Transcriptomic analysis of cell lines derived from a metaplastic breast cancer with squamous metaplasia (MBC-SM) tissue

Although epithelial–mesenchymal transition (EMT) is the favored hypothesis for why cancer metastasis occurs, the cause–effect relationship remains unclear due to inconsistent clinical evidence. In this study, we establised epithelial– and mesenhcymal–predominant cell clones from a patient derived-metaplastic breast carcinoma with squamous metaplasia tissue (MBC-SM), followed by in-depth characterization of the derived cell clones. Before cells reaching confluence, total RNA of each cell clone was extracted with TRIzol reagent (Thermo Fischer Scientific, Waltham, MA, USA), including epithelial-predominant (n=3), E/M hybrid (n=2) and mesenchymal-predominant (n=3). The quality of RNA was validated by a Bioanalyzer (Agilent, Santa Clara, CA, USA) and subjected to Tri-I Biotech Inc. (Taipei, Taiwan) for RNA sequencing. Briefly, transcriptome libraries from the mRNA fractions were generated by MGIEasy RNA Library kit (SE50) and sequenced on a BGI-seq 500 machine. After reads trimming and adaptor removal, clean reads were used for downstream bioinformatic analysis including CLC Genomic Workbench (v10, Qiagen, Hilden, Germany), R limma (v 3.40.6), and GSEA (hallmark v7.4, Broad Institute, MA, USA).