Changing the Waddington landscape to control mesendoderm competence

Abstract

19As pluripotent human embryonic stem cells progress towards one germ layer fate, they lose the 20 ability to adopt alternative fates. It is unknown how the cells' competence for these alternative 21 fates changes along their developmental trajectory or if this competence can be modulated. Here, 22 we show that a differentiating stem cell's probability of adopting a mesendodermal fate when 23 given the appropriate signal falls sharply at a specific point along the ectodermal trajectory, and 24 we further demonstrate that this point can be moved using genetic perturbations. Using a low-25 dimensional reaction coordinate to monitor progression towards ectoderm, we can determine the 26 probability that individual cells at different points along this path can transition to the 27 2 mesendodermal fate upon BMP4 and Activin A signal exposure. Knowing this probability allows 28 us to prospectively isolate and profile differentiating cells based on their mesendoderm 29 competence. Analysis and validation of these RNA-seq and ATAC-seq profiles identified 30 transcription factors that can independently control the cell's mesendoderm competence and its 31 progression along the ectodermal developmental trajectory. In the classical picture of a 32 Waddington landscape, these effects correspond to altering the barrier between fates and changing 33 the cell's location on the landscape, respectively. The ability of the underlying gene regulatory 34 network to modulate these two aspects of the developmental landscape could allow separate 35 control of the dynamics of differentiation and tissue size proportions. 36Main 37 Pluripotent cells have the ability to produce any of the myriad cell types seen in the adult body 1 , 38 but they lose this potential as they differentiate. During initial lineage specification, cells can 39 change their fate choice upon exposure to signals that induce an alternative selection 1-4 , such as 40 by transplantation to a different location in the embryo. In time, however, the cell's fate becomes 41 determined, and it is no longer competent to choose a different lineage in response to the same 42 external signals 5-7 . While lineage specification is relatively well-understood 8-17 , whether and how 43 competence for adopting alternative lineages can be tuned during differentiation is not. 44Determining how this competence is set and modulated is essential for understanding 45 developmental patterning and plasticity. 46There is a fundamental challenge in understanding the competence of a cell to choose a specific 47 Figure 1: Stem cells lose competence to adopt mesendodermal fates upon BMP4 and ActivinA signal exposure with increasing duration of Activin/NODAL inhibition. a, Schematic of a Waddington landscape illustrating the ectoderm (blue) / mesendoderm (yellow) fate choice. In this picture, the competence of a cell to produce mesendoderm depends both on the cell's location along the ectodermal developmental trajectory and on the position of the barrier between the ectoderm and mesendoderm fates...

The time integral of BMP signaling determines fate in a stem cell model for early human development

“…Second, this result implies qualitative differences in signaling behavior between the fates: a smooth static signaling gradient would not allow prediction of cell fate domains because it contains no information on where the downstream thresholds determining fate boundaries are. Third, there have been claims that the initial state of a cell predicts its fate 36,37 which seems at odds with the signaling determining its fate unless the signaling response and initial state are correlated.…”

“…There has been debate about whether heterogeneous differentiation in human pluripotent stem cells is primarily due to a heterogeneous initial state or heterogeneous signaling response 59 and several papers found initial levels of pluripotency markers to be predictive of differentiation 36,37 although the simplest models for tissue patterning assume a fixed relationship between signaling and fate. Intuitively it is clear that both should matter and that it depends on the specific context which dominates.…”

In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm

“…Inhibiting the activity of lineage-specific TFs, especially in key developmental stages, might be a sound differentiation strategy (Graf and Enver 2009;Palii et al 2019). For example, using a gradient of the TFs POU5F1 (OCT4) and SOX2 to control mesendoderm competence towards ectoderm fates (Valcourt et al 2019). Therefore, it is tempting to speculate that a similar gradient of two or more TFs could be used to promote the transition of mesendoderm towards either DE or ME lineages.…”