title: A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.
abstract: Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Hooman
authors.initials: H
authors.lastname: Hefzi
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore.
authors.forename: Kok Siong
authors.initials: KS
authors.lastname: Ang
authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Hanscho
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Aarash
authors.initials: A
authors.lastname: Bordbar
authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
authors.forename: David
authors.initials: D
authors.lastname: Ruckerbauer
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore.
authors.forename: Meiyappan
authors.initials: M
authors.lastname: Lakshmanan
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia.
authors.forename: Camila A
authors.initials: CA
authors.lastname: Orellana
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Deniz
authors.initials: D
authors.lastname: Baycin-Hizal
authors.affiliation: Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA.
authors.forename: Yingxiang
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ley
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia.
authors.forename: Veronica S
authors.initials: VS
authors.lastname: Martinez
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore.
authors.forename: Sarantos
authors.initials: S
authors.lastname: Kyriakopoulos
authors.affiliation: Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile.
authors.forename: Natalia E
authors.initials: NE
authors.lastname: Jiménez
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Zielinski
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia.
authors.forename: Lake-Ee
authors.initials: LE
authors.lastname: Quek
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Tune
authors.initials: T
authors.lastname: Wulff
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Johnny
authors.initials: J
authors.lastname: Arnsdorf
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Shangzhong
authors.initials: S
authors.lastname: Li
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Jae Seong
authors.initials: JS
authors.lastname: Lee
authors.affiliation: Center for Systems Biology, University of Iceland, 101 Reykjavik, Iceland.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Paglia
authors.affiliation: Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Loira
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Philipp N
authors.initials: PN
authors.lastname: Spahn
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Lasse E
authors.initials: LE
authors.lastname: Pedersen
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Jahir M
authors.initials: JM
authors.lastname: Gutierrez
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: King
authors.affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Anne Mathilde
authors.initials: AM
authors.lastname: Lund
authors.affiliation: Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA.
authors.forename: Harish
authors.initials: H
authors.lastname: Nagarajan
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Thomas
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia.
authors.forename: Alyaa M
authors.initials: AM
authors.lastname: Abdel-Haleem
authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
authors.forename: Juergen
authors.initials: J
authors.lastname: Zanghellini
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Helene F
authors.initials: HF
authors.lastname: Kildegaard
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Bjørn G
authors.initials: BG
authors.lastname: Voldborg
authors.affiliation: Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile.
authors.forename: Ziomara P
authors.initials: ZP
authors.lastname: Gerdtzen
authors.affiliation: Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Betenbaugh
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.affiliation: Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Mikael R
authors.initials: MR
authors.lastname: Andersen
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia.
authors.forename: Lars K
authors.initials: LK
authors.lastname: Nielsen
authors.affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria. Electronic address: nicole.borth@boku.ac.at.
authors.forename: Nicole
authors.initials: N
authors.lastname: Borth
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore. Electronic address: cheld@nus.edu.sg.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: nlewisres@ucsd.edu.
authors.forename: Nathan E
authors.initials: NE
authors.lastname: Lewis
mesh_terms: D000818:Animals; D016466:CHO Cells; D032921:Consensus; D006224:Cricetinae; D003412:Cricetulus; D016678:Genome; D006801:Humans; D053858:Metabolic Networks and Pathways; D011994:Recombinant Proteins
chemical_list: D011994:Recombinant Proteins
keywords: CHO; Chinese hamster ovary; biotherapeutic protein production; genome-scale model; metabolic network; systems biology