Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Abstract Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehen...

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Autores principales:	Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/26475bd8b69946bfadfaa2b8d460120a
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spelling	oai:doaj.org-article:26475bd8b69946bfadfaa2b8d460120a2021-12-02T11:40:45ZUse antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation10.1038/s41598-017-07757-w2045-2322https://doaj.org/article/26475bd8b69946bfadfaa2b8d460120a2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07757-whttps://doaj.org/toc/2045-2322Abstract Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 209 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.Ann H. RyuWalter L. EckalbarAnat KreimerNir YosefNadav AhituvNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ann H. Ryu Walter L. Eckalbar Anat Kreimer Nir Yosef Nadav Ahituv Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
description	Abstract Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 209 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
format	article
author	Ann H. Ryu Walter L. Eckalbar Anat Kreimer Nir Yosef Nadav Ahituv
author_facet	Ann H. Ryu Walter L. Eckalbar Anat Kreimer Nir Yosef Nadav Ahituv
author_sort	Ann H. Ryu
title	Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
title_short	Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
title_full	Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
title_fullStr	Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
title_full_unstemmed	Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
title_sort	use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/26475bd8b69946bfadfaa2b8d460120a
work_keys_str_mv	AT annhryu useantibioticsincellculturewithcautiongenomewideidentificationofantibioticinducedchangesingeneexpressionandregulation AT walterleckalbar useantibioticsincellculturewithcautiongenomewideidentificationofantibioticinducedchangesingeneexpressionandregulation AT anatkreimer useantibioticsincellculturewithcautiongenomewideidentificationofantibioticinducedchangesingeneexpressionandregulation AT niryosef useantibioticsincellculturewithcautiongenomewideidentificationofantibioticinducedchangesingeneexpressionandregulation AT nadavahituv useantibioticsincellculturewithcautiongenomewideidentificationofantibioticinducedchangesingeneexpressionandregulation
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

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