Article

This is an unedited manuscript that has been accepted for publication. Nature Research are providing this early version of the manuscript as a service to our customers. The manuscript will undergo copyediting, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

Utx loss causes myeloid transformation

Received:
Revised:
Accepted:
Published online:

Abstract

Recurrent somatic loss-of-function mutations in histone demethylases are frequently detected in cancer. However, whether loss of a histone demethylase can cause cancer has not been determined. Here, we report that knockout of the histone demethylase Utx in mice causes a chronic myelomonocytic leukemia (CMML)-like disease with splenomegaly, monocytosis, and extramedullary hematopoiesis. Mutational analysis of patient data indicated that UTX mutations occur simultaneously with TP53 mutations in myeloid malignancies, and combined inactivation of Utx and Trp53 accelerated the development of CMML in a cell-autonomous manner. Utx loss caused increased self-renewal of hematopoietic stem cells and predisposed hematopoietic stem cells to differentiate into myeloid-derived lineages. Transcriptome and chromatin immunoprecipitation analyses revealed that Utx activates key transcriptional factors required for erythroid differentiation by modulating histone H3 lysine 27 and lysine 4 trimethylation. Our results suggest that Utx suppresses CMML formation by controlling hematopoietic stem cell self-renewal and differentiation.

  • Subscribe to Leukemia for full access:

    $1031

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    Shilatifard A. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem. 2006;75:243–69.

  2. 2.

    Martin C, Zhang Y. The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol. 2005;6:838–49.

  3. 3.

    Mosammaparast N, Shi Y. Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases. Annu Rev Biochem. 2010;79:155–79.

  4. 4.

    Shi Y, Whetstine JR. Dynamic regulation of histone lysine methylation by demethylases. Mol Cell. 2007;25:1–14.

  5. 5.

    Klose RJ, Zhang Y. Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol. 2007;8:307–18.

  6. 6.

    Klose RJ, Kallin EM, Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet. 2006;7:715–27.

  7. 7.

    Greer EL, Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet. 2012;13:343–57.

  8. 8.

    Shi Y. Histone lysine demethylases: emerging roles in development, physiology and disease. Nat Rev Genet. 2007;8:829–33.

  9. 9.

    Hojfeldt JW, Agger K, Helin K. Histone lysine demethylases as targets for anticancer therapy. Nat Rev Drug Discov. 2013;12:917–30.

  10. 10.

    You Jueng S, Jones Peter A. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell. 2012;22:9–20.

  11. 11.

    Dawson Mark A, Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell. 2012;150:12–27.

  12. 12.

    Kim KH, Roberts CWM. Targeting EZH2 in cancer. Nat Med. 2016;22:128–34.

  13. 13.

    Shih AH, Abdel-Wahab O, Patel JP, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer. 2012;12:599–612.

  14. 14.

    Albert M, Helin K. Histone methyltransferases in cancer. Semin Cell Dev Biol. 2010;21:209–20.

  15. 15.

    Krivtsov AV, Armstrong SA. MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer. 2007;7:823–33.

  16. 16.

    Agger K, Cloos PA, Christensen J, Pasini D, Rose S, Rappsilber J, et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature. 2007;449:731–4.

  17. 17.

    Hong S, Cho YW, Yu LR, Yu H, Veenstra TD, Ge K. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. Proc Natl Acad Sci USA. 2007;104:18439–44.

  18. 18.

    Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature. 2007;449:689–94.

  19. 19.

    Lee MG, Villa R, Trojer P, Norman J, Yan KP, Reinberg D, et al. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science. 2007;318:447–50.

  20. 20.

    Van der Meulen J, Sanghvi V, Mavrakis K, Durinck K, Fang F, Matthijssens F, et al. The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia. Blood. 2015;125:13–21.

  21. 21.

    Ntziachristos P, Tsirigos A, Welstead GG, Trimarchi T, Bakogianni S, Xu L, et al. Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia. Nature. 2014;514:513–7.

  22. 22.

    Kar SA, Jankowska A, Makishima H, Visconte V, Jerez A, Sugimoto Y, et al. Spliceosomal gene mutations are frequent events in the diverse mutational spectrum of chronic myelomonocytic leukemia but largely absent in juvenile myelomonocytic leukemia. Haematologica. 2013;98:107–13.

  23. 23.

    Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333–9.

  24. 24.

    Mar BG, Bullinger L, Basu E, Schlis K, Silverman LB, Dohner K, et al. Sequencing histone-modifying enzymes identifies UTX mutations in acute lymphoblastic leukemia. Leukemia. 2012;26:1881–3.

  25. 25.

    Jankowska AM, Makishima H, Tiu RV, Szpurka H, Huang Y, Traina F, et al. Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. Blood. 2011;118:3932–41.

  26. 26.

    van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet. 2009;41:521–3.

  27. 27.

    Van der Meulen J, Speleman F, Van Vlierberghe P. The H3K27me3 demethylase UTX in normal development and disease. Epigenetics. 2014;9:658–68.

  28. 28.

    Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr., Kinzler KW. Cancer genome landscapes. Science. 2013;339:1546–58.

  29. 29.

    Thieme S, Gyarfas T, Richter C, Ozhan G, Fu J, Alexopoulou D, et al. The histone demethylase UTX regulates stem cell migration and hematopoiesis. Blood. 2013;121:2462–73.

  30. 30.

    Patnaik MM, Tefferi A. Cytogenetic and molecular abnormalities in chronic myelomonocytic leukemia. Blood Cancer J. 2016;6:e393.

  31. 31.

    Patnaik MM, Tefferi A. Chronic myelomonocytic leukemia: focus on clinical practice. Mayo Clin Proc. 2016;91:259–72.

  32. 32.

    Patnaik MM, Parikh SA, Hanson CA, Tefferi A. Chronic myelomonocytic leukaemia: a concise clinical and pathophysiological review. Br J Haematol. 2014;165:273–86.

  33. 33.

    Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, et al. Xist RNA is a potent suppressor of hematologic cancer in mice. Cell. 2013;152:727–42.

  34. 34.

    Dey A, Seshasayee D, Noubade R, French DM, Liu J, Chaurushiya MS, et al. Loss of the tumor suppressor BAP1 causes myeloid transformation. Science. 2012;337:1541–6.

  35. 35.

    Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C, et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell. 2011;20:11–24.

  36. 36.

    Klinakis A, Lobry C, Abdel-Wahab O, Oh P, Haeno H, Buonamici S, et al. A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia. Nature. 2011;473:230–3.

  37. 37.

    Xu J, Wang YY, Dai YJ, Zhang W, Zhang WN, Xiong SM, et al. DNMT3A Arg882 mutation drives chronic myelomonocytic leukemia through disturbing gene expression/DNA methylation in hematopoietic cells. Proc Natl Acad Sci USA. 2014;111:2620–5.

  38. 38.

    Schubbert S, Shannon K, Bollag G. Hyperactive Ras in developmental disorders and cancer. Nat Rev Cancer. 2007;7:295–308.

  39. 39.

    Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012;28:2782–8.

  40. 40.

    Lee S, Lee Jae W, Lee S-K. UTX, a histone H3-lysine 27 demethylase, acts as a critical switch to activate the cardiac developmental program. Dev Cell. 2012;22:25–37.

  41. 41.

    Shpargel KB, Sengoku T, Yokoyama S, Magnuson T. UTX and UTY demonstrate histone demethylase-independent function in mouse embryonic development. PLoS Genet. 2012;8:e1002964.

  42. 42.

    Wang C, Lee JE, Cho YW, Xiao Y, Jin Q, Liu C, et al. UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity. Proc Natl Acad Sci USA. 2012;109:15324–9.

  43. 43.

    Welstead GG, Creyghton MP, Bilodeau S, Cheng AW, Markoulaki S, Young RA, et al. X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner. Proc Natl Acad Sci USA. 2012;109:13004–9.

  44. 44.

    Mao J, Ligon KL, Rakhlin EY, Thayer SP, Bronson RT, Rowitch D, et al. A novel somatic mouse model to survey tumorigenic potential applied to the hedgehog pathway. Cancer Res. 2006;66:10171–8.

  45. 45.

    Vardiman JW, Thiele J, Arber DA, Brunning RD, Borowitz MJ, Porwit A, et al. The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes. Blood. 2009;114:937–51.

  46. 46.

    Kogan SC, Ward JM, Anver MR, Berman JJ, Brayton C, Cardiff RD, et al. Bethesda proposals for classification of nonlymphoid hematopoietic neoplasms in mice. Blood. 2002;100:238–45.

  47. 47.

    Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P, et al. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Human Mutat. 2007;28:622–9.

  48. 48.

    Jacks T, Remington L, Williams BO, Schmitt EM, Halachmi S, Bronson RT, et al. Tumor spectrum analysis in p53-mutant mice. Curr Biol. 1994;4:1–7.

  49. 49.

    Cantor AB, Orkin SH. Transcriptional regulation of erythropoiesis: an affair involving multiple partners. Oncogene. 2002;21:3368–76.

  50. 50.

    Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, et al. Chromatin state dynamics during blood formation. Science. 2014;345:943–9.

  51. 51.

    Olivier M, Hollstein M, Hainaut P. TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol. 2010;2:a001008.

  52. 52.

    Bally C, Adès L, Renneville A, Sebert M, Eclache V, Preudhomme C, et al. Prognostic value of TP53 gene mutations in myelodysplastic syndromes and acute myeloid leukemia treated with azacitidine. Leuk Res. 2014;38:751–5.

  53. 53.

    Ler LD, Ghosh S, Chai X, Thike AA, Heng HL, Siew EY, et al. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci Transl Med. 2017;9:eaai8312.

  54. 54.

    Grossmann V, Kohlmann A, Eder C, Haferlach C, Kern W, Cross NCP, et al. Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in >80% of patients with TET2 and EZH2 being of high prognostic relevance. Leukemia 2011;25:877–9.

  55. 55.

    Mochizuki-Kashio M, Aoyama K, Sashida G, Oshima M, Tomioka T, Muto T, et al. Ezh2 loss in hematopoietic stem cells predisposes mice to develop heterogeneous malignancies in an Ezh1-dependent manner. Blood. 2015;126:1172–83.

Download references

Acknowledgements

We thank Lijian Hui (SIBCB, Shanghai, China) for sharing p53 KO mice. This work was supported by the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDB19000000), National Basic Research Program of China (2014CB943100), and the National Natural Science Foundation of China (91519303). Accession numbers: RNA-Seq data are available in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) under the accession numbers: GSE97737.

Author contributions

LTZ and LYX designed and performed the experiments and wrote the manuscript. QX, DFZ, and GH performed the animal experiments. LY performed the bioinformatic analyses. PC analyzed the mouse phenotype. WW and YQW performed the cell experiments. CDC conceived and supervised the project and revised the manuscript.

Author information

Author notes

    Affiliations

    1. State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China

      • Liting Zheng
      • , Longyong Xu
      • , Qing Xu
      • , Lu Yu
      • , Danfeng Zhao
      • , Wei Wang
      • , Yiqin Wang
      • , Gang Han
      •  & Charlie Degui Chen
    2. Clinical Laboratory of Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, China

      • Pu Chen

    Authors

    1. Search for Liting Zheng in:

    2. Search for Longyong Xu in:

    3. Search for Qing Xu in:

    4. Search for Lu Yu in:

    5. Search for Danfeng Zhao in:

    6. Search for Pu Chen in:

    7. Search for Wei Wang in:

    8. Search for Yiqin Wang in:

    9. Search for Gang Han in:

    10. Search for Charlie Degui Chen in:

    Conflict of interest

    The authors declare that they have no conflict of interest.

    Corresponding author

    Correspondence to Charlie Degui Chen.

    Electronic supplementary material