Building a Virtual Cell
Our cells are made up of extremely intricate networks of genes, proteins and other molecules that move around, carry messages, respond to changes in the environment and perform functions, like producing insulin or beating in unison. Researchers who study these processes usually focus on just one thing, such as studying a single gene or protein.
To provide researchers with a more global view of cells and their networks, University of California San Diego School of Medicine researchers created Active Interaction Mapping, a program that organizes raw data into a model of the cell.
“This tool is meant to guide researchers interested in any aspect of cellular function, helping them select the next logical experiments to learn about that process,” said Michael Kramer, an MD/PhD student who helped develop the program in the lab of Trey Ideker, PhD, professor of genetics and bioengineering.
Not only do researchers benefit from Active Interaction Mapping, they also contribute. The model becomes more powerful as more researchers roll their data back into it.
To test Active Interaction Mapping, Ideker and team used autophagy in yeast cells as an example cellular process. Autophagy is the process by which cells recycle their components — a system that can go awry in cancer, neurodegenerative diseases and many other conditions. The model told them that genetic experiments were needed, so they went back to the lab to do them. In doing so, the team uncovered previously unknown autophagy roles for a number of genes — information they then fed back into the model.
The study published January 26 in Molecular Cell. Researchers can download the Active Interaction Mapping software at atgo.ucsd.edu
Ideker, Kramer and team have already started modeling human cells. In the future, they hope to offer not just healthy cell models, but models for diseased cells. The ultimate goal is to offer personalized cell modeling — a window not just into a cancer cell, but your unique cancer cell.
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