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| Status |
Public on Feb 08, 2021 |
| Title |
Comparative transcriptomics of epithelial cells grown under static and microfluidic gut-on-chip conditions and benchmarked against human in vivo intestinal cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
Microarray analysis was performed on Caco-2 cells cultured statically or in a gut-on-chip device for 21 days.
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| Contributor(s) |
Kulthong K, Hooiveld GJ, van der Zande M, Bouwmeester H |
| Citation(s) |
33547413, 36680592 |
| Submission date |
Aug 14, 2020 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
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| Organization name |
Wageningen University
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| Department |
Div. Human Nutrition & Health
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| Lab |
Nutrition, Metabolism & Genomics Group
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| Street address |
HELIX, Stippeneng 4
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| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
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| Platforms (1) |
| GPL17692 |
[HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [transcript (gene) version] |
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| Samples (8)
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| GSM4728034 |
Caco-2 cells, grown on Transwell inserts, replicate 1 |
| GSM4728035 |
Caco-2 cells, grown on Transwell inserts, replicate 2 |
| GSM4728036 |
Caco-2 cells, grown on Transwell inserts, replicate 3 |
| GSM4728037 |
Caco-2 cells, grown on Transwell inserts, replicate 4 |
| GSM4728038 |
Caco-2 cells, grown in a microfluidic device, replicate 1 |
| GSM4728039 |
Caco-2 cells, grown in a microfluidic device, replicate 2 |
| GSM4728040 |
Caco-2 cells, grown in a microfluidic device, replicate 3 |
| GSM4728041 |
Caco-2 cells, grown in a microfluidic device, replicate 4 |
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| Relations |
| BioProject |
PRJNA657247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156269_RAW.tar |
39.5 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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