Comprehensive resistance profiling of chronic myeloid leukaemia associated ABL1 variants against five tyrosine kinase inhibitors using prime editing.

There are four generations of tyrosine kinase inhibitors (TKIs) that target BCR-ABL1 mutations, a fusion oncogene, in chronic myeloid leukaemia, but predicting the resistance profiles of these TKIs for patients with ABL1 mutations is sometimes difficult, especially when the mutations are not included by clinical guidelines. Here we use prime editing to generate 97% (2,802/2,892) of all possible single-nucleotide variants in the sequence encoding the ABL1 kinase domain, which covers 98% (1,954/1,998) of all possible corresponding single amino acid variants. We evaluated their effects on resistance to five TKIs (imatinib, nilotinib, bosutinib, ponatinib and asciminib), spanning all four TKI generations by using K562 cells. We identified 361 pairs of resistance-conferring single amino acid variants and the corresponding TKIs. Our comprehensive resistance map will complement clinical guidelines in drug selection for patients with chronic myeloid leukaemia based on ABL1 mutations, facilitating precision medicine.