Deducing cell fate choreography using light

Summary by Allison Saul: Farahani, P. E., Reed, E. H., Underhill, E. J., Aoki, K., & Toettcher, J. E. (2021). Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annual review of biomedical engineering, 23, 61–87. https://doi.org/10.1146/annurev-bioeng-083120-111648

Image credit: scillystuff, Wikimedia Commons

Understanding how cells choreograph development through a convoluted web of signaling pathways has proven to be difficult, given the challenges involved in developing precision tools to interrogate how these pathways collaborate. Molecular optogenetics can be a powerful new tool in the toolbox. Using light sensitive domains, researchers are now able to engineer tools to methodically investigate pathways and perturb signaling dynamics, in a manner that is precise, acute, and reversible (1). Protocols to repurpose light sensitive domains from fungi, bacteria, and plants to generate functional tools have been increasing exponentially in the last few decades across a variety of scientific fields, beginning in the mid 2000s (2,3).

The application of optogenetics to the field of developmental biology is revolutionizing our scientific understanding of the when, the where, and the how of cell fate differentiation.

“When” tells the story of how signaling duration can influence cell fate. Sako at al. speaks to this: They showed that duration-dependent Nodal signaling leads to either endodermal or prechordal plate formation (4). To do this, photoactivatable Nodal constructs were introduced into zebrafish embryos and exposed to light for varying lengths of time, thus demonstrating that Nodal signal duration plays a crucial role in cell fate determination: longer exposures supported development of endodermal fates whereas shorter exposures led to prechordal plate formation.

“Where” addresses the spatial location of cells in a developing embryo and how this influences signal interpretation directing fate. For example, Johnson et al. 2020 erased endogenous ERK signaling and restored function using synthetic, light-based patterning. When introducing an optogenetic construct capable of controlling Ras/extracellular signal-related kinase (ERK) to a system lacking tyrosine-kinase-driven terminal signaling, it was revealed that there are different signal thresholds that prompt three separate developmental programs to initiate (5).  

Finally, “how” illustrates the logic behind a single pathway that can direct differentiation into multiple distinct fates. Beautifully, Johnson & Toettcher 2019 answers the question “when a single kinase like Erk is activated, how does a developing cell know which fate to adopt?”. Choregraphing light pulses demonstrated that a 30-minute ERK pulse specified intermediate neuroblasts (ectodermal cell type) and greater than one hour of ERK signaling drove gut endoderm fate differentiation. In summary, the study illustrated that the fate switch between endoderm and ectoderm relies on the cumulative load of Erk, rather that the specific pulse duration (6).

Through the application of light in varying durations, amplitudes, and timings, biologists can decode concealed features of biochemical networks and “walk up and down” pathways. One challenge is building a wider suite of tools for multicolor control. For example, it would be useful to trigger independent pathways in the same cell using tools with different spectral overlap. Optogenetics has matured beyond “proofs of principal” to discovering new insights into biological systems. As described in Farahani et al., a third phase is on the horizon, where collaboration between biologists and engineers can provide insight into how a biological system can be controlled therapeutically.

References

1. Farahani, P. E., Reed, E. H., Underhill, E. J., Aoki, K. & Toettcher, J. E. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng 23, 61-87 (2021). https://doi.org:10.1146/annurev-bioeng-083120-111648

2. Johnson, H. E. & Toettcher, J. E. Illuminating developmental biology with cellular optogenetics. Curr Opin Biotechnol 52, 42-48 (2018). https://doi.org:10.1016/j.copbio.2018.02.003

3. Kolar, K., Knobloch, C., Stork, H., Znidaric, M. & Weber, W. OptoBase: A Web Platform for Molecular Optogenetics. ACS Synth Biol 7, 1825-1828 (2018). https://doi.org:10.1021/acssynbio.8b00120

4. Sako, K. et al. Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.  (2016).

5. Johnson, H. E., Djabrayan, N. J. V., Shvartsman, S. Y. & Toettcher, J. E. Optogenetic Rescue of a Patterning Mutant. Curr Biol 30, 3414-3424 e3413 (2020). https://doi.org:10.1016/j.cub.2020.06.059

6. Johnson, H. E. & Toettcher, J. E. Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo. Dev Cell 48, 361-370 e363 (2019). https://doi.org:10.1016/j.devcel.2019.01.009