Recording signaling histories to predict cell fates

Summary by Selvaraj Velanganni: Teague, S., Primavera, G., Chen, B., Freeburne, E., Khan, H., Jo, K., Johnson, C., and Heemskerk, I. (2023). The time integral of BMP signaling determines fate in a stem cell model for early human development. bioRxiv. 10.1101/2023.04.10.536068

Image credit: Midjourney

Morphogens are secreted signaling molecules that guide cell fate decisions during embryogenesis [1]. One pervasive idea in developmental biology is that morphogen concentration determines cell fates in the developing embryo [2,3]. However, embryos are dynamic systems where cells are actively dividing and moving; therefore, cells experience changes in morphogen concentration during the process of making cell fate decisions. To establish how morphogens guide cell fate determination, in a recent preprint from the Heemskerk lab, Teague et al. assessed the signaling histories of human pluripotent stem cells (hPSCs) in response to BMP signaling and found that cell fate is determined by both the level and duration of BMP signaling [4].

To understand cell fate determination in a constantly changing cellular environment, a model system with a well-controlled environment along with live imaging techniques to capture signaling histories is useful. Teague et al. first used a well-established 2D micropatterned hPSC culture [5] to quantify signaling histories in response to signaling manipulations. To record BMP signaling activity, the authors used live reporters in which the signaling effectors SMAD1 or SMAD4 are tagged with fluorescent proteins. Measuring the cytoplasmic to nuclear localization of SMAD1 and SMAD4 provides quantification of BMP signaling activity. To identify cell fates after recording signaling activity, they used multiplexed immunofluorescence staining for markers of either amnion-like cell fates or pluripotency cell fates. They found that high levels of prolonged BMP signaling correlated with amnion-like cell fates, while transient BMP signaling (without additional inputs from other pathways) correlated with a more pluripotent cell fate, consistent with previous observations.

Next, to determine how the combination of signaling level and duration control cell fate, they performed experiments in which they independently manipulated signaling levels and durations. The authors found that high signaling levels with short duration or low signaling levels with longer duration could lead to the same amnion-like fate. In other words, the duration required for amnion-like cell fate with varying signaling level differed, but the total amount of signaling required remained the same. This suggests that the concentration of morphogen alone cannot decide the cell fate. Instead, Teague et al. suggest that cell fates are specified by a “time integral model” in which both signaling level and duration of signaling combine to instruct cell fate decisions.

The authors also explored possible mechanisms through which the BMP signaling response is interpreted. They hypothesized the existence of an “integrator gene”, which either increases or decreases proportionally in response to BMP signaling during cell differentiation. A combination of immunofluorescence, bulk RNA-sequencing, and overexpression experiments identified SOX2 as a putative integrator gene because it decreases proportionately as BMP signaling increases. SOX2 represses differentiation genes, and to differentiate into an amnion-like cell fate, the cell loses its pluripotency by downregulating the core gene SOX2 in response to BMP signaling.

Overall, the authors established a powerful pipeline using an automated cell tracking approach to record signaling histories at the single cell level. This tool provides a platform to better understand how morphogens guide axis pattering and cell fate differentiation.

1. Jones, W.D., and Mullins, M.C. (2022). Cell signaling pathways controlling an axis organizing center in the zebrafish. Curr Top Dev Biol 150, 149-209. 10.1016/bs.ctdb.2022.03.005.

2. Ashe, H.L., and Briscoe, J. (2006). The interpretation of morphogen gradients. Development 133, 385-394. 10.1242/dev.02238.

3. Rogers, K.W., and Schier, A.F. (2011). Morphogen gradients: from generation to interpretation. Annu Rev Cell Dev Biol 27, 377-407. 10.1146/annurev-cellbio-092910-154148.

4. Teague, S., Primavera, G., Chen, B., Freeburne, E., Khan, H., Jo, K., Johnson, C., and Heemskerk, I. (2023). The time integral of BMP signaling determines fate in a stem cell model for early human development. bioRxiv. 10.1101/2023.04.10.536068.

5. Warmflash, A., Sorre, B., Etoc, F., Siggia, E.D., and Brivanlou, A.H. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat Methods 11, 847-854. 10.1038/nmeth.3016.