Figure 5.

On-Chip culture enhances biological processes related to the maturation of the intestinal epithelium. (A) Principal component analysis shows that the presence of endothelium clearly separates the epithelial transcriptome of the Chips cultured with and without endothelium. (B) Heatmap representation of the 1000 most variant genes. Samples cultured in the presence of endothelium are clustered separately from all other conditions. (C) The volcano plot resulting from the differential gene expression analysis between the epithelial cells on day 5 of culture, where stretch (10% strain, 0.15 Hz) is applied in the presence and absence of endothelium. The number of the up-regulated and down-regulated differentially expressed genes in the presence of endothelium is shown in green and red, respectively. (D) The volcano plot resulting from the differential gene expression analysis between the epithelial cells on day 8 of culture, where stretch (10% strain, 0.15 Hz) is applied in the presence and absence of endothelium. The number of the up-regulated and down-regulated genes in the presence of endothelium is shown as green and red, respectively. (E) List of biological processes identified by the GO enrichment analysis using the differentially expressed genes between the epithelial cells on day 5 of culture, where stretch (10% strain, 0.15 Hz) is applied in the presence and absence of endothelium. The results indicate the significant enrichment of biological processes related to the morphogenesis and function of the epithelial barrier. (F) List of biological processes identified by the GO enrichment analysis, using the differentially expressed genes between the epithelial cells on day 8 of culture, where stretch (10% strain, 0.15 Hz) is applied in the presence and absence of endothelium. The results indicate significant enrichment of biological processes related to the morphogenesis of the epithelial barrier. (G) The volcano plot resulting from the differential gene expression analysis between the epithelial cells cultured in the absence of endothelium and the presence of stretch (10% strain, 0.15 Hz), on days 5 and 8 of culture. The number of up-regulated and down-regulated genes at the end of the culture is shown in green and red, respectively. (H) The volcano plot resulting from the differential gene expression analysis between the epithelial cells cultured in the presence of endothelium and stretch (10% strain, 0.15 Hz), on days 5 and 8 of culture. The number of the up-regulated and down-regulated genes at the end of the culture is shown in green and red, respectively. n = 3–6 chips/condition. (I) The volcano plots resulting from the differential gene expression analysis between the epithelial cells cultured on chip on days 5 and 8, with the presence of stretch (10% strain, 0.15 Hz) and the presence or absence of endothelium and colonoids. The number of the up-regulated and down-regulated differentially expressed genes in chips is shown in green and red, respectively. (J) The volcano plot of the differential gene expression analysis between the epithelial cells on day 5 of culture with endothelium, in the presence and absence of stretch (10% strain, 0.15 Hz). The number of the up-regulated and down-regulated differentially expressed genes in the presence of stretch is shown in green and red, respectively. (K) The volcano plot resulting from the differential gene expression analysis between the epithelial cells on day 8 of culture with endothelium, in the presence and absence of stretch (10% strain, 0.15 Hz). The number of the up-regulated and down-regulated differentially expressed genes in the presence of stretch is shown in green and red, respectively. (L) List of biological processes identified by the GO enrichment analysis, using the differentially expressed genes between the epithelial cells on day 5 of culture with endothelium, in the presence and absence of stretch (10% strain, 0.15 Hz). The results indicate the significant enrichment of biological processes related to the homeostasis and function of the epithelial barrier. (M) List of biological processes identified by the GO enrichment analysis, using the differentially expressed genes between the epithelial cells on day 8 of culture with endothelium, in the presence and absence of stretch (10% strain, 0.15 Hz). The results indicate the significant enrichment of biological processes related to the morphogenesis, function, and homeostasis of the epithelial barrier. n = 3–6 chips/condition.