Fig. 1: Trametinib induces a cellular state resembling the ground state of embryonic stem cells (ESCs).

a Uniform manifold approximation and projection (UMAP) of patient-derived organoids (PDOs) carrying a KRAS G12A mutation. Single PDOs (HCT24-8) derived from a trametinib-resistant culture were treated with trametinib or left untreated, and multiplexed single-cell expression profiling was performed. Cells are colored by clusters (left), cell cycle score (middle), and treatment (right). A total of 1554 cells from the control group and 1657 cells from the trametinib-treated group were analyzed. b Proportion of cells in each cluster of untreated (control) and trametinib-treated (trametinib) PDOs. Enrichment analysis of C2 using Gene Ontology cellular component (GOCC) (c) and Hallmark (d). Statistical significance was evaluated using permutation testing (n = 1000). P-values were adjusted for multiple comparisons using the false discovery rate. e Immunoblot analysis of ribosomal proteins. Protein levels of indicated proteins in trametinib-treated (trametinib) and untreated (control) PDOs were evaluated. β-actin was shown as the loading control. n = 3 biological replicates. Data are presented as fold-change mean ± SD (shown in parentheses). Gene set enrichment analysis of C2 with ground-state ESCs (f)²⁸ and epiblast (g)²⁹. Schematic drawings are shown in the upper panels. h Violin plot depicting the expression of ground state genes in each cluster in CRC organoids. The expression of gene sets identified in the enrichment analysis of ground state ESCs (f) and epiblasts (g) were shown. Statistical analyses are provided in Supplementary Table 1. i Heatmap of genes known to have high expression levels in ESC. Statistical analyses are provided in Supplementary Table 2. Altered fibrillarin expression (j), global protein synthesis (k), and EdU incorporation (l) in trametinib-treated PDOs. Representative images are shown in the upper panels. Data of 40 PDOs (j, k) or 20 PDOs (l), obtained from four independent experiments are presented. Bar = 100 µm. The black line within the boxplot indicates the median. Bottom and top of the boxplot represent the 25th and 75th percentiles, respectively. Whiskers extend to 1.5 × IQR. P values were calculated using a two-sided Welch’s two-sample t-test. Source data are provided as a Source data file.