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Novel column generation-based optimization approach for poly-pathway kinetic model applied to CHO cell culture.

ABSTRACT: Mathematical modelling can provide precious tools for bioprocess simulation, prediction, control and optimization of mammalian cell-based cultures. In this paper we present a novel method to generate kinetic models of such cultures, rendering complex metabolic networks in a poly-pathway kinetic model. The model is based on subsets of elementary flux modes (EFMs) to generate macro-reactions. Thanks to our column generation-based optimization algorithm, the experimental data are used to identify the EFMs, which are relevant to the data. Here the systematic enumeration of all the EFMs is eliminated and a network including a large number of reactions can be considered. In particular, the poly-pathway model can simulate multiple metabolic behaviors in response to changes in the culture conditions. We apply the method to a network of 126 metabolic reactions describing cultures of antibody-producing Chinese hamster ovary cells, and generate a poly-pathway model that simulates multiple experimental conditions obtained in response to variations in amino acid availability. A good fit between simulated and experimental data is obtained, rendering the variations in the growth, product, and metabolite uptake/secretion rates. The intracellular reaction fluxes simulated by the model are explored, linking variations in metabolic behavior to adaptations of the intracellular metabolism.

SUBMITTER: Hagrot E

PROVIDER: S-EPMC6376161 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Novel column generation-based optimization approach for poly-pathway kinetic model applied to CHO cell culture.

Hagrot Erika E Oddsdóttir Hildur Æsa HÆ Mäkinen Meeri M Forsgren Anders A Chotteau Véronique V

Metabolic engineering communications 20181225

Mathematical modelling can provide precious tools for bioprocess simulation, prediction, control and optimization of mammalian cell-based cultures. In this paper we present a novel method to generate kinetic models of such cultures, rendering complex metabolic networks in a poly-pathway kinetic model. The model is based on subsets of elementary flux modes (EFMs) to generate macro-reactions. Thanks to our column generation-based optimization algorithm, the experimental data are used to identify t ...[more]

PMID: 30809468

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Project description:Over the past decade, global interest in the development of therapeutic monoclonal antibodies (mAbs) has risen rapidly. As therapeutic agents, antibodies have shown marked efficacy in combatting a range of cancers and immune diseases with high target specificity and low toxicity (Carla Lucia et al. in PLoS ONE 6:e24071, 2011; Donaghy in MAbs 8:659-671, 2016; Nasiri et al. in J Cell Physiol 9:6441-6457, 2018; Teo et al. in Cancer Immunol Immunother 61:2295-2309, 2012). Recent advances in cell culture technology, such as high-throughput clone screening, have facilitated antibody production at concentrations exceeding 10 g/L (Chen et al. in BMC Immunol 19:35, 2018; Huang et al. in Biotechnol Prog 26:1400-1410, 2010; Lu et al. in Biotechnol Bioeng 110:191-205, 2013; Singh et al. in Biotechnol Bioeng 113:698-716, 2016). As titers have improved, the industry has begun to focus on the adjustment of target antibody quality profiles to improve efficacy. Cell lines, culture media, and culture conditions impact protein quality (Van Beers and Bardor in Biotechnol J 7:1473-1484, 2012). Optimization of critical quality attributes (CQAs), such as charge variants, can be achieved through bioprocess development and is the preferred approach as changes to the cell line or growth media used is considered unfavorable by regulatory bodies (Gawlitzek et al. in Biotechnol Bioeng 103:1164-1175, 2009; Jordan et al. in Cytotechnology 65:31-40, 2013; Pan et al. in Cytotechnology 69:39-56, 2016). In this study, the effect of process control and ion supplementation on charge variants of mAbs produced by Chinese hamster ovary (CHO) cells was investigated. Results of this study demonstrated that the concentration of Zn2+, duration of culturing, and temperature affect charge variants of a given mAb. Under the optimum conditions of 3L bioreactors, the most significant was that Zn2 + and temperature shift could further improve the quality of antibody. The main peak increased by 12%, and the acid peak decreased by 16%. At the same time, there was no significant loss of titer. This study provided supporting evidence for methods to improve charge variants arising during mAb production.

Project description:BackgroundWith the challenges that dengue fever (DF) presents to healthcare systems and societies, public health officials must determine where best to allocate scarce resources and restricted budgets. Constrained optimization (CO) helps to address some of the acknowledged limitations of conventional health economic analyses and has typically been used to identify the optimal allocation of resources across interventions subject to a variety of constraints.MethodsA dynamic transmission model was developed to predict the number of dengue cases in Thailand at steady state. A CO was then applied to identify the optimal combination of interventions (release of Wolbachia-infected mosquitoes and paediatric vaccination) within the constraints of a fixed budget, set no higher than cost estimates of the current vector control programme, to minimize the number of dengue cases and disability-adjusted life years (DALYs) lost. Epidemiological, cost, and effectiveness data were informed by national data and the research literature. The time horizon was 10 years. Scenario analyses examined different disease management and intervention costs, budget constraints, vaccine efficacy, and optimization time horizon.ResultsUnder base-case budget constraints, the optimal coverage of the two interventions to minimize dengue incidence was predicted to be nearly equal (Wolbachia 50%; paediatric vaccination 49%) with corresponding coverages under lower bound (Wolbachia 54%; paediatric vaccination 10%) and upper bound (Wolbachia 67%; paediatric vaccination 100%) budget ceilings. Scenario analyses indicated that the most impactful situations related to the costs of Wolbachia and paediatric vaccination with decreases/ increases in costs of interventions demonstrating a direct correlation with coverage (increases/ decreases) of the respective control strategies under examination.ConclusionsDetermining the best investment strategy for dengue control requires the identification of the optimal mix of interventions to implement in order to maximize public health outcomes, often under fixed budget constraints. A CO model was developed with the objective of minimizing dengue cases (and DALYs lost) over a 10-year time horizon, within the constraints of the estimated budgets for vector control in the absence of vaccination and Wolbachia. The model provides a tool for developing estimates of optimal coverage of combined dengue control strategies that minimize dengue burden at the lowest budget.

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Novel column generation-based optimization approach for poly-pathway kinetic model applied to CHO cell culture.

Publications

Novel column generation-based optimization approach for poly-pathway kinetic model applied to CHO cell culture.

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