A Common Deletion Polymorphism in the BIM Gene Contributes to Intrinsic Imatinib Resistance in Chronic Myelogenous Leukemia
Authors: Hillmer Axel M , Ng King-Pan , Chuah Charles , Juan Wen Chun , Ko Tun-Kiat , Teo Audrey S.M. , Ariyaratne Pramila N , Takahashi Naoto , Sawada Kenichi , Fei Yao , Lee Wah Heng , Huang Weijie , Allen John C , Woo Xing Yi , Nagarajan Niranjan , Kumar Vikrant , Thalamuthu Anbupalam , Poh Wan Ting , Ang Ai Leen , Mya Hae Tha , How Gee Fung , Yang Li Yi , Koh Liang Piu , Nadarajan Veera S , Chng Wee-Joo , Than Hein , Lim Lay Cheng , Goh Yeow-Tee , Nöthen Markus M , Wong Tien Y , Shahab Atif , Ruan Xiaoan , Cacheux-Rataboul Valère , Sung Wing-Kin , Ruan Yijun , Ong S. Tiong 
Published: October 2019

Abstract
Abstract 1666
The use of the tyrosine kinase inhibitor (TKI), imatinib (IM), to target the oncogenic BCR-ABL kinase has resulted in profound responses in patients with chronic phase (CP) chronic myelogenous leukemia (CML). However, a subset of patients do not respond to TKIs, and are deemed to have primary resistance. Importantly, patients with European LeukemiaNet (ELN)-defined ‘failure’ or ‘suboptimal response’ are at increased risk of poorer long-term outcomes. Little is known about mechanisms underlying primary resistance, where only a minority of patients have BCR-ABL kinase domain (KD) mutations. Interestingly, East-Asian CML patients are reported to have lower complete cytogenetic response rates compared to the West (∼50 vs 80% respectively, Au et al. 2009). We used massively parallel DNA sequencing of paired-end ditags to identify genetic factors associated with resistance in CML patient samples. We discovered a novel deletion polymorphism in the BIM gene that correlated with resistance, and which represented a common polymorphism in normal East-Asian (12.3% carriers), but not African or Caucasian (0%), populations (n=2465). BIM is a pro-apoptotic BCL2 family member, and plays a central role in CML pathophysiology. Here, BCR-ABL suppresses FoxO3a-mediated BIM transcription to maintain a survival advantage, while preventing BIM expression following BCR-ABL inhibition results in TKI resistance. Inspection of BIM gene structure suggested the polymorphism would result in mutually exclusive splicing of exon 3 (E3) vs 4 (E4), leading to decreased expression of BIM transcripts encoding the pro-apoptotic BH3 domain (found only in E4). To test this hypothesis, we constructed a minigene to measure E3 vs E4 splicing, and found the polymorphism decreased splicing to E4 over E3 by >5-fold. Importantly, primary CML cells exhibited the same phenomenon, since polymorphism-containing samples expressed lower levels of E4- vs E3-containing transcripts (p=0.008), while general BIM transcription was unaffected. Our observations suggested a novel mechanism for intrinsic TKI resistance. Here, upon IM exposure, polymorphism-containing CML cells would favor induction of E3- vs E4-containing BIM transcripts, decreased expression of BH3-containing BIM isoforms, and impaired apoptosis. To facilitate these studies, we identified a Japanese CML cell line, KCL22, which contained the polymorphism, and confirmed it had a decreased E4/E3 transcript ratio compared to cells without the polymorphism. KCL22 cells also had decreased induction of E4-containing transcripts following IM, as well as lower levels of BIMEL protein, a major BH3-containing BIM isoform. Consistent with prior reports, KCL22 cells were resistant to IM, despite effective BCR-ABL inhibition, and had impaired apoptotic signalling upon IM exposure. Importantly, and as predicted by our model, pharmacologic restoration of BH3 activity (using the BH3-mimetic drug, ABT-737) sensitized cells to IM-induced death. Next, we used zinc finger nuclease-facilitated gene targeting to precisely create the polymorphism in the BIM gene of IM-sensitive K562 CML cells. We generated subclones that were heterozygous or homozygous for the polymorphism, and confirmed a decreased E4/E3 ratio in these cells in a polymorphism-dosage-dependent manner. Polymorphism-containing cells exhibited decreased induction of E4-containing transcripts following IM exposure, as well as impaired upregulation of BIMEL protein, and diminished apoptotic cell death. As in KCL22 cells, ABT-737 enhanced the ability of IM to activate apoptosis in polymorphism-containing cells. Using an expanded East-Asian CML cohort (n=203), we found the polymorphism correlated with TKI resistance (defined as ‘failure’ or ‘suboptimal’ per ELN criteria) in CP patients treated with 400 mg IM daily (p=0.02). Further, patients with the polymorphism were more likely to have resistance in the absence of a KD mutation than those without (OR=2.24, 95% CI of 1.22–4.12). In sum, we have found an East-Asian polymorphism in BIM that is associated with intrinsic resistance to TKIs. Screening for this polymorphism may be useful in identifying patients at risk of TKI resistance; a resistance we show can be overcome by BH3 mimetics. Our findings may also apply to other cancers and proliferative disorders in which drug-sensitivity is BIM-dependent.

Disclosures:
No relevant conflicts of interest to declare.