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

1 Scopus citations

Abstract

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
Volume80
Issue number3
DOIs
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

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 Minnesota) and the Minnesota Supercomputing Institute. This work and Z. Sachs were supported by the American Cancer Society, Frederick A. DeLuca Foundation, Mentored Research Scholar Grant (MRSG-16-195-01-DDC); the Clinical and Translational Science Institute at the University of Minnesota KL2 Career Development and K to R01 awards (NIH's National Center for Advancing Translational Sciences, grants KL2TR002492 and UL1TR002494); the Lois and Richard King Assistant Professorship in Medicine, the American Cancer Society Institutional Research Grant at the University of Minnesota (124166-IRG-58-001-55-IRG12); the Masonic Cancer Center at the University of Minnesota Translational Working Group Award and Genetic Mechanisms of Cancer Award; the University of Minnesota Department of Medicine Women's Early Research Career Award; the University of Minnesota Genomic Center Pilot Award; the Randy Shaver Cancer Research and Community Fund, the Masonic Cancer Center, the Division of Hematology, Oncology, and Transplantation, Department of Medicine; and the University of Minnesota Foundation donors. K. Sachs was supported in part by an award from the Muscular Dystrophy Association (MDA Award #574137). D. Largaespada was supported by an American Cancer Society Research Professorship.

Publisher Copyright:
© 2020 American Association for Cancer Research.

PubMed: MeSH publication types

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

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