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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The high-throughput DNA sequencing data have been deposited in the database of Genotypes and Phenotypes (dbGaP) .
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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).
Supplementary Figures 1–15
Genes for targeted capture sequencing
Somatic mutations detected by targeted capture sequencing in each patient
Antibodies for FACS experiments
Primers for single-cell targeted sequencing with Fluidigm platform
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Nature Cell Biology (2019)