Biological engineers have devised a way to record complex histories in the DNA of human cells, allowing them to retrieve ‘memories’ of past events.
This analogue memory storage system is the first that can record the duration and/or intensity of events in human cells and could also help scientists study how cells differentiate into various tissues during embryonic development, experience environmental conditions, and how they undergo genetic changes that lead to disease.
“To enable a deeper understanding of biology, we engineered human cells that are able to report on their own history based on genetically encoded recorders,” said Timothy Lu, an associate professor of electrical engineering and computer science, and of biological engineering. “This technology should offer insights into how gene regulation and other events within cells contribute to disease and development.”
Many scientists have devised ways to record digital information in living cells. Using enzymes called recombinases, they program cells to flip sections of their DNA when a particular event occurs, such as exposure to a particular chemical. However, that method only reveals whether the event occurred, not how much exposure there was or how long it lasted. Lu and other researchers have previously devised ways to record that kind of analogue information in bacteria, but until now, no one has achieved it in human cells.
The new MIT approach is based on the genome-editing system known as CRISPR, which consists of a DNA-cutting enzyme called Cas9 and a short RNA strand that guides the enzyme to a specific area of the genome, directing Cas9 where to make its cut. To encode memories, the MIT team took a different approach: They designed guide strands that recognise the DNA that encodes the very same guide strand, creating what they call “self-targeting guide RNA.”
By using sensors for specific biological events to regulate Cas9 or self-targeting guide RNA activity, this system enables progressive mutations that accumulate as a function of those biological inputs, thus providing genomically encoded memory.
For example, the researchers engineered a gene circuit that only expresses Cas9 in the presence of a target molecule, such as TNF-alpha, which is produced by immune cells during inflammation. Whenever TNF- alpha is present, Cas9 cuts the DNA encoding the guide sequence, generating mutations. The longer the exposure to TNF-alpha or the greater the TNF-alpha concentration, the more mutations accumulate in the DNA sequence. By sequencing the DNA later on, researchers can determine how much exposure there was.
“This is the rich analogue behaviour that we are looking for, where, as you increase the amount or duration of TNF-alpha, you get increases in the amount of mutations,” said Samuel Perli, a lead author of the paper reporting this study.
“Moreover, we wanted to test our system in living animals. Being able to record and extract information from live cells in mice can help answer meaningful biological questions,” noted graduate student Cheryl Cui.
The researchers showed that the system is capable of recording inflammation in mice and that they could engineer cells to detect and record more than one input, by producing multiple self-targeting RNA guide strands in the same cell.
Currently this method is most likely to be used for studies of human cells, tissues, or engineered organs, the researchers say. By programming cells to record multiple events, scientists could use this system to monitor inflammation or infection, or to monitor cancer progression.