Network Reconstruction and In Silico Metabolic Model of Chinese Hamster Ovary cells

Cyrielle Calmels*

*Corresponding author for this work

Research output: Book/ReportPh.D. thesisResearch

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Abstract

Biotechnology can be defined by the use of biological processes, organisms, or systems to manufacture products intended to improve the quality of human life. At the forefront of biotechnology, Chinese Hamster Ovary (CHO) cells have been studied and cultured for 60 years, to now become the most important cell line used for the production of therapeutic proteins, including monoclonal antibodies. As antibody therapies require large doses over a long period of time, manufacturing capacity becomes an issue and improvements are still needed to decrease time and effort associated to bioprocess development, despite great advances in terms of protein yields. Since productivity levels are currently met by iterative empirical approaches, which are both time consuming and costly, there is a drive for a deeper understanding of the cellular characteristics of the host cell. In this context, mathematical models provide promising applications in guiding experimental work at reduced cost and reduced time of tedious laboratory experiments. The first publication of CHO genome sequences in 2011 allowed a better interpretation of the results in all the omics fields, such as proteomics, transcriptomics and metabolomics. Combined together, all this information allowed for the reconstruction of detailed genome-scale models, which represent innovative tools that became available by the start of this thesis, and thus were never applied to CHO cells in the context of industrial bioprocesses.
In this thesis, the development of a curated genome-scale model is reported, which aims at gaining an in-depth knowledge of cellular metabolism in different biopharmaceutical production conditions. The core of this thesis is revolved around the development, validation and application of a reliable metabolic network model of CHO cells. A genome-scale model was carefully curated and adapted to the phenotype of industrially relevant cell lines. Several cell lines were modeled to characterize their metabolic differences and signatures at different stages of the process. A detailed description of their metabolism is provided, and is compared to experimental measurements that were used to refine the model and support predicted intracellular states. As a final milestone, the model was used to provide cell line engineering targets and to explore the possibility of developing an optimum feeding solution.
Overall, the results of this thesis illustrate a successful application of a curated metabolic model to industrial CHO cell cultures. The curation process realized in the model sheds light on metabolic specificities of high yielding cell lines. The actual model is an advanced tool to support cell line engineering, and improve the therapeutic production capabilities of CHO cell factories. This thesis contributes to accelerate drug development process, in order to reduce both manufacturing cost and delivery time to market, which would benefit a broader range of patients around the globe.
Original languageEnglish
Place of PublicationKgs. Lyngby
PublisherTechnical University of Denmark
Number of pages225
Publication statusPublished - 2018

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