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Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions

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 u...

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Autores principales: Elzinga, Janneke, Grouls, Menno, Hooiveld, Guido J. E. J., van der Zande, Meike, Smidt, Hauke, Bouwmeester, Hans
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9862247/
https://www.ncbi.nlm.nih.gov/pubmed/36680592
http://dx.doi.org/10.1007/s00204-022-03430-y
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author Elzinga, Janneke
Grouls, Menno
Hooiveld, Guido J. E. J.
van der Zande, Meike
Smidt, Hauke
Bouwmeester, Hans
author_facet Elzinga, Janneke
Grouls, Menno
Hooiveld, Guido J. E. J.
van der Zande, Meike
Smidt, Hauke
Bouwmeester, Hans
author_sort Elzinga, Janneke
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00204-022-03430-y.
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spelling pubmed-98622472023-01-23 Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions Elzinga, Janneke Grouls, Menno Hooiveld, Guido J. E. J. van der Zande, Meike Smidt, Hauke Bouwmeester, Hans Arch Toxicol In Vitro Systems 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00204-022-03430-y. Springer Berlin Heidelberg 2023-01-21 2023 /pmc/articles/PMC9862247/ /pubmed/36680592 http://dx.doi.org/10.1007/s00204-022-03430-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle In Vitro Systems
Elzinga, Janneke
Grouls, Menno
Hooiveld, Guido J. E. J.
van der Zande, Meike
Smidt, Hauke
Bouwmeester, Hans
Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title_full Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title_fullStr Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title_full_unstemmed Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title_short Systematic comparison of transcriptomes of Caco-2 cells cultured under different cellular and physiological conditions
title_sort systematic comparison of transcriptomes of caco-2 cells cultured under different cellular and physiological conditions
topic In Vitro Systems
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9862247/
https://www.ncbi.nlm.nih.gov/pubmed/36680592
http://dx.doi.org/10.1007/s00204-022-03430-y
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