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A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes

Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which...

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Bibliographic Details
Published in:Metabolic engineering 2021-07, Vol.66, p.114-122
Main Authors: Karottki, Karen Julie la Cour, Hefzi, Hooman, Li, Songyuan, Pedersen, Lasse Ebdrup, Spahn, Philipp N., Joshi, Chintan, Ruckerbauer, David, Bort, Juan A.Hernandez, Thomas, Alex, Lee, Jae Seong, Borth, Nicole, Lee, Gyun Min, Kildegaard, Helene Faustrup, Lewis, Nathan E.
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Language:English
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Summary:Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we present a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. Using this screen, we identified a glutamine response network in CHO cells. Glutamine is particularly important since it is often over-fed to drive increased TCA cycle flux, but toxic ammonia may accumulate. With the screen we found one orphan glutamine-responsive gene with no clear connection to our network. Knockout of this novel and poorly characterized lipase, Abhd11, substantially increased growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait, and elucidate novel regulators of metabolism. •A large-scale CHO specific CRISPR knockout screening platform is established in CHO cells.•This platform identified known and novel genes involved in glutamine metabolism.•Abhd11 plays a critical role in growth in media supplemented with glutamine.•Abhd11 decreases lag-time in glutamine free media.
ISSN:1096-7176
1096-7184
DOI:10.1016/j.ymben.2021.03.017