Next-gen CRISPR system allows precise search-and-replace gene editing
The CRISPR gene-editing system is one of the most important developments in medicine in recent years. By making cut-and-paste edits to DNA, scientists can correct a whole range of health problems – but the tool has its own issues, too. Now, Harvard and MIT scientists have created a new approach called prime editing, which could correct almost 90 percent of disease-causing genes.
The first CRISPR system made to edit the human genome worked using an enzyme called Cas9. After guide RNAs directed the tool to the desired section of the genome, Cas9 would then cut both strands of DNA in two places, removing a section of DNA and replacing it with something else. The idea was that troublesome genes – such as those that cause certain genetic diseases – could be completely cut out and replaced with more benign or beneficial bits of DNA.
As powerful as that system is, it isn’t without its risks. Completely cutting sections of DNA and then introducing new ones can create some mistakes, with some studies suggesting that it could increase a patient’s chances of cancer. On top of that, the tool may sometimes miss the right spot, instead making “off-target” edits that can cause all sorts of problems. A study saying just that was criticized and later retracted, but concerns remain.
Enter prime editing. This new version of the tool is designed to be gentler and more precise, coupling the Cas9 enzyme to two new components – a reverse transcriptase (RT) protein and a prime editing guide RNA (pegRNA). It was developed by scientists at MIT’s Broad Institute and Harvard.
First, the pegRNA guides the prime editor to the desired section of the genome. There, instead of cutting both strands of DNA, the Cas9 enzyme nicks just one strand. The pegRNA also contains a sequence of letters that will be inserted into the genome – the RT protein reads that sequence and writes the corresponding DNA letters to the end of the nicked piece of DNA. It can do this by converting individual DNA letters into others.
Next, the cell itself will naturally cut out the original, unwanted DNA sequence, and seal the new letters into the genome. But that creates a mismatch between the two strands – one half of the DNA sequence will be edited and the other won’t be. To fix that, another guide RNA will then direct the prime editor to nick the unedited strand. That small “injury” tells the cell to repair the strand, and it will do so by copying the edited strand.
The end result is a section of DNA that’s fully edited, with less chance for off-target mutations and a more precise edit.
“A major aspiration in the molecular life sciences is the ability to precisely make any change to the genome in any location,” says David Liu, senior author of the study. “We think prime editing brings us closer to that goal. We’re not aware of another editing technology in mammalian cells that offers this level of versatility and precision with so few byproducts.”
In tests, the researchers were able to correct gene variants that cause sickle-cell anemia and Tay-Sachs disease – the first involves changing one specific T in the DNA code to an A, and the second requires removing four letters from a specific location. According to the researchers, this tool has the potential to correct up to 89 percent of genetic variations that can cause diseases.
The team also tested the new prime editing system in human cells and primary mouse neurons, successfully performing a range of edit types. They managed to pull off all 12 possible DNA letter substitutions, inserted new DNA segments up to 44 letters long, and deleted segments up to 80 letters long. Combining bits of these different edit types also worked as hoped.
“The versatility of prime editing quickly became apparent as we developed this technology,” says Andrew Anzalone, first author of the study. “The fact that we could directly copy new genetic information into a target site was a revelation. We were really excited.”
The team plans to continue testing the prime editing technique in human cells and animal models, investigating how it affects cells, and ultimately getting it ready for potential clinical trials in humans.
The research was published in the journal Nature.