Cystic fibrosis is one of the most common genetic disorders and causes thick mucus buildup in the lungs and other parts of the body, breathing problems and infections. A three-drug cocktail known as Trikafta has greatly improved patients’ quality of life since its development in 2019, but it can cause cataracts and liver damage and must be taken daily at a cost of about $300,000 per year.
Now, researchers at the Broad Institute of MIT and Harvard and the University of Iowa have developed a gene-editing method that effectively corrects the most common mutation causing cystic fibrosis, present in 85 percent of patients. If further developed, it could pave the way for treatments that are administered once and have fewer side effects.
The new method, published today in Biomedical Engineering of Natureprecisely and durably corrects the mutation in human lung cells, restoring cellular function to levels similar to those of Trikafta. The approach relies on a technique called prime editing, which can make insertions, deletions, and substitutions of up to hundreds of base pairs in the genome with few unwanted byproducts. Prime editing was developed in 2019 by the lab of David Liu, who is the Richard Merkin Professor and director of the Merkin Institute for Transformative Technologies in Health Care at the Broad, as well as a professor at Harvard University and an investigator at the Howard Hughes Medical Institute.
“We hope that using prime editing to correct the predominant cause of cystic fibrosis could lead to a unique and permanent treatment for this serious disease,” said Liu, senior author of the study. “Developing a strategy to efficiently correct this challenging mutation also provided a model for optimizing prime editing to precisely correct other mutations that cause devastating disorders.”
Postdoctoral researcher Alex Sousa and graduate student Colin Hemez, both in Liu’s lab, were first authors of the study.
Genetic repair
Cystic fibrosis is caused by mutations in the CFTR A gene that disrupts cell membrane ion channels that pump chloride out of cells. There are over 2,000 known variants of the gene. CFTR Gene, 700 of which cause disease. The most common is a three-base pair deletion of CTT that causes the ion channel protein to fold incorrectly and become degraded.
Fixed CTT removal in CFTR It has long been the goal of gene-editing therapies from labs like Liu’s, but most attempts have either not been efficient enough to confer therapeutic benefit or used approaches like CRISPR/Cas9 nuclease editing that generate double-strand breaks in DNA, potentially leading to unintended changes in the target gene and other locations in the genome.
Prime editing, a more flexible and controlled type of gene editing that does not require double-strand breaks, could help address this limitation. To more efficiently correct the CFTR To correct the mutation, Liu’s team combined six different improvements to the technology. These included improving the primary editing guide RNAs that program primary editing proteins to find their target and perform the desired edit, as well as modifying the primary editing protein itself and other changes that make the target site more accessible. In combination, these refinements corrected about 60 percent of the CTT deletions in human lung cells and about 25 percent in cells taken directly from patient lungs and grown in a dish — an increase over previous methods that corrected less than 1 percent of the mutation in the cells. The new approach also generated 3.5 times fewer unwanted insertions and deletions per edit than previous methods using the Cas9 nuclease enzyme.
Next, researchers will need to develop ways to package and deliver the primary editing machinery to the airways of mice and, ultimately, humans. The team is hopeful that recent advances, such as lipid nanoparticles that reach the lungs of mice, could help speed up the translation of this approach.