Mutations of all sorts—deletions, amplifications, single nucleotide changes—initiate cancer and drive its evolution. But it has not been possible to swiftly and comprehensively assess the different biological effects of the thousands of distinct mutations found in cancer genomes. Researchers led by Ludwig MIT’s Francisco J. Sánchez-Rivera reported in a March publication in Nature Biotechnology their adaptation of a type of CRISPR genome-editing system known as prime editing (PE) to do just that. PE, which employs a PE guide RNA (pegRNA) to target and directly edit the genome at specific sites, can be used to generate any type of small mutation without interfering with surrounding sequences. Francisco and his colleagues devised a method to measure the efficiency and accuracy of each pegRNA used for editing and integrated it with experimental and computational methods to interrogate the cellular effects of thousands of mutations at once. They applied their system, which could be a useful tool for precision medicine, to examine the effects of more than 1,000 mutations in the tumor suppressor p53 that are frequently observed in cancer genomes. Aside from validating their methods, Francisco and his colleagues showed that some p53 mutations are far more pro-cancerous than previous studies relying on gene overexpression had suggested—demonstrating the value of examining mutations in the more physiological context permitted by PE.
High-throughput evaluation of genetic variants with prime editing sensor libraries
Nature Biotechnology, 2024 March 12