Introduction: While the acquisition of mutations in the ABL1 kinase domain (KD) has been identified as a common mechanism behind tyrosine kinase inhibitor (TKI) resistance, recent genetic studies have revealed that patients with TKI resistance or intolerance frequently harbor one or more genetic alterations implicated in myeloid malignancies. This suggests that additional mutations other than ABL1 KD mutations might contribute to disease progression.
Methods: We performed targeted-capture sequencing of 127 known and putative cancer-related genes of 63 patients with CML using next-generation sequencing (NGS), including 42 patients with TKI resistance and 21 with TKI intolerance.
Results: The differences in the number of mutations between groups had no statistical significance. This could be explained in part by not all of the patients having achieved major molecular remission in the early period as expected. Overall, 66 mutations were identified in 96.8% of the patients, most frequently in the KTM2C  (31.82%), ABL1  (31.82%), FAT1  (25.76%), and ASXL1  (22.73%) genes. CUX1 , KIT , and GATA2  were associated with TKI intolerance, and two of them (CUX1 , GATA2 ) are transcription factors in which mutations were identified in 82.61% of patients with TKI intolerance. ASXL1  mutations were found more frequently in patients with ABL1  KD mutations (38.1% vs 15.21%, P=0.041). Although the number of mutations was low, pairwise interaction between mutated genes showed that ABL1  KD mutations cooccurred with SH2B3  mutations (P< 0.05). In Kaplan–Meier analyses, only TET2  mutations were associated with shorter progression-free survival (P=0.026).
Conclusion: Our data suggested that the CUX1 , KIT , and GATA2  genes may play important roles in TKI intolerance. ASXL1  and TET2  mutations may be associated with poor patient prognosis. NGS helps improving the clinical risk stratification, which enables the identification of patients with TKI resistance or intolerance in the era of TKI therapy.
Keywords: chronic myeloid leukemia, mutations, tyrosine kinase inhibitor, intolerance, resistance