Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions.
3R
Caco-2
Good in vitro method practices
Gut-on-a-chip
In vitro
Transcriptome
Journal
Archives of toxicology
ISSN: 1432-0738
Titre abrégé: Arch Toxicol
Pays: Germany
ID NLM: 0417615
Informations de publication
Date de publication:
03 2023
03 2023
Historique:
received:
31
10
2022
accepted:
13
12
2022
pubmed:
22
1
2023
medline:
3
3
2023
entrez:
21
1
2023
Statut:
ppublish
Résumé
There is a need for standardized in vitro models emulating the functionalities of the human intestinal tract to study human intestinal health without the use of laboratory animals. The Caco-2 cell line is a well-accepted and highly characterized intestinal barrier model, which has been intensively used to study intestinal (drug) transport, host-microbe interactions and chemical or drug toxicity. This cell line has been cultured in different in vitro models, ranging from simple static to complex dynamic microfluidic models. We aimed to investigate the effect of these different in vitro experimental variables on gene expression. To this end, we systematically collected and extracted data from studies in which transcriptome analyses were performed on Caco-2 cells grown on permeable membranes. A collection of 13 studies comprising 100 samples revealed a weak association of experimental variables with overall as well as individual gene expression. This can be explained by the large heterogeneity in cell culture practice, or the lack of adequate reporting thereof, as suggested by our systematic analysis of experimental parameters not included in the main analysis. Given the rapidly increasing use of in vitro cell culture models, including more advanced (micro) fluidic models, our analysis reinforces the need for improved, standardized reporting protocols. Additionally, our systematic analysis serves as a template for future comparative studies on in vitro transcriptome and other experimental data.
Identifiants
pubmed: 36680592
doi: 10.1007/s00204-022-03430-y
pii: 10.1007/s00204-022-03430-y
pmc: PMC9862247
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
737-753Subventions
Organisme : Nederlandse Organisatie voor Wetenschappelijk Onderzoek
ID : 737.016.003
Organisme : Dutch Ministry of Agriculture, Nature and Food Quality
ID : KB-37-002-020
Informations de copyright
© 2023. The Author(s).
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