Cells use signal and noise to make gut decisions

Summary by Katherine Rogers: Economou, A. D., Guglielmi, L., East, P. and Hill, C. S. (2022). Nodal signaling establishes a competency window for stochastic cell fate switching. Dev Cell 57, 2604-2622 e2605.

Image credit: Midjourney (Input = Post title)

Adult animals can contain hundreds of different types of cells with distinct functions, such as gut and muscle cells. How do pluripotent cells in developing embryos make “fate decisions” and differentiate into these diverse types? The popular “morphogen” model suggests that a gradient of signaling across a tissue could cause cells to experience different signaling levels that result in different fate decisions (Rogers and Schier, 2011). However, recent work from the Hill lab suggests a fundamentally distinct mechanism underlying fate choices in at least one context: Instead of signaling levels instructing fate decisions, they argue that signaling simply makes cells competent to choose between fates—but the choice is ultimately stochastic (Economou et al., 2022).

In zebrafish embryos, a Nodal signaling gradient is needed for cells to acquire one of two identities: mesoderm, which produces tissues including muscle, and endoderm, the future gut, marked by sox32 expression (Hill, 2022). The morphogen model suggests that high levels of Nodal cause cells to activate sox32 and become endoderm, whereas lower levels specify sox32- mesoderm. However, the “salt and pepper” distribution of sox32+ cells contradicts this. In regions of the embryo thought to experience identical Nodal levels, some cells are sox32+, whereas neighbors are negative. Why would cells presumably experiencing the same signaling level make different decisions?   

The Hill lab measured Nodal signaling levels and sox32 expression in fixed cells and found that a snapshot of Nodal levels indeed failed to predict whether a cell expressed sox32. A second signaling pathway, FGF, decreases the likelihood of sox32 activation—but even considering FGF and Nodal levels together was not predictive. If different signaling levels don’t determine fate decisions, what does? Perhaps cells are biased toward sox32 activation by preexisting gene expression differences. However, assessment of gene expression in single cells (Farrell et al., 2018) showed that cells that very recently activated sox32 had similar transcriptomes compared to sox32- neighbors, ruling out a preexisting bias.

The Hill lab proposes instead that Nodal acts as a “necessary but not sufficient” signal for endoderm specification: Exposure to Nodal creates a state where cells are competent to activate sox32. The activation “decision” itself appears to be stochastic and perhaps governed by gene expression noise—but without Nodal, there can be no sox32 activation. Each Nodal-exposed cell has a fixed probability of switching on sox32. Signaling duration does not affect that probability, but the longer cells are exposed to Nodal, the greater the likelihood a cell activates sox32, similar to radioactive decay. In the zebrafish embryo, cells therefore harness both signal and noise to make “gut decisions” about fate.

Noise is often considered to be an obstacle to robust development. How do embryos ensure the right proportion of mesoderm and endoderm with a noise-driven mechanism? Intriguingly, using a Nodal inhibitor to decrease the number of endodermal progenitors in early embryos, the Hill lab found that numbers recovered later in development (also observed in (Rogers et al., 2017))—suggesting an unknown mechanism that ensures the correct number of endodermal cells. Future studies exploring this, as well as the role of signaling dynamics in fate decisions, promise exciting insights.

References

Economou, A. D., Guglielmi, L., East, P. and Hill, C. S. (2022). Nodal signaling establishes a competency window for stochastic cell fate switching. Dev Cell 57, 2604-2622 e2605.

Farrell, J. A., Wang, Y., Riesenfeld, S. J., Shekhar, K., Regev, A. and Schier, A. F. (2018). Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360.

Hill, C. S. (2022). Establishment and interpretation of NODAL and BMP signaling gradients in early vertebrate development. Curr Top Dev Biol 149, 311-340.

Rogers, K. W., Lord, N. D., Gagnon, J. A., Pauli, A., Zimmerman, S., Aksel, D. C., Reyon, D., Tsai, S. Q., Joung, J. K. and Schier, A. F. (2017). Nodal patterning without Lefty inhibitory feedback is functional but fragile. Elife 6, e28785.

Rogers, K. W. and Schier, A. F. (2011). Morphogen gradients: from generation to interpretation. Annu Rev Cell Dev Biol 27, 377-407.