Fig. 3: Inhibition of ribosome biogenesis with trametinib to reduce the viability of KRAS-mutant colorectal cancer (CRC) PDOs.

Chou–Talalay plot depicting the synergistic effects of cyclin-dependent kinase (CDK) inhibitors (a) and CX-5461 (e) with trametinib. Combination index (CI) value was determined using constant-ratio drug combinations. (Means ± SD, N = 4 wells) Heatmap showing the synergistic effects of dinaciclib (b) and CX-5461 (f) with trametinib. CI value was determined using nonconstant-ratio drug combinations. Top 10 most significantly enriched signatures in the Gene Ontology cellular component (GOCC) in dinaciclib (c) or CX-5461 (g)-treated PDOs. Enrichment scores were calculated using differentially expressed genes (DEGs) obtained via comparison between treated and untreated PDOs using one-sided Fisher exact tests. Volcano plot showing the gene expression levels in dinaciclib (d)- and CX-5461 (h)-treated PDOs compared with those in untreated PDOs. Genes in the GOCC ribosome gene sets are shown by red dots. Differential expression was assessed using edgeR’s exact test for negative binomially distributed counts. i Reduced EU incorporation in CX-5461-treated CRC organoids. Representative images of EU (red) and nuclei (blue) in control and CX-5461-treated organoids are shown. High magnification views of the white boxed regions are shown in the insets. Bar = 50 µm, Bar in inset = 10 µm. j The percentage of EU-positive nuclei per organoid is shown in the boxplot. The central line of each box indicates the median, the box bounds represent the interquartile range (IQR), and whiskers extend to 1.5 × IQR. CX-5461 treatment markedly reduced the proportion of EU-positive cells, indicating suppression of RNA synthesis. Data of 20 PDOs obtained from four independent experiments are shown. Statistical significance was assessed using a two-sided Welch’s t-test. Source data are provided as a Source data file.