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Updated: Oct 5, 2025

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
Published on: November 1, 2024
ON-Target Adverse Events of CRISPR-Cas9 Nuclease: More Chaotic than Expected
Julian Boutin1,2,3, David Cappellen1,2,4, Juliette Rosier1,2
1Bordeaux University, Bordeaux, France.
Abstract:
CRISPR-Cas9 is a highly promising technology for clinical development. However, this powerful tool can induce adverse genomic events. The off-target genotoxicity is well described, predictable, detectable, and resolved by the use of new generations of Cas9 nucleases with high fidelity. In contrast, the ON-target genotoxicity due to a DNA double-strand break at the targeted locus is still underestimated. Here, we review several genomic outcomes induced by CRISPR-Cas9 from the insertion/deletion of a few bases to megabase-scale rearrangements. We hope to highlight this barely detectable complex safety concern to promote further studies to understand the mechanisms better, to detect these unwanted events, and to prevent them for the safety management of future CRISPR-Cas9 clinical trials.
Insights
CRISPR-Cas9 gene editing can cause unintended DNA damage at the target site, which is underestimated. Further research is needed to understand and prevent these on-target genotoxic events for safe clinical applications.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- CRISPR-Cas9 is a powerful gene editing tool with significant clinical potential.
- While off-target effects are understood, on-target genotoxicity remains a concern.
- Genomic alterations at the targeted locus can occur following CRISPR-Cas9 activity.
Purpose of the Study:
- To review the spectrum of genomic outcomes induced by CRISPR-Cas9 at the on-target locus.
- To highlight the underappreciated safety concern of on-target genotoxicity.
- To emphasize the need for better detection and prevention strategies for CRISPR-Cas9 clinical trials.
Main Methods:
- Literature review of studies investigating CRISPR-Cas9 induced genomic alterations.
- Analysis of reported on-target genotoxic events, including insertions, deletions, and large-scale rearrangements.
- Discussion of the implications for CRISPR-Cas9 safety and clinical translation.
Main Results:
- CRISPR-Cas9 can lead to a range of on-target genomic events, from small indels to megabase-scale rearrangements.
- These on-target genotoxic effects are complex and often difficult to detect.
- Current high-fidelity Cas9 variants primarily address off-target, not on-target, genotoxicity.
Conclusions:
- On-target genotoxicity is a critical, underestimated safety issue for CRISPR-Cas9 therapies.
- Understanding the mechanisms underlying these events is crucial for developing robust safety protocols.
- Further research and improved detection methods are essential for the safe clinical deployment of CRISPR-Cas9 technology.
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