Extended Data Fig. 4: Cells eliminated during early mouse embryogenesis have activated stress responses.
a, Overlap of genes differentially expressed along the trajectory joining winning and losing epiblast cells in CI-treated embryos (Fig. 2a and Extended Data Fig. 3a) and genes related to the unfolded protein response and integrated protein response pathways (UPR_ISR, see Supplementary Table 3). From the 32 genes related to the UPR & ISR pathways, 12 are down-regulated in loser cells, 8 genes are up-regulated in loser cells, and 12 genes are not differentially expressed between loser and winner cells. There is a statistically significant enrichment of UPR&ISR genes among the up-regulated genes in loser cells (odds ratio=3.0, p-value=0.012). The intersection between UPR-ISR genes and the down regulated genes is not significant (odds ratio=1.2, p value=0.69). b-c, List of genes from UPR-ISR pathways that are statistically significantly up-regulated (b) or down-regulated (c) in loser cells. d, Scatterplots with the expression levels of genes involved in stress responses in epiblast cells from CI-treated embryos as a function of cells’ losing score. e, Experimental design with the approach taken to validate the expression of the stress response marker DDIT3 in epiblast cells from DMSO or CI-treated embryos. f, Representative micrographs of DMSO (upper panel) or CI-treated embryos (100 μM, lower panel) stained for DDIT3, quantified in (g). Nuclei are labelled with Hoechst. In control embryos (DMSO-treated), dying cells in the cavity show very high DDIT3 expression (arrow), while live cells in the epiblast of the CI-treated embryos show more modest levels of DDIT3 expression (arrowheads). Scale bar = 20 μm. g, Quantification of the percentage of epiblast cells with nuclear DDIT3 expression. N = 10 DMSO and N = 9 CI-treated embryos. Data shown as mean ± SEM. See methods for details on statistical analysis.
