title: Transcriptomic changes in CHO cells after adaptation to suspension growth in protein-free medium analysed by a species-specific microarray.
abstract: Chinese Hamster Ovary (CHO) cells are the preferred cell line for production of biopharmaceuticals. These cells are capable to grow without serum supplementation, but drastic changes in their phenotype occur during adaptation to protein-free growth, which typically include the change to a suspension phenotype with reduced growth rate. A possible approach to understand this transformation, with the intention to counteract the reduction in growth by targeted supplementation of protein-free media, is gene expression profiling. The increasing availability of genome-scale data for CHO now facilitates quests for a better understanding of metabolic pathways and gene networks. So far, systematic large-scale expression profiling in CHO cells by microarray was limited due to lack of publicly available array designs and limitations of alternative approaches. Based on the recent release of CHO and Chinese Hamster genome sequences, including an annotated RefSeq genome, we have constructed a publicly available microarray design for effective genome-scale expression profiling. The design employed microarray probes optimized for uniformity, sensitivity, and specificity, with probe properties computed using the latest thermodynamic models. We validated the platform in an analysis of gene expression changes in response to serum-free adaptation. The observed effects on the lipid metabolism as well as on nucleotide synthesis were used to successfully select media supplements that were able to increase growth rate.
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Smriti
authors.initials: S
authors.lastname: Shridhar
authors.affiliation: Austrian Centre of Industrial Biotechnology, Austria.
authors.forename: Gerald
authors.initials: G
authors.lastname: Klanert
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Norbert
authors.initials: N
authors.lastname: Auer
authors.affiliation: Austrian Centre of Industrial Biotechnology, Austria.
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Hernandez-Lopez
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Maciej M
authors.initials: MM
authors.lastname: Kańduła
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hackl
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Johannes
authors.initials: J
authors.lastname: Grillari
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria.
authors.forename: Nancy
authors.initials: N
authors.lastname: Stralis-Pavese
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria. Electronic address: david.kreil@boku.ac.at.
authors.forename: David P
authors.initials: DP
authors.lastname: Kreil
authors.affiliation: Department of Biotechnology, BOKU University, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Austria. Electronic address: nicole.borth@boku.ac.at.
authors.forename: Nicole
authors.initials: N
authors.lastname: Borth
mesh_terms: D000818:Animals; D016466:CHO Cells / Q000378:metabolism*; D018929:Cell Culture Techniques; D003412:Cricetulus; D003470:Culture Media / Q000737:chemistry; D016895:Culture Media, Serum-Free / Q000032:analysis* / Q000737:chemistry; D015342:DNA Probes; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D050356:Lipid Metabolism / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013535:Suspensions; D059467:Transcriptome / Q000235:genetics
chemical_list: D003470:Culture Media; D016895:Culture Media, Serum-Free; D015342:DNA Probes; D013535:Suspensions
keywords: CHO; Chinese Hamster Ovary; Gene ontology; KEGG; Microarray; Probe design; Serum deprivation; Specificity; Transcriptome