• A Corrigendum to this article was published on 16 April 2014

Abstract

In acute myeloid leukaemia (AML), the cell of origin, nature and biological consequences of initiating lesions, and order of subsequent mutations remain poorly understood, as AML is typically diagnosed without observation of a pre-leukaemic phase. Here, highly purified haematopoietic stem cells (HSCs), progenitor and mature cell fractions from the blood of AML patients were found to contain recurrent DNMT3A mutations (DNMT3Amut) at high allele frequency, but without coincident NPM1 mutations (NPM1c) present in AML blasts. DNMT3Amut-bearing HSCs showed a multilineage repopulation advantage over non-mutated HSCs in xenografts, establishing their identity as pre-leukaemic HSCs. Pre-leukaemic HSCs were found in remission samples, indicating that they survive chemotherapy. Therefore DNMT3Amut arises early in AML evolution, probably in HSCs, leading to a clonally expanded pool of pre-leukaemic HSCs from which AML evolves. Our findings provide a paradigm for the detection and treatment of pre-leukaemic clones before the acquisition of additional genetic lesions engenders greater therapeutic resistance.

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Acknowledgements

We thank all members of the Dick laboratory for critical assessment of this work, A. Khandani, P. Penttilä, N. Simard, T. Velauthapillai and the SickKids-UHN flow facility for technical support, J. Claudio for management of the HALT studies that enabled the genetic analysis described herein, and J. Cui and X.-Z. Yang for curating the human AML samples used in these studies. This work was supported by a Postdoctoral Fellowship Award from the McEwen Centre for Regenerative Medicine with funding made available through the Gentle Ben Charity (L.I.S.), a Canadian Institutes for Health Research (CIHR) fellowship in partnership with the Aplastic Anemia and Myelodysplasia Association of Canada and an award from Vetenskapsradet (S.Z.), and by grants from CIHR, Canadian Cancer Society, Terry Fox Foundation, Genome Canada through the Ontario Genomics Institute, Ontario Institute for Cancer Research with funds from the province of Ontario, a Canada Research Chair, and the Ontario Ministry of Health and Long Term Care (OMOHLTC). The views expressed do not necessarily reflect those of the OMOHLTC. This work was also supported by the Cancer Stem Cell Consortium with funding from the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-047), and through the Canadian Institutes of Health Research (CSC-105367). Contributors to the HALT Pan-Leukemia Gene Panel are listed in Supplementary Note 1.

Author information

Author notes

    • Liran I. Shlush
    •  & Sasan Zandi

    These authors contributed equally to this work.

Affiliations

  1. Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada

    • Liran I. Shlush
    • , Sasan Zandi
    • , Amanda Mitchell
    • , Weihsu Claire Chen
    • , Joseph M. Brandwein
    • , Vikas Gupta
    • , James A. Kennedy
    • , Aaron D. Schimmer
    • , Andre C. Schuh
    • , Karen W. Yee
    • , Jessica L. McLeod
    • , Monica Doedens
    • , Jessie J. F. Medeiros
    • , Rene Marke
    • , Mark D. Minden
    • , Jean C. Y. Wang
    •  & John E. Dick
  2. Department of Medicine, University of Toronto, Toronto, Ontario M5S 2J7, Canada

    • Joseph M. Brandwein
    • , Vikas Gupta
    • , Aaron D. Schimmer
    • , Andre C. Schuh
    • , Karen W. Yee
    • , Mark D. Minden
    •  & Jean C. Y. Wang
  3. Division of Medical Oncology and Hematology, UHN, Toronto, Ontario M5G 2M9, Canada

    • Joseph M. Brandwein
    • , Vikas Gupta
    • , Aaron D. Schimmer
    • , Andre C. Schuh
    • , Karen W. Yee
    • , Mark D. Minden
    •  & Jean C. Y. Wang
  4. Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada

    • Aaron D. Schimmer
    • , John D. McPherson
    • , Thomas J. Hudson
    •  & Mark D. Minden
  5. Radboud University, Nijmegen Medical Centre, Nijmegen 6500 HB, The Netherlands

    • Rene Marke
  6. Chonnam National University Hwasun Hospital, Genome Research Center for Hematopoietic Diseases, Gwangju 519-809, South Korea

    • Hyeoung Joon Kim
    •  & Kwon Lee
  7. Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada

    • John D. McPherson
    • , Thomas J. Hudson
    • , Andrew M. K. Brown
    • , Fouad Yousif
    • , Quang M. Trinh
    •  & Lincoln D. Stein
  8. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada

    • Thomas J. Hudson
    • , Lincoln D. Stein
    •  & John E. Dick
  9. †Lists of participants and their affiliations appear in Supplementary Information.

    • The HALT Pan-Leukemia Gene Panel Consortium

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Contributions

L.I.S. and S.Z. designed and performed experiments, analysed data and wrote the manuscript; A.M., W.C.C screened AML engraftment in xenotransplantation assays; J.M.B., V.G., J.A.K., A.D.S., A.C.S., K.W.Y., M.D.M. collected AML samples and assembled clinical information; J.A.K. correlated xenotransplantation engraftment data with clinical information; J.L.M., M.D. performed xenotransplantation experiments; J.J.F.M., R.M. performed ddPCR; H.J.K., K.L. performed Sanger sequencing; J.D.M., T.J.H., supervised the targeted sequencing; A.M.K.B. and F.Y. performed and analysed targeted sequencing; Q.M.T., L.D.S. performed DNMT3A data mining. M.D.M. designed the study; J.C.Y.W. supervised AML xenotransplantation screening experiments, designed the study and wrote the manuscript; J.E.D. supervised the study and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to John E. Dick.

Extended data

Supplementary information

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    Supplementary Information

    This file contains the legends for Supplementary Tables 1-5 (see separate excel files) and Supplementary Notes 1-2.

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  1. 1.

    Supplementary Table 1

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    Supplementary Table 2

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    Supplementary Table 3

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    Supplementary Table 4

    This file contains Supplementary Table 4 (see Supplementary Information file for legend).

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    Supplementary Table 5

    This file contains Supplementary Table 5 (see Supplementary Information file for legend).

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https://doi.org/10.1038/nature13038

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