Fig. 2: Defining cellular ribosome biogenesis levels.
From: Targeting ribosomes reprograms the tumour microenvironment and augments cancer immunotherapy
a, b Schematic representation of the analysis strategy to identify ribosome-related programs. In this tumor, UMAP plots showing each NMF program and its program score (a) heatmaps showing correlation coefficients between NMF program score and ribosome signature scores (b). c, d Hierarchically clustered heatmaps showing all correlation coefficients between NMF program scores and ribosome signature, including (c) and excluding (d) ≤ 10%-programs. e GSEA plots showing the enrichment of ribosome biogenesis levels in samples from independent GEO datasets. f Spikes plots showing ribosomal states (Up) and AUC (bottom) within cancer cell lines of the Depmap. RKO, MCF7 and A498 cells were selected represent relative higher, middle and lower ribosome biogenesis activity cell lines used in our drug sensitivity validation. g IC50 curves of CX-5461 for RKO, MCF7 and A498 cell lines. h Multi-color immunostaining of rRNA (Y10B), epithelial cells (EPCAM) and immune cells (PTPRC/CD45) in tissues of CRC, STAD (stomach adenocarcinoma) and LIHC (hepatocellular carcinoma). Scale bar for all immunostaining images = 100 µm. i Pseudo immunofluorescence based on Visium HD images of CRC showing the spatial organization of spots assigned to cellular ribosome biogenesis levels, epithelial (EPCAM), stromal (DCN) and immune (PTPRC/CD45) cell markers. j Dotplot showing associations of ribosome biogenesis levels with patient overall survival in cancer types from the TCGA. Dot size indicates P values, dot color indicates HR values.
