As cells function, a large number of genes and biological pathways are triggered. Thanks to the work of MIT scientists, the history of these events has now been preserved by cells in a long protein chain that can be observed under a light microscope.
Cells that have been designed to create these sequences constantly accumulate the building pieces that encode certain biological functions. The organised protein chains can then have fluorescent molecules added to them, which can be examined under a microscope to determine the sequence of events. This method might help illuminate the phases involved in processes including memory formation, pharmacological response, and gene expression.
According to Edward Boyden, the Y. Eva Tan Professor in Neurotechnology, a professor of biological engineering and brain and cognitive sciences at MIT, a Howard Hughes Medical Institute investigator, and a member of MIT’s McGovern Institute for Brain Research and Koch Institute for Integrative Cancer Research, “there are a lot of changes that happen at organ or body scale, over hours to weeks, which cannot be tracked over time.” According to the researchers, if the method could be improved to operate over longer time periods, it may potentially be used to examine processes like ageing and illness progression.
The paper, which was written by Boyden in the lead, was published in Nature Biotechnology today. The paper’s primary author is Changyang Linghu, a former J. Douglas Tan Postdoctoral Fellow at the McGovern Institute who is currently an assistant professor at the University of Michigan.
Organs and other biological systems are made up of many different types of cells, each of which performs a specific purpose. Imaging proteins, RNA, or other molecules inside the cells, which give clues as to what the cells are doing, is one technique to explore their processes. The majority of techniques for achieving this, meanwhile, only provide a snapshot in time or are ineffective when dealing with very large populations of cells.
” Biological systems are often composed of a large number of different types of cells. For example, the human brain has 86 billion cells,” Linghu says. “To understand those kinds of biological systems, we need to observe physiological events over time in these large cell populations.”
The research team came up with the concept of storing biological events as a succession of protein subunits that are continually added to a chain in order to do that. The scientists developed protein components that can self-assemble into lengthy filaments but are not typically seen in live cells in order to make their chains.
One of these subunits is continually produced inside cells in the system the researchers created using genetic coding, but the other is only made when a particular event takes place. Each subunit also has an epitope tag, which is a very short peptide; in this instance, the researchers selected the tags HA and V5.
These tags can all attach to various fluorescent antibodies, which makes it simple to see the tags afterwards and identify the order of the protein subunits.
The creation of the V5-containing subunit was rendered dependent in this work on the activation of the c-fos gene, which is involved in the encoding of new memories. The majority of the chain is made up of HA-tagged subunits, however anytime the V5 tag is present, c-fos was active at that moment.
“We’re hoping to use this kind of protein self-assembly to record activity in every single cell,” Linghu says. “It’s not only a snapshot in time, but also records past history, just like how tree rings can permanently store information over time as the wood grows.”
In this work, the researchers initially recorded the activation of c-fos in developing neurons in a lab dish using their technique. Chemically induced neuronal activation, which resulted in the V5 subunit being added to the protein chain, activated the c-fos gene.
The researchers designed the brain cells of mice to produce protein chains that would show when the animals were exposed to a certain medicine in order to test if this method would function in the brains of animals. Later, by conserving the tissue and using a light microscope to examine it, the researchers were able to identify that exposure.
In order to detect many physiological processes, including, theoretically, cell division or the activation of enzymes known as protein kinases that help regulate several cellular pathways, the researchers built their system to be modular.
Additionally, the researchers want to increase the length of time they can keep records. Before imaging the tissue in this investigation, events were documented for a number of days. Because the length of the protein chain is constrained by the size of the cell, there is a trade-off between the amount of time that can be recorded and the temporal resolution, or frequency of event recording.
According to Linghu, “The total quantity of information it could hold is fixed, but we could theoretically slow down or speed up the expansion of the chain.” “If we wanted to keep track of the data for a longer period of time, we could slow down the synthesis so that it would fill the cell in, say, two weeks. So, while we could record for a longer duration, the temporal resolution would be worse.” By increasing the variety of subunits that may be integrated, the researchers are also aiming to design the system so that it can record many sorts of events in the same chain.