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Gene expression profiling of Chinese Hamster Ovary production cell lines

ABSTRACT: The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined

ORGANISM(S): Cricetulus griseus

PROVIDER: GSE30321 | GEO | 2011/07/28

SECONDARY ACCESSION(S): PRJNA143557

REPOSITORIES: GEO

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Gene expression profiling of Chinese Hamster Ovary production cell lines

Project description:The dataset set consists of 295 microarrays from 121 individual CHO cultures producing a range of biologics including monoclonal antibodies, fusion proteins and therapeutic factors; non-producing cell lines were also included. Samples were taken from a wide range of process scales and formats that varied in terms of seeding density, temperature, medium, feed medium, culture duration and product type. Cells were sampled for gene expression analysis at various stages of the culture and bioprocess-relevant characteristics including cell density, growth rate, viability, lactate, ammonium and cell specific productivity (Qp) were determined A total of 295 microarray samples were assayed. In addition 9 continous bioprocess variables were also measured.

2011-07-27 | E-GEOD-30321 | biostudies-arrayexpress

Gene expression profiling of Fast vs. Slow Chinese Hamster Ovary cell lines using Wye3aHamster array

Project description:A 3rd generation Wye3aHamster microarray chip was used to carry out a differential expression microarray study of a panel of 30 slow- and fast-growing production cell lines, identifying a priority list of 240 transcripts (110 Up; 130 Down) that passed a statisical filter (ANOVA p-value <0.05, 1.3 fold-change) when the samples were grouped into fast versus slow and pairwise compared and a minimum Pearson Correlation Coefficent (PCC) of >0.7 when growth rate was used as a continuous variable (i.e. included genes have to satisfy BOTH criteria, not just one). This yielded a list of 240 genes. The 240-member genelist yielded 223 Annotated IDs, 203 of which are Unique and all of which are associated with contributing to a high rate of growth in production CHO cell lines. Prospective samples were isolated from 2 distinct groups of clones (slow growers and fast growers), all chosen from the same project (transfection of product transgene into parent line) generated at Pfizer Inc., Bioprocess R&D, Andover, MA, USA. Each group comprised 5 distinct clones, all of which had comparable Qp characteristics. The clones were passaged for 3 or 4 passages over 3-4 days to stabilise the phenotype and freeze stocks. Samples for array hybridization were generated in batch shake flask culture (60ml working volume) with AS1 medium and without feeds or temperature shift. Samples were collected at a single time point (72hrs - mid/late log) and each clone was grown in triplicate flasks, yielding a total of 30 samples for collection and processing. Two bioprocess-relevant variables, viable cell density (VCD) and viability were measured. From the VCD, the growth rate (h-1) was calculated.

2013-01-01 | E-GEOD-37251 | biostudies-arrayexpress

Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture

2011-05-24 | GSE29439 | GEO

The Suppression of Medium Acidosis Improves the Maintenance and Differentiation of Human Pluripotent Stem Cells at High Density in Defined Cell Culture Medium

Project description:We use a chemically defined medium to systemically examine cellular activities and the impact of medium components in high-density culture. We show that medium acidosis is the main factor that alters cell cycle, gene expression and cellular metabolism at high cell density. The low medium pH leads to inhibition of glucose consumption, cell cycle arrest, and subsequent cell death. At high cell density, the suppression of medium acidosis with sodium bicarbonate (NaHCO3) significantly increases culture capacity for stem cell survival, derivation, maintenance and differentiation.

2018-04-12 | GSE113016 | GEO

Transcriptome analysis of human erythroid cells differentiated from iPSCs, cord blood and adult peripheral blood

Project description:The aim of the study is to develop a scalable continuous agitation suspension culture bioprocess for differentiation of hiPSCs towards erythroid cells. Using process optimization, we developed the entire process completely in agitation suspension culture condition starting from hiPSC expansion through to hematopoietic induction and erythroid differentiation. Transcriptome profiling was carried out to facilitate comparisons between erythroid cells differentiated from hiPSCs using this bioprocess, and erythroid cells differentiated from cord blood and adult CD34+ cells.

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Mucosal Glycan Foraging Enhances the Fitness and Transmission of a Saccharolytic Human Distal Gut Symbiont

Project description:Gene expression profiles of Bacteroides thetaiotaomicron in vitro during growth on host mucosal polysaccharides as sole carbon sources. All substrates in this series are derived from porcine gastric mucin and include mucin O-glycans and glycosaminoglycans. Two different culture formats used: 800ml batch-culture bioreactors and 5ml tube cultures (format is indicated within each sample title). Each set of growths was referenced to a minimal medium glucose reference corressponding to the same culture format. Unfractionated porcine mucosal glycan (PMG) growths were compared to previously published in vivo datasets, which were referenced to the 800ml minimal medium glucose reference dataset.

2008-11-20 | E-GEOD-11944 | biostudies-arrayexpress

Genomic instability in human embryonic stem cells is associated to culture density and medium acidification.

Project description:Human embryonic stem cells (hESC) show great promise for clinical and research applications, but genomic instability hampers the development of their full potential. Here we demonstrate that increased culture density causes medium acidification due to lactic acid accumulation. hESC are able to cope with this, but acquire increased DNA damage associated to DNA replication stress. Also, single-cell genomics analysis reveals a strong correlation of the occurrence of de novo CNVs and culture density after only five days of culture. However, by an improved control over the accumulation of metabolites through more frequent medium changes, we were able to counter the effect of culture density on DNA damage and CNVs. These data underline the importance of optimal culture conditions, even at short-term, in the light of bringing hESC to their full potential.

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Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture

Project description:Strong production of recombinant proteins interfere with cellular processes in many ways. The extent of the bacterial stress response is determined by the specific properties of the recombinant protein, and by the rates of transcription and translation. The consideration of bacterial stress and starvation responses is of crucial importance for the successful establishment of an industrial large scale bioprocess. Stress genes can be used as marker genes in order to monitor the fitness of industrial bacterial hosts during fermentation processes. For this purpose, here in our study we have applied transcriptome analysis for the description of general and specific stress and starvation responses of Escherichia coli. Producing recombinant protein (Xylanase) in high cell density fed batch culture. Cells were grown in batch mode in TB media till an OD600 of 15. The specific growth rate of 0.3 h-1 was maintained by fed batch started at OD600 of 15. Cells were induced at an OD600 of 30 using 1 mM IPTG and the growth and product profile was monitored. Samples at different time points (2hrs, 4hrs, and 6hrs) were taken and frozen in liquid nitrogen quickly for transcriptome analysis.

2011-05-23 | E-GEOD-29439 | biostudies-arrayexpress

Chinese hamster ovary (CHO) cell Surfaceome LC-MSMS and mRNA expression analysis

Project description:The production of biopharmaceuticals relies on robust cell systems that can produce recombinant proteins at high levels, and grow and survive in the stressful bioprocess environment. Chinese hamster ovary cells (CHO) as the main production hosts offer a variety of advantages including robust growth and survival in a bioprocess environment. Cell surface proteins are of special interest for the understanding of how CHO cells react to their environment while maintaining growth and survival phenotypes, since they enable cellular reactions to external stimuli and potentially initiate signaling pathways. To provide deeper insight into functions of this special cell surface sub-proteome, pathway enrichment analysis of the determined CHO surfaceome was conducted. Enrichment of growth/ survival pathways such as the phosphoinositide-3-kinase (PI3K/AKT), Mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK-STAT) and RAP1 pathways was observed, offering novel insights into how cell surface receptors and ligand mediated signaling enable the cells to grow and survive in a bioprocess environment. When supplementing surfaceome data with RNA expression data, several growth/ survival-receptors were shown to be co-expressed with their respective ligands and thus suggesting self-induction mechanisms, while other receptors or ligands were not detectable. As data about the presence of surface receptors and their associated expressed ligands may serve as base for future studies, further pathway characterization will enable the implementation of optimization strategies to further enhance cellular growth and survival behavior.

2022-10-15 | PXD033581 | Pride

A novel and simple strategy to isolate extracellular vesicles from human plasma and tissue culture medium with high yield and purity

Project description:Extracellular vesicles (EVs) function in intercellular communication and can be indicative of the biological status of their producing cells, for example in disease. Isolation of EVs from blood or tissue culture medium is instrumental for the discovery of novel EV associated disease biomarkers as well as for functional studies. Current protocols for EV isolation from blood are limited by low recovery yield and in their capacity to remove contaminating particles, including lipoprotein particles and protein aggregates. In this study, we designed and evaluated a three step protocol to isolate EVs from blood or tissue culture media, with high yield and purity. EVs were first collected and separated from the majority of soluble plasma protein by precipitation with polyethylene glycol (PEG). PEG precipitation resulted in near to absolute recovery, while the yield of EVs collected by ultracentrifugation was only 15%. PEG precipitated EVs were then separated from co-precipitated proteins and protein complexes, low density lipoproteins (LDL), and the majority of high density lipoproteins (HDL) by upward displacement into a iohexol density gradients, yielding 493 fold purification relative to total plasma protein with 76% recovery. Finally, remaining HDL and iohexol was effectively removed by size exclusion chromatography (SEC). Near to absolute pure of isolated EVs was confirmed by cryo-electron microscopy.

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