Revolutionary Prime Editing Technique Reduces Gene Editing Errors for Safer Therapies

A cutting-edge genome-editing technique known as prime editing holds significant promise for treating a wide range of genetic diseases by converting faulty genes into functional ones. While this innovative method boasts remarkable potential, it does carry a minimal risk of introducing errors that could pose health risks. Researchers at MIT have recently made strides to substantially reduce the error rate associated with prime editing by employing modified versions of the proteins involved in the process. This advancement is expected to facilitate the development of gene therapy treatments for various ailments. Phillip Sharp, an esteemed Professor Emeritus at MIT and a member of MIT’s Koch Institute for Integrative Cancer Research, emphasizes that this research presents a novel approach to gene editing. It simplifies the delivery system without adding unnecessary complexity, resulting in more precise edits with fewer unintended mutations. The MIT team’s new strategy improved the error rate of prime editors significantly; from one error in seven edits to one in 101 for the most commonly used editing mode, and from one error in 122 edits to one in 543 for a high-precision mode. Robert Langer, a prominent professor at MIT, highlights the importance of developing effective therapies with minimal side effects. He believes this refined method could lead to safer and more efficient genome editing solutions for various diseases. Vikash Chauhan, the lead author of the study published in Nature, notes that the evolution of gene therapy began in the 1990s with viral delivery systems. The introduction of gene-editing technologies, including zinc finger nucleases, provided scientists with tools to correct genetic anomalies but proved to be challenging to engineer for various DNA targets. The discovery of the CRISPR genome-editing system revolutionized the field by allowing for more straightforward genome modifications. This system utilizes an enzyme called Cas9 to make precise cuts in double-stranded DNA, guided by RNA. Researchers have successfully adapted this technology to remove faulty gene sequences or introduce new ones using an RNA template. Prime editing emerged in 2019 as a more accurate CRISPR-based method that minimizes off-target effects. In recent studies, prime editors have been successfully employed to treat patients with chronic granulomatous disease (CGD), underscoring its potential for addressing numerous genetic disorders by directly correcting small mutations in cells and tissues. One notable advantage of prime editing is its ability to perform edits without creating double-stranded breaks in the target DNA. Instead, it employs a modified version of Cas9 that only cuts one strand, allowing a new sequence to be inserted without substantial risk of error. However, there remains a challenge as the newly inserted sequence must compete with the original DNA strand for incorporation into the genome, which can sometimes lead to mistakes. The current error rate ranges from one per seven edits to one per 121 edits across different modes of editing. Chauhan acknowledges that while existing technologies are superior to earlier gene therapy methods, there is always a possibility for unintended consequences. To enhance precision and minimize errors, the MIT researchers capitalized on observations made in previous studies regarding Cas9’s behavior. They discovered that certain mutated versions of Cas9 exhibited less constraint and could cut DNA at varying locations, which ultimately destabilized old DNA strands and facilitated successful incorporation of new sequences. Through identifying specific mutations in Cas9, the researchers achieved a dramatic reduction in error rates—down to one-twentieth of the original value. By combining these mutations, they developed a new version of Cas9 that further lowered the error rate, achieving an impressive reduction to one-thirty-sixth of the original rate. To further enhance accuracy, the team integrated their advanced Cas9 proteins into a prime editing system featuring an RNA binding protein that effectively stabilizes RNA template ends. The resulting editor, referred to as vPE, exhibited an outstanding error rate of just one-sixtieth of the original values—ranging from one error in 101 edits to one in 543 edits for various modes tested in mouse and human cells. The MIT team is committed to ongoing improvements in prime editor efficiency through further modifications to Cas9 and RNA templates. Additionally, they aim to develop targeted delivery methods for these editors to specific body tissues—addressing a long-standing challenge in gene therapy. The researchers are eager for other laboratories to adopt their novel prime editing techniques in various research applications. Genome editors are extensively utilized in research settings, and the therapeutic implications are exciting as they anticipate seeing how their editors will be integrated into diverse research workflows. This innovative research received funding from various esteemed organizations including the Life Sciences Research Foundation and the National Cancer Institute.