by Greta Friar – Link to Full Article with Video
Imagine a ball thrown in the air: it curves up, then down, tracing an arc to a point on the ground some distance away. The path of the ball can be described with a simple mathematical equation, and if you know the equation, you can figure out where the ball is going to land. Biological systems tend to be harder to forecast, but Whitehead Institute Member Jonathan Weissman, postdoc in his lab Xiaojie Qiu, and collaborators at the University of Pittsburgh School of Medicine are working on making the path taken by cells as predictable as the arc of a ball. Rather than looking at how cells move through space, they are considering how cells change with time.
Weissman, Qiu, and collaborators Jianhua Xing, professor of computational and systems biology at the University of Pittsburgh School of Medicine, and Xing lab graduate student Yan Zhang have built a machine learning framework that can define the mathematical equations describing a cell’s trajectory from one state to another, such as its development from a stem cell into one of several different types of mature cell. The framework, called dynamo, can also be used to figure out the underlying mechanisms—the specific cocktail of gene activity—driving changes in the cell. Researchers could potentially use these insights to manipulate cells into taking one path instead of another, a common goal in biomedical research and regenerative medicine.
The researchers describe dynamo in a paper published in the journal Cell on February 1. They explain the framework’s many analytical capabilities and use it to help understand mechanisms of human blood cell production, such as why one type of blood cell forms first (appears more rapidly than others).
“We want to be able to map how a cell changes in relation to the interplay of regulatory genes as accurately as an astronomer can chart a planet’s movement in relation to gravity.”
“Our goal is to move towards a more quantitative version of single cell biology,” Qiu says. “We want to be able to map how a cell changes in relation to the interplay of regulatory genes as accurately as an astronomer can chart a planet’s movement in relation to gravity, and then we want to understand and be able to control those changes.”
How to map a cell’s future journey
Dynamo uses data from many individual cells to come up with its equations. The main information that it requires is how the expression of different genes in a cell changes from moment to moment. The researchers estimate…
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