Comprehensive resistance profiling of ABL1 variants against various kinase inhibitors for CML treatment

Variants of uncertain significance (VUSs) hinder the clinical application of genetic information, particularly for precision medicine. A prime example is chronic myeloid leukemia (CML); there are four generations of tyrosine kinase inhibitors (TKIs), but predicting the resistance profiles of these TKIs for a given patient with ABL1 mutations is sometimes difficult, especially when the mutations are not covered by clinical guidelines. Here, we used prime editing to generate 97% (2,802/2,892) of all possible single nucleotide variants in the sequence encoding the ABL1 kinase domain, which encode 98% (1,954/1,998) of all possible corresponding single amino acid variants (SAAVs), and evaluated their effects on resistance to five TKIs (imatinib, nilotinib, bosutinib, ponatinib, and asciminib), covering all four TKI generations, in CML-relevant K562 cells. We identified 361 novel pairs of resistance-conferring SAAVs and the corresponding TKIs. Our comprehensive resistance map will complement clinical guidelines in drug selection for CML patients based on ABL1 mutations, facilitating precision medicine.

意义未明变异（Variants of Uncertain Significance, VUSs）阻碍了遗传信息的临床应用，尤其对精准医学领域而言。慢性髓系白血病（chronic myeloid leukemia, CML）便是典型例证：当前临床已有四代酪氨酸激酶抑制剂（tyrosine kinase inhibitors, TKIs），但针对携带ABL1突变的患者预测这些TKIs的耐药谱时常颇具难度，尤其是当突变未被临床指南覆盖时。本研究利用先导编辑（prime editing）技术，构建了ABL1激酶结构域编码序列中97%（2802/2892）的所有可能单核苷酸变异，这些变异对应编码了98%（1954/1998）的潜在单氨基酸变异（single amino acid variants, SAAVs）；随后在与CML相关的K562细胞中，评估了这些变异对五种TKIs（伊马替尼、尼洛替尼、博舒替尼、普纳替尼及阿西米尼）的耐药影响，覆盖了全部四代TKIs。本研究共鉴定出361组全新的耐药相关单氨基酸变异与对应酪氨酸激酶抑制剂配对组合。我们构建的全面耐药图谱可作为临床指南的有益补充，用于基于ABL1突变的CML患者的用药选择，助力精准医学的发展。