As cells perform their daily functions, they turn on various genes and cellular pathways. Engineers at MIT induced cells to engrave the history of these events into long protein chains that can be imaged using light microscopy.
Cells programmed to generate these chains continually add building blocks that encode specific cellular events. The ordered protein chains can then be labeled with fluorescent molecules and read under a microscope, allowing researchers to reconstruct the timing of events.
This technique could help shed light on the steps underlying processes such as memory formation, response to drug therapy, and gene expression.
“At the scale of organs and bodies, there are many untraceable changes that occur over time, from hours to weeks,” says Y. Eva Tan, professor of bioengineering, brain and cognition and professor of neurotechnology. One Edward Boyden said: He is an investigator at the Howard Hughes Medical Institute and a member of the Massachusetts Institute of Technology’s McGovern Brain Institute and the Koch Institute for Integrative Cancer.
If the technology can be scaled up to work over time, the researchers say, it could also be used to study processes such as aging and disease progression.
Boyden is the senior author of the study and today nature biotechnologyChangyang Linghu, a former J. Douglas Tan postdoctoral fellow at the McGovern Institute and now an assistant professor at the University of Michigan, is the lead author of the paper.
Biological systems such as organs contain various types of cells, each with its own characteristic function. One of his ways of studying these functions is by imaging proteins, RNA, or other molecules inside cells, which provide clues as to what the cells are doing. However, most methods for doing this only provide a glimpse of a single moment in time or do not work well with very large cell populations.
Biological systems are often composed of many different types of cells. For example, the human brain has 86 billion cells of her. To understand this kind of biological system, we need to observe physiological events in these large cell populations over time. ”
Changyang Linghu, first author
To achieve that, the research team came up with the idea of recording cellular events as a series of protein subunits, continually adding to the chain. We used engineered protein subunits not normally found in living cells that can self-assemble into long filaments.
The researchers engineered a genetically-encoded system in which one of these subunits is produced continuously within the cell and another subunit is produced only when a specific event occurs. Did. Each subunit also contains a very short peptide called an epitope tag. In this case, the researchers chose tags called her HA and V5. Each of these tags can be conjugated to a different fluorescent antibody, making it easier to later visualize the tags and determine the sequence of the protein subunits.
For this study, the researchers generated V5-containing subunits contingent on the activation of a gene called c-fos, which is involved in encoding new memories. HA-tagged subunits make up the bulk of the chain, but whenever the V5 tag appears in the chain, it means that c-fos was activated during that time.
“We hope to use this kind of self-assembly of proteins to record the activity of all cells,” Linghu said. “It is not only a snapshot of time, but also a record of past history, just as tree rings can permanently store information over time as wood grows.”
In this study, researchers first used the system to record c-fos activation in neurons growing in experimental dishes. The c-fos gene was activated by chemically induced neuronal activation and the V5 subunit was added to the protein chain.
To test whether this approach works in animal brains, the researchers programmed mouse brain cells to produce protein chains when the animals were exposed to certain drugs. The researchers were then able to detect the exposure by preserving the tissue and analyzing it with a light microscope.
Researchers designed the system to be modular, allowing different epitope tags to be exchanged and different types of cellular events to be detected. This, in principle, involves cell division and the activation of enzymes called protein kinases that help regulate many cellular pathways. .
Researchers also hope to extend the record duration that can be achieved. In this study, they recorded events for several days before imaging the tissue. Since protein chain length is limited by cell size, there is a trade-off between the time that can be recorded and temporal resolution, or frequency of event recording.
“The total amount of information that can be stored is fixed, but in principle the chain can grow slower or faster,” Linghu says. “If you want to record for a longer period of time, you can slow down the synthesis so that the cell size is reached, say, within two weeks. That way you can record longer, but at the expense of temporal resolution.” .”
Researchers are also working on designing the system so that it can record multiple types of events in the same chain by increasing the number of different subunits that can be incorporated.
This study was funded by the Hock E. Tan and K. Lisa Yang Center for Autism Research, John Doerr, National Institutes of Health, National Science Foundation, U.S. Army Research Service, and Howard Hughes Medical Institute. rice field.
Massachusetts Institute of Technology
Linghu, C., and others. (2022) Recording cell physiological history along optically readable self-assembling protein chains. nature biotechnology. doi.org/10.1038/s41587-022-01586-7.