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DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction

Nature Genetics volume 41, pages 1207–1215 (2009)Cite this article

Abstract

DNA methylation is a dynamic epigenetic mark that undergoes extensive changes during differentiation of self-renewing stem cells. However, whether these changes are the cause or consequence of stem cell fate remains unknown. Here, we show that alternative functional programs of hematopoietic stem cells (HSCs) are governed by gradual differences in methylation levels. Constitutive methylation is essential for HSC self-renewal but dispensable for homing, cell cycle control and suppression of apoptosis. Notably, HSCs from mice with reduced DNA methyltransferase 1 activity cannot suppress key myeloerythroid regulators and thus can differentiate into myeloerythroid, but not lymphoid, progeny. A similar methylation dosage effect controls stem cell function in leukemia. These data identify DNA methylation as an essential epigenetic mechanism to protect stem cells from premature activation of predominant differentiation programs and suggest that methylation dynamics determine stem cell functions in tissue homeostasis and cancer.

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Figure 1: DNMT1 is indispensable for early hematopoiesis.
Figure 2: DNA methylation is required for HSC homeostasis and self-renewal.
Figure 3: DNA methylation controls myeloerythroid versus lymphoid differentiation of HSCs.
Figure 4: DNA methylation controls LSC functions.
Figure 5: DNA hypomethylation leads to derepression of myeloerythroid genes in HSCs.
Figure 6: Epigenetic Gata1 and Cd48 activation in renewal of myeloid leukemia cells.

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References

  1. Weissman, I. Stem cell research: paths to cancer therapies and regenerative medicine. J. Am. Med. Assoc. 294, 1359–1366 (2005).

    Article  CAS  Google Scholar 

  2. Passegué, E., Jamieson, C.H., Ailles, L.E. & Weissman, I.L. Normal and leukemic hematopoiesis: are leukemias a stem cell disorder or a reacquisition of stem cell characteristics? Proc. Natl. Acad. Sci. USA 100 (Suppl. 1), 11842–11849 (2003).

    Article  Google Scholar 

  3. Morrison, S.J. & Weissman, I.L. The long-term repopulating subset of hematopoietic stem cells is deterministic and isolatable by phenotype. Immunity 1, 661–673 (1994).

    Article  CAS  Google Scholar 

  4. Osawa, M., Hanada, K., Hamada, H. & Nakauchi, H. Long-term lymphohematopoietic reconstitution by a single CD34-low/negative hematopoietic stem cell. Science 273, 242–245 (1996).

    Article  CAS  Google Scholar 

  5. Orkin, S.H. Diversification of haematopoietic stem cells to specific lineages. Nat. Rev. Genet. 1, 57–64 (2000).

    Article  CAS  Google Scholar 

  6. Rosenbauer, F. & Tenen, D.G. Transcription factors in myeloid development: balancing differentiation with transformation. Nat. Rev. Immunol. 7, 105–117 (2007).

    Article  CAS  Google Scholar 

  7. Bottardi, S., Ghiam, A.F., Bergeron, F. & Milot, E. Lineage-specific transcription factors in multipotent hematopoietic progenitors: a little bit goes a long way. Cell Cycle 6, 1035–1039 (2007).

    Article  CAS  Google Scholar 

  8. Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33 Suppl. 245–254 (2003).

    Article  CAS  Google Scholar 

  9. Bibikova, M., Laurent, L.C., Ren, B., Loring, J.F. & Fan, J.B. Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell 2, 123–134 (2008).

    Article  CAS  Google Scholar 

  10. Tadokoro, Y., Ema, H., Okano, M., Li, E. & Nakauchi, H. De novo DNA methyltransferase is essential for self-renewal, but not for differentiation, in hematopoietic stem cells. J. Exp. Med. 204, 715–722 (2007).

    Article  CAS  Google Scholar 

  11. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).

    Article  CAS  Google Scholar 

  12. Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat. Genet. 27, 31–39 (2001).

    Article  CAS  Google Scholar 

  13. Kühn, R., Schwenk, F., Aguet, M. & Rajewsky, K. Inducible gene targeting in mice. Science 269, 1427–1429 (1995).

    Article  Google Scholar 

  14. Gaudet, F. et al. Induction of tumors in mice by genomic hypomethylation. Science 300, 489–492 (2003).

    Article  CAS  Google Scholar 

  15. Adolfsson, J. et al. Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential a revised road map for adult blood lineage commitment. Cell 121, 295–306 (2005).

    Article  CAS  Google Scholar 

  16. Månsson, R. et al. Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity 26, 407–419 (2007).

    Article  Google Scholar 

  17. Kiel, M.J. et al. SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121, 1109–1121 (2005).

    Article  CAS  Google Scholar 

  18. Domen, J., Gandy, K.L. & Weissman, I.L. Systemic overexpression of BCL-2 in the hematopoietic system protects transgenic mice from the consequences of lethal irradiation. Blood 91, 2272–2282 (1998).

    CAS  PubMed  Google Scholar 

  19. Busslinger, M. Transcriptional control of early B cell development. Annu. Rev. Immunol. 22, 55–79 (2004).

    Article  CAS  Google Scholar 

  20. Medina, K.L. & Singh, H. Genetic networks that regulate B lymphopoiesis. Curr. Opin. Hematol. 12, 203–209 (2005).

    Article  CAS  Google Scholar 

  21. Rickert, R.C., Roes, J. & Rajewsky, K. B lymphocyte-specific, Cre-mediated mutagenesis in mice. Nucleic Acids Res. 25, 1317–1318 (1997).

    Article  CAS  Google Scholar 

  22. Srinivas, S. et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus. BMC Dev. Biol. 1, 4 (2001).

    Article  CAS  Google Scholar 

  23. Luo, H. et al. c-Myc rapidly induces acute myeloid leukemia in mice without evidence of lymphoma-associated antiapoptotic mutations. Blood 106, 2452–2461 (2005).

    Article  CAS  Google Scholar 

  24. Somervaille, T.C. & Cleary, M.L. Identification and characterization of leukemia stem cells in murine MLL-AF9 acute myeloid leukemia. Cancer Cell 10, 257–268 (2006).

    Article  CAS  Google Scholar 

  25. Krivtsov, A.V. et al. Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 442, 818–822 (2006).

    Article  CAS  Google Scholar 

  26. Huntly, B.J. et al. MOZ-TIF2, but not BCR-ABL, confers properties of leukemic stem cells to committed murine hematopoietic progenitors. Cancer Cell 6, 587–596 (2004).

    Article  CAS  Google Scholar 

  27. Deshpande, A.J. et al. Acute myeloid leukemia is propagated by a leukemic stem cell with lymphoid characteristics in a mouse model of CALM/AF10-positive leukemia. Cancer Cell 10, 363–374 (2006).

    Article  CAS  Google Scholar 

  28. Landgrebe, J., Wurst, W. & Welzl, G. Permutation-validated principal components analysis of microarray data. Genome Biol. 3, RESEARCH0019 (2002).

    Article  Google Scholar 

  29. Akashi, K., Traver, D., Miyamoto, T. & Weissman, I.L. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 404, 193–197 (2000).

    Article  CAS  Google Scholar 

  30. Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).

    Article  CAS  Google Scholar 

  31. Iwasaki, H. et al. GATA-1 converts lymphoid and myelomonocytic progenitors into the megakaryocyte/erythrocyte lineages. Immunity 19, 451–462 (2003).

    Article  CAS  Google Scholar 

  32. Pongubala, J.M. et al. Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5. Nat. Immunol. 9, 203–215 (2008).

    Article  CAS  Google Scholar 

  33. Klug, M. & Rehli, M. Functional analysis of promoter CpG methylation using a CpG-free luciferase reporter vector. Epigenetics 1, 127–130 (2006).

    Article  Google Scholar 

  34. Fouse, S.D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008).

    Article  CAS  Google Scholar 

  35. Yoo, C.B. & Jones, P.A. Epigenetic therapy of cancer: past, present and future. Nat. Rev. Drug Discov. 5, 37–50 (2006).

    Article  CAS  Google Scholar 

  36. Flotho, C. et al. The DNA methyltransferase inhibitors azacitidine, decitabine and zebularine exert differential effects on cancer gene expression in acute myeloid leukemia cells. Leukemia 23, 1019–1028 (2009).

    Article  CAS  Google Scholar 

  37. Ehlers, A. et al. Histone acetylation and DNA demethylation of B cells result in a Hodgkin-like phenotype. Leukemia 22, 835–841 (2008).

    Article  CAS  Google Scholar 

  38. Hackanson, B. et al. Epigenetic modification of CCAAT/enhancer binding protein alpha expression in acute myeloid leukemia. Cancer Res. 68, 3142–3151 (2008).

    Article  CAS  Google Scholar 

  39. Walsh, J.C. et al. Cooperative and antagonistic interplay between PU.1 and GATA-2 in the specification of myeloid cell fates. Immunity 17, 665–676 (2002).

    Article  CAS  Google Scholar 

  40. Prinz, M. et al. Distinct and nonredundant in vivo functions of IFNAR on myeloid cells limit autoimmunity in the central nervous system. Immunity 28, 675–686 (2008).

    Article  CAS  Google Scholar 

  41. Seet, C.S., Brumbaugh, R.L. & Kee, B.L. Early B cell factor promotes B lymphopoiesis with reduced interleukin 7 responsiveness in the absence of E2A. J. Exp. Med. 199, 1689–1700 (2004).

    Article  CAS  Google Scholar 

  42. Rosenbauer, F. et al. Acute myeloid leukemia induced by graded reduction of a lineage-specific transcription factor, PU.1. Nat. Genet. 36, 624–630 (2004).

    Article  CAS  Google Scholar 

  43. Walsh, C.P., Chaillet, J.R. & Bestor, T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117 (1998).

    Article  CAS  Google Scholar 

  44. Ushijima, T. et al. Establishment of methylation-sensitive-representational difference analysis and isolation of hypo- and hypermethylated genomic fragments in mouse liver tumors. Proc. Natl. Acad. Sci. USA 94, 2284–2289 (1997).

    Article  CAS  Google Scholar 

  45. Cheshier, S.H., Morrison, S.J., Liao, X. & Weissman, I.L. In vivo proliferation and cell cycle kinetics of long-term self-renewing hematopoietic stem cells. Proc. Natl. Acad. Sci. USA 96, 3120–3125 (1999).

    Article  CAS  Google Scholar 

  46. Kaiho, S. & Mizuno, K. Sensitive assay systems for detection of hemoglobin with 2,7-diaminofluorene: histochemistry and colorimetry for erythrodifferentiation. Anal. Biochem. 149, 117–120 (1985).

    Article  CAS  Google Scholar 

  47. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785–15790 (2005).

    Article  CAS  Google Scholar 

  48. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57, 289–300 (1995).

    Google Scholar 

  49. Nicolis, S. et al. An erythroid specific enhancer upstream to the gene encoding the cell-type specific transcription factor GATA-1. Nucleic Acids Res. 19, 5285–5291 (1991).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank V. Malchin, C. Graubmann and J.F. Zinke for their excellent technical assistance; J. Schoenheit for his help with real-time PCR; H.P. Rahn and Z. Ma for assistance with high-speed cell sorting; M.L. Cleary (Stanford University School of Medicine), S. Fillatreau (Deutsches Rheuma-Forschungszentrum), A. Müller (University of Würzburg), K. Rajewsky (Harvard Medical School), M. Rehli (University of Regensburg), M. Tomasson (Washington University School of Medicine), B.L. Kee (University of Chicago) and T. Somervaille (Stanford University School of Medicine) for reagents; members of the Rosenbauer lab for discussions; D.G. Tenen for support during the initial phase of this study; and C. Plass, C. Müller-Tidow, C. Bonifer and D.G. Tenen for advice on the manuscript. This work was supported by grants from the German Research Foundation, the German Cancer Aid (Mildred Scheel) and the Helmholtz Association of German Research Centers to F.R. S.E.W.J. is the recipient of a strategic appointment grant from the UK Medical Research Council.

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  1. Ann-Marie Bröske and Lena Vockentanz: These authors contributed equally to this work.

Authors and Affiliations

  1. Max Delbrück Center for Molecular Medicine, Berlin, Germany

    Ann-Marie Bröske, Lena Vockentanz, Matthew R Huska, Marina Scheller, Christiane Kuhl, Andreas Enns, Achim Leutz, Miguel A Andrade-Navarro & Frank Rosenbauer

  2. Hematopoietic Stem Cell Laboratory, Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden

    Shabnam Kharazi & Sten Eirik W Jacobsen

  3. European Molecular Biology Laboratory, Mouse Biology Unit, Monterotondo, Italy

    Elena Mancini & Claus Nerlov

  4. Department of Neuropathology, University of Freiburg, Freiburg, Germany

    Marco Prinz

  5. The Whitehead Institute, Cambridge, Massachusetts, USA

    Rudolf Jaenisch

  6. Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England

    Sten Eirik W Jacobsen

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  1. Ann-Marie Bröske
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Contributions

A.-M.B., L.V., S.K., E.M., C.K., M.S. and A.E. conducted experiments. M.R.H. and M.A.A.-N. analyzed the microarray data. A.-M.B., L.V. and F.R. wrote the manuscript. R.J. provided key mouse strains and gave advice on the manuscript. M.P. conducted the pathological analysis. C.N., A.L. and S.E.W.J. provided essential ideas, experimental support and suggestions on the manuscript. F.R. designed and supervised the project and provided financial support.

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Correspondence to Frank Rosenbauer.

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Bröske, AM., Vockentanz, L., Kharazi, S. et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet 41, 1207–1215 (2009). https://doi.org/10.1038/ng.463

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