A genome-wide cell-free DNA methylation analysis identifies an episignature associated with metastatic luminal B breast cancer.

Breast cancers of the luminal B subtype are frequent tumors with high proliferation and poor prognosis. Epigenetic alterations have been found in breast tumors and in biological fluids. We aimed to profile the cell-free DNA (cfDNA) methylome of metastatic luminal B breast cancer (LBBC) patients using an epigenomic approach to discover potential noninvasive biomarkers. Plasma cfDNA was analyzed using the Infinium MethylationEpic array (EPIC array) in a cohort of 14 women, including metastatic LBBC patients and healthy controls. Fifteen nanograms of each individual sample of plasma cfDNA was bisulfite-converted using the EZ DNA Methylation Lightning Kit (Zymo Research). Subsequently, the bisulfite-modified cfDNA was then subjected to whole genome amplification (WGA) using the EpiTect Whole Bisulfitome Kit (Qiagen). After the WGA of cfDNA, the Illumina Infinium HD methylation protocol was followed using MethylationEPIC BeadChips that were analyzed in a HiScan (Illumina).