title: Enhanced protein production by microRNA-30 family in CHO cells is mediated by the modulation of the ubiquitin pathway.
abstract: Functional genomics represent a valuable approach to improve culture performance of Chinese hamster ovary (CHO) cell lines for biopharmaceutical manufacturing. Recent advances in applied microRNA (miRNAs) research suggest that these small non-coding RNAs are critical for the regulation of cell phenotypes in CHO cells. However, the notion that individual miRNAs usually control the expression of hundreds of different genes makes miRNA target identification highly complex. We have recently reported that the entire miR-30 family enhances recombinant protein production in CHO cells. To better understand the pro-productive effects of this miRNA family, we set out to identify their downstream target genes in CHO cells. Computational target prediction combined with a comprehensive functional validation enabled the discovery of a set of twenty putative target genes for all productivity enhancing miR-30 family members. We demonstrate that all miR-30 isoforms contribute to the regulation of the ubiquitin pathway in CHO cells by directly targeting the ubiquitin E3 ligase S-phase kinase-associated protein 2 (Skp2). Finally, we provide several lines of evidence that miR-30-mediated modulation of the ubiquitin pathway may enhance recombinant protein expression in CHO cells. In summary, this study supports the importance of non-coding RNAs, especially of miRNAs, in the context of cell line engineering.
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Medicine, Albert-Einstein-Allee 11, 89081 Ulm, Germany. Electronic address: simon.fischer@hochschule-bc.de.
authors.forename: Simon
authors.initials: S
authors.lastname: Fischer
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Natural Sciences, Albert-Einstein-Allee 11, 89081 Ulm, Germany. Electronic address: sven.mathias@hochschule-bc.de.
authors.forename: Sven
authors.initials: S
authors.lastname: Mathias
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany; University of Ulm, Faculty of Natural Sciences, Albert-Einstein-Allee 11, 89081 Ulm, Germany. Electronic address: simonehelena.schaz@hochschule-bc.de.
authors.forename: Simone
authors.initials: S
authors.lastname: Schaz
authors.affiliation: University of Ulm, Faculty of Medicine, Albert-Einstein-Allee 11, 89081 Ulm, Germany; Rentschler Biotechnologie GmbH, Erwin-Rentschler-Straße 21, 88471 Laupheim, Germany. Electronic address: verena.emmerling@uni-ulm.de.
authors.forename: Verena Vanessa
authors.initials: VV
authors.lastname: Emmerling
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany. Electronic address: theresa.buck@gmail.com.
authors.forename: Theresa
authors.initials: T
authors.lastname: Buck
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany. Electronic address: kleemann@hochschule-bc.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Kleemann
authors.affiliation: TAmiRNA GmbH, Muthgasse 18, 1190 Vienna, Austria. Electronic address: matthias.hackl@tamirna.com.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hackl
authors.affiliation: Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; Evercyte GmbH, Muthgasse 18, 1190 Vienna, Austria. Electronic address: johannes.grillari@boku.ac.at.
authors.forename: Johannes
authors.initials: J
authors.lastname: Grillari
authors.affiliation: Department of Neuroinformatics, Donders Institute for Brain Function, Cognition and Behaviour, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. Electronic address: a.aschrafi@donders.ru.nl.
authors.forename: Armaz
authors.initials: A
authors.lastname: Aschrafi
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany. Electronic address: handrick@hochschule-bc.de.
authors.forename: René
authors.initials: R
authors.lastname: Handrick
authors.affiliation: Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany. Electronic address: otte@hochschule-bc.de.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Otte
mesh_terms: D000818:Animals; D016466:CHO Cells; D006224:Cricetinae; D003412:Cricetulus; D057809:HEK293 Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics; D011994:Recombinant Proteins / Q000378:metabolism; D044786:S-Phase Kinase-Associated Proteins / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction; D025801:Ubiquitin / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D011994:Recombinant Proteins; D044786:S-Phase Kinase-Associated Proteins; D025801:Ubiquitin
keywords: CHO; Cell engineering; MicroRNA; Skp2; Ubiquitin pathway; miR-30