Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors


Acute myeloid leukemia (AML) is mostly driven by oncogenic transcription factors, which have been classically viewed as intractable targets using small-molecule inhibitor approaches. Here we demonstrate that AML driven by repressive transcription factors, including AML1-ETO (encoded by the fusion oncogene RUNX1-RUNX1T1) and PML-RARα fusion oncoproteins (encoded by PML-RARA) are extremely sensitive to poly (ADP-ribose) polymerase (PARP) inhibition, in part owing to their suppressed expression of key homologous recombination (HR)-associated genes and their compromised DNA-damage response (DDR). In contrast, leukemia driven by mixed-lineage leukemia (MLL, encoded by KMT2A) fusions with dominant transactivation ability is proficient in DDR and insensitive to PARP inhibition. Intriguingly, genetic or pharmacological inhibition of an MLL downstream target, HOXA9, which activates expression of various HR-associated genes, impairs DDR and sensitizes MLL leukemia to PARP inhibitors (PARPis). Conversely, HOXA9 overexpression confers PARPi resistance to AML1-ETO and PML-RARα transformed cells. Together, these studies describe a potential utility of PARPi-induced synthetic lethality for leukemia treatment and reveal a novel molecular mechanism governing PARPi sensitivity in AML.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: PARPi targets AML1-ETO– and PML-RARα–transformed leukemic cells in vitro and in vivo.
Figure 2: PARPis induce differentiation, senescence, and apoptosis of AML1-ETO– and PML-RARα–transformed leukemic cells.
Figure 3: AML1-ETO– and PML-RARα–transformed cells show a defect in the HR pathway and accumulate DNA damage in response to PARPi treatment.
Figure 4: HOXA9 modulates sensitivity to PARPi.
Figure 5: HOXA9 modulates PARPi sensitivity.
Figure 6: Combined PARPi and GSK3i treatment impairs in vivo survival of MLL leukemia cells.

Accession codes


Gene Expression Omnibus


  1. 1

    Krishnakumar, R. & Kraus, W.L. The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol. Cell 39, 8–24 (2010).

  2. 2

    McLornan, D.P., List, A. & Mufti, G.J. Applying synthetic lethality for the selective targeting of cancer. N. Engl. J. Med. 371, 1725–1735 (2014).

  3. 3

    De Lorenzo, S.B., Patel, A.G., Hurley, R.M. & Kaufmann, S.H. The elephant and the blind men: making sense of PARP inhibitors in homologous recombination-deficient tumor cells. Front. Oncol. 3, 228 (2013).

  4. 4

    Helleday, T. The underlying mechanism for the PARP and BRCA synthetic lethality: clearing up the misunderstandings. Mol. Oncol. 5, 387–393 (2011).

  5. 5

    El-Khamisy, S.F., Masutani, M., Suzuki, H. & Caldecott, K.W. A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage. Nucleic Acids Res. 31, 5526–5533 (2003).

  6. 6

    Masson, M. et al. XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage. Mol. Cell. Biol. 18, 3563–3571 (1998).

  7. 7

    Bryant, H.E. et al. PARP is activated at stalled forks to mediate Mre11-dependent replication restart and recombination. EMBO J. 28, 2601–2615 (2009).

  8. 8

    Haince, J.F. et al. PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites. J. Biol. Chem. 283, 1197–1208 (2008).

  9. 9

    Haince, J.F. et al. Ataxia telangiectasia mutated (ATM) signaling network is modulated by a novel poly(ADP-ribose)-dependent pathway in the early response to DNA-damaging agents. J. Biol. Chem. 282, 16441–16453 (2007).

  10. 10

    Paddock, M.N. et al. Competition between PARP-1 and Ku70 control the decision between high-fidelity and mutagenic DNA repair. DNA Repair (Amst.) 10, 338–343 (2011).

  11. 11

    Roy, R., Chun, J. & Powell, S.N. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nat. Rev. Cancer 12, 68–78 (2012).

  12. 12

    Carreira, A. et al. The BRC repeats of BRCA2 modulate the DNA-binding selectivity of RAD51. Cell 136, 1032–1043 (2009).

  13. 13

    Fong, P.C. et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N. Engl. J. Med. 361, 123–134 (2009).

  14. 14

    Tutt, A. et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and advanced breast cancer: a proof-of-concept trial. Lancet 376, 235–244 (2010).

  15. 15

    Bryant, H.E. et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature 434, 913–917 (2005).

  16. 16

    Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917–921 (2005).

  17. 17

    Helleday, T., Petermann, E., Lundin, C., Hodgson, B. & Sharma, R.A. DNA repair pathways as targets for cancer therapy. Nat. Rev. Cancer 8, 193–204 (2008).

  18. 18

    Kraus, W.L. Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr. Opin. Cell Biol. 20, 294–302 (2008).

  19. 19

    Esposito, M.T. & So, C.W. DNA damage accumulation and repair defects in acute myeloid leukemia: implications for pathogenesis, disease progression, and chemotherapy resistance. Chromosoma 123, 545–561 (2014).

  20. 20

    Cheung, N. & So, C.W. Transcriptional and epigenetic networks in haematological malignancy. FEBS Lett. 585, 2100–2111 (2011).

  21. 21

    Zeisig, B.B., Kulasekararaj, A.G., Mufti, G.J. & So, C.W. Acute myeloid leukemia: snapshot. Cancer Cell 22, 698 (2012).

  22. 22

    Zeisig, B.B. & So, C.W. Retroviral/lentiviral transduction and transformation assay. Methods Mol. Biol. 538, 207–229 (2009).

  23. 23

    Yeung, J. et al. β-Catenin mediates the establishment and drug resistance of MLL leukemic stem cells. Cancer Cell 18, 606–618 (2010).

  24. 24

    Smith, L.L. et al. Functional crosstalk between Bmi1 and MLL/Hoxa9 axis in establishment of normal hematopoietic and leukemic stem cells. Cell Stem Cell 8, 649–662 (2011).

  25. 25

    Arteaga, M.F. et al. The histone demethylase PHF8 governs retinoic acid response in acute promyelocytic leukemia. Cancer Cell 23, 376–389 (2013).

  26. 26

    Fung, T.K. & So, C.W. Overcoming treatment resistance in acute promyelocytic leukemia and beyond. Oncotarget 4, 1128–1129 (2013).

  27. 27

    Santos, M.A. et al. DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier. Nature 514, 107–111 (2014).

  28. 28

    Turner, N., Tutt, A. & Ashworth, A. Hallmarks of ′BRCAness′ in sporadic cancers. Nat. Rev. Cancer 4, 814–819 (2004).

  29. 29

    Mah, L.J., El-Osta, A. & Karagiannis, T.C. γH2AX: a sensitive molecular marker of DNA damage and repair. Leukemia 24, 679–686 (2010).

  30. 30

    Baumann, P., Benson, F.E. & West, S.C. Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell 87, 757–766 (1996).

  31. 31

    Moynahan, M.E. & Jasin, M. Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat. Rev. Mol. Cell Biol. 11, 196–207 (2010).

  32. 32

    Valk, P.J. et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N. Engl. J. Med. 350, 1617–1628 (2004).

  33. 33

    Verhaak, R.G. et al. Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling. Haematologica 94, 131–134 (2009).

  34. 34

    Gaymes, T.J., Mufti, G.J. & Rassool, F.V. Myeloid leukemias have increased activity of the nonhomologous end-joining pathway and concomitant DNA misrepair that is dependent on the Ku70/86 heterodimer. Cancer Res. 62, 2791–2797 (2002).

  35. 35

    Pierce, A.J., Johnson, R.D., Thompson, L.H. & Jasin, M. XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev. 13, 2633–2638 (1999).

  36. 36

    Yip, B.H. & So, C.W. Mixed-lineage leukemia protein in normal and leukemic stem cells. Exp. Biol. Med. (Maywood) 238, 315–323 (2013).

  37. 37

    Krivtsov, A.V. & Armstrong, S.A. MLL translocations, histone modifications and leukaemia stem-cell development. Nat. Rev. Cancer 7, 823–833 (2007).

  38. 38

    Golub, T.R. et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537 (1999).

  39. 39

    Costa, B.M. et al. Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. Cancer Res. 70, 453–462 (2010).

  40. 40

    Gaspar, N. et al. MGMT-independent temozolomide resistance in pediatric glioblastoma cells associated with a PI3-kinase-mediated HOX/stem cell gene signature. Cancer Res. 70, 9243–9252 (2010).

  41. 41

    Kumar, A.R. et al. Hoxa9 influences the phenotype but not the incidence of Mll-AF9 fusion gene leukemia. Blood 103, 1823–1828 (2004).

  42. 42

    So, C.W., Karsunky, H., Wong, P., Weissman, I.L. & Cleary, M.L. Leukemic transformation of hematopoietic progenitors by MLL-GAS7 in the absence of Hoxa7 or Hoxa9. Blood 103, 3192–3199 (2004).

  43. 43

    So, C.W. et al. MLL-GAS7 transforms multipotent hematopoietic progenitors and induces mixed lineage leukemias in mice. Cancer Cell 3, 161–171 (2003).

  44. 44

    Faber, J. et al. HOXA9 is required for survival in human MLL-rearranged acute leukemias. Blood 113, 2375–2385 (2009).

  45. 45

    Huang, Y. et al. Identification and characterization of Hoxa9 binding sites in hematopoietic cells. Blood 119, 388–398 (2012).

  46. 46

    Wang, Z. et al. GSK-3 promotes conditional association of CREB and its coactivators with MEIS1 to facilitate HOX-mediated transcription and oncogenesis. Cancer Cell 17, 597–608 (2010).

  47. 47

    Wang, Z. et al. Glycogen synthase kinase 3 in MLL leukaemia maintenance and targeted therapy. Nature 455, 1205–1209 (2008).

  48. 48

    Viale, A. et al. Cell-cycle restriction limits DNA damage and maintains self-renewal of leukaemia stem cells. Nature 457, 51–56 (2009).

  49. 49

    Boichuk, S., Hu, L., Makielski, K., Pandolfi, P.P. & Gjoerup, O.V. Functional connection between Rad51 and PML in homology-directed repair. PLoS ONE 6, e25814 (2011).

  50. 50

    Yeung, P.L. et al. Promyelocytic leukemia nuclear bodies support a late step in DNA double-strand break repair by homologous recombination. J. Cell. Biochem. 113, 1787–1799 (2012).

  51. 51

    Zhong, S. et al. A role for PML and the nuclear body in genomic stability. Oncogene 18, 7941–7947 (1999).

  52. 52

    Alcalay, M. et al. Acute myeloid leukemia fusion proteins deregulate genes involved in stem cell maintenance and DNA repair. J. Clin. Invest. 112, 1751–1761 (2003).

  53. 53

    Armstrong, S.A. et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat. Genet. 30, 41–47 (2002).

  54. 54

    Liu, H. et al. Phosphorylation of MLL by ATR is required for execution of mammalian S-phase checkpoint. Nature 467, 343–346 (2010).

  55. 55

    Rubin, E. et al. A role for the HOXB7 homeodomain protein in DNA repair. Cancer Res. 67, 1527–1535 (2007).

  56. 56

    Chiba, N. et al. Homeobox B9 induces epithelial-to-mesenchymal transition-associated radioresistance by accelerating DNA damage responses. Proc. Natl. Acad. Sci. USA 109, 2760–2765 (2012).

  57. 57

    Blanpain, C., Mohrin, M., Sotiropoulou, P.A. & Passegue, E. DNA-damage response in tissue-specific and cancer stem cells. Cell Stem Cell 8, 16–29 (2011).

  58. 58

    Takacova, S. et al. DNA damage response and inflammatory signaling limit the MLL-ENL–induced leukemogenesis in vivo. Cancer Cell 21, 517–531 (2012).

  59. 59

    Santos, M.A. et al. DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier. Nature 514, 107–111 (2014).

  60. 60

    Lawrence, H.J. et al. Loss of expression of the Hoxa-9 homeobox gene impairs the proliferation and repopulating ability of hematopoietic stem cells. Blood 106, 3988–3994 (2005).

  61. 61

    Yeung, J. & So, C.W. Identification and characterization of hematopoietic stem and progenitor cell populations in mouse bone marrow by flow cytometry. Methods Mol. Biol. 538, 301–315 (2009).

  62. 62

    Dimri, G.P. et al. A biomarker that identifies senescent human cells in culture and in aging skin in vivo. Proc. Natl. Acad. Sci. USA 92, 9363–9367 (1995).

  63. 63

    Choi, E.J., Kim, S.M., Song, K.J., Lee, J.M. & Kee, S.H. Axin1 expression facilitates cell death induced by aurora kinase inhibition through PARP activation. J. Cell. Biochem. 112, 2392–2402 (2011).

  64. 64

    Schmittgen, T.D. & Livak, K.J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108 (2008).

  65. 65

    Gaymes, T.J. et al. Increased error-prone non-homologous DNA end-joining–a proposed mechanism of chromosomal instability in Bloom’s syndrome. Oncogene 21, 2525–2533 (2002).

  66. 66

    Gautier, L., Cope, L., Bolstad, B.M. & Irizarry, R.A. Affy–analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307–315 (2004).

  67. 67

    Martin, N. et al. Interplay between homeobox proteins and polycomb repressive complexes in p16INK(4)a regulation. EMBO J. 32, 982–995 (2013).

Download references


We thank G. Mufti, S. Shall, T. Ng, and D. Weekes for insightful discussion; A. Zelent (Miller School of Medicine, University of Miami), M. Greaves (The Institute of Cancer Research, London ) and O. Heidenreich (Northern Institute for Cancer Research, Newcastle University) for providing NB4-LR2, THP1 and Kasumi cell lines, respectively; I. Ahel (Sir William Dunn School of Pathology, University of Oxford), I. Gibbs-Seymour (Sir William Dunn School of Pathology, University of Oxford), and D. Livingston (Dana-Farber Cancer Institute, Harvard University) for tagged ALPF and PARP1 constructs; E. Soutoglou (Institut de Genetique de Biologie Moleculaire et Celluraire) and M. Jasin (Memorial Sloan Kettering Cancer Center) for DR-GFP HR reporter systems; H. Lee (School of Biological Sciences, Seoul National University) and M. Tarsounas (Oxford University for Radiation Oncology) for BRCA2-specific antibody; J. Hess (Department of Pathology, University of Michigan School of Medicine) for the MSCV-HA-Hoxa9-IRES-GFP construct; C. Lourenco and W. Vetharoy for technical assistance with mice experiments and FACS analysis; S. Tung, A. Innes and P. Lau for technical assistance with gene expression profiling; T. Gaymes for support with DNA damage repair experiments; and P. Tse for graphical illustration. This work was supported by program grants from Bloodwise and Cancer Research UK (to C.W.E.S.).

Author information

M.T.E., L.Z. T.K.F. and J.K.R. performed experiments and analyzed the data. A.W. provided technical support for the in vivo experiments. N.M. and J.G. performed mass spectrometry and data analysis. A.Y.L. and A.A. provide essential reagents and data interpretation. M.T.E and C.W.E.S. wrote the manuscript. C.W.E.S. conceptualized, designed and supervised the study.

Correspondence to Chi Wai Eric So.

Ethics declarations

Competing interests

A.A. has a consulting or advisory role at Genentech, Sun Pharma, GlaxoSmithKline, and Novartis; he also is a co-inventor on patents (US patent nos. US7449464, US7981889, US7692006, US8247416) related to the use of PARP inhibitors held by AstraZeneca. As a consequence, A.A. has and may in the future benefit financially from the Institute of Cancer Research's ‘rewards to inventors’ scheme.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1–8 (PDF 4464 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Esposito, M., Zhao, L., Fung, T. et al. Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors. Nat Med 21, 1481–1490 (2015).

Download citation

Further reading