MIT Scientists Drastically Reduce Errors in Prime Gene Editing

CAMBRIDGE, MA – Researchers at the Massachusetts Institute of Technology (MIT) have engineered a significant breakthrough in prime editing, a precise gene-editing technique, by dramatically lowering its potential error rate. The advance, detailed in a new paper published today in the journal Nature, could make it safer and easier to develop gene therapies for a wide array of genetic disorders.

The MIT team improved the safety profile by engineering the proteins that power the prime editing system, achieving error rates as low as one unintended change per 543 edits in its high-precision mode. This is a vast improvement over the previous rate of one error per 122 edits for the same mode, and a near 60-fold reduction in errors for the most refined editor.

Solving the Precision Problem

Prime editing, developed in 2019, is a gene-editing method based on the popular CRISPR system. Unlike earlier methods that make a double-stranded cut in the DNA, prime editing cuts only one strand, allowing a new sequence to be directly inserted using an RNA template.

The potential for error arises when the newly edited DNA strand has to compete with the old strand to be incorporated into the genome. If the old strand prevails, the leftover flap of new DNA can accidentally integrate elsewhere, leading to “unwanted mutations.”

Lead author Vikash Chauhan, a research scientist at MIT’s Koch Institute for Integrative Cancer Research, explained that the goal was to achieve maximal efficacy with minimal side effects.

“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,” said Phillip Sharp, an MIT Institute Professor Emeritus and senior author of the study.

Creating the ‘vPE’ Editor

To achieve this precision, the MIT researchers initially introduced subtle mutations into the Cas9 enzyme used in prime editing. They found that these changes made the old DNA strands less stable, facilitating their degradation and allowing the new, corrected DNA strand to be incorporated more cleanly.

By combining pairs of these Cas9 mutations, the team lowered the error rate to about 1/36th of its original amount.

The final system, dubbed vPE (variant Prime Editor), incorporated these enhanced Cas9 proteins into a prime editing system that also included an RNA-binding protein to stabilize the RNA template. This combined approach resulted in the final, highly accurate editor, with the error rate reduced to just 1/60th of the original.

“For any disease where you might do genome editing, I would think this would ultimately be a safer, better way of doing it,” said Robert Langer, the David H. Koch Institute Professor at MIT and a senior author of the study.

The MIT team is now focused on further improving the efficiency of the vPE editor and tackling the longstanding challenge of delivering the editors to specific tissues in the body. They also anticipate the vPE system will be rapidly adopted by other labs, accelerating basic research into cancer evolution and cellular development.