An extended model for culture-dependent heterogeneous gene expression and proliferation dynamics in mouse embryonic stem cells

During development, pluripotency is a transient state describing a cell’s ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells (mESCs), isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mESCs into a ground state of pluripotency, while serum/LIF cultures promote the co-existence of ground- and primed-like mESC subpopulations. The latter heterogeneity correlates with temporal fluctuations of pluripotency markers, including the master regulator Nanog, in single cells. We propose a mathematical model of Nanog dynamics in both media, accounting for recent experimental data showing the persistence of a small Nanog-low subpopulation in ground state pluripotency mESC cultures. The model integrates into the core pluripotency Gene Regulatory Network both inhibitors present in 2i/LIF (PD and Chiron), and feedback interactions with genes found to be differentially expressed in the two media. Our simulations and bifurcation analysis show that, in ground-state cultures, Nanog dynamics result from the combination of reduced noise in gene expression and the shift of the system towards monostable, but still excitable, regulation. Experimental data and agent-based modelling simulations indicate that mESC proliferation dynamics vary in the two media, and cannot be reproduced only accounting for Nanog-dependent cell-cycle regulation. We further demonstrate that both PD and Chiron play a key role in regulating transcription factors heterogeneity and, ultimately, mESC fate decision.