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Spotlight on Epigenetics in Hematologic Malignancies

Origins of aberrant DNA methylation in acute myeloid leukemia

Abstract

Aberrant DNA methylation patterns are a characteristic feature of cancer including myeloid malignancies such as acute myeloid leukemia (AML). The mechanisms behind aberrant DNA methylation have long remained obscure. New genome-wide studies have elucidated the genome and epigenome of solid tumors and AML. Molecular subtypes of AML were found to exhibit highly distinct DNA methylation profiles. Clonal evolution patterns of AML were recently dissected and might shape epigenetic dysregulation. Also, recurrent mutations in epigenetic modifying enzymes were identified in AML and linked to distinct DNA methylation signatures. The genetic background, thus, takes center stage as a driver of epigenetic dysregulation in AML. First mechanistic insights into the dysregulation of DNA methylation by recurrent mutations have already been gained. Other studies suggest that epigenomic plasticity and aging-associated changes in DNA methylation also contribute extensively to aberrant DNA methylation in cancer. Epigenetic dysregulation, therefore, seems to also occur independently of the genetic background. Furthermore, global changes in chromatin conformation and nuclear organization have also been proposed as potential contributors to aberrant DNA methylation. This review will summarize and discuss current concepts regarding the mechanisms behind aberrant DNA methylation in cancer and specifically AML.

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References

  1. Holliday R, Pugh JE . DNA modification mechanisms and gene activity during development. Science 1975; 187: 226–232.

    CAS  PubMed  Google Scholar 

  2. Riggs AD . X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 1975; 14: 9–25.

    CAS  PubMed  Google Scholar 

  3. Feinberg AP, Tycko B . The history of cancer epigenetics. Nat Rev Cancer 2004; 4: 143–153.

    CAS  PubMed  Google Scholar 

  4. Jones PA . Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13: 484–492.

    CAS  PubMed  Google Scholar 

  5. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43: 768–775.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41: 178–186.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell 2010; 17: 13–27.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 2012; 8: e1002781.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013; 368: 2059–2074.

    Google Scholar 

  10. Schoofs T, Rohde C, Hebestreit K, Klein HU, Gollner S, Schulze I et al. DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Blood 2013; 121: 178–187.

    CAS  PubMed  Google Scholar 

  11. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med 2010; 363: 2424–2433.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Delhommeau F, Dupont S, Della Valle V, James C, Trannoy S, Masse A et al. Mutation in TET2 in myeloid cancers. N Engl J Med 2009; 360: 2289–2301.

    Article  PubMed  Google Scholar 

  13. Patel JP, Gonen M, Figueroa ME, Fernandez H, Sun Z, Racevskis J et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med 2012; 366: 1079–1089.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Shih AH, Abdel-Wahab O, Patel JP, Levine RL . The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer 2012; 12: 599–612.

    CAS  PubMed  Google Scholar 

  15. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC et al. The origin and evolution of mutations in acute myeloid leukemia. Cell 2012; 150: 264–278.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Sasaki M, Knobbe CB, Munger JC, Lind EF, Brenner D, Brustle A et al. IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics. Nature 2012; 488: 656–659.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Busque L, Patel JP, Figueroa ME, Vasanthakumar A, Provost S, Hamilou Z et al. Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis. Nat Genet 2012; 44: 1179–1181.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Yan XJ, Xu J, Gu ZH, Pan CM, Lu G, Shen Y et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 2011; 43: 309–315.

    CAS  PubMed  Google Scholar 

  19. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 2010; 18: 553–567.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 2002; 295: 1079–1082.

    CAS  PubMed  Google Scholar 

  21. Liu S, Shen T, Huynh L, Klisovic MI, Rush LJ, Ford JL et al. Interplay of RUNX1/MTG8 and DNA methyltransferase 1 in acute myeloid leukemia. Cancer Res 2005; 65: 1277–1284.

    CAS  PubMed  Google Scholar 

  22. Krivtsov AV, Armstrong SA . MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer 2007; 7: 823–833.

    CAS  PubMed  Google Scholar 

  23. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E et al. The accessible chromatin landscape of the human genome. Nature 2012; 489: 75–82.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Yang H, Ye D, Guan KL, Xiong Y . IDH1 and IDH2 mutations in tumorigenesis: mechanistic insights and clinical perspectives. Clin Cancer Res 2012; 18: 5562–5571.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Tiwari VK, McGarvey KM, Licchesi JD, Ohm JE, Herman JG, Schubeler D et al. PcG proteins, DNA methylation, and gene repression by chromatin looping. PLoS Biol 2008; 6: 2911–2927.

    CAS  PubMed  Google Scholar 

  26. Rickman DS, Soong TD, Moss B, Mosquera JM, Dlabal J, Terry S et al. Oncogene-mediated alterations in chromatin conformation. Proc Natl Acad Sci USA 2012; 109: 9083–9088.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Sexton T, Schober H, Fraser P, Gasser SM . Gene regulation through nuclear organization. Nat Struct Mol Biol 2007; 14: 1049–1055.

    CAS  PubMed  Google Scholar 

  28. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2012; 44: 40–46.

    CAS  Google Scholar 

  29. Hsu PY, Hsu HK, Singer GA, Yan PS, Rodriguez BA, Liu JC et al. Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res 2010; 20: 733–744.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ . Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 2006; 38: 540–549.

    CAS  PubMed  Google Scholar 

  31. Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T et al. Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 2013; 23: 9–22.

    CAS  PubMed  Google Scholar 

  32. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005; 102: 10604–10609.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, Sommer IE et al. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One 2009; 4: e6767.

    PubMed  PubMed Central  Google Scholar 

  34. Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell 2013; 49: 359–367.

    CAS  PubMed  Google Scholar 

  35. Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A et al. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell 2013; 12: 413–425.

    CAS  PubMed  Google Scholar 

  36. Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010; 468: 839–843.

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Smith ZD, Meissner A . DNA methylation: roles in mammalian development. Nat Rev Genet 2013; 14: 204–220.

    CAS  PubMed  Google Scholar 

  38. Schoofs T, Muller-Tidow C . DNA methylation as a pathogenic event and as a therapeutic target in AML. Cancer Treat Rev 2011; 37 (Suppl 1): S13–S18.

    CAS  PubMed  Google Scholar 

  39. Ehrlich M . DNA methylation in cancer: too much, but also too little. Oncogene 2002; 21: 5400–5413.

    CAS  PubMed  Google Scholar 

  40. Bullinger L, Ehrich M, Dohner K, Schlenk RF, Dohner H, Nelson MR et al. Quantitative DNA methylation predicts survival in adult acute myeloid leukemia. Blood 2010; 115: 636–642.

    CAS  PubMed  Google Scholar 

  41. Deneberg S, Grovdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A et al. Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia 2010; 24: 932–941.

    CAS  PubMed  Google Scholar 

  42. Wong IH, Ng MH, Huang DP, Lee JC . Aberrant p15 promoter methylation in adult and childhood acute leukemias of nearly all morphologic subtypes: potential prognostic implications. Blood 2000; 95: 1942–1949.

    CAS  PubMed  Google Scholar 

  43. Shimamoto T, Ohyashiki JH, Ohyashiki K . Methylation of p15(INK4b) and E-cadherin genes is independently correlated with poor prognosis in acute myeloid leukemia. Leuk Res 2005; 29: 653–659.

    CAS  PubMed  Google Scholar 

  44. Agrawal S, Hofmann WK, Tidow N, Ehrich M, van den Boom D, Koschmieder S et al. The C/EBPdelta tumor suppressor is silenced by hypermethylation in acute myeloid leukemia. Blood 2007; 109: 3895–3905.

    CAS  PubMed  Google Scholar 

  45. Agrawal S, Unterberg M, Koschmieder S, zur Stadt U, Brunnberg U, Verbeek W et al. DNA methylation of tumor suppressor genes in clinical remission predicts the relapse risk in acute myeloid leukemia. Cancer Res 2007; 67: 1370–1377.

    CAS  PubMed  Google Scholar 

  46. Jiang Y, Dunbar A, Gondek LP, Mohan S, Rataul M, O'Keefe C et al. Aberrant DNA methylation is a dominant mechanism in MDS progression to AML. Blood 2009; 113: 1315–1325.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M et al. Genetic alterations during colorectal-tumor development. N Engl J Med 1988; 319: 525–532.

    CAS  PubMed  Google Scholar 

  48. Magrangeas F, Avet-Loiseau H, Gouraud W, Lode L, Decaux O, Godmer P et al. Minor clone provides a reservoir for relapse in multiple myeloma. Leukemia 2013; 27: 473–481.

    CAS  PubMed  Google Scholar 

  49. Greaves M, Maley CC . Clonal evolution in cancer. Nature 2012; 481: 306–313.

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Walter MJ, Shen D, Shao J, Ding L, White BS, Kandoth C et al. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia 2013; 27: 1275–1282.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med 2012; 4: 149ra118.

    PubMed  PubMed Central  Google Scholar 

  52. Fernandez C, Santos-Silva MC, Lopez A, Matarraz S, Jara-Acevedo M, Ciudad J et al. Newly diagnosed adult AML and MPAL patients frequently show clonal residual hematopoiesis. Leukemia 2013; ; e-pub ahead of print 12 April 2013; doi:10.1038/leu.2013.109.

    CAS  PubMed  Google Scholar 

  53. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012; 481: 506–510.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Stratton MR . Exploring the genomes of cancer cells: progress and promise. Science 2011; 331: 1553–1558.

    CAS  PubMed  Google Scholar 

  55. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ et al. The genomic landscapes of human breast and colorectal cancers. Science 2007; 318: 1108–1113.

    CAS  PubMed  Google Scholar 

  56. Timp W, Feinberg AP . Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013; 13: 497–510.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Pina C, Fugazza C, Tipping AJ, Brown J, Soneji S, Teles J et al. Inferring rules of lineage commitment in haematopoiesis. Nat Cell Biol 2012; 14: 287–294.

    CAS  PubMed  Google Scholar 

  58. Krivtsov AV, Figueroa ME, Sinha AU, Stubbs MC, Feng Z, Valk PJ et al. Cell of origin determines clinically relevant subtypes of MLL-rearranged AML. Leukemia 2013; 27: 852–860.

    CAS  PubMed  Google Scholar 

  59. Broske AM, Vockentanz L, Kharazi S, Huska MR, Mancini E, Scheller M et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet 2009; 41: 1207–1215.

    PubMed  Google Scholar 

  60. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 2010; 467: 338–342.

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Rideout WM 3rd, Coetzee GA, Olumi AF, Jones PA . 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science 1990; 249: 1288–1290.

    CAS  PubMed  Google Scholar 

  62. de The H, Lavau C, Marchio A, Chomienne C, Degos L, Dejean A . The PML-RAR alpha fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR. Cell 1991; 66: 675–684.

    CAS  PubMed  Google Scholar 

  63. Nucifora G, Rowley JD . AML1 and the 8;21 and 3;21 translocations in acute and chronic myeloid leukemia. Blood 1995; 86: 1–14.

    CAS  PubMed  Google Scholar 

  64. Tenen DG . Disruption of differentiation in human cancer: AML shows the way. Nat Rev Cancer 2003; 3: 89–101.

    CAS  PubMed  Google Scholar 

  65. Haferlach T, Kohlmann A, Wieczorek L, Basso G, Kronnie GT, Bene MC et al. Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol 2010; 28: 2529–2537.

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Corral J, Lavenir I, Impey H, Warren AJ, Forster A, Larson TA et al. An Mll-AF9 fusion gene made by homologous recombination causes acute leukemia in chimeric mice: a method to create fusion oncogenes. Cell 1996; 85: 853–861.

    CAS  PubMed  Google Scholar 

  67. Rhoades KL, Hetherington CJ, Harakawa N, Yergeau DA, Zhou L, Liu LQ et al. Analysis of the role of AML1-ETO in leukemogenesis, using an inducible transgenic mouse model. Blood 2000; 96: 2108–2115.

    CAS  PubMed  Google Scholar 

  68. Schwieger M, Lohler J, Friel J, Scheller M, Horak I, Stocking C . AML1-ETO inhibits maturation of multiple lymphohematopoietic lineages and induces myeloblast transformation in synergy with ICSBP deficiency. J Exp Med 2002; 196: 1227–1240.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Westervelt P, Lane AA, Pollock JL, Oldfather K, Holt MS, Zimonjic DB et al. High-penetrance mouse model of acute promyelocytic leukemia with very low levels of PML-RARalpha expression. Blood 2003; 102: 1857–1865.

    CAS  PubMed  Google Scholar 

  70. Welch JS, Yuan W, Ley TJ . PML-RARA can increase hematopoietic self-renewal without causing a myeloproliferative disease in mice. J Clin Invest 2011; 121: 1636–1645.

    PubMed  PubMed Central  Google Scholar 

  71. Wojiski S, Guibal FC, Kindler T, Lee BH, Jesneck JL, Fabian A et al. PML-RARalpha initiates leukemia by conferring properties of self-renewal to committed promyelocytic progenitors. Leukemia 2009; 23: 1462–1471.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Miyamoto T, Nagafuji K, Akashi K, Harada M, Kyo T, Akashi T et al. Persistence of multipotent progenitors expressing AML1/ETO transcripts in long-term remission patients with t(8;21) acute myelogenous leukemia. Blood 1996; 87: 4789–4796.

    CAS  PubMed  Google Scholar 

  73. Lengfelder E, Hanfstein B, Haferlach C, Braess J, Krug U, Spiekermann K et al. Outcome of elderly patients with acute promyelocytic leukemia: results of the German Acute Myeloid Leukemia Cooperative Group. Ann Hematol 2013; 92: 41–52.

    PubMed  Google Scholar 

  74. Lugthart S, Figueroa ME, Bindels E, Skrabanek L, Valk PJ, Li Y et al. Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1. Blood 2011; 117: 234–241.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Liu S, Klisovic RB, Vukosavljevic T, Yu J, Paschka P, Huynh L et al. Targeting AML1/ETO-histone deacetylase repressor complex: a novel mechanism for valproic acid-mediated gene expression and cellular differentiation in AML1/ETO-positive acute myeloid leukemia cells. J Pharmacol Exp Ther 2007; 321: 953–960.

    CAS  PubMed  Google Scholar 

  76. Hoemme C, Peerzada A, Behre G, Wang Y, McClelland M, Nieselt K et al. Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood 2008; 111: 2887–2895.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Steffen B, Serve H, Berdel WE, Agrawal S, Linggi B, Buchner T et al. Specific protein redirection as a transcriptional therapy approach for t(8;21) leukemia. Proc Natl Acad Sci USA 2003; 100: 8448–8453.

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F et al. PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia. Cancer Cell 2010; 17: 173–185.

    CAS  PubMed  Google Scholar 

  79. Saeed S, Logie C, Francoijs KJ, Frige G, Romanenghi M, Nielsen FG et al. Chromatin accessibility, p300, and histone acetylation define PML-RARalpha and AML1-ETO binding sites in acute myeloid leukemia. Blood 2012; 120: 3058–3068.

    CAS  PubMed  Google Scholar 

  80. Alvarez S, Suela J, Valencia A, Fernandez A, Wunderlich M, Agirre X et al. DNA methylation profiles and their relationship with cytogenetic status in adult acute myeloid leukemia. PLoS One 2010; 5: e12197.

    PubMed  PubMed Central  Google Scholar 

  81. Bernt KM, Armstrong SA . Targeting epigenetic programs in MLL-rearranged leukemias. Hematol Am Soc Hematol Educ Prog 2011; 2011: 354–360.

    Google Scholar 

  82. de Boer J, Walf-Vorderwulbecke V, Williams O . In focus: MLL-rearranged leukemia. Leukemia 2013; 27: 1224–1228.

    CAS  PubMed  Google Scholar 

  83. Maiques-Diaz A, Chou FS, Wunderlich M, Gomez-Lopez G, Jacinto FV, Rodriguez-Perales S et al. Chromatin modifications induced by the AML1-ETO fusion protein reversibly silence its genomic targets through AML1 and Sp1 binding motifs. Leukemia 2012; 26: 1329–1337.

    CAS  PubMed  Google Scholar 

  84. Ptasinska A, Assi SA, Mannari D, James SR, Williamson D, Dunne J et al. Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding. Leukemia 2012; 26: 1829–1841.

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Wang J, Hoshino T, Redner RL, Kajigaya S, Liu JM . ETO, fusion partner in t(8;21) acute myeloid leukemia, represses transcription by interaction with the human N-CoR/mSin3/HDAC1 complex. Proc Natl Acad Sci USA 1998; 95: 10860–10865.

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Wang K, Wang P, Shi J, Zhu X, He M, Jia X et al. PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia. Cancer Cell 2010; 17: 186–197.

    CAS  PubMed  Google Scholar 

  87. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011; 480: 490–495.

    CAS  PubMed  Google Scholar 

  88. Renneville A, Roumier C, Biggio V, Nibourel O, Boissel N, Fenaux P et al. Cooperating gene mutations in acute myeloid leukemia: a review of the literature. Leukemia 2008; 22: 915–931.

    CAS  PubMed  Google Scholar 

  89. Langabeer SE, Gale RE, Rollinson SJ, Morgan GJ, Linch DC . Mutations of the AML1 gene in acute myeloid leukemia of FAB types M0 and M7. Genes Chromosomes Cancer 2002; 34: 24–32.

    CAS  PubMed  Google Scholar 

  90. Leroy H, Roumier C, Huyghe P, Biggio V, Fenaux P, Preudhomme C . CEBPA point mutations in hematological malignancies. Leukemia 2005; 19: 329–334.

    CAS  PubMed  Google Scholar 

  91. Kamashev D, Vitoux D, De The H . PML-RARA-RXR oligomers mediate retinoid and rexinoid/cAMP cross-talk in acute promyelocytic leukemia cell differentiation. J Exp Med 2004; 199: 1163–1174.

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009; 361: 1058–1066.

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Ward PS, Patel J, Wise DR, Abdel-Wahab O, Bennett BD, Coller HA et al. The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Cancer Cell 2010; 17: 225–234.

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 2009; 462: 739–744.

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell 2011; 19: 17–30.

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011; 333: 1300–1303.

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Williams K, Christensen J, Helin K . DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep 2012; 13: 28–35.

    CAS  Google Scholar 

  98. Bhutani N, Burns DM, Blau HM . DNA demethylation dynamics. Cell 2011; 146: 866–872.

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 2011; 20: 11–24.

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Losman JA, Looper RE, Koivunen P, Lee S, Schneider RK, McMahon C et al. (R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible. Science 2013; 339: 1621–1625.

    CAS  PubMed  Google Scholar 

  101. Goll MG, Bestor TH . Eukaryotic cytosine methyltransferases. Annu Rev Biochem 2005; 74: 481–514.

    CAS  PubMed  Google Scholar 

  102. Holz-Schietinger C, Matje DM, Reich NO . Mutations in DNA methyltransferase (DNMT3A) observed in acute myeloid leukemia patients disrupt processive methylation. J Biol Chem 2012; 287: 30941–30951.

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Yamashita Y, Yuan J, Suetake I, Suzuki H, Ishikawa Y, Choi YL et al. Array-based genomic resequencing of human leukemia. Oncogene 2010; 29: 3723–3731.

    CAS  PubMed  Google Scholar 

  104. 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 2007; 204: 715–722.

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet 2012; 44: 23–31.

    CAS  Google Scholar 

  106. Harley CB, Futcher AB, Greider CW . Telomeres shorten during ageing of human fibroblasts. Nature 1990; 345: 458–460.

    CAS  PubMed  Google Scholar 

  107. de Magalhaes JP, Curado J, Church GM . Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009; 25: 875–881.

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Bahar R, Hartmann CH, Rodriguez KA, Denny AD, Busuttil RA, Dolle ME et al. Increased cell-to-cell variation in gene expression in ageing mouse heart. Nature 2006; 441: 1011–1014.

    CAS  PubMed  Google Scholar 

  109. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL et al. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 2009; 5: e1000602.

    PubMed  PubMed Central  Google Scholar 

  110. Bell JT, Tsai PC, Yang TP, Pidsley R, Nisbet J, Glass D et al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet 2012; 8: e1002629.

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Alisch RS, Barwick BG, Chopra P, Myrick LK, Satten GA, Conneely KN et al. Age-associated DNA methylation in pediatric populations. Genome Res 2012; 22: 623–632.

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci USA 2012; 109: 10522–10527.

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GH, Wong AH et al. DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 2009; 41: 240–245.

    CAS  PubMed  Google Scholar 

  114. Murgatroyd C, Patchev AV, Wu Y, Micale V, Bockmuhl Y, Fischer D et al. Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat Neurosci 2009; 12: 1559–1566.

    CAS  PubMed  Google Scholar 

  115. Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 2009; 323: 1074–1077.

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD et al. Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet 2012; 131: 1565–1589.

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Rossi DJ, Bryder D, Zahn JM, Ahlenius H, Sonu R, Wagers AJ et al. Cell intrinsic alterations underlie hematopoietic stem cell aging. Proc Natl Acad Sci USA 2005; 102: 9194–9199.

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 2010; 12: 235–246.

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37: 853–862.

    CAS  PubMed  Google Scholar 

  120. Easwaran H, Baylin SB . Epigenetic abnormalities in cancer find a "home on the range". Cancer Cell 2013; 23: 1–3.

    CAS  PubMed  PubMed Central  Google Scholar 

  121. Cremer T, Cremer C . Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001; 2: 292–301.

    CAS  PubMed  Google Scholar 

  122. Shumaker DK, Dechat T, Kohlmaier A, Adam SA, Bozovsky MR, Erdos MR et al. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc Natl Acad Sci USA 2006; 103: 8703–8708.

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453: 948–951.

    CAS  PubMed  Google Scholar 

  124. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 2010; 107: 139–144.

    CAS  PubMed  Google Scholar 

  125. Aran D, Toperoff G, Rosenberg M, Hellman A . Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 2011; 20: 670–680.

    CAS  PubMed  Google Scholar 

  126. Easwaran H, Johnstone SE, Van Neste L, Ohm J, Mosbruger T, Wang Q et al. A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res 2012; 22: 837–849.

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Remeseiro S, Losada A . Cohesin, a chromatin engagement ring. Curr Opin Cell Biol 2013; 25: 63–71.

    CAS  PubMed  Google Scholar 

  128. Cuadrado A, Remeseiro S, Gomez-Lopez G, Pisano DG, Losada A . The specific contributions of cohesin-SA1 to cohesion and gene expression: implications for cancer and development. Cell Cycle 2012; 11: 2233–2238.

    CAS  PubMed  Google Scholar 

  129. Guillou E, Ibarra A, Coulon V, Casado-Vela J, Rico D, Casal I et al. Cohesin organizes chromatin loops at DNA replication factories. Genes Dev 2010; 24: 2812–2822.

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res 2013; 23: 555–567.

    CAS  PubMed  PubMed Central  Google Scholar 

  131. Goodell MA, Godley LA . Perspectives and future directions for epigenetics in hematology. Blood 2013; 121: 5131–5137.

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A . The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010; 5: e8888.

    PubMed  PubMed Central  Google Scholar 

  133. Bernot KM, Siebenaler RF, Whitman SP, Zorko NA, Marcucci GG, Santhanam R et al. Towards personalized therapy in AML: in vivo benefit of targeting aberrant epigenetics in MLL-PTD-associated AML. Leukemia 2013; ; e-pub ahead of print 10 May 2013; doi:10.1038/leu.2013.147.

    CAS  PubMed  Google Scholar 

  134. Krug U, Koschmieder A, Schwammbach D, Gerss J, Tidow N, Steffen B et al. Feasibility of azacitidine added to standard chemotherapy in older patients with acute myeloid leukemia—a randomised SAL pilot study. PLoS ONE 2012; 7: e52695.

    CAS  PubMed  PubMed Central  Google Scholar 

  135. Schenk T, Chen WC, Gollner S, Howell L, Jin L, Hebestreit K et al. Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia. Nat Med 2012; 18: 605–611.

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Wang F, Travins J, Delabarre B, Penard-Lacronique V, Schalm S, Hansen E et al. Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Science 2013.

  137. Saeed S, Logie C, Stunnenberg HG, Martens JH . Genome-wide functions of PML-RARalpha in acute promyelocytic leukaemia. Br J Cancer 2011; 104: 554–558.

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We are grateful to members of the Müller-Tidow lab and to Frank Rosenbauer for helpful comments and critical discussions. We apologize to all colleagues whose work could not be cited due to space restrictions. Work on epigenetics or AML in our lab are supported by the Deutsche Forschungsgemeinschaft (SPP1463-MU 1328/9-1, SFB1009A07), the Deutsche Krebshilfe (110807), the José-Carreras Leukämiestiftung (R10/35f), the Else-Kröner Fresenius Stiftung (2012_A76) and the Innovative Medizinische Forschung at the University of Münster (I-BÄ111116).

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Correspondence to C Müller-Tidow.

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Schoofs, T., Berdel, W. & Müller-Tidow, C. Origins of aberrant DNA methylation in acute myeloid leukemia. Leukemia 28, 1–14 (2014). https://doi.org/10.1038/leu.2013.242

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