The BIM Deletion Polymorphism: A Paradigm Of a Permissive Interaction Between Germline and Acquired TKI Resistance Factors In Chronic Myeloid Leukemia
Authors: Ko Tun Kiat , Chuah Charles , Huang John W.J. , Ng King-Pan , Ong S. Tiong 
Published: October 2019

Abstract
Germline polymorphisms and tumor-specific genetic mutations together contribute to the behavior of human cancers, including the response to therapy. However, few specific models allow for the detailed study of how inherited and acquired genetic factors interact to cause clinical drug resistance, nor how their interaction can be prevented or overcome. We recently reported a germline deletion polymorphism in the BIM gene that was sufficient to mediate intrinsic resistance to targeted therapies in cancer, including the example of imatinib in chronic myeloid leukemia (CML) (Ng et al. Nature Medicine, 2012). Mechanistically, the deletion polymorphism led to the generation of BIM splice forms that lacked the pro-apoptotic BH3 domain, and that were incapable of activating apoptosis in response to targeted therapy. Clinically, we found that CML patients with the deletion polymorphism experienced inferior responses to imatinib. Furthermore, within the cohort of resistant patients harboring the BIM deletion polymorphism, we found that the majority developed cross-resistance to second or third generation TKI (nilotinib, dasatinib, and bosutinib), and that TKI resistance-conferring BCR-ABL kinase domain mutations were less frequent in patients with the BIM deletion polymorphism than those without. These observations suggested that the BIM deletion polymorphism cooperates with both BCR-ABL-independent and -dependent TKI resistance mechanisms to produce broad resistance to TKI.
We generated K562 cells with and without the BIM deletion polymorphism that were resistant to imatinib by using the method described by Mahon et al (Blood, 2000). We found that deletion-containing cells exhibited 3- to 4-fold increased viability as compared to wildtype cells, and this was due to reduced apoptosis in the deletion-containing cells. We then compared the panel of wildtype and deletion-containing cells for the development of known TKI resistance mechanisms. The table below summarizes our findings. Importantly, we also found that, in a number of cells, both ERK and LYN activation occurred independently of BCR-ABL.Known TKI resistance mechanismWildtypeHeterozygous for BIM deletion polymorphismHomozygous for BIM deletion polymorphismSomatic mutation in BCR-ABL kinase domain--G250EBCR-ABL gene amplification--+++LYN activation+++++ERK activation+++-++
Next, we tested the ability of second-generation TKI, including dasatinib and nilotinib, to overcome resistance induced by long-term culture. We also determined if the addition of ABT-737, a BH3-mimetic, to the TKI could overcome resistance in our cell lines. First, we found that prolonged incubation with imatinib induced cross-resistance to both nilotinib and dasatinib, a result that reproduced our observation in patients with the BIM deletion polymorphism. Next, we found that a combination of second generation TKI, especially dasatinib, and ABT-737 induced maximal cell death in cells with the BIM deletion polymorphism. Based on the information generated from our cell lines, we evaluated the viability of TKI-resistant primary CML cells when treated with TKI with and without ABT-737. In TKI-resistant primary CML cells, regardless of their BIM deletion status, maximal reduction in cell viability was observed when both TKI and ABT-737 were used.
We conclude that: 1. The BIM deletion polymorphism is permissive for the acquisition of somatic events that mediate both BCR-ABL-dependent and -independent mechanisms of TKI resistance. 2. The permissive action of the BIM deletion polymorphism is associated with reduced apoptosis, and likely accounts for the ability of BIM deletion polymorphism-containing CML cells to acquire secondary resistance-conferring events. 3. The combined use of TKI with ABT-737 represents a potential therapeutic strategy to overcome TKI resistance in CML patients with and without the BIM deletion polymorphism. 4. In our cell line system, dasatinib with ABT-737 induced maximum cell death. Finally, our results demonstrate that germline and acquired resistance factors can interact to produce resistance to targeted therapies in cancer, and that cell line systems allow us to both elucidate these mechanisms as well as devise therapeutic strategies to overcome such resistance.

Disclosures:
Chuah: Novartis: Honoraria; Bristol-Myers Squibb: Honoraria.