Expression profiles of MCF7-CV and MCF7-6SA

Gene set enrichment analysis links several pathways are upregulated or downregulated in MCF7-6SA, compared to MCF7-CV. To elucidate the downstream signaling by which 6SA-Snail suppresses colonization, we first compared the expression profiles of MCF7-CV and MCF7-6SA with the use of microarray data. Through gene set enrichment analysis (GSEA), we found that several pathways were upregulated or downregulated in MCF7-6SA, compared to MCF7-CV. Of these, estrogen-dependent gene expression and estrogen receptor (ESR)-mediated signaling were among the most downregulated pathways in MCF7-6SA, which may contribute to the previously observed phenotypic changes in these ER+ cancer cell lines. Total RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany). The generation of labelled cRNA and its hybridization to Human U133 Plus 2 GeneChip arrays (Affymetrix, Santa Clara, CA) were carried out at the genomic core facilities in the National Yang-Ming University (Taipei, Taiwan) according to the standard procedures. Functional annotation and identification of over-represented functional themes were performed using Reactome database of GSEA.