CRISPR-Cas9 genome editing causes previously underappreciated deletions and rearrangements near the target site, reports a paper published online this week in Nature Biotechnology. This finding suggests that researchers overseeing CRISPR-Cas9-based human therapies must closely monitor sequence changes in genome-edited cells.

CRISPR-Cas9 genome editing is widely hailed as a promising therapeutic strategy for diseases such as cancer, HIV, haemophilia and sickle cell disease. Cas9 works by cutting the two strands of cellular DNA at a target site within the genome. Cells repair these breaks through pathways that often introduce small DNA insertions or deletions. This process can be harnessed to inactivate disease-causing genes, or correct genetic mutations. Previously, safety concerns have mainly arisen from the low likelihood that Cas9 will cut the genome at sites other than the intended target.

Studying mouse and human laboratory cell lines, Allan Bradley and colleagues find that, in addition to the small DNA errors that are known to accompany the repair of double-strand breaks, CRISPR-Cas9 can cause large deletions and, in some cases, complex rearrangements around the target site. In mouse stem cells and human pigmented retinal epithelial cells, the authors find that these deletions can be as large as several thousand DNA bases, raising the possibility that neighboring genes or regulatory sequences could be affected and cell function could be altered.

The relevance of these findings to clinical applications of Cas9 is unknown. The experiments were not designed to detect deleterious effects of the chromosomal changes beyond knockout of the target gene - but they do highlight a potential safety concern that warrants further study.