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Molecular-defined clonal evolution in patients with chronic myeloid leukemia independent of the BCR-ABL status

Leukemia volume 28, pages 2292–2299 (2014)Cite this article

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Abstract

To study clonal evolution in chronic myeloid leukemia (CML), we searched for BCR-ABL-independent gene mutations in both Philadelphia chromosome (Ph)-negative and Ph-positive clones in 29 chronic-phase CML patients by targeted deep sequencing of 25 genes frequently mutated in myeloid disorders. Ph-negative clones were analyzed in 14 patients who developed clonal cytogenetic abnormalities in Ph-negative cells during treatment with tyrosine kinase inhibitors (TKI). Mutations were detected in 6/14 patients (43%) affecting the genes DNMT3A, EZH2, RUNX1, TET2, TP53, U2AF1 and ZRSR2. In two patients, the mutations were also found in corresponding Ph-positive diagnostic samples. To further investigate Ph-positive clones, 15 randomly selected CML patients at diagnosis were analyzed. Somatic mutations additional to BCR-ABL were found in 5/15 patients (33%) affecting ASXL1, DNMT3A, RUNX1 and TET2. Analysis of individual hematopoietic colonies at diagnosis revealed that most mutations were part of the Ph-positive clone. In contrast, deep sequencing of subsequent samples during TKI treatment revealed one DNMT3A mutation in Ph-negative cells that was also present in Ph-positive cells at diagnosis, implying that the mutation preceded the BCR-ABL rearrangement. In summary, BCR-ABL-independent gene mutations were frequently found in Ph-negative and Ph-positive clones of CML patients and may be considered as important cofactors in the clonal evolution of CML.

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Acknowledgements

The excellent technical assistance of Mrs Anja Waldau is gratefully acknowledged. The study was funded by the Deutsche José Carreras Leukämie-Stiftung e.V. (DJCLS R12/24) and the Interdisziplinäres Zentrum für Klinische Forschung (IZKF, Jena, Germany). This work was supported by Roche Diagnostics (Mannheim, Germany) as a subproject within the Interlaboratory Robustness of Next-Generation Sequencing (IRON)-II study.

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  1. M Schmidt and J Rinke: These authors contributed equally to this work.

Authors and Affiliations

  1. Abteilung Hämatologie und Internistische Onkologie, Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany

    M Schmidt, J Rinke, V Schäfer, E Obstfelder, C Kunert, J Ziermann, N Winkelmann, E Eigendorff, A Hochhaus & T Ernst

  2. MLL Münchner Leukämie Labor, München, Germany

    S Schnittger, A Kohlmann, T Haferlach & C Haferlach

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Correspondence to T Ernst.

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SS, TH and CH are part owners of the MLL Munich Leukemia Laboratory. AK is employed by the MLL Munich Leukemia Laboratory and has received honoraria from Roche. The remaining authors declare no conflict of interest.

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Schmidt, M., Rinke, J., Schäfer, V. et al. Molecular-defined clonal evolution in patients with chronic myeloid leukemia independent of the BCR-ABL status. Leukemia 28, 2292–2299 (2014). https://doi.org/10.1038/leu.2014.272

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