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Title: DNA Methylation Profiling of Breast Cancer Cell Lines along the Epithelial Mesenchymal Spectrum-Implications for the Choice of Circulating Tumour DNA Methylation Markers.
Austin Authors: Le, Anh Viet-Phuong;Szaumkessel, Marcin;Tan, Tuan Zea;Thiery, Jean-Paul;Thompson, Erik W;Dobrovic, Alexander 
Affiliation: School of Cancer Medicine, La Trobe University Bundoora, Bundoora, VIC 3086, Australia
Translational Research Institute, Woolloongabba, QLD 4102, Australia
Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
Department of Clinical Pathology, University of Melbourne, Parkville, VIC 3010, Australia
Cancer Science Institute of Singapore, 14 Medical Drive, National University of Singapore, Singapore 117599, Singapore
INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, Université Paris-Sud, 94805 Villejuif, France
Department of Surgery, St. Vincent's Hospital, University of Melbourne, Melbourne, VIC 3065, Australia
Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
Issue Date: 28-Aug-2018 2018-08-28
Publication information: International journal of molecular sciences 2018; 19(9): E2553
Abstract: (1) Background: Epithelial⁻mesenchymal plasticity (EMP) is a dynamic process whereby epithelial carcinoma cells reversibly acquire morphological and invasive characteristics typical of mesenchymal cells. Identifying the methylation differences between epithelial and mesenchymal states may assist in the identification of optimal DNA methylation biomarkers for the blood-based monitoring of cancer. (2) Methods: Methylation-sensitive high-resolution melting (MS-HRM) was used to examine the promoter methylation status of a panel of established and novel markers in a range of breast cancer cell lines spanning the epithelial⁻mesenchymal spectrum. Pyrosequencing was used to validate the MS-HRM results. (3) Results: VIM, DKK3, and CRABP1 were methylated in the majority of epithelial breast cancer cell lines, while methylation of GRHL2, MIR200C, and CDH1 was restricted to mesenchymal cell lines. Some markers that have been used to assess minimal residual disease such as AKR1B1 and APC methylation proved to be specific for epithelial breast cell lines. However, RASSF1A, RARβ, TWIST1, and SFRP2 methylation was seen in both epithelial and mesenchymal cell lines, supporting their suitability for a multimarker panel. (4) Conclusions: Profiling DNA methylation shows a distinction between epithelial and mesenchymal phenotypes. Understanding how DNA methylation varies between epithelial and mesenchymal phenotypes may lead to more rational selection of methylation-based biomarkers for circulating tumour DNA analysis.
DOI: 10.3390/ijms19092553
ORCID: 0000-0003-3414-112X
PubMed URL: 30154364
Type: Journal Article
Subjects: DNA methylation
Breast cancer
circulating tumour DNA
epithelial–mesenchymal plasticity
methylation-sensitive high-resolution melting (MS-HRM), pyrosequencing
minimal residual disease
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