CRISPR's New CAMERA is a Cellular Data Recorder
News Feb 21, 2018 | by Ruairi J Mackenzie, Science Writer, Technology Networks
CRISPR gene editing technology is making a name as a genetic swiss army knife. The genetics research community, seemingly limited by only their imagination, have been creating CRISPR applications at a breakneck speed - DNA detective work, stem cell creation and saving the world’s supply of chocolate are just some of the tasks CRISPR has proved capable of in recent months.
Its latest party trick, as unveiled by scientists at the Broad Institute of MIT and Harvard and Harvard’s Department of Chemistry and Chemical Biology, is to become a cellular black box recorder.
The recorder system, dubbed CAMERA1, can track the sequence and duration of events within the cell. Authors demonstrated that the system could record stimuli in the cell’s environment such as exposure to viruses and antibiotics. The ultimate aim for this technology is to use the recorders to achieve a deeper understanding of complex cellular processes, such as expression of genes into proteins.
Lights, CAMERA, Action
The study, published in Science, exploited CRISPR’s Cas-9 enzyme, a pair of genetic scissors that can chop DNA at pre-determined points. The scissors, aimed by a short chunk of genetic material called a guide RNA, were directed to cut bacterial cell DNA. This allowed researchers to insert plasmids, small circles of DNA. Some of these plasmids had been genetically modified by the researchers to allow Cas-9 to target them.
When Cas-9 cuts DNA, mammalian cells usually have repair mechanisms in place to fix the break, although sometimes creating errors in the process (which science readily exploits). In this study, the bacterial cells used had no such repair mechanisms meaning the targeted plasmids were degraded instead. The researchers’ final genetic alteration was to make sure that the host cells would only start producing Cas-9 if a particular antibiotic was present.
The antibiotic was added, and detected by the bacterial cells, which produced Cas-9. The enzyme started cutting the plasmids that were sensitive to Cas-9, whilst leaving other plasmids intact. The targeted plasmids then degraded, meaning authors simply had to monitor the relative levels of the two types of plasmid to get a readout in which increased antibiotic concentration and duration meant relatively fewer Cas-9 plasmids.
This readout was incredibly sensitive. The researchers could detect a signal from tiny populations of just tens of cells. As a final flourish, the authors developed a technique which could reset the altered: non-altered plasmid ratio, meaning multiple recordings could be taken from the same cell.
CRISPR Sewing Scissors
The authors didn’t stop there. A second device, CAMERA2, exploited another CRISPR method which more delicately altered single base letters of DNA, the sewing scissors to CAMERA1’s rough scythe. This method, base editing, was developed by Liu and his group in 2016. Editing DNA in such a fashion has the risk of damaging the cell. To prevent this, the system was set up the system so that the base editor would only function in a specific gene called a “safe harbor” gene, a testing ground where there is no risk of cell damage.
This system was able to record up to four stimuli, and the exact sequence in which the stimuli occurred. This second system was modified to work with mammalian cells, through bypassing the need for plasmids altogether and monitoring changes made directly to the cell’s genome.
And For My Next Trick…
This is only one of multiple CRISPR recording systems proposed recently, but Liu’s innovation is to require so few cells. Indeed, the simplicity and flexibility of this approach is highly promising for the field, where the grand goal is to make these CRISPR recording systems work in animal models, rather than just in cell lines. Such analysis would provide an entirely new level of detail about what exactly goes on in our cells. At that point, CRISPR would just be showing off.