Toward genomic cell culture engineering

Abstract

Genomic and proteomic based global gene expression profiling has altered the landscape of biological research in the past few years. Its potential impact on cell culture bioprocessing has only begun to emanate, partly due to the lack of genomic sequence information for the most widely used industrial cells, Chinese hamster ovary (CHO) cells. Transcriptome and proteome profiling work for species lacking extensive genomic resources must rely on information for other related species or on data obtained from expressed sequence tag (EST) sequencing projects, for which burgeoning efforts have only recently begun. This article discusses the aspects of EST sequencing in those industrially important, genomic resources-poor cell lines, articulates some of the unique features in employing microarray in the study of cultured cells, and highlights the infrastructural needs in establishing a platform for genomics based cell culture research. Recent experience has revealed that generally, most changes in culture conditions only elicit a moderate level of alteration in gene expression. Nevertheless, by broadening the conventional scope of microarray analysis to consider estimated levels of transcript abundance, much physiological insight can be gained. Examples of the application of microarray in cell culture are discussed, and the utility of pattern identification and process diagnosis are highlighted. As genomic resources continue to expand, the power of genomic tools in cell culture processing research will be amply evident. The key to harnessing the immense benefit of these genomic resources resides in the development of physiological understanding from their application.

Gene expression profiling for mechanistic understanding of cellular aggregation in mammalian cell perfusion cultures

“…The amount of genomic information on BHK cells is limited in the GenBank database and as a result, PCR arrays specific to BHK are not commercially available. Nevertheless, the study of gene expression in BHK is possible through cross‐species hybridization to mouse, which in addition to being closely related to BHK, has abundant genomic sequence information (Bult et al, 2008; Eppig et al, 2005; Wlaschin et al, 2006). Because the level of identity between the mouse and BHK sequences is between 75% and 97% and the level of homology varies with each gene (Wlaschin et al, 2006), the reproducibility of the PCR arrays and the specificity to the BHK genes of interest must be assessed.…”

Cell culture processes for monoclonal antibody production

“…These advances have resulted from intensive research in cell line engineering, media development, feeding strategies, cell metabolism, better process understanding and their impact on product quality and scale-up. It is expected that better understanding of cell biology fueled by advances in genomics, proteomics and metabolomics, including the application of gene expression analysis using CHO chips and genomic scale models, 99,100 combined with further improvements in media, high throughput technologies, online monitoring and automation, will allow researchers to broaden the experimental design space, as well as lower the cost of process development.…”

Identifying the CHO Secretome using Mucin-type O-Linked Glycosylation and Click-chemistry

“…Unfortunately, unlike other rodent cells, CHO cell genetic and proteomic data are limited and the genomic sequence for the CHO-K1 cell line has only recently been published . Increasing these resources could potentially aid in understanding and improving recombinant protein production processes to help enhance therapeutic protein development. , In particular, a CHO proteome has yet to be well established and the few CHO proteomic studies performed to-date have generally focused on changes in the CHO intracellular proteome relative to the expression level of the recombinant protein. , An important area of the proteome typically overlooked even though it plays an integral role in cell culture media conditions is the cellular secretome, often called host cell proteins (HCP) in conditioned media of transfected cells. The secretome generally refers to the collection of proteins that contain the signal peptide and are processed through the classical secretory pathway.…”