Sex-biased genome-editing effects of CRISPR-Cas9 across cancer cells dependent on p53 status

The CRISPR-Cas9 system has emerged as the dominant technology for gene editing and clinical applications. One major concern is its off-target effect after the introduction of exogenous CRISPR-Cas9 into cells. Several previous studies have investigated either Cas9 alone or CRISPR-Cas9 interactions with p53. Here, we reanalyzed previously reported data of p53-associated Cas9 activities and observed large significant sex differences between p53-wildtype and p53-mutant cells. To expand the impact of this finding, we further examined all protein-coding genes for sex-specific dependencies in a large-scale CRISPR-Cas9 screening dataset from the DepMap project. We highlighted the p53-dependent sex bias of gene knockouts (including MYC, PIK3CA, KAT2B, KDM4E, SUV39H1, FANCB, TLR7, and APC2) across cancer types and potential mechanisms (mediated by transcriptional factors, including SOX9, FOXO4, LEF1, and RYBP) underlying this phenomenon. Our results suggest that the p53-dependent sex bias may need to be considered in future clinical applications of CRISPR-Cas9, especially in cancer. [Display omitted] •Large sex-biased difference of Cas9 activities between cell lines with wildtype and mutant p53•>100 genes (including MYC and PIK3CA) showed knockout sex bias in CRISPR-Cas9 screens•Four TFs (SOX9, FOXO4, LEF1, and RYBP) responsible for sex bias effects of CRISPR-Cas9 Genetics; Molecular genetics; Cancer