ABOVE: Researchers used a new and improved prime editing system to correct the gene mutation responsible for a majority of cystic fibrosis cases. ©istock, magicmine
In cystic fibrosis (CF), patients’ organs become overwhelmed by thick mucus, which affects breathing and can result in serious bacterial infections. The outlook for patients with CF has improved significantly since scientists identified the gene mutation responsible for the disease in 1989.1 A majority of cases are caused by a three-base-pair mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This mutation, called F508del, results in ion channel defects throughout the patients’ bodies.
Gene therapies have huge potential for diseases like CF because they provide long-lasting treatments. However, genetic editing techniques used to develop these promising treatments, including the Nobel Prize-winning CRISPR-Cas9, have proved inefficient at correcting F508del. Now, published in Nature Biomedical Engineering, researchers used an optimized version of the genome editing technology prime editing to alter this mutation in lung cells from patients with CF.2 The approach restored function to the same degree as a powerful CF drug combination therapy. The findings could lead to CF treatments that permanently correct the disease’s genetic origin.
David Liu, a geneticist at the Broad Institute of MIT and Harvard and coauthor on the study, recognized that complex genetic diseases require flexible and precise gene therapies. In 2019, he developed prime editing, a gene editing technique that takes a different approach from CRISPR.3 The latter technique cuts the genome like scissors, snipping through both strands of the DNA, which can lead to unintended, off-target edits. In contrast, prime editors, said Liu, are like “DNA word processors in that we develop them to do true search and replace editing.” He added that this allows the technology to make more precise and controllable changes, making it ideal for the repair job needed to correct the F508del mutation: the addition of only a few DNA letters at specific locations.
In their 2019 paper, Liu’s team used prime editing to alter the gene mutations causing sickle cell disease and Tay-Sachs disease. Liu explained that they attempted to edit mutated CFTR as well but with limited success. “That was a very difficult correction to make,” said Liu. The genetic machinery that guided the prime editor proved unstable and corrected less than one percent of mutations.
Researchers have made improvements to prime editing over the last five years. In the latest paper, Liu’s team took another crack at editing CFTR using what he calls a “kitchen sink approach” that utilized six major enhancements to prime editing. These changes improved the accuracy and stability of the molecular machinery.
Liu said much effort went into incorporating an enhancement that allowed the system to make edits to the DNA without attracting the attention of cells’ built-in repair pathways. This protein machinery—the DNA mismatch repair system—reversed the prime editor’s changes if it noticed the rewriting. By adding in silent mutations near the edits they made to F508del, Liu’s team found that the mismatch repair system was less likely to undo edits.
The new and improved prime editing system proved far more effective. The editing efficiency varied between cell types studied but the editor corrected the mutation in 58 percent of human epithelial cells carrying the F508del mutation. When Liu and his team tested the machinery in airway cells taken from patients with CF, they found that it restored the function of ion channels to the same level as the leading combination therapy Trikafta, which works by boosting ion channel function.
Liu is optimistic about the approach’s efficacy, but he pointed out that treating cells in a dish is far from treating those in the bodies of affected patients. He added that the delivery method for prime editors will be a key determinant of how effective any future treatment is for patients.
“It’s encouraging to see the positive results in these studies correcting the most common CF gene mutation, F508del, and we hope future research could lead to the development of genetic therapy treatments for those with rarer CF mutations too,” said Lucy Allen, a lung biologist and research director at Cystic Fibrosis Trust, who was not involved in the research.
Trikafta, which specifically targets the F508del mutation carried by 90 percent of patients with CF, gives patients a “very significant improvement in all of the clinical parameters,” said Scott Bell, a clinician scientist at the University of Queensland who was not involved in the study. Trikafta must be taken at least daily for the rest of a patient’s life and costs over $300,000 per year.4
Bell said these recent advances have still left roughly 10 percent of the CF population, who have rarer mutations, with limited options.5 Liu said that the new technique’s flexibility provides hope that it could contribute to efforts to reverse rarer CF mutations and correct other genetic diseases.
Reflecting on the arduous journey to correcting the F508del mutation, Liu said, “When you're faced with a stubborn problem in science, there might be a temptation to move on.” In this case, persistence paid off, producing a genetic tool that could correct disease mutations beyond CF. “The long-term benefit of overcoming that challenge is you learn a lot about the system and therefore about how to best apply it in the future,” he added.
- Marx JL. The cystic fibrosis gene is found. Science. 1989;245(4921):923-925.
- Sousa AA, et al. Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells. Nat Biomed Eng. 2024:1-15.
- Anzalone AV, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576(7785):149-157.
- Zaher A, et al. A review of Trikafta: Triple cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy. Cureus. 13(7):e16144.
- Taylor-Cousar JL, et al. Clinical development of triple-combination CFTR modulators for cystic fibrosis patients with one or two F508del alleles. ERJ Open Res. 2019;5(2):00082-02019.