DNA Methylation Profiling of Breast Cancer Cell Lines along the Epithelial Mesenchymal Spectrum—Implications for the Choice of Circulating Tumour DNA Methylation Markers

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.

Liquid Biopsy as a Tool for Differentiation of Leiomyomas and Sarcomas of Corpus Uteri

“…We, therefore, suggest a way to identify LB biomarkers suitable for UMT differentiation by searching for abnormal patterns already established in solid UMT in LB samples. This possibility is very promising also because reports identify that solid tumor abnormalities should remain unchanged in CNA [35,36,37,38,39,67,70,71,72,73,74,75] and eventually also in vesicles and CTC. Therefore, all abnormal patterns listed below are noted in solid tumors and their summary can form the basis for designing LB-based analysis in patients with UMT.…”

“…Whereas, both targeted and nontargeted approaches are used mainly for detecting point mutations, insertions and deletions, amplifications, translocations, and copy number alterations [36,67]; identifying abnormal epigenetic patterns and especially changes in promoter region methylation levels can be a suitable alternative to genomic alterations. It is supposed that ctDNA epigenetic patterns should also usually remain the same as in the tumors from which they were released and also be specific for both cancer type and progression [35,67,70,71,72,73,74,75].…”

“…The methylation profiles of ULM and sarcoma promoter regions provide further possibilities for tumor differentiation based on LB, because changes in DNA methylation patterns can be identified in ctDNA and have been proposed as potential biomarkers for tumor staging, prognosis, and monitoring of the treatment response [31,98,162]. It has also been suggested that abnormal methylation patterns should remain identical in both the primary tumors and the ctDNAs released by the tumor [35,67,70,71,72,73,74,75]. Maekawa et al [163] reported great variability in ULM methylation patterns.…”

<p>Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer</p>

“…A distinction in profiling DNA methylation was revealed between epithelial and mesenchymal phenotypes. 74 This study provided important insight into selecting an optimal panel of methylation markers to assess minimal residual disease, which is a major determinant of the initiation of metastatic tumors. 75 Panagopoulou et al assessed the methylation status of a panel of cancer-related genes in BC.…”

Modern approaches for the screening of epigenetically active xenobiotics

“…В свою очередь, для анализа метилирования траспозируемых элементов и специфичных локусов используют клеточные линии MDA-MB-468, SiHa, CaSki, HCT-116, SW-480, WI-38 VA-13 и др. [64][65][66][67][68]. На моделях in vitro был получен большой перечень данных о влиянии на эпигенетические механизмы таких ксенобиотиков, как 2,3,7,8-тетрахлордибенз-пара-диоксин, генистеин, соединения никеля и кадмия [59,69,70].…”