Fig. 3: PQL phenotype is associated with the acquisition of a fetal intestinal stem cell (feISC) signature.
A PCA of the RNA-seq analysis from the indicated replicates performed on PDO5 and PDO66 (untreated; CT) or 5-FU + Iri.-treated either at IC20 or IC30 as indicated. B, C Barplots depicting the normalized enrichment score of statistically significant enriched pathways obtained by GSEA analysis of PDO5 (B) and PDO66 (C) with the Hallmark gene set for treated samples (NOM p val < 0.05). D WB analysis of control and 5-FU + Iri.-treated PDO5 cells collected at the indicated time points (from one out of three biologically independent experiments). E RT-qPCR analysis of selected p53 target genes from control and IC20-treated PDO5 cells (n = 4 biologically independent experiments). F GSEA of an intestinal stem cell (ISC) gene set, according to Muñoz et al., in untreated (C) versus treated (T) PDO5/PDO66 condition. G Heat map showing the expression levels of the indicated ISC genes in untreated, IC20 and IC30-treated PDO5 cells and untreated and IC30-treated PDO66 cells. H, I GSEA of a fetal down (H) and a fetal up (I) stem cell gene set, according to Mustata et al., in control (C) versus treated (T) PDO5/PDO66 condition. J RT-qPCR analysis of selected fetal ISC and EMT genes from untreated and IC20-treated sorted GFPhigh or GFPlow PDO5 cells (from 1 out of 2 biologically independent experiments). For all applicable figure panels, data are mean ± SD. Significance (p) was calculated in E with two-sided Student’s t test and in J with one-way ANOVA test. For F, H, I p.value is nominal p value given by the GSEA program. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; n.s., no significant; CT, control; IC20 and IC30, 5-FU + Iri. are doses imposing 20 and 30% cell death, respectively; GSEA, gene set enrichment analysis; NES, normalized enriched score. Source data are provided as a Source Data file.
