Scientists have developed a powerful new research tool that can help researchers reveal the intricate details of cell function. Reporting in Nature, researchers have created CytoTape, a protein fiber that can act like a thread that moves through cells to measure various activities over time with the help of computational tools.
Scientists already have many advanced methods to study cells. They can freeze molecules and study their structures, or use expansion microscopy, which can take a small piece of tissue and make it much larger so that small details are easier to see. But it is challenging to monitor live cells and molecules in action over long periods of time, as they move through different processes.
In this work, researchers created an approach that can embed a timestamp into cells while they're working. This tool can behave like a kind of tape recorder that the cell generates and maintains, so that previous interactions can be analyzed over long time periods.
“Just like tree rings, which encode physiological histories of a growing tree, CytoTape records temporal cell activities in situ along a flexible intracellular protein fiber for post-mortem readout at scale under conventional light microscopy, breaking through the tradeoff between resolution and scale,” said corresponding study author Changyang Linghu, Ph.D., Assistant Professor of Cell and Developmental Biology and Biomedical Engineering and Principal Investigator at the Michigan Neuroscience Institute.
The researchers engineered a method that utilizes existing methods to send genes into cells. But for this effort, they sent genes that encode for the synthetic CytoTape into cells. Tests indicated that these genes do not alter the normal function of cells, nor did they change brain cell function in a mouse model. The cell simply recognizes these synthetic genes and produces the proteins they encode for, so that CytoTape is continuously made in the cell.
Once the CytoTape is present, it makes molecular tags with color codes that are only about fifteen amino acids long, and can be linked to signals in cells that are generated over as long as three weeks.
Tagging is a common method in molecular biology research, so that scientists can see certain things in the cells that they are interested in; these tags are often fluorescent, or can be detected with fluorescent antibodies, so they can be seen through a microscope.
“The presence of these tagged tape monomers are controlled by individual cell activity-dependent promoters, to leave an imprint on this tape when there is a corresponding kind of cell activity,” said study co-author Dongqing Shi, a postdoctoral fellow in the Linghu lab.
The researchers used this novel technology to assess gene activity in over 14,000 live neurons in a mouse brain. They also tested it in cell lines like human cancer cells. This work illuminated how certain pathways behaved over time.
“With our tool, we hope to collaborate with biomedical researchers to dissect various cell plasticity processes that span over days and weeks,” said Linghu. “By comparing the results between healthy and diseases brains, we may be able to pinpoint what goes wrong exactly across space and time in these processes and provide insights into future therapeutic interventions to correct these differences.”
Sources: University of Michigan, Nature
