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Genetic variegation of clonal architecture and propagating cells in leukaemia

Nature volume 469, pages 356–361 (2011)Cite this article

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Abstract

Little is known of the genetic architecture of cancer at the subclonal and single-cell level or in the cells responsible for cancer clone maintenance and propagation. Here we have examined this issue in childhood acute lymphoblastic leukaemia in which the ETV6–RUNX1 gene fusion is an early or initiating genetic lesion followed by a modest number of recurrent or ‘driver’ copy number alterations. By multiplexing fluorescence in situ hybridization probes for these mutations, up to eight genetic abnormalities can be detected in single cells, a genetic signature of subclones identified and a composite picture of subclonal architecture and putative ancestral trees assembled. Subclones in acute lymphoblastic leukaemia have variegated genetics and complex, nonlinear or branching evolutionary histories. Copy number alterations are independently and reiteratively acquired in subclones of individual patients, and in no preferential order. Clonal architecture is dynamic and is subject to change in the lead-up to a diagnosis and in relapse. Leukaemia propagating cells, assayed by serial transplantation in NOD/SCID IL2Rγnull mice, are also genetically variegated, mirroring subclonal patterns, and vary in competitive regenerative capacity in vivo. These data have implications for cancer genomics and for the targeted therapy of cancer.

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Figure 1: Examples of subclonal architecture in ALL.
Figure 2: Changes in clonal architecture in ALL.
Figure 3: Genetics of cells propagating NOD/SCID IL2Rγ null mice.
Figure 4: Shift in clonal architecture of ALL after in vivo NOD/SCID IL2Rγ null transplantation.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

SNP array data have been deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession code GSE24412.

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Acknowledgements

This work is supported by specialist programme grants from The Kay Kendall Leukaemia Fund (M.G.) and Leukaemia & Lymphoma Research (M.G., T.E.) and a Deutsche Forschungsgemeinschaft fellowship LU 1474/1-1 (to C.L.). T.E. and C.L. acknowledge support from the Oxford BRC.

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Author notes

  1. Tariq Enver

    Present address: Present address: University College London Cancer Institute, London WC1E 6BT, UK.,

Authors and Affiliations

  1. Section of Haemato-Oncology, The Institute of Cancer Research, Sutton SM2 5NG, UK ,

    Kristina Anderson, Frederik W. van Delft, Caroline M. Bateman, Susan M. Colman, Ian Titley, John Swansbury, Lyndal Kearney & Mel Greaves

  2. MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK ,

    Christoph Lutz, Yanping Guo & Tariq Enver

  3. Paediatric Malignancy Unit, Great Ormond Street Hospital & UCL Institute of Child Health, London WC1N 3JH, UK ,

    Helena Kempski

  4. Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 4LP, UK ,

    Anthony V. Moorman

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Contributions

K.A. carried out the FISH analyses. C.L. and Y.G. conducted the in vivo experiments. C.M.B. analysed the SNP array and FISH analysis of the patient with aplasia and ALL. S.M.C. and I.T. performed cell immunostaining and sorting. F.W.v.D. provided SNP array data. H.K., A.V.M. and J.S. provided patient data and samples. T.E. advised on design and interpretation of in vivo experiments. L.K. supervised the FISH studies. L.K. and M.G. designed the overall study. M.G. wrote the paper with critical input from T.E., L.K. and other authors.

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Correspondence to Mel Greaves.

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Anderson, K., Lutz, C., van Delft, F. et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469, 356–361 (2011). https://doi.org/10.1038/nature09650

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