Single-cell gene expression analyses reveal distinct self-renewing and proliferating subsets in the leukemia stem cell compartment in acute myeloid leukemia

Karen Sachs, Aaron L. Sarver, Klara E. Noble-Orcutt, Rebecca S. LaRue, Marie Lue Antony, Daniel Chang, Yoonkyu Lee, Connor M. Navis, Alexandria L. Hillesheim, Ian R. Nykaza, Ngoc A. Ha, Conner J. Hansen, Fatma K. Karadag, Rachel J. Bergerson, Michael R. Verneris, Matthew M. Meredith, Matthew L. Schomaker, Michael A. Linden, Chad L. Myers, David A. LargaespadaZohar Sachs

Research output: Contribution to journalArticlepeer-review


Standard chemotherapy for acute myeloid leukemia (AML) targets proliferative cells and efficiently induces complete remission; however, many patients relapse and die of their disease. Relapse is caused by leukemia stem cells (LSC), the cells with self-renewal capacity. Self-renewal and proliferation are separate functions in normal hematopoietic stem cells (HSC) in steady-state conditions. If these functions are also separate functions in LSCs, then antiproliferative therapies may fail to target self-renewal, allowing for relapse. We investigated whether proliferation and self-renewal are separate functions in LSCs as they often are in HSCs. Distinct transcriptional profiles within LSCs of Mll-AF9/NRASG12V murine AML were identified using single-cell RNA sequencing. Single-cell qPCR revealed that these genes were also differentially expressed in primary human LSCs and normal human HSPCs. A smaller subset of these genes was upregulated in LSCs relative to HSPCs; this subset of genes constitutes “LSC-specific” genes in human AML. To assess the differences between these profiles, we identified cell surface markers, CD69 and CD36, whose genes were differentially expressed between these profiles. In vivo mouse reconstitution assays resealed that only CD69High LSCs were capable of self-renewal and were poorly proliferative. In contrast, CD36High LSCs were unable to transplant leukemia but were highly proliferative. These data demonstrate that the transcriptional foundations of self-renewal and proliferation are distinct in LSCs as they often are in normal stem cells and suggest that therapeutic strategies that target self-renewal, in addition to proliferation, are critical to prevent relapse and improve survival in AML.

Original languageEnglish (US)
Pages (from-to)458-470
Number of pages13
JournalCancer Research
Issue number3
StatePublished - Feb 1 2020

Bibliographical note

Funding Information:
The authors thank Michael Franklin for editorial assistance. The authors thank Katy Richards-Hrdlicka and Jason McKinney from Fluidigm for helping us to assess and ensure the quality of the single-cell qPCR data. This work utilized the resources of the University of Minnesota Hematological Malignancies Tissue Bank, which is supported by the NCI (5P30CA077598-18), Minnesota Masonic Charities, and the Killebrew-Thompson Memorial Fund through the Cancer Experimental Therapeutics Initiative (CETI); the Flow Cytometry Resource and other services of the Masonic Cancer Center (which is supported by NIH 2P30CA077598-21) at the University of Minnesota; Jerry Daniel and Darrell Johnson and the University of Minnesota Genomics Center Fluidigm C1 single-cell capture and BioMark qPCR and next-generation sequencing services; the Mass Cytometry Shared Resource at the University of Minnesota (which is supported by the Office of the Vice President for Research, University of

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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