Geburtshilfe Frauenheilkd 2011; 71 - O_3
DOI: 10.1055/s-0031-1286459

Identification of new targets of cisplatin resistance in ovarian cancer patients using combined transcriptome and methylation analyses

H Neubauer 1, J Hoffmann 2, M Walter 2, A Staebler 3, S Poths 2, O Riess 2, D Wallwiener 1, M Bonin 2, T Fehm 1
  • 1Department of Obstetrics and Gynecology, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
  • 2Microarray Facility Tuebingen, Eberhard-Karls-University Tuebingen, Tuebingen, Germany
  • 3Institute for Pathology, Eberhard-Karls-University Tuebingen, Tuebingen, Germany

The standard therapy for Ovarian cancer consists of aggressive cytoreductive surgery followed by platinum-based chemotherapy. However, intrinsic or acquired platinum resistance in the majority of patients leads to high mortality rate.

To gain new insights in resistance mechanisms and modified pathways, we performed combined whole-genome expression and methylation studies using Illumina BeadArrays.

Eleven cryopreserved tissue samples from each platinum resistant and platinum sensitive ovarian carcinomas were selected. From consecutive tissue sections RNA and DNA was extracted and analysed for differences in gene expression and methylation patterns by using Illumina BeadArray platforms. Results obtained were confirmed using qRT-PCR and pyrosequencing.

We assessed the DNA methylation profile of approx. 27,000 CpG sites (associated with approx. 14000 transcripts) and found 613 differenzially methylated promoter sites using M-value statistics. To investigate the relationship between DNA methylation status and gene expression, we measured levels of transcripts from the same set of genes in the same samples. After normalization and biostatistical analysis we detected 115 significantly differenzially expressed transcripts with a fold change >1.6 and a p-value <0.05. Promoter DNA methylation and levels of the corresponding gene's transcript have been found to be inversely correlated in some cases. Overall, we were able to detect 14 negatively correlated transcripts. Pathway and network analyses indicate a strong enrichment of genes involved in cell differentiation and tumorigenesis processes.

By combining whole-genome expression and methylation analyses we reveal molecular changes in ovarian cancers which might be involved in establishing platinum resistance. Functional verification and pathway analysis is under way.