Abstract

The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL) cases, is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of non-templated sequence at junctions, 30-fold enrichment at promoters and enhancers of genes actively transcribed in B cell development and an unexpectedly high ratio of recurrent to non-recurrent structural variants. Single-cell tracking shows that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions. Integration of data on point mutations and rearrangements identifies ATF7IP and MGA as two new tumor-suppressor genes in ALL. Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1–positive lymphoblasts, targeting the promoters, enhancers and first exons of genes that normally regulate B cell differentiation.

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Acknowledgements

This work was supported by the Kay Kendall Leukaemia Fund (KKLF; grant reference KKL407), Leukemia and Lymphoma Research (grant reference 11021) and the Wellcome Trust (grant reference 077012/Z/05/Z). P.J.C. is personally funded through a Wellcome Trust Senior Clinical Research Fellowship (grant reference WT088340MA). P.V.L. is supported by a postdoctoral research fellowship from Research Foundation–Flanders (FWO). S.N.-Z. is a Wellcome Trust Intermediate Clinical Fellow (grant reference WT100183MA). F.W.v.D. is funded by KKLF (grant reference KKL417). J.Z. is supported by University Hospital Motol (grant MH-CR DRO 00064203).

Author information

Author notes

    • Mel Greaves
    •  & Peter J Campbell

    These authors jointly directed this work.

Affiliations

  1. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.

    • Elli Papaemmanuil
    • , Yilong Li
    • , David C Wedge
    • , Jose Tubio
    • , Ludmil B Alexandrov
    • , Peter Van Loo
    • , Susanna L Cooke
    • , John Marshall
    • , Inigo Martincorena
    • , Jonathan Hinton
    • , Gunes Gundem
    • , Serena Nik-Zainal
    • , David R Jones
    • , Manasa Ramakrishna
    • , Lucy Stebbings
    • , Catherine Leroy
    • , Andrew Menzies
    • , John Gamble
    • , Ben Robinson
    • , Laura Mudie
    • , Keiran Raine
    • , Sarah O'Meara
    • , Jon W Teague
    • , Adam P Butler
    • , Michael R Stratton
    •  & Peter J Campbell
  2. Hospital Universitario 12 de Octubre, Madrid, Spain.

    • Inmaculada Rapado
  3. Institute for Cancer Research, Sutton, London, UK.

    • Nicola E Potter
    • , Frederik W van Delft
    • , Ian Titley
    • , Anthony M Ford
    •  & Mel Greaves
  4. Department of Human Genetics, VIB and University of Leuven, Leuven, Belgium.

    • Peter Van Loo
  5. Northern Institute for Cancer Research, University of Newcastle, Newcastle-upon-Tyne, UK.

    • Frederik W van Delft
  6. Centro Ricerca Tettamanti, Hospital San Gerardo, Monza, Italy.

    • Giovanni Cazzaniga
    •  & Andrea Biondi
  7. Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic.

    • Jan Zuna
  8. Paediatric Malignancy Unit, Molecular Haematology & Cancer Biology Unit, Camelia Botnar Laboratories, Great Ormond Street Hospital for Children and University College London (UCL) Institute of Child Health, London, UK.

    • Helena Kempski
  9. Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA.

    • Markus Muschen
  10. Addenbrooke's National Health Service (NHS) Foundation Trust, Cambridge, UK.

    • Peter J Campbell
  11. Department of Haematology, University of Cambridge, Cambridge, UK.

    • Peter J Campbell

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Contributions

E.P., M.G. and P.J.C. designed the study and wrote the manuscript, with assistance from M.R.S. E.P. designed experiments, performed experiments, analyzed sequencing data and performed and reviewed bioinformatics and statistical analyses. I.R. performed sample preparation, validation experiments and evaluation of sequencing data. Y.L. performed bioinformatics and statistical analyses and wrote the manuscript. D.C.W., L.B.A., I.M. and P.V.L. performed statistical analysis. N.E.P., I.T., F.W.v.D. and A.M.F. performed experiments. G.G., J.T., C.L., S.L.C., J.M., J.H., A.M., K.R., S.N.-Z., M.R., L.S., D.R.J., A.P.B., J.G. and J.W.T. support variant calling algorithms and sequencing analysis platforms. L.M., B.R. and S.O. performed sample preparation and experiments. J.Z., H.K., G.C., M.M. and A.B. provided and prepared samples and experimental materials. All authors reviewed the manuscript during its preparation.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Mel Greaves or Peter J Campbell.

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https://doi.org/10.1038/ng.2874

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