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:

Molecular targets for therapy

Synthetic lethal targeting of TET2-mutant hematopoietic stem and progenitor cells (HSPCs) with TOP1-targeted drugs and PARP1 inhibitors

Leukemia volume 34, pages 2992–3006 (2020)Cite this article

Subjects

Abstract

Inactivating mutations in TET2 serve as an initiating genetic lesion in the transformation of hematopoietic stem and progenitor cells (HSPCs). Thus, effective therapy for this subset of patients would ideally include drugs that are selectively lethal in TET2-mutant HSPCs, at dosages that spare normal HSPCs. In this study, we tested 129 FDA-approved anticancer drugs in a tet2-deficient zebrafish model and showed that topoisomerase 1 (TOP1)-targeted drugs and PARP1 inhibitors selectively kill tet2-mutant HSPCs. We found that Tet2-deficient murine bone marrow progenitors and CRISPR-Cas9-induced TET2-mutant human AML cells were more sensitive to both classes of drugs compared with matched control cells. The mechanism underlying the selective killing of TET2-mutant blood cells by these drugs was due to aberrantly low levels of tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that is important for removing TOP1 cleavage complexes (TOP1cc). Low TDP1 levels yield sensitivity to TOP1-targeted drugs or PARP1 inhibitors and an inability to remove TOP1 cleavage complexes, leading to DNA double-strand breaks and cell death. The finding that TET2 mutations render HSPCs uniquely vulnerable to disruption of TOP1 and PARP1 activity may therefore represent a unique opportunity to use relatively low dosages of these drugs for the “precision therapy” of TET2-mutant myeloid malignancies.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: tet2-mutant HSPCs are hypersensitive to topotecan.
Fig. 2: Topotecan treatment induces DNA double-strand breaks and triggers apoptosis in tet2-mutant zebrafish HSPCs.
Fig. 3: A decrease in tdp1 expression confers topotecan hypersensitivity to tet2-mutant HSPCs.
Fig. 4: A decrease in tdp1 expression confers hypersensitivity to PARP1 inhibition in tet2-mutant HSPCs.
Fig. 5: Topotecan selectively kills Tet2-mutant murine progenitor cells and human OCI-AML2 cells.
Fig. 6: Olaparib selectively kills Tet2-mutant murine progenitor cells and human OCI-AML2 cells.

Similar content being viewed by others

References

  1. Bowman RL, Levine RL. TET2 in normal and malignant hematopoiesis. Cold Spring Harb Persp Med. 2017;7:a026518.

    Article  Google Scholar 

  2. Alderton GK. Leukaemia and lymphoma: the expansive reach of TET2. Nat Rev Cancer. 2011;11:535.

    Article  CAS  Google Scholar 

  3. Nakajima H, Kunimoto H. TET2 as an epigenetic master regulator for normal and malignant hematopoiesis. Cancer Sci. 2014;105:1093–9.

    Article  CAS  Google Scholar 

  4. Chou WC, Chou SC, Liu CY, Chen CY, Hou HA, Kuo YY, et al. TET2 mutation is an unfavorable prognostic factor in acute myeloid leukemia patients with intermediate-risk cytogenetics. Blood. 2011;118:3803–10.

    Article  CAS  Google Scholar 

  5. Liu WJ, Tan XH, Luo XP, Guo BP, Wei ZJ, Ke Q, et al. Prognostic significance of Tet methylcytosine dioxygenase 2 (TET2) gene mutations in adult patients with acute myeloid leukemia: a meta-analysis. Leuk lymphoma. 2014;55:2691–8.

    Article  CAS  Google Scholar 

  6. Sato H, Wheat JC, Steidl U, Ito K. DNMT3A and TET2 in the pre-leukemic phase of hematopoietic disorders. Front Oncol. 2016;6:187.

    Article  Google Scholar 

  7. Genovese G, Kahler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N. Engl J Med. 2014;371:2477–87.

    Article  Google Scholar 

  8. Jaiswal S, Fontanillas P, Flannick J, Manning A, Grauman PV, Mar BG, et al. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl J Med. 2014;371:2488–98.

    Article  Google Scholar 

  9. Jae-Sook A, Hyeoung-Joon K, Yeo-Kyeoung K, Sung-Hoon J, Deok-Hwan Y, Je-Jung L, et al. Adverse prognostic effect of homozygous TET2 mutation on the relapse risk of acute myeloid leukemia in patients of normal karyotype. Haematologica. 2015;100:e351–3.

    Article  Google Scholar 

  10. Wakita S, Yamaguchi H, Omori I, Terada K, Ueda T, Manabe E, et al. Mutations of the epigenetics-modifying gene (DNMT3a, TET2, IDH1/2) at diagnosis may induce FLT3-ITD at relapse in de novo acute myeloid leukemia. Leukemia. 2013;27:1044–52.

    Article  CAS  Google Scholar 

  11. Chen ES. Targeting epigenetics using synthetic lethality in precision medicine. Cell Mol Life Sci. 2018;75:3381–92.

    Article  CAS  Google Scholar 

  12. Mair B, Moffat J, Boone C, Andrews BJ. Genetic interaction networks in cancer cells. Curr Opin Genet Dev. 2019;54:64–72.

    Article  CAS  Google Scholar 

  13. Ryan CJ, Bajrami I, Lord CJ. Synthetic lethality and cancer—penetrance as the major barrier. Trends Cancer. 2018;4:671–83.

    Article  CAS  Google Scholar 

  14. Smith LM, Willmore E, Austin CA, Curtin NJ. The novel poly(ADP-Ribose) polymerase inhibitor, AG14361, sensitizes cells to topoisomerase I poisons by increasing the persistence of DNA strand breaks. Clin Cancer Res. 2005;11:8449–57.

    Article  CAS  Google Scholar 

  15. El-Khamisy SF, Caldecott KW. TDP1-dependent DNA single-strand break repair and neurodegeneration. Mutagenesis. 2006;21:219–24.

    Article  CAS  Google Scholar 

  16. Das BB, Huang SY, Murai J, Rehman I, Ame JC, Sengupta S, et al. PARP1-TDP1 coupling for the repair of topoisomerase I-induced DNA damage. Nucleic Acids Res. 2014;42:4435–49.

    Article  CAS  Google Scholar 

  17. Pommier Y, Barcelo JM, Rao VA, Sordet O, Jobson AG, Thibaut L, et al. Repair of topoisomerase I‐mediated DNA damage. Prog Nucleic Acid Res Mol Biol. 2006;81:179–229.

    Article  CAS  Google Scholar 

  18. Gilbert DC, Chalmers AJ, El-Khamisy SF. Topoisomerase I inhibition in colorectal cancer: biomarkers and therapeutic targets. Br J cancer. 2012;106:18–24.

    Article  CAS  Google Scholar 

  19. Gjini E, Mansour MR, Sander JD, Moritz N, Nguyen AT, Kesarsing M, et al. A zebrafish model of myelodysplastic syndrome produced through tet2 genomic editing. Mol Cell Biol. 2015;35:789–804.

    Article  Google Scholar 

  20. Choy H, MacRae R. Irinotecan and radiation in combined-modality therapy for solid tumors. Oncol (Williston Park). 2001;15:22–8.

    CAS  Google Scholar 

  21. Chen AY, Chen PM, Chen YJ. DNA topoisomerase I drugs and radiotherapy for lung cancer. J Thorac Dis. 2012;4:390–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Bolli N, Payne EM, Grabher C, Lee JS, Johnston AB, Falini B, et al. Expression of the cytoplasmic NPM1 mutant (NPMc+) causes the expansion of hematopoietic cells in zebrafish. Blood. 2010;115:3329–40.

    Article  CAS  Google Scholar 

  23. Metscher BD, Ahlberg PE. Zebrafish in context: uses of a laboratory model in comparative studies. Dev Biol. 1999;210:1–14.

    Article  CAS  Google Scholar 

  24. Liu D, Wang Z, Xiao A, Zhang Y, Li W, Zu Y, et al. Efficient gene targeting in zebrafish mediated by a zebrafish-codon-optimized cas9 and evaluation of off-targeting effect. J Genet Genomics. 2014;41:43–6.

    Article  Google Scholar 

  25. North TE, Goessling W, Peeters M, Li P, Ceol C, Lord AM, et al. Hematopoietic stem cell development is dependent on blood flow. Cell. 2009;137:736–48.

    Article  CAS  Google Scholar 

  26. Gjini E, Jing CB, Nguyen AT, Reyon D, Gans E, Kesarsing M, et al. Disruption of asxl1 results in myeloproliferative neoplasms in zebrafish. Dis Model Mech. 2019;12:dmm035790.

    Article  CAS  Google Scholar 

  27. An J, Gonzalez-Avalos E, Chawla A, Jeong M, Lopez-Moyado IF, Li W, et al. Acute loss of TET function results in aggressive myeloid cancer in mice. Nat Commun. 2015;6:10071.

    Article  CAS  Google Scholar 

  28. Kushner BH, Kramer K, Modak S, Cheung NK. Camptothecin analogs (irinotecan or topotecan) plus high-dose cyclophosphamide as preparative regimens for antibody-based immunotherapy in resistant neuroblastoma. Clin Cancer Res. 2004;10:84–7.

    Article  CAS  Google Scholar 

  29. Linda JK, Yang L-X. γ-H2AX-A novel biomarker for Double-strand Breaks. In vivo 2008;22:305–9.

    Google Scholar 

  30. North TE, Goessling W, Walkley CR, Lengerke C, Kopani KR, Lord AM, et al. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature. 2007;447:1007–11.

    Article  CAS  Google Scholar 

  31. Gao R, Das BB, Chatterjee R, Abaan OD, Agama K, Matuo R, et al. Epigenetic and genetic inactivation of tyrosyl-DNA-phosphodiesterase 1 (TDP1) in human lung cancer cells from the NCI-60 panel. DNA Repair. 2014;13:1–9.

    Article  CAS  Google Scholar 

  32. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013;31:227–9.

    Article  CAS  Google Scholar 

  33. Cimmino L, Dolgalev I, Wang Y, Yoshimi A, Martin GH, Wang J, et al. Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell. 2017;170:1079–95. e1020.

    Article  CAS  Google Scholar 

  34. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819–23.

    Article  CAS  Google Scholar 

  35. Meisenberg C, Ward SE, Schmid P, El-Khamisy SF. TDP1/TOP1 ratio as a promising indicator for the response of small cell lung cancer to topotecan. J Cancer Sci Ther. 2014;6:258–67.

    Article  CAS  Google Scholar 

  36. Duma N, Gast KC, Choong GM, Leon-Ferre RA, O’Sullivan CC. Where do we stand on the integration of PARP inhibitors for the treatment of breast cancer? Curr Oncol Rep. 2018;20:63.

    Article  Google Scholar 

  37. Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, Perez-Lopez R, et al. DNA-repair defects and olaparib in metastatic prostate cancer. N. Engl J Med. 2015;373:1697–708.

    Article  CAS  Google Scholar 

  38. Wang L, Hamard PJ, Nimer SD. PARP inhibitors: a treatment option for AML? Nat Med. 2015;21:1393–4.

    Article  CAS  Google Scholar 

  39. Esposito MT, Zhao L, Fung TK, Rane JK, Wilson A, Martin N, et al. Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors. Nat Med. 2015;21:1481–90.

    Article  CAS  Google Scholar 

  40. Zhao L, So CW. PARP-inhibitor-induced synthetic lethality for acute myeloid leukemia treatment. Exp Hematol. 2016;44:902–7.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Cicely Jette and John Gilbert for editorial assistance and critical comments. This work was supported by Edward P. Evans Foundation (to ATL); the Andrew McDonough B+ Foundation (to C-BJ), and an International Award of Lady Tata Memorial Trust (to C-BJ).

Author information

Author notes

  1. These authors contributed equally: Chang-Bin Jing, Cong Fu

Authors and Affiliations

  1. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    Chang-Bin Jing, Cong Fu, Nicole Prutsch, Shuning He & A. Thomas Look

  2. Department of Dermatology and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA

    Meng Wang

Authors
  1. Chang-Bin Jing
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cong Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicole Prutsch
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Meng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shuning He
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. Thomas Look
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C-BJ and CF contributed to experimental work, experimental design, writing, and data analysis and interpretation. NP contributed to serial plating experimental work on Tet2-mutant progenitor cells. MW contributed to the bioinformatics analysis in AML database. SH analyzed the data. ATL directed all experimental activity and contributed to data interpretation, analysis, and writing of manuscript.

Corresponding author

Correspondence to A. Thomas Look.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jing, CB., Fu, C., Prutsch, N. et al. Synthetic lethal targeting of TET2-mutant hematopoietic stem and progenitor cells (HSPCs) with TOP1-targeted drugs and PARP1 inhibitors. Leukemia 34, 2992–3006 (2020). https://doi.org/10.1038/s41375-020-0927-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41375-020-0927-5

This article is cited by

Search

Advanced search

Quick links