Introduction to Cell Development
During early development, tissues and organs begin to bloom through the shifting, splitting, and growing of many thousands of cells. A team of MIT engineers has now developed a way to predict, minute by minute, how individual cells will fold, divide, and rearrange during a fruit fly’s earliest stage of growth.
The New Method
The new method may one day be applied to predict the development of more complex tissues, organs, and organisms. It could also help scientists identify cell patterns that correspond to early-onset diseases, such as asthma and cancer. In a study, the team presents a new deep-learning model that learns, then predicts, how certain geometric properties of individual cells will change as a fruit fly develops.
How it Works
The model records and tracks properties such as a cell’s position, and whether it is touching a neighboring cell at a given moment. The team applied the model to videos of developing fruit fly embryos, each of which starts as a cluster of about 5,000 cells. They found the model could predict, with 90 percent accuracy, how each of the 5,000 cells would fold, shift, and rearrange, minute by minute, during the first hour of development.
Gastrulation: The Initial Phase
This very initial phase is known as gastrulation, which takes place over roughly one hour, when individual cells are rearranging on a time scale of minutes. By accurately modeling this early period, scientists can start to uncover how local cell interactions give rise to global tissues and organisms. The researchers hope to apply the model to predict the cell-by-cell development in other species, such zebrafish and mice.
Potential Applications
Then, they can begin to identify patterns that are common across species. The team also envisions that the method could be used to discern early patterns of disease, such as in asthma. Lung tissue in people with asthma looks markedly different from healthy lung tissue. How asthma-prone tissue initially develops is an unknown process that the team’s new method could potentially reveal.
Capturing Cell Dynamics
“Asthmatic tissues show different cell dynamics when imaged live,” says co-author and MIT graduate student Haiqian Yang. “We envision that our model could capture these subtle dynamical differences and provide a more comprehensive representation of tissue behavior, potentially improving diagnostics or drug-screening assays.”
The Dual-Graph Structure
Scientists typically model how an embryo develops in one of two ways: as a point cloud, where each point represents an individual cell as point that moves over time; or as a “foam,” which represents individual cells as bubbles that shift and slide against each other, similar to the bubbles in shaving foam. Rather than choose between the two approaches, the researchers embraced both.
Combining Point Cloud and Foam
“There’s a debate about whether to model as a point cloud or a foam,” Yang says. “But both of them are essentially different ways of modeling the same underlying graph, which is an elegant way to represent living tissues. By combining these as one graph, we can highlight more structural information, like how cells are connected to each other as they rearrange over time.”
Training the Model
At the heart of the new model is a “dual-graph” structure that represents a developing embryo as both moving points and bubbles. Through this dual representation, the researchers hoped to capture more detailed geometric properties of individual cells. As a proof of principle, the team trained the new model to “learn” how individual cells change over time during fruit fly gastrulation.
Conclusion
The team believes that, in principle, the new model, and the dual-graph approach, should be able to predict the cell-by-cell development of other multiceullar systems, such as more complex species, and even some human tissues and organs. The limiting factor is the availability of high-quality video data. This work is supported, in part, by the U.S. National Institutes of Health.
FAQs
Q: What is the main goal of the new method developed by MIT engineers?
A: The main goal is to predict, minute by minute, how individual cells will fold, divide, and rearrange during a fruit fly’s earliest stage of growth.
Q: What is gastrulation?
A: Gastrulation is the initial phase of development, which takes place over roughly one hour, when individual cells are rearranging on a time scale of minutes.
Q: What are the potential applications of the new method?
A: The method could be used to predict the development of more complex tissues, organs, and organisms, and to identify cell patterns that correspond to early-onset diseases, such as asthma and cancer.
Q: What is the dual-graph structure?
A: The dual-graph structure represents a developing embryo as both moving points and bubbles, combining the point cloud and foam approaches to model how an embryo develops.
Q: What is the limiting factor for applying the new model to other species?
A: The limiting factor is the availability of high-quality video data.
