Strong Association between Cancer Gene Variants at Diagnosis, Especially ASXL1, and Emergence of Kinase Domain Mutation-Driven Resistance in CML Patients Despite Frontline Treatment with More Potent BCR::ABL1 Inhibitors
Authors: Shanmuganathan Naranie , Wadham Carol , Yeung David T , Shahrin Nur Hezrin , Fernandes Adelina , Maqsood Muneeza , Kok Chung Hoow , Saunders Verity A , Pagani Ilaria Stefania , Kenyon Rosalie , Lin Ming , Ross David M , Hughes Timothy P , Branford Susan 
Published: December 2024

Background
We previously demonstrated that additional genetic abnormalities (AGAs) detected at diagnosis had a negative impact on failure-free survival (FFS, as defined by ELN 2020) and molecular response for 200 frontline imatinib-treated patients (pts), despite proactive treatment intervention. The effect was evident for blood cancer related gene variants (CGVs) and aberrant structural rearrangements associated with the formation of the Philadelphia chromosome (Ph-associated). We have now sequenced the diagnosis samples of 315 pts treated with more potent frontline BCR::ABL1 inhibitors.
Aim
To determine if frontline more potent BCR::ABL1 inhibitors overcome the negative impact of AGAs detected at diagnosis.
Methods
An RNA-based targeted myeloid and lymphoid cancer-related gene next-generation sequencing method was used to detect single nucleotide variants, RNA splice altering variants, small insertions/deletions, gene fusions and focal gene deletions. Blood samples from pts enrolled in consecutive Australasian frontline CML clinical trials were investigated; 200 imatinib-treated pts (TIDEL II) and 315 of 335 pts treated with more potent BCR::ABL1 inhibitors (dasatinib: DIRECT n=76; nilotinib: PINNACLE n=59 and ENESTxtnd n=81; asciminib: ASCEND n=99). Kaplan-Meier and cumulative incidence analyses were performed to assess the effect of AGAs on FFS, kinase domain (KD) mutation acquisition (including ATP-site and myristoyl-site) and molecular response.
Results
The incidence of AGAs in the total cohort of 515 pts was 32%: cancer gene variants (CGVs 18%) and Ph-associated rearrangements (Ph-ass 18%). ASXL1 variants were most frequently detected: 41/515 pts (8%).
We previously demonstrated that AGAs at diagnosis were associated with inferior FFS and molecular response for the imatinib-treated pts. Notably, Ph-associated rearrangements were strongly associated with the acquisition of KD mutations. No differences were observed for overall or transformation-free survival. For pts treated with more potent inhibitors, the negative impact of Ph-ass for FFS, KD mutations and molecular response was overcome. However, CGVs were associated with a significantly higher rate of treatment failure (2-year FFS 76 vs 92%, P&lt;0.001), acquisition of KD mutations at 2 years (11% vs 0.3%, P&lt;0.001), and a lower rate of major molecular response (12-month MMR 63% vs 82%, P=0.002) for pts treated with more potent inhibitors with a median follow up of 24 months. These inferior responses were observed irrespective of whether pts were treated with nilotinib/dasatinib or asciminib. Notably, ASXL1 variants at diagnosis were associated with inferior 12-month MMR (55% vs 82%, P=0.033), 2-year FFS (68% vs 93%, P&lt;0.001) and higher 2-year KD mutation acquisition (27% vs &lt;0.3%, P&lt;0.001) compared to pts without CGVs. Among asciminib-treated pts with ASXL1 variants, the cumulative incidence of KD mutations at 24 months was 37%. Non-ASXL1 variants also predicted for inferior 12-month MMR.
Irrespective of whether pts with CGVs at diagnosis were treated with frontline imatinib or more potent inhibitors, there was no significant difference in 12-month MMR (53% vs 63%, P=0.34), 24-month FFS (71% vs 76%, P=0.57) or 24-month KD mutation acquisition (12% vs 11%, P=0.95).
Prognostic factors for pts treated with more potent inhibitors were examined in multivariable models. CGVs at diagnosis were the only predictors of all 3 outcomes: 12-month MMR [HR 0.54 (0.36-0.80), P=0.003], 2-year FFS [HR 3.57 (1.55-8.19), P=0.003] and KD mutations [HR 30.4 (3.75-246.9), P=0.001]. In a separate model, ASXL1 variants also predicted 12-month MMR [HR 0.47 (0.24-0.92), P=0.003], 2-year FFS [HR 1.65 (1.04-2.64), P=0.035] and KD mutations [HR 73.9 (8.8-619), P&lt;0.001]. High risk ELTS also predicted 12-month MMR [HR 0.50 (0.30-0.80), P=0.009]. No difference was observed for 24-month MR4 and overall or transformation-free survival.
Conclusion
CGVs at diagnosis were associated with inferior outcomes, even with more potent frontline inhibitor therapy. KD mutations almost exclusively developed in pts with CGVs at diagnosis. However, the negative impact of Ph-associated rearrangements observed for imatinib-treated pts was abrogated by more potent inhibitors. The data suggest a potential beneficial role for combination therapy in this cohort of pts where the risk of treatment failure driven by KD mutations is high.