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Cited by 139Genomics and Chromatin DynamicsBacterial Genetics and BiotechnologyEpigenetics and DNA Methylation

Use Antibiotics in Cell Culture with Caution: Genome-wide Identification of Antibiotic-Induced Changes in Gene Expression and Regulation

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Ryu, Ann H., Eckalbar, Walter L., Kreimer, Anat, Yosef, Nir, Ahituv, Nadav·2017·Scientific Reports
DOI 10.1038/s41598-017-07757-wPMC PMC5548911

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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.

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  • Non-physiological concentrations of growth factors and antibiotics are commonly used in cell culture.

    “Such factors include, but are not limited to, the common usage non-physiological concentrations of growth factors (Rubin, 2007; Holohan et al., 2013; Langhans, 2018), and antibiotics (Ryu et al., 2017)”

    From Toward Best Practices for Controlling Mammalian Cell Culture Environments (2022) · cites this paper as Ryu et al., 2017

    The Introduction and Discussion say that antibiotics are routinely used in cell culture, and the Methods specify a standard antibiotic concentration. The paper does not characterize that concentration as non-physiological. The growth-factor portion of the sentence is attributed to other citations, not Ryu et al.; our copy provides no page numbers for these passages. (LLM, conf=0.84)

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Authors
Ryu, A. H., Eckalbar, W. L., Kreimer, A., Yosef, N., & Ahituv, N.
Affiliations
  • University of California, San Francisco (US)
  • Ragon Institute of MGH, MIT and Harvard (US)
Corresponding author
Ahituv, Nadav
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2017-08-08
Volume
7
Issue
1
Pages
7533-7533
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-017-07757-w
PMC
PMC5548911
OpenAlex
W2951597545
Cited by
139
References
54
Citations by year
2026: 14 · 2025: 24 · 2024: 23 · 2023: 19 · 2022: 21 · 2021: 13 · 2020: 14 · 2019: 8 · 2018: 2 · 2017: 1
FWCI
2.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • eScholarship (California Digital Library) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • National Science Foundation
  • National Institutes of Health (1s10od021596-01)
  • National Institute of Mental Health (R01MH109907)
  • National Human Genome Research Institute
  • National Cancer Institute (R01CA197139)
  • National Institute of General Medical Sciences (GM61390, U19GM061390, T32GM007175, U01GM061390)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (P01HD084387)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
penicillin-streptomycin, HepG2 cells, gene expression changes, H3K27ac, chromatin regulation, ATF3, xenobiotic metabolism, liver cell lines
MeSH terms
Acetylation, Anti-Bacterial Agents, Histones, Humans, Liver, Lysine, Signal Transduction, Genome, Human, Gene Expression Regulation, Neoplastic, Sequence Analysis, RNA, Chromatin Immunoprecipitation, Hep G2 Cells

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