Kyoto University Develops a Comprehensive Framework to Improve CRISPR Safety Evaluation

Researchers led by Professor Akitsu Hotta from the Center for iPS Cell Research and Application (CIRA), Kyoto University, have developed a comprehensive framework to evaluate the safety of CRISPR-Cas9 genome editing therapies. The approach combines computer-based predictions, laboratory validation, and whole-genome analysis to identify both intended and unintended genetic changes.

The team focused on CRISPR delivered through lipid nanoparticles (LNPs) and assessed its performance compared with adeno-associated virus (AAV) delivery. In a mouse model, LNPs produced fewer unwanted DNA insertions and showed no detectable integration of delivery-related genetic material at the target site. The researchers also evaluated 13 commonly used computational tools for predicting off-target effects and found that while many detected potential sites, they often generated large numbers of false positives.

Using whole-genome sequencing and a newly developed “indel cluster” method, the researchers identified only a small number of high-confidence off-target sites across the genome. The findings revealed limited off-target activity in genes and minimal functional consequences, suggesting that LNP-based CRISPR delivery is generally safe. The team concluded that integrating multiple assessment methods offers a practical and scalable strategy to improve the safety evaluation of future genome-editing therapies.

For more information, read the article from CIRA, Kyoto University.