Cited by 236Acute Myeloid Leukemia ResearchEpigenetics and DNA MethylationHematopoietic Stem Cell Transplantation

DNA methylation disruption reshapes the hematopoietic differentiation landscape

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Izzo, Franco, Lee, Stanley C., Poran, Asaf, Chaligne, Ronan, Gaiti, Federico, Gross, Baptiste, Murali, Rekha R., Deochand, Sunil D. +14 more·2020·Nature Genetics

Abstract

Mutations in genes involved in DNA methylation (DNAme; for example, TET2 and DNMT3A) are frequently observed in hematological malignancies 1-3 and clonal hematopoiesis 4,5. Applying single-cell sequencing to murine hematopoietic stem and progenitor cells, we observed that these mutations disrupt hematopoietic differentiation, causing opposite shifts in the frequencies of erythroid versus myelomonocytic progenitors following Tet2 or Dnmt3a loss. Notably, these shifts trace back to transcriptional priming skews in uncommitted hematopoietic stem cells. To reconcile genome-wide DNAme changes with specific erythroid versus myelomonocytic skews, we provide evidence in support of differential sensitivity of transcription factors due to biases in CpG enrichment in their binding motif. Single-cell transcriptomes with targeted genotyping showed similar skews in transcriptional priming of DNMT3A-mutated human clonal hematopoiesis bone marrow progenitors. These data show that DNAme shapes the topography of hematopoietic differentiation, and support a model in which genome-wide methylation changes are transduced to differentiation skews through biases in CpG enrichment of the transcription factor binding motif.

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  • Analysis of DNA methylation and gene expression patterns in mouse and human systems has yet to identify a unifying molecular mechanism to explain the increased fitness of Dnmt3a-mutant hematopoietic stem cells.

    “However, analysis of DNA methylation and gene expression patterns in mouse (15,17) and human (17,18) systems have yet to identify a unifying molecular mechanism to explain the increased fitness of these mutant HSCs.”

    From <i>Txnip</i> Enhances Fitness of <i>Dnmt3a</i> -Mutant Hematopoietic Stem Cells via <i>p21</i> (2022) · cites this paper as [17]

    The paper reports gene-expression and methylation analyses in Dnmt3a-deficient mice and a human DNMT3A-mutant sample (Abstract section; page unavailable). It proposes a potential mechanism for altered lineage priming, but does not establish whether a unifying molecular mechanism explains the increased fitness of mutant HSCs. That specific fitness claim is not supported by the cited passages. (LLM, conf=0.77)

    Experimental — accuracy not yet measured
  • Focal methylation alterations appear physiologically relevant.

    “yet focal methylation alterations appear physiologically relevant (17,18,37,41).”

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Authors
Izzo, F., Lee, S. C., Poran, A., Chaligne, R., Gaiti, F., Gross, B., Murali, R. R., Deochand, S. D., Ang, C., Jones, P. W., Nam, A. S., Kim, K.-T., Kothen-Hill, S., Schulman, R. C., Ki, M., Lhoumaud, P., Skok, J. A., Viny, A. D., Levine, R. L., Kenigsberg, E., Abdel-Wahab, O., & Landau, D. A.
Affiliations
  • New York Genome Center (US)
  • Memorial Sloan Kettering Cancer Center (US)
  • Weill Cornell Medicine (US)
  • NYU Langone Health (US)
  • Icahn School of Medicine at Mount Sinai (US)
Corresponding author
Landau, Dan A.
Venue
Nature Genetics
Published
2020-03-23
Volume
52
Issue
4
Pages
378-387
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
OpenAlex
W3012899267
Cited by
236
References
86
Citations by year
2026: 16 · 2025: 25 · 2024: 46 · 2023: 42 · 2022: 45 · 2021: 38 · 2020: 24
FWCI
23.53
Type
journal article
Language
en
Open access
Locations
  • Nature Genetics (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Burroughs Wellcome Fund
  • Pershing Square Foundation
  • Foundation for the National Institutes of Health (DP2-CA239065)
  • EIF | Stand Up To Cancer (SU2C-AACR-IRG-0616)
  • American Society of Hematology
  • Marie Skłodowska-Curie
  • National Cancer Center
  • U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI R00 CA218896, K08 CA215317)
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (1R35GM122515)
  • Damon Runyon Cancer Research Foundation (DRG 117-15)
  • Edward P. Evans Foundation
  • Leukemia and Lymphoma Society
  • U.S. Department of Health & Human Services | National Institutes of Health (P30 CA008748)
Topics
  • Health Sciences › Medicine › Hematology › Acute Myeloid Leukemia Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Health Sciences › Medicine › Hematology › Hematopoietic Stem Cell Transplantation
Keywords
DNA methylation, hematopoietic differentiation, TET2, DNMT3A, clonal hematopoiesis, hematologic malignancies, hematopoietic stem cells, erythroid progenitor cells, transcriptional priming, transcription factor binding motifs, single-cell transcriptomics, targeted genotyping
MeSH terms
Animals, Cell Differentiation, DNA (Cytosine-5-)-Methyltransferases, DNA-Binding Proteins, Hematopoiesis, Hematopoietic Stem Cells, Humans, Male, Mice, Transgenic, Mutation, Transcription, Genetic, DNA Methylation, Mice, Transcriptome

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