Cell line used in biopharmaseutical manufacturing process must maintain their productivity and sustain the same product quality over the production period as well as the life cycle of the product. Although the productivity is often thought of as a critical characteristic of the cell line, it is actually a complex trait that are the manifestation of many cellular properties and influenced by numerous genetic, epigenetic and other physiological factors. Many events in the course of a cell line’s life cycle, including chromosomal rearrangement, loss of the secretory capacity, reduction of the transgene expression, or loss of gene copies, may affect the productivity and product quality. This work aims to develop a better understanding of these factors, and to develop better means for rapidly isolating the stable cell lines. Using a high producing cell line that has been cultured in the laboratory over an extensive period, we performed subcloning to examine the distribution of the productivity. The productivity of low and high producing clones spread over a wide range of more than 10 fold. After a number of cell doubling of those clones to expand their population, the isolated high and low producing cell clones were further subcloned and their productivity distribution was examined again. Selected subclones were analyzed at transcriptome and genome reorganization levels using expression microarrays and comparative genomic hybridization microarrays. Although some genes were differentially expressed, reasonable clonal consistency of transcriptome was found among the offsprings derived from the same clones. However, regions in the genome with copy number differences was detected between high and low producing clones. Furthermore, the DNA methylation extent was examined by whole genome bisulfite sequencing. Total methylation content in CpG sites was reasonablely stable in high and low producing clones and their offsprings. While conclusive evidence that any causal relationship between those genomic and transcriptomic alterations and the productivity cannot be dran, the data does spur further hypothesis to enhance our mechanistic understanding of cell line stability and may provide new insight on the selection of stable high producing cell lines..

Transcriptome, methylome, and genome analysis in clonal variability

249th National Meeting (2015)

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