A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies
Kirsten Grønbæk, Carsten Müller-Tidow, Giovanni Perini, Sören Lehmann, Marianne Bach Treppendahl, Ken Mills, Christoph Plass, Brigitte Schlegelberger

Author Affiliations

  1. Kirsten Grønbæk1,
  2. Carsten Müller-Tidow2,
  3. Giovanni Perini3,
  4. Sören Lehmann4,
  5. Marianne Bach Treppendahl1,
  6. Ken Mills5,
  7. Christoph Plass6 and
  8. Brigitte Schlegelberger7
  9. on behalf of the European Genomics and Epigenomics Study on MDS and AML (EuGESMA), COST Action BM0801
  1. 1Department of Hematology, Rigshospitalet, Copenhagen, Denmark
  2. 2Department of Medicine, Hematology/Oncology, University of Münster, Germany
  3. 3Department of Biology, University of Bologna, Italy
  4. 4Department of Internal Medicine/Hematology, Karolinska University Hospital Huddinge, Stockholm, Sweden
  5. 5Centre for Cancer Research and Cell Biology, Queen’s University Belfast, UK
  6. 6Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
  7. 7Centre for Pathology and Forensic and Genetic Medicine, Institute of Cell and Molecular Pathology, Hannover Medical School, Germany
  1. Correspondence: Kirsten Grønbæk, Department of Hematology, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark. Phone: international +45.3545.8895; Fax: international +45.3545.4295; E-mail: kirsten.groenbaek{at}rh.regionh.dk
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Abstract

Research over the past decade has confirmed that epigenetic alterations act in concert with genetic lesions to deregulate gene expression in acute myeloid leukemia and myelodysplastic syndromes. Epigenetic alterations may serve as markers of disease, and may potentially be used for classification, prognostication and to monitor minimal residual disease. In addition, we now have the capability to pharmaceutically target epigenetic modifications, and there is an urgent need for early validation of the efficacy of the drugs. Also, an improved understanding of the functionality of epigenetic modifications may further pave the road towards individualized therapy. The recent advances in biotechnology and bioinformatics provide a plethora of novel tools for characterizing the epigenome in clinical samples, but at this point the practical, clinical utility of these methodologies needs further exploration. Here, we provide the pros and cons of the currently most feasible methods used for characterizing the methylome in clinical samples, and give a brief introduction to novel approaches to sequencing that may revolutionize our abilities to characterize the genomes and epigenomes in acute myeloid leukemia and myelodysplastic syndrome patients.

  • Received November 9, 2011.
  • Revision received February 15, 2012.
  • Accepted March 9, 2012.
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