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

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. [Display omitted] •Established mammalian systems biotechnology framework for cell-line development•Unraveled cellular adaptation upon transgene integration in wild-type CHO cells•Studied genomic rearrangements and transcriptional re-wiring in recombinant CHO cells•Identified key regulatory/metabolic signatures for improved cell-line engineering A knowledge-based systems biotechnology approach integrates multi-omics data and genome-scale model to characterize the cellular transfection of a Chinese hamster ovary cell line, thereby identifying key engineering targets for cell-line development and engineering.