Identify novel TGF-β-regulated genes by RNA-sequencing from MCF10A cells

TGF-β signaling and its induced EMT (Epithelial to mesenchymal transition) play fundamental roles in development and disease including cancers. Although, TGF-β-regulated genes have been extensively studied, with RNA-sequencing (RNA-seq) analysis, new TGF-β-regulated genes are still been identified. Moreover, many significantly regulated genes by TGF-β are not emphasized. This study employs RNA-seq on MCF10A cells treated by TGF-β for 1.5 (this GEO), 24, 48, and 72 (GSE74377) hours and aims to identify novel TGF-β-regulated genes. With 1.5 fold gene expression change (log2 0.58) and p<0.05 at any length of the treatment, 1166 and 861 genes were found to be upregulated and downregulated by TGF-β, respectively. These genes were analyzed for their enrichments in KEGG pathways and prognostic markers of cancers. Several genes of interest were further analyzed for their regulation by TGF-β across cell lines and their functions in context of TGF-β were further studied. This study systematically analyzed TGF-β-regulated genes and revealed novel factors mediating the pro-migratory role of TGF-β signaling, hence, sheds a light on the understanding of the mechanisms underlying the role of TGF-β signaling in cancer development. mRNA profiles of MCF10A cells stably expressing a scramble shRNA with TGF-β1 treatment for 0, 1.5 hours were generated by RNA-seq, in duplicate, using HiSeq2500 instrument.