Video 1: Synthetic symmetry breaking between two daughter cells. The mammalian cell line engineered with a synthetic lateral inhibition circuit spontaneously bifurcates into red and green cell types (modified from Matsuda M et al., Nat Commun, 2015).

Figure 1: The period of the segmentation clock differs among species. Our plan is to investigate the interspecies difference by comparing the segmentation clock organoids of differently sized animals in vitro.

Figure 1: The period of the segmentation clock differs among species. Our plan is to investigate the interspecies difference by comparing the segmentation clock organoids of differently sized animals in vitro.

The Ebisuya group reconstitutes developmental mechanisms by making artificial gene circuits, and studies interspecies differences by comparing organoids of different animals.

Previous and current research

In our lab we take two different synthetic biology approaches, reconstituting or recapitulating developmental mechanisms in vitro to better understand them.

Reconstitution of developmental mechanisms

We make artificial gene circuits in mammalian cell culture to reconstitute developmental mechanisms of interest. Our aim is to test how well we currently understand these mechanisms, as well as to discover unexplained or unexpected elements through observation. Since the fundamental principles of development include cell autonomous differentiation, pattern formation, and tissue deformation, we have been trying to reconstitute these principles one by one. So far, we have succeeded in reconstituting cell autonomous differentiation. We created an artificial gene circuit mimicking Delta-Notch lateral inhibition in a mammalian cell line, causing spontaneous bifurcation of initially identical cells into two different cell types (Video 1). We are now working on the reconstitution of reaction-diffusion pattern formation as well as 3D tissue deformation.

Interspecies comparisons of organoids

The second approach is making organoids to recapitulate developmental mechanisms of interest in vitro. Our primary aim in culturing organoids is to study interspecies differences in timing: why do larger animals tend to have slower developmental times? Organoids offer powerful tools to tackle this big question because iPSCs/ESCs from diverse species are now available, and because the organoids of different species can be compared under the same experimental conditions. As a model system of interspecies differences, we have focused on the segmentation clock: the oscillatory gene expression that regulates the timing of somite formation during embryogenesis. Interestingly, the period of the human segmentation clock is approximately 5 hours, while that of a mouse is approximately 2 hours (Figure 1). We are now investigating the cause of the period difference by making organoids that display the segmentation clock from human iPSCs, mouse ESCs, and the stem cells of other mammals.

Future projects and goals

  • Reconstituting the mechanism of 3D tissue deformation.
  • Finding out the cause of the different periods of the segmentation clock in different species. We are also interested in other interspecies differences in timing, as well as in the size of organoids.
  • Our synthetic cell cultures also have the advantage of facilitating measurements and the modification of parameters, which we hope will contribute to the quantitative understanding of developmental principles.