Abstract 2308: Heterogeneous and low-level methylation of novel biomarker candidates for breast cancer clinical management
Authors: Wojdacz Tomasz K. , Windeløv Johanne A. , Thestrup Britta B. , Damsgaard Tine E. , Overgaard Jens , Hansen Lise Lotte 
Published: May 2015

Abstract
Breast cancer is a highly heterogeneous malignancy, which is best exemplified by the fact that despite similar clinical and pathological features large number breast cancer patients experience different outcome of the disease. Therefore there is an urgent need for identification of new biomarkers to stratify patients for personalized treatment.
Methylation of gene promoters regulates genes transcription and provides normal cell function. At the same time, changes of the normal pattern of methylation are directly involved in malignant transformation, and have been shown to provide a good source of clinical biomarkers for cancer management. Nevertheless it is still challenging to firstly identify methylation changes suitable for clinical biomarkers and secondly evaluate the clinical specificity and sensitivity of those biomarkers.
We used ultra high-resolution microarrays to compare genome wide methylation patterns of breast carcinomas (N=20) with non-malignant breast tissue (N=5) and identified 1000+ differentially methylated regions (DMR) in the genome, which undergo methylation changes during breast cancer development. The results of genome wide screening technologies (due to the high complexity of those methods) require validation with PCR based technology. Therefore, we validated 19 of the regions identified in the genome wide screening with the Methylation Sensitive High Resolution Melting (MS-HRM) technique in a panel of breast carcinomas (N=275) and non-malignant controls (N=74).
The validation experiments corroborated the results, confirming that methylation changes within the identified regions can potentially be used as biomarkers.
Interestingly, we have observed two types of methylation gain at the validated loci: 1) loci undergoing predominantly complete methylation, and 2) loci acquiring mainly heterogeneous methylation during carcinogenesis. It can be speculated that the different types of methylation gain have different physiological consequences for transcriptional activity of the affected genes. Consequently the involvement of the gene in carcinogenesis may depend on the type of methylation acquired. However more research is needed to elaborate these findings.
Our validation experiments also showed that almost all tested DMRs (17 out of 19) displayed low-level methylation in non-malignant breast tissue. The physiological consequences of the low level methylation of non-malignant tissue are largely unknown. These changes does not seem to have immediate pathological consequences but may predispose to breast cancer and hence have significant impact on evaluation of the clinical sensitivity and specificity of methylation biomarkers.
Summarizing in our study, we have identified two phenomena that have significant consequences for the locus specific methylation biomarker development and need to be further researched.
Citation Format: Tomasz K. Wojdacz, Johanne A. Windeløv, Britta B. Thestrup, Tine E. Damsgaard, Jens Overgaard, Lise Lotte Hansen. Heterogeneous and low-level methylation of novel biomarker candidates for breast cancer clinical management. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2308. doi:10.1158/1538-7445.AM2014-2308