A gene-editing approach called prime editing could one day help treat many illnesses by turning faulty genes into healthy ones. However, the technique sometimes introduces small mistakes into DNA, which can occasionally be harmful.

Researchers at MIT have now discovered a way to significantly reduce these errors by altering the key proteins that drive the editing process. They believe this improvement could make gene therapy safer and more practical for treating a wide range of diseases.

“This paper outlines a new approach to doing gene editing that doesn’t complicate the delivery system and doesn’t add additional steps, but results in a much more precise edit with fewer unwanted mutations,” says Phillip Sharp, an MIT Institute Professor Emeritus, a member of MIT’s Koch Institute for Integrative Cancer Research, and one of the senior authors of the new study.

Using their refined method, the MIT team lowered the rate of mistakes in prime editing from roughly one in seven edits to about one in 101 for the most common editing type. In a more precise editing mode, the improvement went from one in 122 to one in 543.

“For any drug, what you want is something that is effective, but with as few side effects as possible,” says Robert Langer, the David H. Koch Institute Professor at MIT, a member of the Koch Institute, and one of the senior authors of the new study. “For any disease where you might do genome editing, I would think this would ultimately be a safer, better way of doing it.”

Koch Institute research scientist Vikash Chauhan led the study, which was recently published in Nature.

The potential for error

In the 1990s, early gene therapy efforts relied on inserting new genes into cells using modified viruses. Later, scientists developed techniques that used enzymes like zinc finger nucleases to directly repair genes. These enzymes worked but were difficult to reengineer for new DNA targets, making them slow and cumbersome to use.

The discovery of the CRISPR system in bacteria changed everything. CRISPR uses an enzyme called Cas9, guided by a piece of RNA, to cut DNA at a specific location. Researchers adapted it to remove faulty DNA sequences or insert corrected ones using an RNA-based template, making gene editing faster and more flexible.

In 2019, scientists at the Broad Institute of MIT and Harvard introduced prime editing, a new version of CRISPR that is even more precise and less likely to affect unintended areas of the genome. More recently, prime editing was used successfully to treat a patient with chronic granulomatous disease (CGD), a rare disorder that weakens white blood cells.

“In principle, this technology could eventually be used to address many hundreds of genetic diseases by correcting small mutations directly in cells and tissues,” Chauhan says.

One of the advantages of prime editing is that it doesn’t require making a double-stranded cut in the target DNA. Instead, it uses a modified version of Cas9 that cuts just one of the complementary strands, opening up a flap where a new sequence can be inserted. A guide RNA delivered along with the prime editor serves as the template for the new sequence.

One reason prime editing is considered safer is that it doesn’t cut both strands of DNA. Instead, it makes a gentler, single-strand cut using a modified Cas9 enzyme. This opens a small flap in the DNA where a new, corrected sequence can be inserted, guided by an RNA template.

Once the corrected sequence is added, it must replace the original DNA strand. If the old strand reattaches instead, the new fragment can sometimes end up in the wrong spot, leading to unintended errors.

Most of these mistakes are harmless, but in rare cases they could contribute to tumor growth or other health issues. In current prime editing systems, the error rate can vary from about one in seven edits to one in 121, depending on the editing mode.

“The technologies we have now are really a lot better than earlier gene therapy tools, but there’s always a chance for these unintended consequences,” Chauhan says.

Precise editing

To reduce those error rates, the MIT team decided to take advantage of a phenomenon they had observed in a 2023 study. In that paper, they found that while Cas9 usually cuts in the same DNA location every time, some mutated versions of the protein show a relaxation of those constraints. Instead of always cutting the same location, those Cas9 proteins would sometimes make their cut one or two bases further along the DNA sequence.

This relaxation, the researchers discovered, makes the old DNA strands less stable, so they get degraded, making it easier for the new strands to be incorporated without introducing any errors.

In the new study, the researchers were able to identify Cas9 mutations that dropped the error rate to 1/20th its original value. Then, by combining pairs of those mutations, they created a Cas9 editor that lowered the error rate even further, to 1/36th the original amount.

To make the editors even more accurate, the researchers incorporated their new Cas9 proteins into a prime editing system that has an RNA binding protein that stabilizes the ends of the RNA template more efficiently. This final editor, which the researchers call vPE, had an error rate just 1/60th of the original, ranging from one in 101 edits to one in 543 edits for different editing modes. These tests were performed in mouse and human cells.

The MIT team is now working on further improving the efficiency of prime editors, through further modifications of Cas9 and the RNA template. They are also working on ways to deliver the editors to specific tissues of the body, which is a longstanding challenge in gene therapy.

They also hope that other labs will begin using the new prime editing approach in their research studies. Prime editors are commonly used to explore many different questions, including how tissues develop, how populations of cancer cells evolve, and how cells respond to drug treatment.

“Genome editors are used extensively in research labs,” Chauhan says. “So the therapeutic aspect is exciting, but we are really excited to see how people start to integrate our editors into their research workflows.”

The research was funded by the Life Sciences Research Foundation, the National Institute of Biomedical Imaging and Bioengineering, the National Cancer Institute, and the Koch Institute Support (core) Grant from the National Cancer Institute.