New Gene Editing Technique Outperforms Existing Therapies

Cystic fibrosis, a prevalent genetic disorder, leads to thick mucus accumulation in the lungs and other parts of the body, resulting in breathing difficulties and infections. Since its introduction in 2019, the three-drug regimen Trikafta has significantly enhanced patient quality of life. However, it can cause cataracts and liver damage and must be taken daily, costing approximately $300,000 annually.

Researchers at the Broad Institute of MIT and Harvard, along with the University of Iowa, have developed a gene-editing technique that efficiently corrects the most common mutation causing cystic fibrosis, present in 85% of patients. With further development, this approach could lead to treatments that are administered only once and have fewer side effects.

The newly published method in Nature Biomedical Engineering achieves precise and long-lasting correction of the mutation in human lung cells, restoring cell function to levels comparable to those seen with Trikafta.

This approach utilizes prime editing, a technique developed in 2019 by David Liu's lab at the Broad Institute, where he serves as the Richard Merkin Professor and Director of the Merkin Institute of Transformative Technologies in Healthcare.

Additionally, Liu is a Professor at Harvard University and an investigator at the Howard Hughes Medical Institute. Prime editing allows for insertions, deletions, and substitutions in the genome, spanning hundreds of base pairs, with minimal unintended side effects.

We are hopeful that the use of prime editing to correct the predominant cause of cystic fibrosis might lead to a one-time, permanent treatment for this serious disease. Developing a strategy to efficiently correct this challenging mutation also provided a blueprint for optimizing prime editing to precisely correct other mutations that cause devastating disorders.”

David Liu, Richard Merkin Professor, Broad Institute

Postdoctoral researcher Alex Sousa and graduate student Colin Hemez, both from Liu’s lab, were the first authors of the study.

Gene Repair

Cystic fibrosis is caused by mutations in the CFTR gene, which impair ion channels in the cell membrane responsible for pumping chloride out of cells. There are over 2,000 known variants of the CFTR gene, with 700 causing disease. The most common mutation is a three base-pair deletion (CTT) that results in the ion channel protein misfolding and degrading.

Efforts to correct the CTT deletion in CFTR have been a longstanding objective of gene-editing therapies pursued by labs, including Liu’s. However, many attempts have proven inefficient in providing therapeutic benefits.

Some approaches, such as CRISPR/Cas9 nuclease editing, involve generating double-stranded breaks in DNA, which can lead to unintended changes in the target gene and other locations within the genome.

Prime editing, a more adaptable and controlled form of gene editing that avoids the need for double-stranded breaks, offers the potential to overcome this challenge. To enhance the efficiency of correcting the CFTR mutation, Liu’s team integrated six distinct improvements into the technology.

These enhancements included refining the guide RNAs used to direct prime editor proteins to their targets and execute desired edits, optimizing the prime editor protein itself, and making adjustments to enhance accessibility to the target site. Together, these refinements resulted in the correction of approximately 60% of CTT deletions in human lung cells and around 25% in cells directly derived from patient lungs and cultured in vitro.

This marks a significant improvement over previous methods, which corrected less than 1% of the mutation in cells. Furthermore, the new approach produced 3.5 times fewer unintended insertions and deletions per edit compared to methods utilizing the Cas9 nuclease enzyme.

The next step for researchers is to develop methods to package and deliver the prime editing machinery to the airways of mice and, eventually, humans. The team is optimistic that recent advancements, such as lipid nanoparticles that successfully reach the lungs in mice, may accelerate the translation of this approach to clinical applications.