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

Kornphimol Kulthong,Loes Duivenvoorde,Meike Van Der Zande,Guido J E J Hooiveld,Ignacio Miro Estruch,Victor Marin,Hans Bouwmeester

doi:10.1038/s41598-021-82853-6

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.

Highlights

Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods
Caco-2 cells grown under continuous flow showed a comparable monolayer formation and cell morphology at day 21 to cells grown under static conditions, as reflected by immunofluorescence staining of nuclei, actin filaments and tight junctions
Monolayers of Caco-2 cells grown in conventional static systems have been widely used to study effects of exposure to chemicals to predict the in vivo human intestinal epithelial responses[25,26,27]

Summary

Introduction

Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could 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. The differential expression of intestine-specific genes in Caco-2 cells was compared to those reported for different regions of human intestinal tissues in vivo[22]

Objectives

Results

Conclusion