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Kopp MRG, Grigolato F, Zürcher D, Das TK, Chou D, Wuchner K, Arosio P. Surface-Induced Protein Aggregation and Particle Formation in Biologics: Current Understanding of Mechanisms, Detection and Mitigation Strategies. J Pharm Sci 2023; 112:377-385. [PMID: 36223809 DOI: 10.1016/j.xphs.2022.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 01/12/2023]
Abstract
Protein stability against aggregation is a major quality concern for the production of safe and effective biopharmaceuticals. Amongst the different drivers of protein aggregation, increasing evidence indicates that interactions between proteins and interfaces represent a major risk factor for the formation of protein aggregates in aqueous solutions. Potentially harmful surfaces relevant to biologics manufacturing and storage include air-water and silicone oil-water interfaces as well as materials from different processing units, storage containers, and delivery devices. The impact of some of these surfaces, for instance originating from impurities, can be difficult to predict and control. Moreover, aggregate formation may additionally be complicated by the simultaneous presence of interfacial, hydrodynamic and mechanical stresses, whose contributions may be difficult to deconvolute. As a consequence, it remains difficult to identify the key chemical and physical determinants and define appropriate analytical methods to monitor and predict protein instability at these interfaces. In this review, we first discuss the main mechanisms of surface-induced protein aggregation. We then review the types of contact materials identified as potentially harmful or detected as potential triggers of proteinaceous particle formation in formulations and discuss proposed mitigation strategies. Finally, we present current methods to probe surface-induced instabilities, which represent a starting point towards assays that can be implemented in early-stage screening and formulation development of biologics.
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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Capasso Palmiero U, Paganini C, Kopp MRG, Linsenmeier M, Küffner AM, Arosio P. Programmable Zwitterionic Droplets as Biomolecular Sorters and Model of Membraneless Organelles. Adv Mater 2022; 34:e2104837. [PMID: 34664748 DOI: 10.1002/adma.202104837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Increasing evidence indicates that cells can regulate biochemical functions in time and space by generating membraneless compartments with well-defined mesoscopic properties. One important mechanism underlying this control is simple coacervation driven by associative disordered proteins that encode multivalent interactions. Inspired by these observations, programmable droplets based on simple coacervation of responsive synthetic polymers that mimic the "stickers-and-spacers" architecture of biological disordered proteins are developed. Zwitterionic polymers that undergo an enthalpy-driven liquid-liquid phase separation process and form liquid droplets that remarkably exclude most molecules are developed. Starting from this reference material, different functional groups in the zwitterionic polymer are progressively added to encode an increasing number of different intermolecular interactions. This strategy allowed the multiple emerging properties of the droplets to be controlled independently, such as stimulus-responsiveness, polarity, selective uptake of client molecules, fusion times, and miscibility. By exploiting this high programmability, a model of cellular compartmentalization is reproduced and droplets capable of confining different molecules in space without physical barriers are generated. Moreover, these biomolecular sorters are demonstrated to be able to localize, separate, and enable the detection of target molecules even within complex mixtures, opening attractive applications in bioseparation, and diagnostics.
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Affiliation(s)
- Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Carolina Paganini
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Andreas M Küffner
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
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Kopp MRG, Wolf Pérez AM, Zucca MV, Capasso Palmiero U, Friedrichsen B, Lorenzen N, Arosio P. An accelerated surface-mediated stress assay of antibody instability for developability studies. MAbs 2021; 12:1815995. [PMID: 32954930 PMCID: PMC7577746 DOI: 10.1080/19420862.2020.1815995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High physical stability is required for the development of monoclonal antibodies (mAbs) into successful therapeutic products. Developability assays are used to predict physical stability issues such as high viscosity and poor conformational stability, but protein aggregation remains a challenging property to predict. Among different types of stresses, air–water and solid–liquid interfaces are well known to potentially trigger protein instability and induce aggregation. Yet, in contrast to the increasing number of developability assays to evaluate bulk properties, there is still a lack of experimental methods to evaluate antibody stability against interfaces. Here, we investigate the potential of a hydrophobic nanoparticle surface-mediated stress assay to assess the stability of mAbs during the early stages of development. We evaluate this surface-mediated accelerated stability assay on a rationally designed library of 14 variants of a humanized IgG4, featuring a broad span of solubility values and other developability properties. The assay could identify variants characterized by high instability against agitation in the presence of air–water interfaces. Remarkably, for the set of investigated molecules, we observe strong correlations between the extent of aggregation induced by the surface-mediated stress assay and other developability properties of the molecules, such as aggregation upon storage at 45°C, self-association (evaluated by affinity-capture self-interaction nanoparticle spectroscopy) and nonspecific interactions (estimated by cross-interaction chromatography, stand-up monolayer chromatography (SMAC), SMAC*). This highly controlled surface-mediated stress assay has the potential to complement and increase the ability of the current set of screening techniques to assess protein aggregation and developability potential of mAbs during the early stages of drug development. Abbreviations:AC-SINS: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy; AMS: Ammonium sulfate precipitation; ANS: 1-anilinonaphtalene-8-sulfonate; CIC: Cross-interaction chromatography; DLS: Dynamic light scattering; HIC: Hydrophobic interaction chromatography; HNSSA: Hydrophobic nanoparticles surface-stress assay; mAb: Monoclonal antibody; NP: Nanoparticle; SEC: Size exclusion chromatography; SMAC: Stand-up monolayer chromatography; WT: Wild type
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Adriana-Michelle Wolf Pérez
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark.,Aarhus University, iNANO , Aarhus C, Denmark
| | - Marta Virginia Zucca
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | | | - Nikolai Lorenzen
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
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Linsenmeier M, Kopp MRG, Stavrakis S, de Mello A, Arosio P. Analysis of biomolecular condensates and protein phase separation with microfluidic technology. Biochim Biophys Acta Mol Cell Res 2020; 1868:118823. [PMID: 32800925 DOI: 10.1016/j.bbamcr.2020.118823] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.
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Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Andrew de Mello
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland.
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Kopp MRG, Linsenmeier M, Hettich B, Prantl S, Stavrakis S, Leroux JC, Arosio P. Microfluidic Shrinking Droplet Concentrator for Analyte Detection and Phase Separation of Protein Solutions. Anal Chem 2020; 92:5803-5812. [DOI: 10.1021/acs.analchem.9b05329] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Britta Hettich
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Sebastian Prantl
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Jean-Christophe Leroux
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
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Affiliation(s)
- Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich 8093, Switzerland
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanoulidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Berichtigung: Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201913379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanouilidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Corrigendum: Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019; 58:17902. [DOI: 10.1002/anie.201913379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanoulidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019; 58:14489-14494. [DOI: 10.1002/anie.201907278] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Leonidas Emmanoulidis
- Institute of Molecular Biology and Biophysics Department of Biology ETH Zurich 8093 Zurich Switzerland
| | - Dany Liu
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Maria Hondele
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Karsten Weis
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
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10
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Linsenmeier M, Kopp MRG, Grigolato F, Emmanoulidis L, Liu D, Zürcher D, Hondele M, Weis K, Capasso Palmiero U, Arosio P. Dynamics of Synthetic Membraneless Organelles in Microfluidic Droplets. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Leonidas Emmanoulidis
- Institute of Molecular Biology and Biophysics Department of Biology ETH Zurich 8093 Zurich Switzerland
| | - Dany Liu
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Dominik Zürcher
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Maria Hondele
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Karsten Weis
- Department of Biology Institute of Biochemistry ETH Zürich 8093 Zurich Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich 8093 Zurich Switzerland
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11
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Grignaschi E, Cereghetti G, Grigolato F, Kopp MRG, Caimi S, Faltova L, Saad S, Peter M, Arosio P. A hydrophobic low-complexity region regulates aggregation of the yeast pyruvate kinase Cdc19 into amyloid-like aggregates in vitro. J Biol Chem 2018; 293:11424-11432. [PMID: 29853641 DOI: 10.1074/jbc.ra117.001628] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/15/2018] [Indexed: 11/06/2022] Open
Abstract
Cells form stress granules (SGs) upon stress stimuli to protect sensitive proteins and RNA from degradation. In the yeast Saccharomyces cerevisiae, specific stresses such as nutrient starvation and heat-shock trigger recruitment of the yeast pyruvate kinase Cdc19 into SGs. This RNA-binding protein was shown to form amyloid-like aggregates that are physiologically reversible and essential for cell cycle restart after stress. Cellular Cdc19 exists in an equilibrium between a homotetramer and monomer state. Here, we show that Cdc19 aggregation in vitro is governed by protein quaternary structure, and we investigate the physical-chemical basis of Cdc19's assembly properties. Equilibrium shift toward the monomer state exposes a hydrophobic low-complexity region (LCR), which is prone to induce intermolecular interactions with surrounding proteins. We further demonstrate that hydrophobic/hydrophilic interfaces can trigger Cdc19 aggregation in vitro Moreover, we performed in vitro biophysical analyses to compare Cdc19 aggregates with fibrils produced by two known dysfunctional amyloidogenic peptides. We show that the Cdc19 aggregates share several structural features with pathological amyloids formed by human insulin and the Alzheimer's disease-associated Aβ42 peptide, particularly secondary β-sheet structure, thermodynamic stability, and staining by the thioflavin T dye. However, Cdc19 aggregates could not seed aggregation. These results indicate that Cdc19 adopts an amyloid-like structure in vitro that is regulated by the exposure of a hydrophobic LCR in its monomeric form. Together, our results highlight striking structural similarities between functional and dysfunctional amyloids and reveal the crucial role of hydrophobic/hydrophilic interfaces in regulating Cdc19 aggregation.
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Affiliation(s)
- Erica Grignaschi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Gea Cereghetti
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Fulvio Grigolato
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Stefano Caimi
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Shady Saad
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute for Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, 8093 Zurich, Switzerland.
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Kopp MRG, Villois A, Capasso Palmiero U, Arosio P. Microfluidic Diffusion Analysis of the Size Distribution and Microrheological Properties of Antibody Solutions at High Concentrations. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00666] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie R. G. Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - Alessia Villois
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
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13
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Karst DJ, Steinhoff RF, Kopp MRG, Soos M, Zenobi R, Morbidelli M. Isotope labeling to determine the dynamics of metabolic response in CHO cell perfusion bioreactors using MALDI-TOF-MS. Biotechnol Prog 2017; 33:1630-1639. [PMID: 28840654 DOI: 10.1002/btpr.2539] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/22/2017] [Indexed: 01/09/2023]
Abstract
The steady-state operation of Chinese hamster ovary (CHO) cells in perfusion bioreactors requires the equilibration of reactor dynamics and cell metabolism. Accordingly, in this work we investigate the transient cellular response to changes in its environment and their interactions with the bioreactor hydrodynamics. This is done in a benchtop perfusion bioreactor using MALDI-TOF MS through isotope labeling of complex intracellular nucleotides (ATP, UTP) and nucleotide sugars (UDP-Hex, UDP-HexNAc). By switching to a 13 C6 glucose containing feed media during constant operation at 20 × 106 cells and a perfusion rate of 1 reactor volume per day, isotopic steady state was studied. A step change to the 13 C6 glucose medium in spin tubes allowed the determination of characteristic times for the intracellular turnover of unlabeled metabolites pools, τST (≤0.56 days), which were confirmed in the bioreactor. On the other hand, it is shown that the reactor residence time τR (1 day) and characteristic time for glucose uptake τGlc (0.33 days), representative of the bioreactor dynamics, delayed the consumption of 13 C6 glucose in the bioreactor and thus the intracellular 13 C enrichment. The proposed experimental approach allowed the decoupling of bioreactor hydrodynamics and intrinsic dynamics of cell metabolism in response to a change in the cell culture environment. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1630-1639, 2017.
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Affiliation(s)
- Daniel J Karst
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Robert F Steinhoff
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Marie R G Kopp
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Miroslav Soos
- Department of Chemical Engineering, University of Chemistry and Technology, Technicka 3, Prague, 166 28, Czech Republic
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Massimo Morbidelli
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
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Karst DJ, Steinhoff RF, Kopp MRG, Serra E, Soos M, Zenobi R, Morbidelli M. Intracellular CHO Cell Metabolite Profiling Reveals Steady-State Dependent Metabolic Fingerprints in Perfusion Culture. Biotechnol Prog 2017; 33:879-890. [PMID: 27997765 DOI: 10.1002/btpr.2421] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/01/2016] [Indexed: 11/08/2022]
Abstract
Perfusion cell culture processes allow the steady-state culture of mammalian cells at high viable cell density, which is beneficial for overall product yields and homogeneity of product quality in the manufacturing of therapeutic proteins. In this study, the extent of metabolic steady state and the change of the metabolite profile between different steady states of an industrial Chinese hamster ovary (CHO) cell line producing a monoclonal antibody (mAb) was investigated in stirred tank perfusion bioreactors. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of daily cell extracts revealed more than a hundred peaks, among which 76 metabolites were identified by tandem MS (MS/MS) and high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS. Nucleotide ratios (Uridine (U)-ratio, nucleotide triphosphate (NTP)-ratio and energy charge (EC)) and multivariate analysis of all features indicated a consistent metabolite profile for a stable culture performed at 40 × 106 cells/mL over 26 days of culture. Conversely, the reactor was operated continuously so as to reach three distinct steady states one after the other at 20, 60, and 40 × 106 cells/mL. In each case, a stable metabolite profile was achieved after an initial transient phase of approximately three days at constant cell density when varying between these set points. Clear clustering according to cell density was observed by principal component analysis, indicating steady-state dependent metabolite profiles. In particular, varying levels of nucleotides, nucleotide sugar, and lipid precursors explained most of the variance between the different cell density set points. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:879-890, 2017.
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Affiliation(s)
- Daniel J Karst
- Dept. of Chemistry and Applied Biosciences, Inst. for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Robert F Steinhoff
- Dept. of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie R G Kopp
- Dept. of Chemistry and Applied Biosciences, Inst. for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Elisa Serra
- Dept. of Chemistry and Applied Biosciences, Inst. for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Miroslav Soos
- Dept. of Chemistry and Applied Biosciences, Inst. for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.,Dept. of Chemical Engineering, University of Chemistry and Technology, Prague, 166 28, Czech Republic
| | - Renato Zenobi
- Dept. of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Massimo Morbidelli
- Dept. of Chemistry and Applied Biosciences, Inst. for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
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