MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation

Blood. 2009 Oct 15;114(16):3448-58. doi: 10.1182/blood-2009-01-200519. Epub 2009 Aug 3.


Increasing evidence shows aberrant hypermethylation of genes occurring in and potentially contributing to pathogenesis of myeloid malignancies. Several of these diseases, such as myelodysplastic syndromes (MDSs), are responsive to DNA methyltransferase inhibitors. To determine the extent of promoter hypermethylation in such tumors, we compared the distribution of DNA methylation of 14 000 promoters in MDS and secondary acute myeloid leukemia (AML) patients enrolled in a phase 1 trial of 5-azacytidine and the histone deacetylase inhibitor entinostat against de novo AML patients and normal CD34(+) bone marrow cells. The MDS and secondary AML patients displayed more extensive aberrant DNA methylation involving thousands of genes than did the normal CD34(+) bone marrow cells or de novo AML blasts. Aberrant methylation in MDS and secondary AML tended to affect particular chromosomal regions, occurred more frequently in Alu-poor genes, and included prominent involvement of genes involved in the WNT and MAPK signaling pathways. DNA methylation was also measured at days 15 and 29 after the first treatment cycle. DNA methylation was reversed at day 15 in a uniform manner throughout the genome, and this effect persisted through day 29, even without continuous administration of the study drugs. This trial was registered at as J0443.

Trial registration: NCT00101179.

Publication types

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

MeSH terms

  • Antigens, CD34
  • Azacitidine / administration & dosage*
  • Bone Marrow Cells / metabolism
  • DNA Methylation / drug effects*
  • DNA, Neoplasm / metabolism*
  • Enzyme Inhibitors / administration & dosage*
  • Female
  • Histone Deacetylase Inhibitors
  • Histone Deacetylases / metabolism
  • Humans
  • Leukemia, Myeloid, Acute* / drug therapy
  • Leukemia, Myeloid, Acute* / metabolism
  • MAP Kinase Signaling System / drug effects
  • Male
  • Myelodysplastic Syndromes* / drug therapy
  • Myelodysplastic Syndromes* / metabolism
  • Neoplasms, Second Primary / drug therapy*
  • Neoplasms, Second Primary / metabolism*
  • Promoter Regions, Genetic
  • Time Factors
  • Wnt Proteins / metabolism


  • Antigens, CD34
  • DNA, Neoplasm
  • Enzyme Inhibitors
  • Histone Deacetylase Inhibitors
  • Wnt Proteins
  • Histone Deacetylases
  • Azacitidine

Associated data