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Cited by 178Viral Infectious Diseases and Gene Expression in InsectsAdvanced Proteomics Techniques and ApplicationsGlycosylation and Glycoproteins Research

Proteomic analysis of Chinese hamster ovary cells

Open access
Baycin-Hizal, Deniz, Tabb, David L., Chaerkady, Raghothama, Chen, Lily, Lewis, Nathan E., Nagarajan, Harish, Sarkaria, Vishaldeep, Kumar, Amit +10 more·2012·Journal of Proteome Research
DOI 10.1021/pr300476wPMC PMC3772721
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Abstract

To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimensional liquid chromatography, and solid phase extraction of glycopeptides (SPEG). From the 120 different mass spectrometry analyses generating 682,097 MS/MS spectra, 93,548 unique peptide sequences were identified with at most 0.02 false discovery rate (FDR). A total of 6164 grouped proteins were identified from both glycoproteome and proteome analysis, representing an 8-fold increase in the number of proteins currently identified in the CHO proteome. Furthermore, this is the first proteomic study done using the CHO genome exclusively, which provides for more accurate identification of proteins. From this analysis, the CHO codon frequency was determined and found to be distinct from humans, which will facilitate expression of human proteins in CHO cells. Analysis of the combined proteomic and mRNA data sets indicated the enrichment of a number of pathways including protein processing and apoptosis but depletion of proteins involved in steroid hormone and glycosphingolipid metabolism. Five-hundred four of the detected proteins included N-acetylation modifications, and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis will enhance the knowledge base about CHO capabilities for recombinant expression and provide information useful in cell engineering efforts aimed at modifying CHO cellular functions.

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  • This multidimensional study also resolved the codon frequency in these cells, which largely contributed to sequence optimization of genes encoding recombinant proteins for this expression system.

    “This multidimensional study also resolved the codon frequency in these cells, which largely contributed to sequence optimization of genes encoding recombinant proteins for this expression system.”

    From Therapeutic glycoprotein production in mammalian cells (2017) · cites this paper as Baycin-Hizal et al., 2012

    The Results (Codon Frequency) report CHO codon frequencies and compare them with human codon frequencies, then suggest replacing suboptimal codons when producing recombinant proteins. The Discussion likewise describes codon optimization as relevant to improving expression, but neither section establishes that this study largely contributed to actual gene-sequence optimization. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • A first large-scale proteomic analysis identified 6164 proteins from both the proteome and glycoproteome of CHO-K1 cells.

    “A first large-scale proteomic analysis identified 6164 proteins from both the proteome and glycoproteome of CHO-K1 cells (Baycin-Hizal et al., 2012).”

    From Therapeutic glycoprotein production in mammalian cells (2017) · cites this paper as Baycin-Hizal et al., 2012

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Authors
Baycin-Hizal, D., Tabb, D. L., Chaerkady, R., Chen, L., Lewis, N. E., Nagarajan, H., Sarkaria, V., Kumar, A., Wolozny, D., Colao, J., Jacobson, E., Tian, Y., O’Meally, R. N., Krag, S. S., Cole, R. N., Palsson, B. O., Zhang, H., & Betenbaugh, M.
Affiliations
  • Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States
  • Vanderbilt University Medical Center (US)
  • Johns Hopkins University (US)
  • University of California San Diego (US)
  • Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
Corresponding author
Betenbaugh, Michael
ORCID
Venue
Journal of Proteome Research
Publisher
American Chemical Society (ACS)
Published
2012-10-05
Volume
11
Issue
11
Pages
5265-5276
ISSN
  • 1535-3893 (ISSN-L)
  • 1535-3907
DOI
10.1021/pr300476w
PMC
PMC3772721
OpenAlex
W2143346248
Cited by
178
References
2
Citations by year
2026: 7 · 2025: 9 · 2024: 7 · 2023: 13 · 2022: 12 · 2021: 9 · 2020: 10 · 2019: 9 · 2018: 14 · 2017: 17 · 2016: 13 · 2015: 25 · 2014: 15 · 2013: 17
FWCI
7.33
Type
journal article
Language
en
Open access
Locations
  • Journal of Proteome Research (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
Funders
  • Johns Hopkins University
  • Novo Nordisk Fonden (NNF10CC1016517)
  • National Cancer Institute (U01CA152647, U01CA152813)
  • Division of Emerging Frontiers in Research and Innovation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
Keywords
CHO cells, secretome, glycoproteome, N-glycosylation, N-acetylation, codon usage, recombinant protein expression, protein processing, apoptosis, steroid hormone metabolism, glycosphingolipid metabolism, cell engineering
MeSH terms
Acetylation, Animals, Carbohydrates, Chromatography, Liquid, Codon, Cricetulus, Glycosylation, Cricetinae, RNA, Messenger, CHO Cells, Proteome, Tandem Mass Spectrometry

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