Autophagy boosts precision in gene editing

Precision gene editing is crucial for treating genetic diseases, as it enables targeted correction of specific mutations. A Korean research team has become the first in the world to significantly enhance the low efficiency of a key genome editing mechanism-known as homologous recombination (HR)-by inducing autophagy, a natual process whthin cells.

Dr. Hye Jin Nam's team at the Korea Research Institute of Chemical Technology (KRICT), in collaboration with Professors Dong Hyun Jo and Sangsu Bae at Seoul National University College of Medicine, found that autophagy induction via nutrient deprivation or mTOR inhibition markedly enhances the efficiency of HR-based CRISPR–Cas9 gene editing up to threefold. The technique was also successfully validated in patient-derived cells carrying genetic mutations and in live animal models, marking a major step toward applying this method in therapeutic settings.

CRISPR–Cas9 technology works by creating double-strand breaks (DSBs) in DNA to enable gene editing. However, most of these breaks are repaired through an error-prone process called nonhomologous end joining (NHEJ), which often introduces unintended mutations. In contrast, homologous recombination (HR) is a more accurate form of DNA repair-but it occurs infrequently, making precision editing difficult. Previous efforts to enhance HR activity, such as modulating the cell cycle or inhibiting NHEJ, have been limited by toxicity and poor compatibility across diverse systems.

Suspecting that autophagy might promote the use of HR over error-prone repair pathways, the research team investigated its effect on gene editing. When autophagy was triggered-either by nutrient starvation or treatment with mTOR inhibitors-the efficiency of HR-based editing increased by 1.4 to 3.1 times across various target genes and DNA insert sizes. In contrast, cells unable to undergo autophagy showed no such improvement, highlighting autophagy's essential role in promoting precise genome repair.

Even alternate versions of CRISPR, such as nickase Cas9 (nCas9) and dead Cas9 (dCas9), showed improved editing performance under autophagic conditions. This suggests that the strategy is widely applicable across different gene editing platforms. Further analysis revealed that autophagy enhanced the accumulation of HR-associated DNA repair proteins within the Cas9 complex, which may help direct repair activity toward more precise outcomes.

In experiments using patient-derived cells carrying mutations in the MPZL2 gene-linked to hearing loss-the method led to increased expression of the corrected gene up to three-fold. The research team also tested the approach in mouse models. When gene editing was performed in the mouse retina, autophagy induction led to about a threefold improvement in editing efficiency. This confirms that the strategy works not only in cultured cells but also in living organisms.

This study is the first to demonstrate that autophagy can enhance the accuracy of genome editing both in human cells and in animal models. The findings suggest a new path forward for gene therapies, offering a safer and more effective way to precisely rewrite faulty genetic sequences.

Leveraging autophagy to enhance homologous recombination represents a breakthrough strategy to overcome key limitations in current gene editing technologies."

Dr. Hye Jin Nam, Korea Research Institute of Chemical Technology

KRICT President Young-Kuk Lee added, "This achievement significantly improves both the efficiency and safety of genome editing and marks an important milestone in the advancement of precision therapeutics."

This work was published in Nucleic Acids Research (IF: 16.7) in April 2025.