Abstract 1911: A common BIM polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
Authors: Ong S. Tiong , Ng King Pan , Hillmer Axel M. , Chuah Charles T.H. , Juan Wen Chun , Ko Tun-Kiat , Teo Audrey S.M. , Ariyaratne Pramila N. , Takahashi Naoto , Sawada Kenichi , Fei Yao , Lee Wah Heng , Huang John W.J. , Allen John C. , Woo Xing Yi , Nagarajan Niranjan , Kumar Vikrant , Thalamuthu Anbupalam , Poh Wan Ting , Yang Li Yi , Koh Liang Piu , Nadarajan Veera S. , Chng Wee Joo , Than Hein , Lim Lay Cheng , Goh Yeow Tee , Soh Sheila , Zhang Shenli , Poh Dianne , Tan Patrick , Seet Ju-Ee , Ang Mei-Kim , Chau Noan-Minh , Ng Quan-Sing , Tan Daniel S.W. , Nöthen Markus M. , Wong Tien Y. , Shahab Atif , Ruan Xiaoan , Cacheux-Rataboul Valère , Sung Wing-Kin , Soda Manabu , Isobe Kazutoshi , Tan Eng Huat , Yatabe Yasushi , Mano Hiroyuki , Soo Ross A. , Chin Tan Min , Lim Wan-Teck , Ruan Yijun 
Published: August 2012

Abstract
The use of tyrosine kinase inhibitors (TKI) to target oncogenic kinases has led to remarkable responses in patients with chronic myeloid leukemia (CML) and EGFR-mutated non-small cell lung cancer (EGFR NSCLC). However, a significant subset of patients have a minimal or very brief response. It has been suggested that germline polymorphisms may account for this upfront TKI resistance, and that identifying such polymorphisms will allow personalization of targeted therapy to achieve optimal responses in patients. Using paired-end DNA sequencing, we discovered a common (12.3% carrier rate) deletion polymorphism in intron 2 of the BIM gene. BIM is a pro-apoptotic member of the BCL2 family of proteins, and is required for TKIs to induce apoptosis in many cancers. We investigated the effects of the polymorphism on BIM function and TKI resistance in CML and EGFR NSCLC. Inspection of BIM gene structure suggested the polymorphism would result in mutually exclusive splicing of exon 3 (E3) and 4 (E4). Importantly, such an event is predicted to affect TKI sensitivity, since the pro-apoptotic BH3 domain is found only in E4. Using minigenes, we confirmed the deletion favored splicing of E3 over E4 by 5-fold (p=0.008), and that the deletion contained a cis-acting splicing suppressor. Next, using Zn finger nuclease-editing, we recreated the polymorphism in TKI sensitive CML (K562) and EGFR NSCLC (PC9) cell lines. Polymorphism-containing subclones had increased E3/E4 transcript ratios, decreased expression of BH3-containing BIM protein and defective apoptotic signaling, and were intrinsically TKI resistant. Importantly, while manipulation of E3-containing transcript levels did not alter the resistance phenotype, pharmacologic restoration of BH3 function (using a BH3 mimetic ABT-737) restored apoptotic signaling as well as TKI-sensitivity. Finally, we determined if the polymorphism predicted for inferior clinical responses in TKI-treated CML and EGFR NSCLC patients. In 203 CML patients, the polymorphism predicted inferior imatinib responses (defined by EuropeanLeukemiaNet criteria) among those with the polymorphism vs those without (odds ratio=2.94, p=0.02, 95% CI 1.17-7.43). In 141 EGFR NSCLC patients, the polymorphism predicted a shorter PFS of 6.6 vs 11.9 months (p=0.0027), and was independently prognostic for poorer PFS (hazard ratio=2.14, p=0.0026, 95% CI 1.30-3.50). In summary, by altering BIM splicing, the BIM polymorphism is sufficient to cause intrinsic TKI resistance in vitro, and predicts inferior TKI responses in patients. Upfront testing of CML and EGFR NSCLC patients for the BIM polymorphism may identify individuals at risk for developing clinical TKI resistance. Our results also offer an explanation for the heterogeneity of TKI responses among CML and EGFR NSCLC patients, and suggest the possibility of personalizing therapy with BH3 mimetics to improve TKI responses.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1911. doi:1538-7445.AM2012-1911