Transcriptomic analysis of transforming growth factor beta (TGF-beta)-responding SCC cells and Fc epsilon receptor I alpha (FceRIa)-positive macrophages

TGF-beta-responding SCC cells, a tumor-initiating cell population, show a unique gene expression signature, including antioxidant gene expression and IL-33 upregulation. IL-33-responding macrophages in SCC, which also express Fc epsilon receptor I alpha, show a gene expression signature that resembles alternatively-activated macrophages To analyze a unique gene expression in TGF-beta-responding SCC cells, we purified TGF-beta signaling reporter (mScarlet) positive and negative tumor basal cells (Rosa-YFP+ CD49f+ CD29+) by FACS. We used RNA-seq analysis to compare the transcriptomes of these FACS-isolated SCC cells and combined the previous RNA-seq data (GSE64867) to obtain higher confidence (p < 0.01). For macrophage analysis, we purified Fc epsilon receptor I alpha positive and negative macrophages (CD45+ F4/80+) from SCC tumor tissues. We also used RNA-seq analysis to compare their transcriptomes.