Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/12610
Title: Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value.
Austin Authors: Stirzaker, Clare;Zotenko, Elena;Song, Jenny Z;Qu, Wenjia;Nair, Shalima S;Locke, Warwick J;Stone, Andrew;Armstong, Nicola J;Robinson, Mark D;Dobrovic, Alexander ;Avery-Kiejda, Kelly A;Peters, Kate M;French, Juliet D;Stein, Sandra;Korbie, Darren J;Trau, Matt;Forbes, John F;Scott, Rodney J;Brown, Melissa A;Francis, Glenn D;Clark, Susan J
Affiliation: Pathology Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
Translational Genomics &Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria 3084, Australia
Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
Epigenetics Group, Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales 2305, Australia
Pathology Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
Swiss Institute of Bioinformatics and Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
Epigenetics Group, Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales 2308, Australia
Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
St Vincent's Clinical School, University of NSW, Sydney, New South Wales 2010, Australia
School of Mathematics and Statistics, University of Sydney, Sydney, New South Wales 2006, Australia
Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
Division of Molecular Medicine, Hunter Area Pathology Service and the Hunter Medical Research Institute, John Hunter Hospital, Newcastle, New South Wales 2305, Australia
Issue Date: 2-Feb-2015
Publication information: Nature Communications 2015; 6(): 5899
Abstract: Epigenetic alterations in the cancer methylome are common in breast cancer and provide novel options for tumour stratification. Here, we perform whole-genome methylation capture sequencing on small amounts of DNA isolated from formalin-fixed, paraffin-embedded tissue from triple-negative breast cancer (TNBC) and matched normal samples. We identify differentially methylated regions (DMRs) enriched with promoters associated with transcription factor binding sites and DNA hypersensitive sites. Importantly, we stratify TNBCs into three distinct methylation clusters associated with better or worse prognosis and identify 17 DMRs that show a strong association with overall survival, including DMRs located in the Wilms tumour 1 (WT1) gene, bi-directional-promoter and antisense WT1-AS. Our data reveal that coordinated hypermethylation can occur in oestrogen receptor-negative disease, and that characterizing the epigenetic framework provides a potential signature to stratify TNBCs. Together, our findings demonstrate the feasibility of profiling the cancer methylome with limited archival tissue to identify regulatory regions associated with cancer.
Gov't Doc #: 25641231
URI: http://ahro.austin.org.au/austinjspui/handle/1/12610
DOI: 10.1038/ncomms6899
URL: https://pubmed.ncbi.nlm.nih.gov/25641231
Type: Journal Article
Appears in Collections:Journal articles

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