Fig. 1: Detection of a broad spectrum of transitory states and a pEMT endpoint in TGF-β1-treated TKA-organoids. | Oncogenesis

Fig. 1: Detection of a broad spectrum of transitory states and a pEMT endpoint in TGF-β1-treated TKA-organoids.

From: TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoids

Fig. 1

A Schematic overview of the scRNA-seq workflow. The figure was generated with BioRender.com. B Unsupervised clustering and UMAP visualization of 931-TKA organoid cells upon TGF-β1 treatment for 0, 24, 48, and 72 h and scRNA-seq. C Individual organoid cells in the UMAP were annotated according to TGF-β1 treatment times deduced by 10x Genomics sample indices. The color code represents TGF-β1 treatment times. RNA velocity analyses (D) and PAGA-based trajectory prediction (E) of scRNA-seq results from 931-TKA organoids. The arrows in the RNA velocity plot predict the starting point of cell states and directions of future progression projected onto the UMAP space. The thickness of the lines denotes the strength of connectivity between clusters. F Heatmap showing the MSigDB hallmark gene sets enriched in gene expression profiles of organoid cell clusters. The red-blue color scale represents the z-score. G TGF-β pathway activity was evaluated by MSigDB with decoupleR. Enrichment was determined by over-representation analysis (ORA) using the SCANPY function: score_gene function and visualized in the UMAP. H Expression of an EMT signature was scored by MSigDB with decoupleR and projected onto the UMAP space. I UMAP cluster-specific visualization of EMT scores in violin plots. J UMAPs visualizing expression levels of epithelial and mesenchymal marker genes in organoid cells treated with TGF-β1 for 0, 24, 48, and 72 h. The color code represents the normalized counts (Norm. counts) of the indicated genes.

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