Oral Presentation Epigenetics 2013

Epigenetic prognostic biomarker panel has potential to stratify triple negative breast cancers (#19)

Clare Stirzaker 1 , Elena Zotenko 1 , Jenny Song 1 , Wenjia Qu 1 , Warwick Locke 1 , Shalima Nair 1 , Nicola Armstrong 1 , Kelly Keijda 2 , Rodney Scott 2 , Melissa Brown 3 , Alexander Dobrovic 4 , Matt Trau 5 , John Forbes 6 , Sandra Stein 7 , Glenn Francis 7 , Susan Clark 1
  1. Epigenetics Laboratory, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
  2. 2School of Biomedical Sciences, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
  3. School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
  4. Molecular Pathology Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  5. Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
  6. Surgical Oncology, The University of Newcastle, Newcastle, NSW, Australia
  7. Queensland Health Pathology Service, Princess Alexandra Hospital, Brisbane, QLD, Australia

Triple negative or basal-type breast cancers comprise a heterogeneous group of cancers that do not express the genes for estrogen receptor (ER), progesterone receptor (PR) or Her2/neu and account for approximately 15%-25% of all breast cancer cases.  Some triple negative breast cancers are known to be more aggressive with poor prognosis, while others have a prognosis similar or better than hormone receptor positive breast cancers; the ongoing challenge is to stratify this group of tumours to provide better treatment decisions. Advances in genome-wide DNA methylation sequencing technology has now enabled new strategies for the identification of novel DNA methylation loci for potential cancer diagnosis and prognosis biomarkers.  Archival cancer samples are commonly stored as formalin-fixed paraffin embedded tissue (FFPET) and this provides an invaluable resource for identification of epigenetic events associated with the cancer subtypes and survival.

To identify differentially methylated regions that may potentially stratify triple-negative breast cancers, we performed genome-wide DNA methylation profiling using MBDCap-Seq which interrogates over 5 million CpG dinucleotides (ten fold more than using the 450K Illumina array), on a discovery cohort of 6 normal and 19 triple-negative breast cancer tumour DNA samples isolated from archival formalin-fixed paraffin embedded tissue (FFPET).  We identify 822 hyper-methylated and 43 hypo-methylated novel breast cancer-specific marks compared to normal breast cells and using 450K TCGA data validate that 5% of the methylated loci are specific for TNBCs. Moreover, we stratify the TNBCs into three distinct clusters associated with better or worse prognosis, based on the methylation profile and identify 14 regional hypermethylation events associated with poor survival and 3 regions associated with good survival.  Our exciting results identify for the first time a cancer DNA methylation prognostic signature that promises to stratify TNBCs for more personalized management and optimal treatment decisions.