Precision gene editing is essential for addressing genetic diseases by allowing targeted correction of specific mutations. A team of researchers from Korea has made a groundbreaking discovery by boosting the efficiency of homologous recombination (HR) through autophagy induction, a natural cellular process.

Dr. Hye Jin Nam's team at the Korea Research Institute of Chemical Technology (KRICT), in partnership with Professors Dong Hyun Jo and Sangsu Bae at Seoul National University College of Medicine, found that triggering autophagy through nutrient deprivation or mTOR inhibition significantly improves the effectiveness of HR-based CRISPR–Cas9 gene editing by up to threefold. This advancement has been successfully demonstrated in patient-derived cells with genetic mutations and live animal models, paving the way for potential therapeutic applications.

CRISPR–Cas9 technology functions by creating double-strand breaks (DSBs) in DNA to facilitate gene editing. However, most of these breaks are repaired through a less precise process known as nonhomologous end joining (NHEJ), leading to unintended mutations. On the other hand, HR offers a more accurate DNA repair method, but its infrequent occurrence poses challenges for precise editing.

Previous attempts to enhance HR activity have been hindered by toxicity and limited compatibility across different systems. Recognizing the potential of autophagy to favor HR over error-prone repair pathways, the research team explored its impact on gene editing. The results showed that autophagy activation led to a 1.4 to 3.1 times increase in the efficiency of HR-based editing across various target genes and DNA insert sizes.

Even alternative CRISPR versions like nickase Cas9 (nCas9) and dead Cas9 (dCas9) exhibited improved editing performance under autophagic conditions, indicating the broad applicability of this strategy. Further analysis revealed that autophagy enhances the accumulation of HR-associated DNA repair proteins within the Cas9 complex, potentially guiding repair activities towards more precise outcomes.

Experiments involving patient-derived cells with mutations in the MPZL2 gene, associated with hearing loss, showed up to a threefold increase in the corrected gene's expression. Testing the approach in mouse models further confirmed its efficacy, with autophagy induction leading to a threefold enhancement in editing efficiency in the mouse retina.

This study is the first to showcase how autophagy can improve the accuracy of genome editing in both human cells and animal models. These findings open up new possibilities for gene therapies, offering a safer and more efficient method for accurately correcting faulty genetic sequences.

Dr. Nam emphasized, "Utilizing autophagy to enhance homologous recombination represents a groundbreaking approach to address key limitations in current gene editing technologies." KRICT President Young-Kuk Lee added, "This achievement significantly enhances both the efficiency and safety of genome editing, marking a significant milestone in the progress of precision therapeutics."

The research was published in Nucleic Acids Research (IF: 16.7) in April 2025.