Isocitrate dehydrogenase 1 and 2 mutations induce BCL-2 dependence in acute myeloid leukemia


Mutant isocitrate dehydrogenase (IDH) 1 and 2 proteins alter the epigenetic landscape in acute myeloid leukemia (AML) cells through production of the oncometabolite (R)-2-hydroxyglutarate (2-HG). Here we performed a large-scale RNA interference (RNAi) screen to identify genes that are synthetic lethal to the IDH1R132H mutation in AML and identified the anti-apoptotic gene BCL-2. IDH1- and IDH2-mutant primary human AML cells were more sensitive than IDH1/2 wild-type cells to ABT-199, a highly specific BCL-2 inhibitor that is currently in clinical trials for hematologic malignancies, both ex vivo and in xenotransplant models. This sensitization effect was induced by (R)-2-HG–mediated inhibition of the activity of cytochrome c oxidase (COX) in the mitochondrial electron transport chain (ETC); suppression of COX activity lowered the mitochondrial threshold to trigger apoptosis upon BCL-2 inhibition. Our findings indicate that IDH1/2 mutation status may identify patients that are likely to respond to pharmacologic BCL-2 inhibition and form the rational basis for combining agents that disrupt ETC activity with ABT-199 in future clinical studies.

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Figure 1: Identification of BCL-2 as synthetic lethal to mutant IDH1.
Figure 2: (R)-2-HG sensitizes AML cells to pharmacologic BCL-2 inhibition.
Figure 3: ABT-199 targets IDH1/2 mutant primary human AML cells.
Figure 4: (R)-2-HG–mediated inhibition of cytochrome c oxidase activity induces BCL-2 dependence.

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  1. 1

    Raimundo, N., Baysal, B.E. & Shadel, G.S. Revisiting the TCA cycle: signaling to tumor formation. Trends Mol. Med. 17, 641–649 (2011).

  2. 2

    Mardis, E.R. et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med. 361, 1058–1066 (2009).

  3. 3

    Yan, H. et al. IDH1 and IDH2 mutations in gliomas. N. Engl. J. Med. 360, 765–773 (2009).

  4. 4

    Gross, S. et al. Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations. J. Exp. Med. 207, 339–344 (2010).

  5. 5

    Parsons, D.W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807–1812 (2008).

  6. 6

    Patel, J.P. et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N. Engl. J. Med. 366, 1079–1089 (2012).

  7. 7

    Ward, P.S. et al. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 17, 225–234 (2010).

  8. 8

    Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739–744 (2009).

  9. 9

    Xu, W. et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate–dependent dioxygenases. Cancer Cell 19, 17–30 (2011).

  10. 10

    Figueroa, M.E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553–567 (2010).

  11. 11

    Lu, C. et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483, 474–478 (2012).

  12. 12

    Shlush, L.I. et al. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature 506, 328–333 (2014).

  13. 13

    Corces-Zimmerman, M.R., Hong, W.J., Weissman, I.L., Medeiros, B.C. & Majeti, R. Preleukemic mutations in human acute myeloid leukemia affect epigenetic regulators and persist in remission. Proc. Natl. Acad. Sci. USA 111, 2548–2553 (2014).

  14. 14

    Chan, S.M. & Majeti, R. Role of DNMT3A, TET2, and IDH1/2 mutations in pre-leukemic stem cells in acute myeloid leukemia. Int. J. Hematol. 98, 648–657 (2013).

  15. 15

    Jan, M. et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci. Transl. Med. 4, 149ra118 (2012).

  16. 16

    Chou, W.C. et al. The prognostic impact and stability of Isocitrate dehydrogenase 2 mutation in adult patients with acute myeloid leukemia. Leukemia 25, 246–253 (2011).

  17. 17

    Chou, W.C. et al. Distinct clinical and biologic characteristics in adult acute myeloid leukemia bearing the isocitrate dehydrogenase 1 mutation. Blood 115, 2749–2754 (2010).

  18. 18

    Wang, F. et al. Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Science 340, 622–626 (2013).

  19. 19

    Rohle, D. et al. An inhibitor of mutant IDH1 delays growth and promotes differentiation of glioma cells. Science 340, 626–630 (2013).

  20. 20

    Luo, J., Solimini, N.L. & Elledge, S.J. Principles of cancer therapy: oncogene and non-oncogene addiction. Cell 136, 823–837 (2009).

  21. 21

    Souers, A.J. et al. ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat. Med. 19, 202–208 (2013).

  22. 22

    Pan, R. et al. Selective BCL-2 inhibition by ABT-199 causes on target cell death in acute myeloid leukemia. Cancer Discov. 4, 362–375 (2014).

  23. 23

    BCL-2 inhibitor yields high response in CLL and SLL. Cancer Discov. 4, OF5 (2014).

  24. 24

    Dick, J.E. Stem cell concepts renew cancer research. Blood 112, 4793–4807 (2008).

  25. 25

    Saito, Y. et al. Induction of cell cycle entry eliminates human leukemia stem cells in a mouse model of AML. Nat. Biotechnol. 28, 275–280 (2010).

  26. 26

    Craddock, C. et al. Azacitidine fails to eradicate leukemic stem/progenitor cell populations in patients with acute myeloid leukemia and myelodysplasia. Leukemia 27, 1028–1036 (2013).

  27. 27

    Ni Chonghaile, T. & Letai, A. Mimicking the BH3 domain to kill cancer cells. Oncogene 27 (suppl. 1), S149–S157 (2008).

  28. 28

    Ryan, J. & Letai, A. BH3 profiling in whole cells by fluorimeter or FACS. Methods 61, 156–164 (2013).

  29. 29

    Danial, N.N. BAD: undertaker by night, candyman by day. Oncogene 27 (suppl. 1), S53–S70 (2008).

  30. 30

    Ploner, C., Kofler, R. & Villunger, A. Noxa: at the tip of the balance between life and death. Oncogene 27 (suppl. 1), S84–S92 (2008).

  31. 31

    Glaser, S.P. et al. Anti-apoptotic Mcl-1 is essential for the development and sustained growth of acute myeloid leukemia. Genes Dev. 26, 120–125 (2012).

  32. 32

    Shi, J. et al. An IDH1 mutation inhibits growth of glioma cells via GSH depletion and ROS generation. Neurol. Sci. 35, 839–845 (2014).

  33. 33

    Mohrenz, I.V. et al. Isocitrate dehydrogenase 1 mutant R132H sensitizes glioma cells to BCNU-induced oxidative stress and cell death. Apoptosis 18, 1416–1425 (2013).

  34. 34

    Hockenbery, D.M., Oltvai, Z.N., Yin, X.M., Milliman, C.L. & Korsmeyer, S.J. Bcl-2 functions in an antioxidant pathway to prevent apoptosis. Cell 75, 241–251 (1993).

  35. 35

    da Silva, C.G. et al. Inhibition of cytochrome c oxidase activity in rat cerebral cortex and human skeletal muscle by D-2-hydroxyglutaric acid in vitro. Biochim. Biophys. Acta 1586, 81–91 (2002).

  36. 36

    Latini, A. et al. Mitochondrial energy metabolism is markedly impaired by D-2-hydroxyglutaric acid in rat tissues. Mol. Genet. Metab. 86, 188–199 (2005).

  37. 37

    Wajne, M. et al. d-2-Hydroxyglutaric aciduria in a patient with a severe clinical phenotype and unusual MRI findings. J. Inherit. Metab. Dis. 25, 28–34 (2002).

  38. 38

    Rohlena, J., Dong, L.F. & Neuzil, J. Targeting the mitochondrial electron transport chain complexes for the induction of apoptosis and cancer treatment. Curr. Pharm. Biotechnol. 14, 377–389 (2013).

  39. 39

    Rohlena, J., Dong, L.F., Ralph, S.J. & Neuzil, J. Anticancer drugs targeting the mitochondrial electron transport chain. Antioxid. Redox Signal. 15, 2951–2974 (2011).

  40. 40

    Grassian, A.R. et al. IDH1 mutations alter citric acid cycle metabolism and increase dependence on oxidative mitochondrial metabolism. Cancer Res. 74, 3317–3331 (2014).

  41. 41

    Choi, C. et al. 2-hydroxyglutarate detection by magnetic resonance spectroscopy in IDH-mutated patients with gliomas. Nat. Med. 18, 624–629 (2012).

  42. 42

    Kölker, S. et al. NMDA receptor activation and respiratory chain complex V inhibition contribute to neurodegeneration in D-2-hydroxyglutaric aciduria. Eur. J. Neurosci. 16, 21–28 (2002).

  43. 43

    Capaldi, R.A. Structure and function of cytochrome c oxidase. Annu. Rev. Biochem. 59, 569–596 (1990).

  44. 44

    Sherman, D., Kotake, S., Ishibe, N. & Copeland, R.A. Resolution of the electronic transitions of cytochrome c oxidase: evidence for two conformational states of ferrous cytochrome α. Proc. Natl. Acad. Sci. USA 88, 4265–4269 (1991).

  45. 45

    Nicholls, P. & Hildebrandt, V. Binding of ligands and spectral shifts in cytochrome c oxidase. Biochem. J. 173, 65–72 (1978).

  46. 46

    Yoshikawa, S., Mochizuki, M., Zhao, X.J. & Caughey, W.S. Effects of overall oxidation state on infrared spectra of heme a3 cyanide in bovine heart cytochrome c oxidase. Evidence of novel mechanistic roles for CuB. J. Biol. Chem. 270, 4270–4279 (1995).

  47. 47

    Way, J.L. Cyanide intoxication and its mechanism of antagonism. Annu. Rev. Pharmacol. Toxicol. 24, 451–481 (1984).

  48. 48

    Koivunen, P. et al. Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation. Nature 483, 484–488 (2012).

  49. 49

    Li, Y., Park, J.S., Deng, J.H. & Bai, Y. Cytochrome c oxidase subunit IV is essential for assembly and respiratory function of the enzyme complex. J. Bioenerg. Biomembr. 38, 283–291 (2006).

  50. 50

    Skrtić, M. et al. Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia. Cancer Cell 20, 674–688 (2011).

  51. 51

    McClintock, D.S. et al. Bcl-2 family members and functional electron transport chain regulate oxygen deprivation-induced cell death. Mol. Cell. Biol. 22, 94–104 (2002).

  52. 52

    Saikumar, P. et al. Role of hypoxia-induced Bax translocation and cytochrome c release in reoxygenation injury. Oncogene 17, 3401–3415 (1998).

  53. 53

    Hetschko, H. et al. BH3 mimetics reactivate autophagic cell death in anoxia-resistant malignant glioma cells. Neoplasia 10, 873–885 (2008).

  54. 54

    Shimizu, S. et al. Prevention of hypoxia-induced cell death by Bcl-2 and Bcl-xL. Nature 374, 811–813 (1995).

  55. 55

    Shroff, E.H., Snyder, C. & Chandel, N.S. Role of Bcl-2 family members in anoxia induced cell death. Cell Cycle 6, 807–809 (2007).

  56. 56

    Silkjaer, T. et al. Characterization and prognostic significance of mitochondrial DNA variations in acute myeloid leukemia. Eur. J. Haematol. 90, 385–396 (2013).

  57. 57

    Larman, T.C. et al. Spectrum of somatic mitochondrial mutations in five cancers. Proc. Natl. Acad. Sci. USA 109, 14087–14091 (2012).

  58. 58

    Vo, T.T. et al. Relative mitochondrial priming of myeloblasts and normal HSCs determines chemotherapeutic success in AML. Cell 151, 344–355 (2012).

  59. 59

    Konopleva, M. et al. Mechanisms of apoptosis sensitivity and resistance to the BH3 mimetic ABT-737 in acute myeloid leukemia. Cancer Cell 10, 375–388 (2006).

  60. 60

    Lagadinou, E.D. et al. BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells. Cell Stem Cell 12, 329–341 (2013).

  61. 61

    Xu, Q., Thompson, J.E. & Carroll, M. mTOR regulates cell survival after etoposide treatment in primary AML cells. Blood 106, 4261–4268 (2005).

  62. 62

    von Bonin, M. et al. In vivo expansion of co-transplanted T cells impacts on tumor re-initiating activity of human acute myeloid leukemia in NSG mice. PLoS ONE 8, e60680 (2013).

  63. 63

    Ryan, J. & Letai, A. BH3 profiling in whole cells by fluorimeter or FACS. Methods 61, 156–164 (2013).

  64. 64

    Chen, J. et al. The Bcl-2/Bcl-XL/Bcl-w inhibitor, navitoclax, enhances the activity of chemotherapeutic agents in vitro and in vivo. Mol. Cancer Ther. 10, 2340–2349 (2011).

  65. 65

    Ward, P.S. et al. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 17, 225–234 (2010).

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We acknowledge the Hematology Division Tissue Bank and the patients for donating their samples. We acknowledge A. Giaccia for providing access to the Seahorse extracellular flux analyzer. S.M.C. is supported by a Stanford University School of Medicine Dean's Postdoctoral Fellowship and an American Society of Hematology Scholar Award. R.M. holds a Career Award for Medical Scientists from the Burroughs Wellcome Fund and is a New York Stem Cell Foundation Robertson Investigator. This research was supported by the Burroughs Wellcome Fund, the New York Stem Cell Foundation, and a National Institutes of Health grant (R01CA188055) to R.M.

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S.M.C., D.T. and R.M. designed experiments. S.M.C., D.T., M.R.C.-Z., S.X., S.R., W.-J.H. and F.Z. performed the experiments. S.M.C., B.C.M., D.A.T. and R.M. analyzed and interpreted the data. S.M.C. and R.M. wrote the manuscript.

Correspondence to Ravindra Majeti.

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Chan, S., Thomas, D., Corces-Zimmerman, M. et al. Isocitrate dehydrogenase 1 and 2 mutations induce BCL-2 dependence in acute myeloid leukemia. Nat Med 21, 178–184 (2015).

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