Depending on the targeted spot of the human genome, CRISPR gene editing can give rise to cell toxicity and genomic instability, Barcelona Institute for Research in Biomedicine scientists report1. CRISPR/Cas9 is a gene editing technique whose developers were the subject of the 2020 Nobel Prize in Chemistry.
Led by researcher Dr. Fran Supek, the team of researchers used algorithms provided by MAGeCK-VISPR, as well as the R package pROC, to analyze the most popular CRISPR library designed for human cells. They identified 3,300 targeted spots that demonstrate strong toxic effects.
In addition, around 15% of the human genes contained at least one toxic editing point.
The regions of the gene that are important for regulation or have certain epigenetic markers are the ones most likely to trigger the p53 response and should, therefore, be avoided as a general recommendation,"
said Dr. Miguel-Martin Álvarez, one of the study’s lead researchers.
p53 - Guardian of the Genome
p53 is a protein known as the guardian of the genome. It detects DNA damage and leads the cells to stop dividing and can cause programmed cell death.
In this way, p53 prevents cells from reproducing and expanding the “mistakes” in their DNA. p53 underlies a natural protection mechanism against cancer and other DNA damage-related complications.
CRISPR gene editing often calls for cutting both DNA strands. In some cases, this manipulation can trigger a p53 response, in which edited cells can be “tagged” as damaged and are then eliminated, thus reducing the efficiency of the gene editing process.
CRISPR Unstable Genomes
However, the main complication regarding p53 and gene editing is that cells that overcome CRISPR editing might do so precisely because of defective p53 functioning. In other words, these cells may be less able to detect DNA damage and/or tag cells for programmed death.
As a result, the gene editing procedure could end up favoring cell populations that have unstable genomes, meaning they are prone to accumulating further mutations, and so raising the risk of developing malignancies.
This unwanted consequence might incur 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. We hope that our study provides some guidelines on how to design safer CRISPR reagents, and encourages further research into this issue,
concluded Dr. Supek.
Álvarez, M.M., Biayna, J. & Supek, F. TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening. Nat Commun 13, 4520 (2022) ↩︎