Abstract

Myelodysplastic syndromes (MDS) frequently progress to acute myeloid leukemia (AML); however, the cells leading to malignant transformation have not been directly elucidated. As progression of MDS to AML in humans provides a biological system to determine the cellular origins and mechanisms of neoplastic transformation, we studied highly fractionated stem cell populations in longitudinal samples of patients with MDS who progressed to AML. Targeted deep sequencing combined with single-cell sequencing of sorted cell populations revealed that stem cells at the MDS stage, including immunophenotypically and functionally defined pre-MDS stem cells (pre-MDS-SC), had a significantly higher subclonal complexity compared to blast cells and contained a large number of aging-related variants. Single-cell targeted resequencing of highly fractionated stem cells revealed a pattern of nonlinear, parallel clonal evolution, with distinct subclones within pre-MDS-SC and MDS-SC contributing to generation of MDS blasts or progression to AML, respectively. Furthermore, phenotypically aberrant stem cell clones expanded during transformation and stem cell subclones that were not detectable in MDS blasts became dominant upon AML progression. These results reveal a crucial role of diverse stem cell compartments during MDS progression to AML and have implications for current bulk cell–focused precision oncology approaches, both in MDS and possibly other cancers that evolve from premalignant conditions, that may miss pre-existing rare aberrant stem cells that drive disease progression and leukemic transformation.

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Data availability

The high-throughput DNA sequencing data have been deposited in the database of Genotypes and Phenotypes (dbGaP) .

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Acknowledgements

We thank P. Schultes from the Department of Cell Biology for expert technical assistance. We thank A. Fiallo from the Einstein Genomics Core Facility for technical assistance in single-cell targeted sequencing, and S. Maqbool and S. Mi from Einstein Epigenomics Core Facility for assistance in targeted sequencing with the HiSeq platform. We thank V. Thiruthuvanathan from the Department of Cell Biology for assistance in processing the patient samples. We also thank W. Li for advice regarding whole-genome amplification, and F. C. Chan, C. Steidl, and H. Steidl for helpful discussion. This work was supported by NIH grants no. R01CA166429, no. R01CA217092 (to U.S.), no. R01HL139487, no. R01DK103961 (to A.V.), and no. K01DK105134 (to B.W.); Translational Research Program grants from the Leukemia & Lymphoma Society (to U.S. and A.V., respectively); a research grant from the Taub Foundation for MDS Research (to U.S.); and a research grant from the Evans Foundation (to A.V.). J.C. was supported by The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract (no. C30292GG). U.S. is a Research Scholar of the Leukemia and Lymphoma Society and the Diane and Arthur B. Belfer Faculty Scholar in Cancer Research of the Albert Einstein College of Medicine. This work was supported through the Albert Einstein Cancer Center core support grant (no. P30CA013330).

Author information

Affiliations

  1. Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA

    • Jiahao Chen
    • , Yun-Ruei Kao
    • , Tihomira I. Todorova
    • , Britta Will
    •  & and Ulrich Steidl
  2. Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA

    • Daqian Sun
    • , Swathi-Rao Narayanagari
    • , Britta Will
    • , Amit Verma
    •  & and Ulrich Steidl
  3. Stem Cell Isolation and Xenotransplantation Facility, Albert Einstein College of Medicine, Bronx, NY, USA

    • Daqian Sun
    •  & Swathi-Rao Narayanagari
  4. Genomics Core Facility, Albert Einstein College of Medicine, Bronx, NY, USA

    • David Reynolds
  5. Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA

    • Cristina Montagna
  6. Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA

    • Cristina Montagna
  7. Department of Medicine (Oncology), Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY, USA

    • Britta Will
    • , Amit Verma
    •  & and Ulrich Steidl
  8. Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA

    • Britta Will
    • , Amit Verma
    •  & and Ulrich Steidl
  9. Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA

    • Amit Verma

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Contributions

J.C., U.S., and A.V. designed the study and analyzed and interpreted data. J.C., Y.K., and T.I.T. collected and analyzed clinical samples. J.C., Y.K., D.S., S.N., and B.W. performed the FACS experiments. J.C. and S.N. performed the xenotransplantation assays. J.C. performed the methylcellulose assay and TCR sequencing. J.C. and D.R. performed single-cell targeted sequencing. C.M., A.V., and U.S. designed the targeted capture panel. J.C. analyzed the sequencing data. J.C., A.V., and U.S. wrote the manuscript. All authors reviewed and approved the final version of the manuscript.

Competing interests

U.S. has received research funding from GlaxoSmithKline, Bayer Healthcare, Aileron Therapeutics, and Novartis; has received compensation for consultancy services and for serving on scientific advisory boards from GlaxoSmithKline, Bayer Healthcare, Celgene, Aileron Therapeutics, Stelexis Therapeutics, and Pieris Pharmaceuticals; and has equity ownership in and is serving on the board of directors of Stelexis Therapeutics. A.V. has received research funding from GlaxoSmithKline, Incyte, MedPacto, Novartis, and Eli Lilly and Company, has received compensation as a scientific advisor to Novartis, Stelexis Therapeutics, Acceleron Pharma, and Celgene, and has equity ownership in Stelexis Therapeutics. B.W. has received research support from Novartis Pharmaceuticals.

Corresponding authors

Correspondence to Amit Verma or and Ulrich Steidl.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–15

  2. Reporting Summary

  3. Supplementary Table 1

    Patient characteristics

  4. Supplementary Table 2

    Genes for targeted capture sequencing

  5. Supplementary Table 3

    Somatic mutations detected by targeted capture sequencing in each patient

  6. Supplementary Table 4

    Antibodies for FACS experiments

  7. Supplementary Table 5

    Primers for single-cell targeted sequencing with Fluidigm platform

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DOI

https://doi.org/10.1038/s41591-018-0267-4