Genomic and proteomic exploration of CHO and hybridoma cells under sodium butyrate treatment

Abstract

Sodium butyrate has been known to increase the specific productivity of recombinant proteins in mammalian cells. In quest of physiological mechanisms leading to the increased productivity, DNA microarray and two dimensional gel electrophoresis (2DE) were used to assess the response of Chinese hamster ovary (CHO) and a mouse hybridoma cell (MAK) to butyrate treatment at the transcriptome and proteome level. The expression of the orthologous genes represented on both CHO cDNA and mouse Affymetrix microarray, as well as genes in the same ontological class were compared. Only a relatively small number of orthologs changed their expression consistently between the two cell lines, however, at a functional class level many genes involved in cell cycle and apoptosis were affected in both cell lines. Furthermore, a large number of genes involved in protein processing, secretion and redox activity were upregulated in both CHO and MAK cells. More genes showed a consistent trend of change at both transcript and protein levels than those which showed opposite trend in MAK cells. Overall the results suggested that the changes arising in the protein processing machinery may be responsible for the increased productivity upon butyrate treatment in both CHO and MAK cells.

Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with in‐creased production capacity

“…Overall, the focus on fold changes distracts attention from changes in gene expression that are regulated at a more physiologic scale such as for instance transcription factors that have an effect on the cell upon slight changes in their expression [30]: if within a pathway each individual gene is upregulated 1.4-fold, none of these will show up in the list of differentially expressed genes when using a threshold of 1.5, however, the overall flux through the pathway will increase significantly. [7,66,69,70] Down regulation of growth [7,32,66,68] In case of antibodies: enhanced [4,69,71,[76][77][78]] assembly and secretion due to a surplus of light chain over heavy chain These challenges in identifying relevant genes and understanding their biological roles are further compounded by the fact that many genes have functional assignments in the GO or KEGG annotation databases that reflect the context in which they were first discovered, which may be completely irrelevant to cells grown in suspension in a protein free medium (such as organism development, tissue specific functions and similar). Moreover, pleiotropy, the phenomenon where a single gene may have multiple functions, which may not all be known [31], can make the interpretation of results difficult.…”

Proteomics analysis of chinese hamster ovary cells undergoing apoptosis during prolonged cultivation

“…Genomic and proteomic studies involving CHO cell lines have also been performed to investigate the effects of treatments which can enhance protein production (Yee et al 2008;Baik and Lee 2010), to compare metabolic profiles of different CHO cell lines varied in protein productivities (Pascoe et al 2007), to study protein profiles in resting and proliferating phases (Naryzhny and Lee 2001), to understand cellular response to hyperosmotic pressure and to examine the effect of transfected cell lines (Carlage et al 2009). Currently, there are no studies on proteomic expression of non-induced apoptotic cells that occurred in prolonged cell cultures, regardless of the cell types.…”

Proteomic Analysis of Bioreactor Cultures of an Antibody Expressing CHOGS Cell Line that Promotes High Productivity

“…Proteomics approaches for improving productivity in CHO cells have been used previously [28][29][30][31][32][33]; specifically, a proteomics approach was used by Yee et al [28] to study the effect of sodium butyrate on CHO cells, whereas Kaufmann et al studied the effect of lowering culture temperature on productivity [43]. While similar to these studies, there are several important features that distinguish the current study from the above published studies.…”

“…An optimized combination of these components is expected to lead to an increased proliferation of the cells, which in turn will lead to higher volumetric productivity, even if the specific productivity of the cell line remains unaltered. Similar studies performed in other laboratories have relied on terminal batch cultures in shake flasks [28,32,33], but since cell culture conditions in shake flasks do not necessarily mimic those in bioreactors, and since the manufacturing step is generally carried out in bioreactors either in fed-batch or in perfusion mode, we have performed all our studies in 2L mini-bioreactors in the fed-batch mode. A CHO-GS cell line expressing a therapeutic Ab was cultured in eight independently controlled DasGip CellFerm Pro mini-bioreactors using an 18-day fed batch process.…”

“…'Global protein expression profiling using shotgun proteomics has been used in our laboratory to determine the protease profile of the CHO-GS host cell line [26] as well as gene expression profile of high producing cell lines [27]. Genome, transcriptome and proteome analysis of CHO cells have been reported multiple times [28][29][30][31][32][33]. Unfortunately, in a majority of these studies, the cells were cultured in shake-flasks prior to analysis.…”