Warning: CRISPR therapeutics can damage the genome

Tel Aviv University researchers have identified risks in the use of CRISPR therapeutics — a Nobel Prize-winning method of editing DNA. Investigating the impact of this technology on T cells, the researchers detected a significant loss of genetic material in some treated cells, which could lead to destabilisation of the genome.

CRISPR involves cleaving DNA sequences at certain locations in order to delete unwanted segments, or alternately repair or insert beneficial segments. Developed about a decade ago, the technology has already proved effective in treating a range of diseases.

The first approved clinical trial to use CRISPR was conducted in 2020 at the University of Pennsylvania. Taking T cells (a type of white blood cell) from a donor, they expressed an engineered receptor targeting cancer cells, while using CRISPR to destroy genes coding for the original receptor — which otherwise might have caused the T cells to attack cells in the recipient’s body. The Tel Aviv researchers wondered whether the potential benefits of CRISPR therapeutics might be offset by risks resulting from the cleavage itself, assuming that broken DNA is not always able to recover.

“The genome in our cells often breaks due to natural causes, but usually it is able to repair itself, with no harm done,” explained Tel Aviv’s Dr Uri Ben-David and research associate Eli Reuveni. “Still, sometimes a certain chromosome is unable to bounce back, and large sections, or even the entire chromosome, are lost. Such chromosomal disruptions can destabilise the genome, and we often see this in cancer cells. Thus, CRISPR therapeutics, in which DNA is cleaved intentionally as a means for treating cancer, might, in extreme scenarios, actually promote malignancies.”

The researchers repeated the 2020 experiment, cleaving the T cells’ genome in exactly the same locations — chromosomes 2, 7 and 14 (of the human genome’s 23 pairs of chromosomes). Using single-cell RNA sequencing, they analysed each cell separately and measured the expression levels of each chromosome in every cell, with their results published in Nature Biotechnology. A significant loss of genetic material was detected in some of the cells.

For example, when Chromosome 14 had been cleaved, about 5% of the cells showed little or no expression of this chromosome. When all chromosomes were cleaved simultaneously, the damage increased, with 9%, 10% and 3% of the cells unable to repair the break in chromosomes 14, 7 and 2 respectively. The three chromosomes did differ, however, in the extent of the damage they sustained.

“Single-cell RNA sequencing and computational analyses enabled us to obtain very precise results,” said Dr Asaf Madi and his student, Ella Goldschmidt. “We found that the cause for the difference in damage was the exact place of the cleaving on each of the three chromosomes. Altogether, our findings indicate that over 9% of the T cells genetically edited with the CRISPR technique had lost a significant amount of genetic material. Such loss can lead to destabilisation of the genome, which might promote cancer.”

Based on their findings, the researchers caution that extra care should be taken when using CRISPR therapeutics, while recognising that it can provide substantial advantages. They also propose alternative, less risky, methods for specific medical procedures, and recommend further research into two kinds of potential solutions: reducing the production of damaged cells, or identifying damaged cells and removing them before the material is administered to the patient.

Image credit: ©stock.adobe.com/au/catalin

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