Background
In the earliest stages of life, mammalian embryos start as a disorganized cluster of cells. As development progresses, these cells become organized into well-defined shapes and structures. This process happens again and again during development, yet it unfolds in environments full of noise and variability. So how do individual cells know which way to point? And what determines where the embryo will form its fluid-filled cavity, a crucial step in mammalian embryonic development?
Now, two companion studies published in Nature Physics and Nature Materials by researchers at the Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, and the European Molecular Biology Laboratory (EMBL) offer an answer: the shape and properties of the boundaries between different tissues, combined with the way cells interact with those boundaries, determine how cells orient themselves and where key structures form. The findings shed new light on how order emerges in complex biological systems.
Key findings
Both studies focus on the mouse epiblast, a group of cells that eventually gives rise to all the major tissues. During the period examined here, these cells progressively acquire polarity, developing a biochemically distinct apical end that mediates interactions with their neighbors and a basal end that attaches to the extracellular matrix (ECM), a mesh of structural proteins. The epiblast sits between two tissues: the visceral endoderm (VE), which is lined with an ECM protein called laminin, and the extraembryonic ectoderm (ExE), a neighboring tissue that lacks this layer.
The Nature Physics study captured, for the first time, how epiblast cells gradually reorient themselves in three dimensions relative to these tissue boundaries. Combining a 3D embryo culture system developed in-house with a machine-learning-assisted imaging pipeline, the team tracked individual cells as they shifted from a disordered state into a coherent, tissue-wide pattern. Cells near the VE turned to face perpendicular to it, anchoring their bases to the laminin-rich layer through a receptor called integrin β1. Cells near the ExE, by contrast, lay flat and parallel to the boundary. Building on a theoretical framework from liquid-crystal physics, the team constructed a model, and its comparison with the data revealed that anchoring to the tissue boundary progressively overtakes cell-to-cell interactions and becomes the dominant factor shaping the alignment pattern.
The Nature Materials study used this theoretical framework as a predictive tool. The model showed that the shape of the tissue boundary determines where "topological defects" form. "These are points in space where it is undefined in which direction an object should point," explained Guruciaga. "For example, if a set of arrows is arranged in a starburst pattern, the center is a point where all directions are equivalent." These topological features directly corresponded to where the lumen—a fluid-filled space that gives rise to the future pro-amniotic cavity—later appeared. When the researchers experimentally altered the shape of the epiblast, lumina formed at positions where the model predicted topological defects would appear, including cases in which multiple lumina emerged in a single embryo.
This boundary-guided alignment is not merely structural but functionally important. Knocking out laminin γ1 or integrin β1 caused cells to lose their coordinated orientation, and the knockout embryos failed to develop to later stages. In a parallel experiment, digesting the ECM disrupted cell alignment and reduced the activation of ERK signaling, a pathway essential for cell growth and differentiation.
Looking ahead
Although these findings were obtained in mouse embryos, the mechanisms underlying implantation-stage development and pattern formation are likely conserved across mammals, including humans. Human embryos at this stage are difficult to study because of ethical and technical constraints. Extending the theoretical framework developed in this work may help predict developmental pathways in human embryos and illuminate species-specific features of development. Beyond the embryo, this boundary-based framework may also apply to lumen formation in other organs such as the kidney and intestine, where tissue geometry similarly governs the emergence of internal cavities.
"Given how much biological variability there is between individual embryos, we were genuinely excited when the physics predictions matched the experimental outcomes," said Dr. Ichikawa. "We hope that the principles of tissue boundaries and pattern formation revealed in this work will ultimately contribute to a deeper understanding of human embryonic development and support future advances in reproductive medicine, including treatments for conditions such as implantation failure. "
This work grew out of an international and interdisciplinary collaboration led by Takafumi Ichikawa at ASHBi, Kyoto University, and Anna Erzberger and Pamela Guruciaga at EMBL. The partnership was sustained across time zones through countless video calls and visits to each other's labs. Bridging not just geography but also the very different languages that biologists and physicists use to describe the world, the team found that combining the two fields opened up possibilities that neither could have reached alone.
Glossary
Epiblast: A small cluster of cells in the early embryo that will eventually form the entire body. At first, these cells are randomly arranged, but over time they develop a defined "top" and "bottom" and line up into an organized, cup-shaped structure.
Visceral endoderm (VE) and extraembryonic ectoderm (ExE): Two tissues that wrap around the epiblast in the early mouse embryo, forming its boundaries. Where the VE contacts the epiblast, ECM proteins, including laminin, accumulate. The ExE boundary lacks this layer. This difference turns out to be critical — it is what tells epiblast cells which way to face.
Topological defect: A spot in an otherwise orderly pattern where no single direction can be defined. Think of the whorl at the crown of your head, where hair points in every direction at once. In the epiblast, these spots turn out to be where the embryo opens fluid-filled cavities.
