Modifications to chromosome structure, such as abnormal duplication of DNA sequences, are a frequent event in cancer cells and can underpin malignant transformation. The advent of CRISPR-Cas9 technologies has unlocked our ability to study gene function in cancer at an unprecedented scale, and holds promise to discover new therapies. Nonetheless, the impact of structural rearrangements has not yet been comprehensively assessed.
To find out, Dr Emanuel Gonçalves from Dr Mathew Garnett’s group at the Wellcome Sanger Institute utilised hundreds of CRISPR-Cas9 screens together with whole-genome sequencing, DNA copy-number arrays and fluorescence in situ hybridization techniques to identify determinants of the CRISPR-Cas9 response. It has previously been shown that genes with a high number of copies have strong false-positive effects in CRISPR screens regardless of their function. In this study, Dr Gonçalves demonstrated that ploidy status (the number of each chromosome in a cell) has a strong impact on the false positive effects detected in CRISPR-Cas9 screens. Specifically, whole chromosome duplications have little to no impact, in stark contrast to genomic amplifications arising from tandem-duplications or highly structurally re-arranged regions, which have a strong non-specific loss-of-fitness effect.
This demonstrates the importance of structural rearrangements in mediating CRISPR-Cas9-induced loss-of-fitness effects, and has broad implications for the use of CRISPR-Cas9 gene-editing in cancer cells, for example when performing gene knockout screens.
