

Abstract

Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) and used to simulate cellular responses to combinations of five signaling pathways. Our simulations predicted experimentally verified cell population compositions and input signal combinations controlling specific cell fate transitions. Extending the model to PSC differentiation, we predicted a combination of signaling activators and inhibitors that efficiently and robustly generated a Cdx2Oct4 cells from naïve mESCs. Overall, this platform provides new strategies to simulate cell fate transitions and the heterogeneity that typically occurs during development and differentiation.

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