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:

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

Abstract

Abnormal epigenetic regulation has been implicated in oncogenesis. We report here the identification of somatic mutations by exome sequencing in acute monocytic leukemia, the M5 subtype of acute myeloid leukemia (AML-M5). We discovered mutations in DNMT3A (encoding DNA methyltransferase 3A) in 23 of 112 (20.5%) cases. The DNMT3A mutants showed reduced enzymatic activity or aberrant affinity to histone H3 in vitro. Notably, there were alterations of DNA methylation patterns and/or gene expression profiles (such as HOXB genes) in samples with DNMT3A mutations as compared with those without such changes. Leukemias with DNMT3A mutations constituted a group of poor prognosis with elderly disease onset and of promonocytic as well as monocytic predominance among AML-M5 individuals. Screening other leukemia subtypes showed Arg882 alterations in 13.6% of acute myelomonocytic leukemia (AML-M4) cases. Our work suggests a contribution of aberrant DNA methyltransferase activity to the pathogenesis of acute monocytic leukemia and provides a useful new biomarker for relevant cases.

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: Locations of DNMT3A mutations and structure of DNMT3A protein.
Figure 2: Functional analysis of DNMT3A mutants.
Figure 3: Analysis of gene expression and DNA methylation in individuals with AML-M5.
Figure 4: Kaplan-Meier analysis of the survival of individuals with AML-M5.

Similar content being viewed by others

References

  1. Bennett, J.M. et al. Proposals for the classification of the acute leukaemias. French-American-British (FAB) co-operative group. Br. J. Haematol. 33, 451–458 (1976).

    Article  CAS  Google Scholar 

  2. Fenaux, P. et al. Acute monocytic leukaemia in adults: treatment and prognosis in 99 cases. Br. J. Haematol. 75, 41–48 (1990).

    Article  CAS  Google Scholar 

  3. Bennett, J.M. et al. Long-term survival in acute myeloid leukemia: the Eastern Cooperative Oncology Group experience. Cancer 80, 2205–2209 (1997).

    Article  CAS  Google Scholar 

  4. Porcu, P. et al. Hyperleukocytic leukemias and leukostasis: a review of pathophysiology, clinical presentation and management. Leuk. Lymphoma 39, 1–18 (2000).

    Article  CAS  Google Scholar 

  5. Peterson, L., Dehner, L.P. & Brunning, R.D. Extramedullary masses as presenting features of acute monoblastic leukemia. Am. J. Clin. Pathol. 75, 140–148 (1981).

    Article  CAS  Google Scholar 

  6. Tallman, M.S. et al. Acute monocytic leukemia (French-American-British classification M5) does not have a worse prognosis than other subtypes of acute myeloid leukemia: a report from the Eastern Cooperative Oncology Group. J. Clin. Oncol. 22, 1276–1286 (2004).

    Article  Google Scholar 

  7. Schoch, C. et al. AML with 11q23/MLL abnormalities as defined by the WHO classification: incidence, partner chromosomes, FAB subtype, age distribution, and prognostic impact in an unselected series of 1897 cytogenetically analyzed AML cases. Blood 102, 2395–2402 (2003).

    Article  CAS  Google Scholar 

  8. Koh, Y. et al. Different clinical importance of FLT3 internal tandem duplications in AML according to FAB classification: possible existence of distinct leukemogenesis involving monocyte differentiation pathway. Ann. Hematol. 88, 1089–1097 (2009).

    Article  CAS  Google Scholar 

  9. Boissel, N. et al. Prevalence, clinical profile, and prognosis of NPM mutations in AML with normal karyotype. Blood 106, 3618–3620 (2005).

    Article  CAS  Google Scholar 

  10. Schlenk, R.F. et al. Mutations and treatment outcome in cytogenetically normal acute myeloid leukemia. N. Engl. J. Med. 358, 1909–1918 (2008).

    Article  CAS  Google Scholar 

  11. Ley, T.J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008).

    Article  CAS  Google Scholar 

  12. Stratton, M.R., Campbell, P.J. & Futreal, P.A. The cancer genome. Nature 458, 719–724 (2009).

    Article  CAS  Google Scholar 

  13. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010).

    Article  CAS  Google Scholar 

  14. Dalgliesh, G.L. et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 463, 360–363 (2010).

    Article  CAS  Google Scholar 

  15. Morin, R.D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 42, 181–185 (2010).

    Article  CAS  Google Scholar 

  16. Bestor, T.H. The DNA methyltransferases of mammals. Hum. Mol. Genet. 9, 2395–2402 (2000).

    Article  CAS  Google Scholar 

  17. Lucio-Eterovic, A. K. et al. Role for the nuclear receptor-binding SET domain protein 1 (NSD1) methyltransferase in coordinating lysine 36 methylation at histone 3 with RNA polymerase II function. Proc. Natl. Acad. Sci. USA 107, 16952–16957 (2010).

    Article  CAS  Google Scholar 

  18. Zhang, S.J. et al. Gain-of-function mutation of GATA-2 in acute myeloid transformation of chronic myeloid leukemia. Proc. Natl. Acad. Sci. USA 105, 2076–2081 (2008).

    Article  CAS  Google Scholar 

  19. Weng, A.P. & Aster, J.C. No T without D3: a critical role for cyclin D3 in normal and malignant precursor T cells. Cancer Cell 4, 417–418 (2003).

    Article  CAS  Google Scholar 

  20. Jia, D., Jurkowska, R.Z., Zhang, X., Jeltsch, A. & Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248–251 (2007).

    Article  CAS  Google Scholar 

  21. Ooi, S.K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).

    Article  CAS  Google Scholar 

  22. Xie, S. et al. Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene 236, 87–95 (1999).

    Article  CAS  Google Scholar 

  23. Xie, Z.H. et al. Mutations in DNA methyltransferase DNMT3B in ICF syndrome affect its regulation by DNMT3L. Hum. Mol. Genet. 15, 1375–1385 (2006).

    Article  CAS  Google Scholar 

  24. Shah, N. & Sukumar, S. The Hox genes and their roles in oncogenesis. Nat. Rev. Cancer 10, 361–371 (2010).

    Article  CAS  Google Scholar 

  25. 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).

    Article  CAS  Google Scholar 

  26. Gilliland, D.G. & Tallman, M.S. Focus on acute leukemias. Cancer Cell 1, 417–420 (2002).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  28. Ley, T.J. et al. DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424–2433 (2010).

    Article  CAS  Google Scholar 

  29. Yamashita, Y. et al. Array-based genomic resequencing of human leukemia. Oncogene 29, 3723–3731 (2010).

    Article  CAS  Google Scholar 

  30. El-Maarri, O. et al. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. Hum. Mol. Genet. 18, 1755–1768 (2009).

    Article  CAS  Google Scholar 

  31. Jones, P.A. DNA methylation and cancer. Oncogene 21, 5358–5360 (2002).

    Article  CAS  Google Scholar 

  32. Okano, M., Bell, D.W., Haber, D.A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

    Article  CAS  Google Scholar 

  33. Xu, G.L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).

    Article  CAS  Google Scholar 

  34. Bullinger, L. et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N. Engl. J. Med. 350, 1605–1616 (2004).

    Article  CAS  Google Scholar 

  35. Eklund, E.A. The role of HOX genes in malignant myeloid disease. Curr. Opin. Hematol. 14, 85–89 (2007).

    Article  CAS  Google Scholar 

  36. Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  38. Panarello, C., Rosanda, C. & Morerio, C. Cryptic translocation t(5;11)(q35;p15.5) with involvement of the NSD1 and NUP98 genes without 5q deletion in childhood acute myeloid leukemia. Genes Chromosom. Cancer 35, 277–281 (2002).

    Article  CAS  Google Scholar 

  39. Ng, S.B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790–793 (2010).

    Article  CAS  Google Scholar 

  40. Nikoloski, G. et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat. Genet. 42, 665–667 (2010).

    Article  CAS  Google Scholar 

  41. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article  CAS  Google Scholar 

  42. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  43. Mullighan, C.G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758–764 (2007).

    Article  CAS  Google Scholar 

  44. Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).

    Article  CAS  Google Scholar 

  45. O'=Gara, M., Klimasauskas, S., Roberts, R.J. & Cheng, X. Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol. 261, 634–645 (1996).

    Article  CAS  Google Scholar 

  46. Garrett, M. et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639–1662 (1998).

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported in part by the China National High Tech Program for Biotechnology (863:2006AA02A405), Chinese National Key Basic Research Project (973: 2010CB529203), the National Natural Science Foundation of China (30772744, 30821063, 81000213) and the Shanghai Municipal Commission for Science and Technology (07DZ05908,08DZ2200100). We thank Jiangsu Institute of Hematology of the First Affiliated Hospital of Soochow University, Department of Hematology of the First Affiliated Hospital of Zhejiang University, Department of Hematology of the Tongji Hospital of Tongji University and Department of Hematology of Luwan division of Ruijin Hospital for providing AML-M5 samples. We are grateful to W.-L. Zhao, F. Yang, Y.-Y. Wang and X. Fan for assistance in clinical analysis of the AML-M5 samples, and to B. Chen and S.-M. Xiong for carrying out the hematological morphological analysis.

Author information

Authors and Affiliations

Authors

Contributions

S.-J.C. and Z.C. were the principal investigators who conceived the study. S.-J.C., Z.C. and X.-J.Y. coordinated and oversaw the study. X.-J.Y. and J.X. carried out most of the experiments. Z.-H.G. and G.L. were responsible for bioinformatics investigation. C.-M.P. and H.-D.S. carried out the exome sequencing and participated in the validation experiments. J.-Q.M. and L.T. participated in the preparation of biological samples. Y.S. helped gather detailed clinical information for the study and helped to carry out clinical analysis. Y.-M.Z. and J.-Y.S. participated in the PCR assay and Sequenom analysis. X.-W.Z. and W.-X.L. helped to carry out the biochemical experiments. K.-Q.L. carried out the structural analysis and guided the biochemical experiments. Z.C., S.-J.C. and X.-J.Y. wrote the manuscript.

Corresponding authors

Correspondence to Zhu Chen or Sai-Juan Chen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11 and Supplementary Tables 1–11. (PDF 8066 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yan, XJ., Xu, J., Gu, ZH. et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 43, 309–315 (2011). https://doi.org/10.1038/ng.788

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.788

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