Gene editing via CRISPR/Cas9 can lead to cell toxicity and genome instability
A TP53 wild-type background can confound estimates of gene selection in genetic screens. a Boxplots showing the pooled normalized sgRNA counts per sample (essential and non-essential genes, and non-targeting sgRNAs; 15 day samples are shown). Tested using 1-tailed Mann-Whitney. *** denotes a p <2.2e-16.>Nature Communications (2022). DOI: 10.1038/s41467-022-32285-1

The development of CRISPR/Cas9 was recognized with the 2020 Nobel Prize in chemistry. The term "genetic scissors" is used to describe a tool that allows the introduction of a desired sequence into any spot of the genome. Clinical trials for the treatment of human blood disorders, some types of cancer and HIV are among the conditions that are being treated using this technique.

Dr. Fran Supek is a researcher at IRB Barcelona and ICREA. The unwanted effect is caused by the linchpin tumor suppressor protein p53 and is determined by various epigenetic factors in the surrounding region.

Researchers in the Genome Data Science lab have found 3,300 spots that show toxic effects after analyzing the most popular CRISPR library. Around 15% of the human genes contain at least one toxic editing point according to the work.

"Our work addresses an important issue with TP53-associated toxicity of Cas9 which was a matter of some controversy recently and it also provides guidelines on how to sidestep the problem" Dr. Supek says that avoiding editing in risky spots would make editing more efficient.

There are a number of positions where a specific gene can be edited. The regions of the gene that are important for regulation or have certain epigenetic markers should be avoided as a general recommendation, according to the lead researcher on the study.

Toxicity and tumorigenesis are caused by p 53.

The guardian of the genomes is p 53. It causes cells to stop dividing and can prevent them from reproducing and expanding their "mistakes" in their genes. There is a mechanism that protects against cancer and other damage to the DNA.

It is necessary to cut both DNA strands. In some cases, this manipulation can cause a p53 response, in which edited cells can be tagged as damaged and eliminated, reducing the efficiency of the process.

Cells that overcome CRISPR editing might do so because of defects in p53. The cells may be less able to detect damage to their genetic material. The risk of developing malignancies is increased by the fact that the cell populations that have unstable genomes could end up being favored by the Gene Editing procedure.

This unwanted consequence might cause a risk of genomic instability, which is highly undesirable in the context of ex-vivo CRISPR therapies, in which cells from a patient are edited in the lab and reintroduced back into the patient. Dr. Supek hopes that the study will provide some guidelines on how to design safer CRISPR reagents.

More information: Miguel M. Álvarez et al, TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening, Nature Communications (2022). DOI: 10.1038/s41467-022-32285-1 Journal information: Nature Communications