A Unified Prime Editing Strategy for Mitigating Diverse Genetic Disorders

Advancements in genome editing have introduced a novel approach capable of addressing a substantial proportion of rare genetic conditions, potentially enhancing the scalability of therapeutic interventions for affected individuals.

This innovative prime editing methodology targets nonsense mutations, which prematurely terminate protein synthesis and underlie approximately one-third of inherited diseases. In investigations led by David Liu and colleagues, the technique demonstrated restoration of protein expression and functionality in cellular and animal models representing four distinct rare disorders. By enabling a single editing agent to serve multiple patient populations, this strategy holds promise for expediting the translation of genome-editing therapies.

Under the guidance of David Liu at the Broad Institute, a research team has engineered a genome-editing framework that may offer a singular intervention for various unrelated hereditary diseases. Traditional gene therapies typically require bespoke designs tailored to individual mutations, posing significant challenges in scalability amid the vast array of rare disorders worldwide. The newly developed system, termed PERT (prime editing-mediated readthrough of premature termination codons), leverages a uniform editing tool to maximize therapeutic reach across diverse patient cohorts.

Liu, who serves as a core institute member, Richard Merkin Professor, director of the Merkin Institute for Transformative Technologies in Healthcare at the Broad Institute, Dudley Cabot Professor of the Natural Sciences at Harvard University, and Howard Hughes Medical Institute investigator, emphasized the potential of this method to consolidate resources: a solitary editing agent could evolve into a therapeutic modality benefiting numerous individuals, thereby alleviating the extensive temporal and financial burdens associated with developing mutation-specific treatments.

PERT exploits prime editing—a precise and adaptable DNA modification platform pioneered by Liu’s laboratory in 2019—to counteract nonsense mutations, which constitute around 24% of the 200,000 pathogenic variants cataloged in the ClinVar database. These mutations disrupt normal protein assembly by introducing premature stop signals across various genes, yielding abbreviated and dysfunctional polypeptides that precipitate pathological states.

Rather than directly correcting each nonsense mutation—which would necessitate distinct editing constructs for every variant—PERT introduces an alternative modification that endows cellular machinery with the capacity to synthesize intact, functional proteins irrespective of the affected locus.

In a study detailed in Nature, the approach was evaluated in human cellular models of Batten disease, Tay-Sachs disease, and Niemann-Pick disease type C1, as well as in a murine model of Hurler syndrome. Implementation of PERT reinstated protein production and ameliorated phenotypic manifestations, exhibiting no discernible off-target modifications, perturbations in endogenous RNA or protein homeostasis, or cellular toxicity.

The initiative was primarily driven by co-first authors Sarah Pierce and Steven Erwood, postdoctoral associates in Liu’s group.

Motivated by prior efforts in DNA editing for genetic maladies, Liu’s team recognized the inefficiencies in clinical translation, including regulatory hurdles, production expenses, and economic viability for ultra-rare conditions. This realization prompted exploration of overarching mechanisms underlying multiple disorders to foster more inclusive therapeutic paradigms.

Nonsense mutations, accounting for nearly 30% of genetic pathologies, arise from aberrant stop codons (UAA, UAG, or UGA) that interrupt mRNA translation prematurely, curtailing the assembly of complete amino acid chains by transfer RNAs (tRNAs).

To circumvent this, the researchers engineered suppressor tRNAs that insert an amino acid at premature termination sites, permitting elongation of the polypeptide. Through systematic screening of myriad tRNA variants, an optimized suppressor was identified and integrated into the genome via prime editing, supplanting a dispensable endogenous tRNA.

This prime editing configuration facilitated intricate genomic alterations unattainable with alternative systems, culminating in a suppressor tRNA that enables full-length protein synthesis across disparate nonsense-mutated genes.

In cellular assays for Batten, Tay-Sachs, and Niemann-Pick disease type C1, PERT achieved enzyme restoration ranging from 20% to 70% of wild-type levels—sufficient thresholds to mitigate clinical manifestations. Similarly, in Hurler syndrome mice, approximately 6% restoration in affected tissues (brain, liver, spleen) substantially resolved lysosomal storage anomalies.

PERT exhibited negligible interference with normative translational processes, likely attributable to redundant cellular safeguards and modest suppressor tRNA abundance.

Ongoing refinements aim to enhance PERT’s efficacy across additional animal models of genetic disorders, with aspirations for eventual clinical evaluation.

This paradigm may catalyze the formulation of mutation-agnostic therapies, expanding accessibility for larger patient demographics and bolstering investment in rare disease interventions.

Pierce SE, Erwood S, et al. Prime editing-installed suppressor tRNAs for disease-agnostic genome editing. Nature. Online November 19, 2025. DOI: 10.1038/s41586-025-09732-2.

Support for this research was provided by the National Institutes of Health, the Broad Institute Chemical Biology and Therapeutics Science program, and the Howard Hughes Medical Institute.