Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer

Abstract

Tyrosine kinase inhibitors (TKIs) elicit high response rates among individuals with kinase-driven malignancies, including chronic myeloid leukemia (CML) and epidermal growth factor receptor–mutated non–small-cell lung cancer (EGFR NSCLC). However, the extent and duration of these responses are heterogeneous, suggesting the existence of genetic modifiers affecting an individual's response to TKIs. Using paired-end DNA sequencing, we discovered a common intronic deletion polymorphism in the gene encoding BCL2-like 11 (BIM). BIM is a pro-apoptotic member of the B-cell CLL/lymphoma 2 (BCL2) family of proteins, and its upregulation is required for TKIs to induce apoptosis in kinase-driven cancers. The polymorphism switched BIM splicing from exon 4 to exon 3, which resulted in expression of BIM isoforms lacking the pro-apoptotic BCL2-homology domain 3 (BH3). The polymorphism was sufficient to confer intrinsic TKI resistance in CML and EGFR NSCLC cell lines, but this resistance could be overcome with BH3-mimetic drugs. Notably, individuals with CML and EGFR NSCLC harboring the polymorphism experienced significantly inferior responses to TKIs than did individuals without the polymorphism (P = 0.02 for CML and P = 0.027 for EGFR NSCLC). Our results offer an explanation for the heterogeneity of TKI responses across individuals and suggest the possibility of personalizing therapy with BH3 mimetics to overcome BIM-polymorphism–associated TKI resistance.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: A 2,903-bp deletion polymorphism in intron 2 of BIM is present in TKI-resistant CML samples.
Figure 2: Effects of the deletion polymorphism on BIM gene function.
Figure 3: De novo generation and analysis of CML cell lines with the BIM deletion polymorphism.
Figure 4: The BIM deletion polymorphism is sufficient to cause intrinsic TKI resistance in EGFR NSCLC cell lines.
Figure 5: The BIM deletion polymorphism predicts shorter PFS in individuals with EGFR-mutant NSCLC treated with EGFR TKI therapy.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

References

  1. Jänne, P.A., Gray, N. & Settleman, J. Factors underlying sensitivity of cancers to small-molecule kinase inhibitors. Nat. Rev. Drug Discov. 8, 709–723 (2009).

    Article  Google Scholar 

  2. Carella, A.M. et al. New insights in biology and current therapeutic options for patients with chronic myelogenous leukemia. Haematologica 82, 478–495 (1997).

    CAS  Google Scholar 

  3. Schiller, J.H. et al. Comparison of four chemotherapy regimens for advanced non–small-cell lung cancer. N. Engl. J. Med. 346, 92–98 (2002).

    Article  CAS  Google Scholar 

  4. Keedy, V.L. et al. American Society of Clinical Oncology provisional clinical opinion: epidermal growth factor receptor (EGFR) mutation testing for patients with advanced non–small-cell lung cancer considering first-line EGFR tyrosine kinase inhibitor therapy. J. Clin. Oncol. 29, 2121–2127 (2011).

    Article  Google Scholar 

  5. Baccarani, M. et al. Chronic myeloid leukemia: an update of concepts and management recommendations of European LeukemiaNet. J. Clin. Oncol. 27, 6041–6051 (2009).

    Article  CAS  Google Scholar 

  6. Wang, L., McLeod, H.L. & Weinshilboum, R.M. Genomics and drug response. N. Engl. J. Med. 364, 1144–1153 (2011).

    Article  CAS  Google Scholar 

  7. Youle, R.J. & Strasser, A. The BCL-2 protein family: opposing activities that mediate cell death. Nat. Rev. Mol. Cell Biol. 9, 47–59 (2008).

    Article  CAS  Google Scholar 

  8. Kuroda, J. et al. Bim and Bad mediate imatinib-induced killing of Bcr/Abl+ leukemic cells, and resistance due to their loss is overcome by a BH3 mimetic. Proc. Natl. Acad. Sci. USA 103, 14907–14912 (2006).

    Article  CAS  Google Scholar 

  9. Aichberger, K.J. et al. Low-level expression of proapoptotic Bcl-2-interacting mediator in leukemic cells in patients with chronic myeloid leukemia: role of BCR/ABL, characterization of underlying signaling pathways, and reexpression by novel pharmacologic compounds. Cancer Res. 65, 9436–9444 (2005).

    Article  CAS  Google Scholar 

  10. Kuribara, R. et al. Roles of Bim in apoptosis of normal and Bcr-Abl–expressing hematopoietic progenitors. Mol. Cell. Biol. 24, 6172–6183 (2004).

    Article  CAS  Google Scholar 

  11. Cragg, M.S., Kuroda, J., Puthalakath, H., Huang, D.C. & Strasser, A. Gefitinib-induced killing of NSCLC cell lines expressing mutant EGFR requires BIM and can be enhanced by BH3 mimetics. PLoS Med. 4, 1681–1689 (2007).

    Article  CAS  Google Scholar 

  12. Gong, Y. et al. Induction of BIM is essential for apoptosis triggered by EGFR kinase inhibitors in mutant EGFR-dependent lung adenocarcinomas. PLoS Med. 4, e294 (2007).

    Article  Google Scholar 

  13. Costa, D.B. et al. BIM mediates EGFR tyrosine kinase inhibitor-induced apoptosis in lung cancers with oncogenic EGFR mutations. PLoS Med 4, 1669–1679 (2007).

    Article  CAS  Google Scholar 

  14. Fullwood, M.J., Wei, C.L., Liu, E.T. & Ruan, Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19, 521–532 (2009).

    Article  CAS  Google Scholar 

  15. Hillmer, A.M. et al. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 21, 665–675 (2011).

    Article  CAS  Google Scholar 

  16. Liu, J.W., Chandra, D., Tang, S.H., Chopra, D. & Tang, D.G. Identification and characterization of Bimgamma, a novel proapoptotic BH3-only splice variant of Bim. Cancer Res. 62, 2976–2981 (2002).

    CAS  Google Scholar 

  17. Adachi, M., Zhao, X. & Imai, K. Nomenclature of dynein light chain-linked BH3-only protein Bim isoforms. Cell Death Differ. 12, 192–193 (2005).

    Article  CAS  Google Scholar 

  18. Ladd, A.N. & Cooper, T.A. Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol. 3, reviews0008 (2002).

    Article  Google Scholar 

  19. Carstens, R.P., McKeehan, W.L. & Garcia-Blanco, M.A. An intronic sequence element mediates both activation and repression of rat fibroblast growth factor receptor 2 pre-mRNA splicing. Mol. Cell. Biol. 18, 2205–2217 (1998).

    Article  CAS  Google Scholar 

  20. Cheng, E.H. et al. BCL-2, BCL-X(L) sequester BH3 domain-only molecules preventing BAX- and BAK-mediated mitochondrial apoptosis. Mol. Cell 8, 705–711 (2001).

    Article  CAS  Google Scholar 

  21. Huang, D.C. & Strasser, A. BH3-only proteins-essential initiators of apoptotic cell death. Cell 103, 839–842 (2000).

    Article  CAS  Google Scholar 

  22. Kubonishi, I. & Miyoshi, I. Establishment of a Ph1 chromosome-positive cell line from chronic myelogenous leukemia in blast crisis. Int. J. Cell Cloning 1, 105–117 (1983).

    Article  CAS  Google Scholar 

  23. Mahon, F.X. et al. Selection and characterization of BCR-ABL positive cell lines with differential sensitivity to the tyrosine kinase inhibitor STI571: diverse mechanisms of resistance. Blood 96, 1070–1079 (2000).

    CAS  Google Scholar 

  24. Deininger, M.W., Goldman, J.M., Lydon, N. & Melo, J.V. The tyrosine kinase inhibitor CGP57148B selectively inhibits the growth of BCR-ABL–positive cells. Blood 90, 3691–3698 (1997).

    CAS  Google Scholar 

  25. Shah, N.P. et al. Transient potent BCR-ABL inhibition is sufficient to commit chronic myeloid leukemia cells irreversibly to apoptosis. Cancer Cell 14, 485–493 (2008).

    Article  CAS  Google Scholar 

  26. Ly, C., Arechiga, A.F., Melo, J.V., Walsh, C.M. & Ong, S.T. Bcr-Abl kinase modulates the translation regulators ribosomal protein S6 and 4E–BP1 in chronic myelogenous leukemia cells via the mammalian target of rapamycin. Cancer Res. 63, 5716–5722 (2003).

    CAS  Google Scholar 

  27. Cragg, M.S., Harris, C., Strasser, A. & Scott, C.L. Unleashing the power of inhibitors of oncogenic kinases through BH3 mimetics. Nat. Rev. Cancer 9, 321–326 (2009).

    Article  CAS  Google Scholar 

  28. La Rosée, P. & Hochhaus, A. Resistance to imatinib in chronic myelogenous leukemia: mechanisms and clinical implications. Curr. Hematol. Malig. Rep. 3, 72–79 (2008).

    Article  Google Scholar 

  29. Paez, J.G. et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 304, 1497–1500 (2004).

    Article  CAS  Google Scholar 

  30. Lynch, T.J. et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to gefitinib. N. Engl. J. Med. 350, 2129–2139 (2004).

    Article  CAS  Google Scholar 

  31. Shepherd, F.A. et al. Erlotinib in previously treated non–small-cell lung cancer. N. Engl. J. Med. 353, 123–132 (2005).

    Article  CAS  Google Scholar 

  32. Kim, E.S. et al. Gefitinib versus docetaxel in previously treated non–small-cell lung cancer (INTEREST): a randomised phase III trial. Lancet 372, 1809–1818 (2008).

    Article  CAS  Google Scholar 

  33. Park, K. & Goto, K. A review of the benefit-risk profile of gefitinib in Asian patients with advanced non-small-cell lung cancer. Curr. Med. Res. Opin. 22, 561–573 (2006).

    Article  CAS  Google Scholar 

  34. Lu, Y., Liang, K., Li, X. & Fan, Z. Responses of cancer cells with wild-type or tyrosine kinase domain–mutated epidermal growth factor receptor (EGFR) to EGFR-targeted therapy are linked to downregulation of hypoxia-inducible factor-1α. Mol. Cancer 6, 63 (2007).

    Article  Google Scholar 

  35. Machida, K. et al. Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. PLoS ONE 5, e13470 (2010).

    Article  Google Scholar 

  36. Wu, J.Y. et al. Lung cancer with epidermal growth factor receptor exon 20 mutations is associated with poor gefitinib treatment response. Clin. Cancer Res. 14, 4877–4882 (2008).

    Article  CAS  Google Scholar 

  37. Sasaki, H. et al. EGFR exon 20 insertion mutation in Japanese lung cancer. Lung Cancer 58, 324–328 (2007).

    Article  Google Scholar 

  38. Gordon, P.M. & Fisher, D.E. Role for the proapoptotic factor BIM in mediating imatinib-induced apoptosis in a c-KIT-dependent gastrointestinal stromal tumor cell line. J. Biol. Chem. 285, 14109–14114 (2010).

    Article  CAS  Google Scholar 

  39. Will, B. et al. Apoptosis induced by JAK2 inhibition is mediated by Bim and enhanced by the BH3 mimetic ABT-737 in JAK2 mutant human erythroid cells. Blood 115, 2901–2909 (2010).

    Article  CAS  Google Scholar 

  40. Soda, M. et al. Identification of the transforming EML4-ALK fusion gene in non–small-cell lung cancer. Nature 448, 561–566 (2007).

    Article  CAS  Google Scholar 

  41. Au, W.Y. et al. Chronic myeloid leukemia in Asia. Int. J. Hematol. 89, 14–23 (2009).

    Article  Google Scholar 

  42. Faber, A. et al. BIM expression in treatment naive cancers predicts responsiveness to kinase inhibitors. Cancer Discov. 1, 352–365 (2011).

    Article  CAS  Google Scholar 

  43. Cartegni, L., Chew, S.L. & Krainer, A.R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. 3, 285–298 (2002).

    Article  CAS  Google Scholar 

  44. López-Bigas, N., Audit, B., Ouzounis, C., Parra, G. & Guigo, R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 579, 1900–1903 (2005).

    Article  Google Scholar 

  45. Yano, S. et al. Hepatocyte growth factor induces gefitinib resistance of lung adenocarcinoma with epidermal growth factor receptor–activating mutations. Cancer Res. 68, 9479–9487 (2008).

    Article  CAS  Google Scholar 

  46. Bivona, T.G. et al. FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR. Nature 471, 523–526 (2011).

    Article  CAS  Google Scholar 

  47. Takeda, M. et al. De novo resistance to epidermal growth factor receptor–tyrosine kinase inhibitors in EGFR mutation-positive patients with non-small cell lung cancer. J. Thorac. Oncol. 5, 399–400 (2010).

    Article  Google Scholar 

  48. Egle, A., Harris, A.W., Bouillet, P. & Cory, S. Bim is a suppressor of Myc-induced mouse B cell leukemia. Proc. Natl. Acad. Sci. USA 101, 6164–6169 (2004).

    Article  CAS  Google Scholar 

  49. Foong, A.W. et al. Rationale and methodology for a population-based study of eye diseases in Malay people: the Singapore Malay eye study (SiMES). Ophthalmic Epidemiol. 14, 25–35 (2007).

    Article  Google Scholar 

  50. Lavanya, R. et al. Methodology of the Singapore Indian Chinese Cohort (SICC) eye study: quantifying ethnic variations in the epidemiology of eye diseases in Asians. Ophthalmic Epidemiol. 16, 325–336 (2009).

    Article  Google Scholar 

  51. Hillmer, A.M. et al. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 21, 665–675 (2011).

    Article  CAS  Google Scholar 

  52. Frazer, K.A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007).

    Article  CAS  Google Scholar 

  53. Korn, J.M. et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40, 1253–1260 (2008).

    Article  CAS  Google Scholar 

  54. Urnov, F.D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This study was supported by grants from the National Medical Research Council of Singapore and the Biomedical Research Council (BMRC) of the Agency for Science, Technology and Research (A*STAR), Singapore. Additional support was also provided by the Genome Institute of Singapore internal research funds from the BMRC and the Department of Clinical Research, Singapore General Hospital. We are grateful for insightful conversations regarding this study with G. Bourque, M. Garcia-Blanco, E. Liu, X. Roca, S. Rosen, S. Shenolikar, D. Virshup and M. Voorhoeve. We thank C.-L. Wei and H. Thoreau for management of the sequencing platform, S.T. Leong, S.C. Neo and P.S. Choi for sequencing, J. Chen and C.S. Chan for help in data processing, H.P. Lim, Y.Y. Sia and Y.H. Choy for PCR validation and A. Lim and T.H. Lim for assistance in the fluorescence in situ hybridization (FISH) analysis. We also thank M. Garcia-Blanco (Duke University), K. Itahana (Duke-NUS), A. Vazquez (Institut National de la Santé et de la Recherche Médicale U.1014, Villejuif, France and Université Paris-Sud, Paris, France) and P. Koeffler (Cedars-Sinai Medical Center, Los Angeles, California, USA and Cancer Science Institute of Singapore, Singapore) for the kind gifts of the pl-12 vector, pcDNA3-FLAG3 plasmid, BIM expression vectors and NSCLC cell lines, respectively. Finally, we are grateful to the patients and physicians at the Department of Haematology, Singapore General Hospital, the Department of Hematology-Oncology, Akita University Hospital, Japan, the Toho University Omori Medical Center, Japan, the Aichi Cancer Center, Japan, the National University Cancer Institute, National University Health System, Singapore, National Cancer Centre, Singapore and the University of Malaya Medical Centre, Kuala Lumpur, Malaysia who contributed patient material.

Author information

Authors and Affiliations

Authors

Contributions

K.P.N. and A.M.H. performed data analyses, generated the list of structural variations, validated the paired-end ditag data and wrote the first draft of the manuscript. C.T.H.C. provided CML clinical input and generated and analyzed the clinical data in Table 1. W.C.J. and T.K.K. devised and performed the experiments in Figures 2–4. C.-T.C. performed the experiments in Figures 3 and 4. J.W.J.H. performed FISH and PCR analysis on patient and normal control samples. A.S.M.T. and Y.F. constructed DNA-PET libraries for high-throughput sequencing. P.N.A., W.H.L. and W.-K.S. developed the bioinformatics pipeline for the DNA-PET analysis, N.N. contributed to the pipeline development, and X.Y.W. developed the copy number analysis. W.T.P. ran the bioinformatics pipeline. V.K. and A.T. performed BIM deletion screening in the HapMap samples, and A.T. performed the population-level genetic statistical analysis. X.R. managed the high-throughput sequencing, and A.S. managed the bioinformatics infrastructure. C.T.H.C., N.T., K.S., A.L.A., H.T.M., G.F.H., L.Y.Y., L.P.K., B.C., V.S.N., W.J.C., H.T., L.C.L. and Y.T.G. provided samples from patients with CML, as well as clinical data from the same patients. M.M.N. and T.Y.W. provided samples from normal individuals. K.P.N., J.W.J.H. and W.C.J. analyzed CML samples for the BIM deletion polymorphism. J.C.A. Jr. performed the statistical analysis of the CML clinical data. V.C.-R. performed and interpreted FISH data and provided scientific advice. S.S. compiled the clinical data and, together with J.C.A. Jr., performed the statistical analyses for Figure 5a. K.P.N., J.W.J.H., S.Z., D.P., P.T. and M.S. analyzed samples for EGFR mutations and the BIM deletion polymorphism. J.-E.S., M.-K.A., N.-M.C., Q.-S.N., D.S.W.T., K.I., Y.Y., H.M., E.H.T., R.A.S., T.M.C. and W.-T.L. provided samples from subjects with EGFR NSCLC, as well as the accompanying clinical data. Y.R. and S.T.O. designed and directed the study and analyzed data. S.T.O. wrote the final draft of the manuscript, which was reviewed by K.P.N., A.M.H., C.T.H.C., W.C.J., T.K.K., W.-T.L. and Y.R.

Corresponding authors

Correspondence to Wan-Teck Lim, Yijun Ruan or S Tiong Ong.

Ethics declarations

Competing interests

K.P.N., A.M.H., C.T.H.C., W.C.J., Y.R. and S.T.O. hold a National University of Singapore, Singapore Health Services Pte Ltd and the Agency for Science, Technology and Research, Singapore patent (BRC/P/06094/01/PCT) for a method to detect resistance to cancer therapy and guide therapy to overcome resistance.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1, 3, 4 and 7–12 and Supplementary Note (PDF 1842 kb)

Supplementary Tables 2, 5, 6 and 13

Statistics of massively parallel PET sequencing on the SOLiD platforms (XLS 261 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ng, K., Hillmer, A., Chuah, C. et al. A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nat Med 18, 521–528 (2012). https://doi.org/10.1038/nm.2713

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nm.2713

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing