Chromosomal instability drives convergent and divergent evolution toward advantageous inherited traits in mammalian CHO bioproduction lineages

Huhn, Steven; Chang, Min S.; Kumar, Amit; Liu, Ren; Jiang, Bo; Betenbaugh, Michael J.; Lin, Henry; Nyberg, Gregg; Du, Zhimei

doi:10.1016/j.isci.2022.104074

Cited by 6 publications

(7 citation statements)

References 51 publications

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“…These discrepancies may be explained by the unique features of the CHO cell lines derived from a single host, acquired by genetic drift in separate laboratories [ 60 ]. Differences in terms of the media used and the culture strategies have also shown to give rise to genetic and epigenetic diversity, and this could explain phenotypic differences when distinct processes are used for the production from the same clone [ 61 , 62 ]. This diversity is known to have a major impact on the metabolomic profile of CHO culture.…”

Section: Discussionmentioning

confidence: 99%

Metabolic Profiling of CHO Cells during the Production of Biotherapeutics

Coulet

Kepp

Kroemer

et al. 2022

Cells

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As indicated by an ever-increasing number of FDA approvals, biotherapeutics constitute powerful tools for the treatment of various diseases, with monoclonal antibodies (mAbs) accounting for more than 50% of newly approved drugs between 2014 and 2018 (Walsh, 2018). The pharmaceutical industry has made great progress in developing reliable and efficient bioproduction processes to meet the demand for recombinant mAbs. Mammalian cell lines are preferred for the production of functional, complex recombinant proteins including mAbs, with Chinese hamster ovary (CHO) cells being used in most instances. Despite significant advances in cell growth control for biologics manufacturing, cellular responses to environmental changes need to be understood in order to further improve productivity. Metabolomics offers a promising approach for developing suitable strategies to unlock the full potential of cellular production. This review summarizes key findings on catabolism and anabolism for each phase of cell growth (exponential growth, the stationary phase and decline) with a focus on the principal metabolic pathways (glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle) and the families of biomolecules that impact these circuities (nucleotides, amino acids, lipids and energy-rich metabolites).

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Section: Discussionmentioning

confidence: 99%

Metabolic Profiling of CHO Cells during the Production of Biotherapeutics

Coulet

Kepp

Kroemer

et al. 2022

Cells

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“…A review of the literature suggests two likely explanations for the increased titer produced in the processes with the re-clones. First, clonal CHO cell populations exhibit natural heterogeneity, which could enable the isolation of a re-clone with desired features (i.e., higher productivity) [20,23,29,30,36]. This heterogeneity is generally accepted in the field and, importantly, is not indicative of instability in upstream process performance or product quality [6,23,37,38].…”

Section: Discussionmentioning

confidence: 99%

Improved Titer in Late-Stage Mammalian Cell Culture Manufacturing by Re-Cloning

Rehmann

Tian

et al. 2022

Bioengineering

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Improving productivity to reduce the cost of biologics manufacturing and ensure that therapeutics can reach more patients remains a major challenge faced by the biopharmaceutical industry. Chinese hamster ovary (CHO) cell lines are commonly prepared for biomanufacturing by single cell cloning post-transfection and recovery, followed by lead clone screening, generation of a research cell bank (RCB), cell culture process development, and manufacturing of a master cell bank (MCB) to be used in early phase clinical manufacturing. In this study, it was found that an additional round of cloning and clone selection from an established monoclonal RCB or MCB (i.e., re-cloning) significantly improved titer for multiple late phase monoclonal antibody upstream processes. Quality attributes remained comparable between the processes using the parental clones and the re-clones. For two CHO cells expressing different antibodies, the re-clone performance was successfully scaled up at 500-L or at 2000-L bioreactor scales, demonstrating for the first time that the re-clone is suitable for late phase and commercial manufacturing processes for improvement of titer while maintaining comparable product quality to the early phase process.

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“…[ 2 ] Similar phenotypic and genotypic heterogeneity has also been reported after subcloning or serum‐free adaption. [ 3–5 ]…”

Section: Introductionmentioning

confidence: 99%

“…[2] Similar phenotypic and genotypic heterogeneity has also been reported after subcloning or serum-free adaption. [3][4][5] Suboptimal cell growth is considered as one of the major bottlenecks of recombinant CHO production. While great efforts have been made in process development, optimization of culture conditions may still be restricted by the intrinsic cell biology limiting the growth.…”

Section: Introductionmentioning

confidence: 99%

Duplication of a chromosome 2 segment in production CHO cell lines correlates with age‐related growth improvement

Wei,

Zielewicz,

Zhang

2024

Biotechnology Journal

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Monitoring the stability of recombinant Chinese Hamster Ovary (CHO) cell lines is essential to ensure the selection of production cell lines suitable for biomanufacturing. It has been frequently observed that recombinant CHO cell lines develop phenotypic changes upon aging, such as accelerated cell growth in late generation cultures. However, the mechanism responsible for age‐correlated changes is poorly understood. In this study, we investigated the molecular mechanisms underlying the age‐correlated cell growth improvement in Pfizer's platform fed‐batch production process, by examining multiple cell lines derived from different CHO expression systems, expressing a variety of monoclonal antibodies (mAbs). Comprehensive whole‐genome resequencing analysis revealed duplication of a continuous 50.2 Mbp segment in chromosome 2 (Chr2) specific to clones that showed age‐correlated growth change as compared to clones that did not exhibit age‐correlated growth change. Moreover, such age‐ and growth‐related Chr2 duplication was independent of the presence or type of recombinant monoclonal antibody expression. When we compared transcriptome profiles from low‐growth and high‐growth cell lines, we found that >95% of the genes overexpressed in high‐growth cell lines were in the duplicated Chr2 segment. To the best of our knowledge, this is the first report of large genomic duplication, specific to Chr2, being associated with age‐correlated growth change. Investigation of the cause‐and‐effect relationship between the genes identified in the duplicated regions and age‐correlated growth change is underway. We are confident that this effort will lead to improved cell line screening and targeted rational cell line engineering efforts to develop cell lines with improved stability performance.

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Chromosomal instability drives convergent and divergent evolution toward advantageous inherited traits in mammalian CHO bioproduction lineages

Cited by 6 publications

References 51 publications

Metabolic Profiling of CHO Cells during the Production of Biotherapeutics

Metabolic Profiling of CHO Cells during the Production of Biotherapeutics

Improved Titer in Late-Stage Mammalian Cell Culture Manufacturing by Re-Cloning

Duplication of a chromosome 2 segment in production CHO cell lines correlates with age‐related growth improvement

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