DNA methylation analysis

DNA methylation plays a key role in regulating gene expression by affecting structure and accessibility of chromatin. In mammalian cells, DNA methylation mainly occurs at carbon-5 of cytosine residues followed by guanine (CpGs). Methylation of gene promoters that are rich in CpGs most frequently results in gene silencing.

Alterations in DNA methylation have been reported for a number of diseases including cancer. Since these aberrations occur very early and frequently in cancer, they are considered as potential diagnostic, predictive and/or prognostic biomarkers.

Our group is developing assays to determine the DNA methylation status of candidate genes associated with cancer. In addition to gene promoters we are interested in DNA regions that have not been primarily targets of DNA methylation analysis, including exons, intron-exon boundaries, and enhancers. We aim at investigating the interplay of DNA methylation in these elements with promoter methylation and gene expression. In addition, we investigate whether these DNA regions are aberrantly methylated in cancer and can be used as potential biomarkers.

We are developing assays based on methylation-sensitive high resolution melting (HRM) analysis, yielding information on the average methylation status across all CpGs in PCR products. We are also developing pyrosequencing assays, allowing the determination of the DNA methylation status of single CpGs in PCR products.

One of the genes we are currently dealing with is MGMT, encoding the protein O6-methylguanine-DNA methyltransferase, playing a crucial role in the prevention of genotoxicity. The MGMT promoter methylation status is considered a predictive biomarker for the response of patients suffering from glioblastoma multiforme to the alkylating agent temozolomide. In addition, we are interested in DNA methylation of ATP-binding cassette (ABC) transporters. As efflux pumps, they play a crucial role in multidrug resistance (MDR) of cancers. Increasing evidence suggests that they are also involved in tumor initiation, progression, and metastasis.  

Cooperation partners:

  • Sabine Spiegl-Kreinecker, University Clinic for Neurosurgery, Kepler University Hospital, Linz
  • Georg Pfeiler, Department of Obstetrics and Gynecology, Medical University of Vienna
  • Petra Heffeter, Institute of Cancer Research, Medical University of Vienna