Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line

Abstract

Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner.

A reference genome of the Chinese hamster based on a hybrid assembly strategy

“…In addition, for >30 years, they have been the host cell of choice for production of most biotherapeutics. While the aforementioned research was carried out without genomic resources, new opportunities are arising with published CHO genome sequences [Xu et al, 2011], [Brinkrolf et al, 2013], [Lewis et al, 2013], [Yusufi et al, 2017]. However, the draft nature of these genome sequences pose challenges for many applications.…”

A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

“…The genome sequencing data of CHO-K1 genome was downloaded from NCBI (Xu et al, 2011); rK1-IgG was obtained courtesy of Bioprocessing Technology Institute, Singapore (Yusufi et al, 2016); rDG-IgG-1 was sequenced at University of Minnesota Genomics Center; and hamster liver was sequenced at National Center for Genomic Research. The sequencing depths were 74X, 54X, 75X for the three lines (CHO-K1, rK1-IgG, and rDG-IgG-1), and 89X for Chinese hamster liver, respectively.…”

Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures

“…The researchers now have access to perform in silico metabolic flux simulation and analysis at a system level based on genome‐scale CHO cell metabolic network (Hefzi et al, ; Yusufi et al, ). Furthermore, increasing volumes of omics data in CHO cells are becoming publicly available with the help of advanced analytical techniques (Gao et al, ; Lewis et al, ), and it's believed that genome‐scale constraint‐based metabolic models are a reliable framework to fully utilize these multi‐omics data.…”

“…The researchers now have access to perform in silico metabolic flux simulation and analysis at a system level based on genome-scale CHO cell metabolic network (Hefzi et al, 2016;Yusufi et al, 2017).…”