Pattern and Evolution of BCR-ABL Kinase Domain Mutations in Patients with Philadelphia-Positive Acute Lymphoblastic Leukemia (Ph+ALL) Developing Resistance to Imatinib.
Authors: Pfeifer Heike , Wassmann Barbara , Pavlova Anni , Mueller Martin , Wunderle Lydia , Brueck Patrick , Oldenburg Johannes , Hochhaus Andreas , Gschaidmeier Harald , Hoelzer Dieter , Ottmann Oliver G. 
Published: April 2020

Abstract
Background: Mutations in the kinase domain (KD) of BCR-ABL are the predominant cause of acquired imatinib (IM) resistance in patients with CML and have also been detected at relapse in patients with advanced Ph+ ALL. The contribution of various known KD mutations to IM resistance of advanced or newly diagnosed Ph+ALL receiving different IM-based treatments has not been determined, however. We therefore studied the mutation frequency at relapse in 94 patients receiving IM-based therapy for advanced or newly diagnosed Ph+ALL or CML in lyBC using cDNA sequencing. To further investigate the frequency, distribution and prognostic significance of ABL mutations, we retrospectively analyzed bone marrow (BM) samples that had been collected pre-treatment and serially throughout IM therapy from patients by using RT-PCR based denaturing HPLC-assay.
Methods: 94 pts. enrolled in a) the initial phase II trials of IM monotherapy for advanced Ph+ALL(n=57) and CML lyBC (n=9) or b) in a GMALL study of elderly pts. (&gt;55 yrs.) with de novo Ph+ALL receiving IM in combination with chemotherapy (n=17) or c) in a GMALL study of younger pts. with de novo Ph+ALL receiving IM-based induction therapy (n=11) were screened at the time of relapse. BM and/or PB samples collected at the time of relapse were analyzed by direct sequencing of the abl KD. Samples collected pre-treatment and serially throughout IM were analyzed by denaturing HPLC.
Results: Mutations were detected in 52 of 94 pts (55%). In the phase II trials of IM monotherapy, 32/57 Ph+ALL-pts. (56%) and 4/9 (44%) pts. with lyBC developed a mutation. Mutation frequency in elderly Ph+ALL pts. with de novo Ph+ALL was 82% (14/17). The overall frequencies of these mutations were: Y253F/H (n=12), Q252H (n=6), E255K (n=21), G250E (n=5), M248V(n=3) in the P-loop region and T315I (n=11) - a mutation in direct contact with IM. Only 1 mutation in the catalytic domain (F359V) and 3 mutations in the activation loop (H396R (n=2), L384M) were observed. In 13 pts. (25%) more than 1 mutation was detected. Comparison of patients with p190 bcrabl and p210 bcrabl revealed no significant difference in either the frequency or profile mutations. In pts. harbouring the T315I mutation, it was possible to detect the mutation upfront with dHPLC (sensitivity 0.5%).
Summary: In Ph+ALL clinical resistance to IM is associated with a high frequency of abl KD mutations, with conspicuous predominance of mutations located in the P-loop, most of which confer high level resistance to IM. In addition in 20% of pts. The T315I mutation was detected which confers absolute resistance to IM as well as to 2nd generation ABL TK inhibitors in clinical development. The mutation profile is similar in pts. with advanced leukemia treated with IM monotherapy and in pts. with de novo Ph+ALL receiving IM in combination with chemotherapy.