Outcome of Patients with Chronic Myeloid Leukemia (CML) with Multiple ABL1 Kinase Domain Mutations during Tyrosine Kinase Inhibitor Therapy.
Authors: Quintas-Cardama Alfonso , Kantarjian Hagop M. , Borthakur Gautam , Faderl Stefan , Garcia-Manero Guillermo , Wierda William G. , Burton Elizabeth M , Cortes Jorge 
Published: April 2020

Abstract
BACKGROUND: BCR-ABL1 kinase domain mutations are the main mechanism of resistance to tyrosine kinase inhibitors (TKIs) by destabilizing the inactive conformation of the enzyme or by causing steric hindrance. Although mutations usually affect one amino acid residue within the ABL1 kinase domain, some patients have been shown to carry multiple ABL1 mutations (MAMs). The outcome of these patients is not well defined.
OBJECTIVES: To define the clinical characteristics and outcome of patients harboring MAMs detected by direct sequencing during TKI therapy.
RESULTS: MAMs were detected in 24 patients (5%) among a series of 502 patients assayed during TKI therapy: 22 with CML and 2 with BCR-ABL1-positive acute lymphoblastic leukemia (Ph+ALL). Median age was 57 years (range, 27–92). Median time from diagnosis to ABL1 mutation detection was 54 months (range, 8–254) and to detection of MAMs 77 months (range, 8–261). Overall, 21 different mutations affecting 15 amino acid residues were detected. The most frequent mutations were M351T (n=7), T315I (n=6), Y253H (n=6), G250E (n=6), and F317L (n=5). P-loop mutations (residues 244–255) were found in 16 (67%) patients. At the time of detection of MAMs, 13 patients were in CP, 4 in AP, and 7 in BP. Patients had received a median of 5 prior therapies (range, 2–9), including 2 TKIs (range, 1–4). Best response to TKI therapy prior to detection of MAMs (24 imatinib, 10 nilotinib, 15 dasatinib, 6 SKI- 606, 1 INNO-406, 1 MK-0457) was complete hematologic response (CHR) in 16 (67%) and cytogenetic response in 7 (29%; complete [CCyR] in 4, partial [PCyR] in 1, minor [mCyR] in 1). One patient had achieved a complete molecular response (CMR).
The median follow-up from the detection of MAMs was 10 months (range, 1–51). Twenty-two patients received a 2nd generation TKI after imatinib failure. Among 13 with MAMs prior to start of 2nd generation TKI, 7 (54%) responded (5 CHR, 1 return to CP, and 1 CCyR) for a median of 6.5 months (range, 2–31). By contrast, all 9 (100%) patients without MAMs prior to 2nd generation TKI responded (4 CHR, 3 CCyR, 1 PCyR, 1 CMR) for a median of 43 months (range, 7–48) (p=0.005). Although most patients with MAMs prior to 2nd generation TKIs start had short-lived responses to those agents, those were sustained for significant periods of time in 3 patients: one in BP harboring simultaneously M244V and M351T achieved a CHR and a mCyR with dasatinib 35mg twice daily, sustained for 8 months. A second patient acquired M351T and F359V while receiving imatinib 800mg/d in CP. Therapy with bosutinib 300mg/d rendered a mCyR that has been sustained for more than 9 months. A third patient in AP receiving imatinib 800mg/d acquired G250E and F317L mutations. Therapy with nilotinib 800mg/d resulted in CCyR for 33 months; although F317L became undetectable, CCyR was lost and later regained and has been ongoing for the last 11 months on bosutinib 500mg/d.
Four patients underwent allogeneic stem cell transplant (allo-SCT) and 2 are alive: 1 in CHR 2+ months after allo-SCT and 1 who relapsed 3 months post transplant and is currently in CCyR (BCR-ABL1/ABL1 ratio 0.55%) after 19+ months on dasatinib. Ten (42%) of the 24 patients died. The 2-year survival for patients in CP, AP, or BP at the time of detection of MAMs was 86%, 50%, and 0%, respectively.
CONCLUSION: Patients expressing more than 1 ABL1 kinase domain mutation respond poorly to TKI therapy. Responses to 2nd generation TKIs, when they occur, are mostly hematologic and typically last &lt;12 months. The long-term survival of patients with MAMs is highly influenced by CML phase.