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

Abstract

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, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell 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 mouse embryonic stem cell 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 a monostable, but still excitable, regulation. Experimental data and agent-based modelling simulations indicate that mouse embryonic stem cell proliferation dynamics vary in the two media, and cannot be reproduced by accounting only for Nanog-dependent cell-cycle regulation. We further demonstrate that both PD and Chiron play a key role in regulating heterogeneity in transcription factor expression and, ultimately, mouse embryonic stem cell fate decision.

Modelling gene expression and proliferation dynamics of pluripotent stem cells

Mouse embryonic stem cells (mESCs) are pluripotent cells, having the potential to turn into most other cell types. A team led by Lucia Marucci at the University of Bristol, and involving collaborators from the University of Sheffield, developed mathematical models to describe temporal dynamics of pluripotency genes in mESCs under different culture conditions. The team shows that the combination of feedback loops in the underlying gene regulatory networks, noise, and culture conditions fine-tunes gene expression dynamics and, consequently, the fate of mESCs. Experimental and modelling results highlight the interplay between pluripotency gene dynamics and cellular proliferation. Understanding the dynamical mechanisms that influence the fate of mESCs could guide the optimisation of culture protocols in both pluripotency and differentiation.