AI-Designed CytoTape Records Cellular Events Over Time With High Resolution

Unraveling the mysteries of how biological organisms function begins with understanding the molecular interactions within and across large cell populations.

A revolutionary new tool, developed at the University of Michigan, acts as a sort of tape recorder produced and maintained by the cell itself, enabling scientists to rewind back in time and view interactions on a large scale and over long periods of time.

Developed in the lab of Changyang Linghu, Ph.D., Assistant Professor of Cell and Developmental Biology and Biomedical Engineering and Principal Investigator in Michigan Neuroscience Institute, the so-called "CytoTape" is a flexible, thread-like intracellular protein fiber, designed with the help of AI to act as a tape recorder for large-scale measurement of cellular activities.

The breakthrough was published in the journal Nature.

Current imaging techniques to measure changing biological processes often tradeoff between resolution and scale.

For example, fMRI, commonly used to study the brain, allows large-scale monitoring of brain activity but no ability to reveal what is happening at the single cell level.

And while light microscopy provides single-cell resolution, it is limited due to the tissue's scattering of light.

While researchers can see more detail in non-living tissue using a microscope, it hasn't been possible to view a cell's activity over time.

The team's solution: embedding timestamp signals along spatial dimension when the cell was alive.

"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 Linghu.

To deliver CytoTape to populations of cells, "we applied existing gene delivery methods to introduce the DNA sequence encoding the synthetic tape monomer to cells," said co-lead author Lirong Zheng, Ph.D., a postdoctoral fellow in the Linghu lab.

"We found CytoTape does not alter normal cell physiology or mouse brain function in vivo."

Then the cell, thinking the tape monomer is something it needs, will start to continuously produce it, which self-assembles in cells and elongate the protein tape over time.

What's recorded on the protein tape are color-coded molecular tags that correspond to diverse cellular temporal signals over up to three weeks.

The tags are small, less than 15 amino acids, and are being fused to the tape monomers."

Yixiao Yan, Ph.D. student and co-lead author

Tags, she explained, are widely used in biology and engineered to be recognized by distinct fluorescent antibodies and viewed under a microscope.

They serve as a signature of what was happening inside the cell at a point in time.

"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 Dongqing Shi, a co-lead author and postdoctoral fellow in the Linghu lab.

"With this technology, we recorded spatially resolved transcriptional activity from up to 14,123 neurons in a mouse brain in vivo."

The team applied CytoTape in mouse neurons and glia, as well as human embryonic kidney–derived cells and human cancer–derived cells.

They discovered unexpected temporal modes of regulatory pathways involved in cell plasticity, thanks to the tape enabling them to see what happened before, during and after a cellular event.

"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."