Epigenetic changes play an important role in
leukemia pathogenesis. DNA methylation is among the most common alterations in
leukemia. The potential role of DNA methylation as a
biomarker in
leukemia is unknown. In addition, the lack of molecular markers precludes
minimal residual disease (MRD) estimation for most patients with
hematologic malignancies. We analyzed the potential of aberrant
DNA promoter methylation as a
biomarker for MRD in acute
leukemias. Quantitative real-time PCR methods with
bisulfite-modified
DNA were established to quantify MRD based on
estrogen receptor alpha (
ERalpha) and/or p15(INK4B) methylation. Methylation analyses were done in >370
DNA specimens from 180 acute
leukemia patients and controls. Methylation of
ERalpha and/or p15(INK4B) occurred frequently and specifically in acute
leukemia but not in healthy controls or in nonmalignant
hematologic diseases. Aberrant DNA methylation was detectable in >20% of
leukemia patients during clinical remission. In pediatric
acute lymphoblastic leukemia, methylation levels during clinical remission correlated closely with
T-cell receptor/
immunoglobulin MRD levels (r = +0.7, P < 0.01) and were associated with subsequent relapse. In
acute myelogenous leukemia patients in clinical remission, increased methylation levels were associated with a high relapse risk and significantly reduced relapse-free survival (P = 0.003). Many patients with acute
leukemia in clinical remission harbor increased levels of aberrant DNA methylation. Analysis of methylation MRD might be used as a novel
biomarker for
leukemia patients' relapse risk.