Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination.

Fuqing Wu,Xiao Wang,Ying-Cheng Lai,Ri-Qi Su

doi:10.7554/elife.23702

Abstract

The process of cell fate determination has been depicted intuitively as cells travelling and resting on a rugged landscape, which has been probed by various theoretical studies. However, few studies have experimentally demonstrated how underlying gene regulatory networks shape the landscape and hence orchestrate cellular decision-making in the presence of both signal and noise. Here we tested different topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations to be quadrastable, which enables direct study of quadruple cell fate determination on an engineered landscape. We show that cells indeed gravitate towards local minima and signal inductions dictate cell fates through modulating the shape of the multistable landscape. Experiments, guided by model predictions, reveal that sequential inductions generate distinct cell fates by changing landscape in sequence and hence navigating cells to different final states. This work provides a synthetic biology framework to approach cell fate determination and suggests a landscape-based explanation of fixed induction sequences for targeted differentiation.

Highlights

Multistability is a mechanism that cells use to achieve a discrete number of mutually exclusive states in response to environmental inputs, such as the lysis/lysogeny switch of phage lambda (Arkin et al, 1998; Oppenheim et al, 2005) and sporulation/competence in Bacillus subtilis (Suel et al, 2006; Schultz et al, 2009)
Multistable switches are common in the cellular decision-making including the regulation of cell-cycle oscillator during cell mitosis (Pomerening et al, 2003), Epithelial-to-Mesenchymal transition and cancer metastasis (Jolly et al, 2016; Lee et al, 2014a), and the well-known cell differentiation process, which is a manifestation of cellular state determination in a multistable system (Laurent and Kellershohn, 1999; Guantes and Poyatos, 2008)
Green fluorescent protein (GFP) and mCherry serve as the corresponding readouts of Plux/tet and Para/lac activities in living cells (Figure 1B)

Summary

Introduction

Multistability is a mechanism that cells use to achieve a discrete number of mutually exclusive states in response to environmental inputs, such as the lysis/lysogeny switch of phage lambda (Arkin et al, 1998; Oppenheim et al, 2005) and sporulation/competence in Bacillus subtilis (Suel et al, 2006; Schultz et al, 2009). Multistable switches are common in the cellular decision-making including the regulation of cell-cycle oscillator during cell mitosis (Pomerening et al, 2003), Epithelial-to-Mesenchymal transition and cancer metastasis (Jolly et al, 2016; Lee et al, 2014a), and the well-known cell differentiation process, which is a manifestation of cellular state determination in a multistable system (Laurent and Kellershohn, 1999; Guantes and Poyatos, 2008). C.H. Waddington hypothesized the ‘epigenetic landscape’ to explain canalization and fate determination mechanism during cell differentiation (Waddington, 1957). Waddington hypothesized the ‘epigenetic landscape’ to explain canalization and fate determination mechanism during cell differentiation (Waddington, 1957) In this hypothesis, differentiation is depicted as a marble rolling down a landscape with multiple bifurcating valleys and eventually settles at one of the local minima, corresponding to terminally differentiated cells.

Methods

Results

Conclusion