Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [human]

We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers.To demonstrate a direct association between activation of the EMT program and immunosuppression, we induced EMT programs in vitro in an array of cultured BrCa cell lines via the doxycycline-induced expression of various EMT-inducing transcription factors (EMT-TFs) and proceeded to determine whether activation of the EMT program also alters cell-intrinisc immuno-modulatory markers To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of control E cells or those induced to undergo an EMT RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2