Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia

Abstract

Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.

Social evolution of shared biofilm matrix components

“…During infection, V. cholerae biofilms are primarily localized on the tips of intestinal villi and therefore experience peristaltic flow in the gut 55 . The flow speed and the associated shear stress used in this study fall within the range measured in these environments 56 . The population densities of V. cholerae cells in natural ecosystems have been measured to range from 10 2 to 10 5 cells per liter 57 , corresponding to an average distance between cells on the order of millimeters in 3D space.…”

Level of Murine DDX3 RNA Helicase Determines Phenotype Changes of Hepatocytes In Vitro and In Vivo

“…Comparison of RNA levels (transcriptome data) between in vitro and in vivo studies can reveal discordant gene expression even under close conditions [71,72]. This difference may be determined by varied inhibition or downregulation of the target in these conditions.…”

Recent advances in the translation of drug metabolism and pharmacokinetics science for drug discovery and development

“…More specifically, spheroids, organoids, and organs-on-chips have been introduced as novel systems to assess ADMET properties 116 . For instance, the effects of dynamic flow conditions of a gut-on-chip culture system on the gene expression profiles were investigated 117 . The in vitro gene expression profiles under 3D culture conditions were similar to those of human in vivo duodenum, jejunum, ileum, and colon tissue samples, indicating that the dynamic gut-on-chip platform is a suitable model for studying human intestinal drug transporters, enzymes, and toxicological responses 117 .…”

“…For instance, the effects of dynamic flow conditions of a gut-on-chip culture system on the gene expression profiles were investigated 117 . The in vitro gene expression profiles under 3D culture conditions were similar to those of human in vivo duodenum, jejunum, ileum, and colon tissue samples, indicating that the dynamic gut-on-chip platform is a suitable model for studying human intestinal drug transporters, enzymes, and toxicological responses 117 . In addition, several other intestinal chip models were recently developed to study drug absorption, metabolism, and bioavailability 118 , 119 , 120 , 121 .…”