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Pelz L, Dogra T, Marichal-Gallardo P, Hein MD, Hemissi G, Kupke SY, Genzel Y, Reichl U. Production of antiviral "OP7 chimera" defective interfering particles free of infectious virus. Appl Microbiol Biotechnol 2024; 108:97. [PMID: 38229300 DOI: 10.1007/s00253-023-12959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/21/2023] [Revised: 10/26/2023] [Accepted: 11/05/2023] [Indexed: 01/18/2024]
Abstract
Defective interfering particles (DIPs) of influenza A virus (IAV) are suggested for use as broad-spectrum antivirals. We discovered a new type of IAV DIP named "OP7" that carries point mutations in its genome segment (Seg) 7 instead of a deletion as in conventional DIPs (cDIPs). Recently, using genetic engineering tools, we generated "OP7 chimera DIPs" that carry point mutations in Seg 7 plus a deletion in Seg 1. Together with cDIPs, OP7 chimera DIPs were produced in shake flasks in the absence of infectious standard virus (STV), rendering UV inactivation unnecessary. However, only part of the virions harvested were OP7 chimera DIPs (78.7%) and total virus titers were relatively low. Here, we describe the establishment of an OP7 chimera DIP production process applicable for large-scale production. To increase total virus titers, we reduced temperature from 37 to 32 °C during virus replication. Production of almost pure OP7 chimera DIP preparations (99.7%) was achieved with a high titer of 3.24 log10(HAU/100 µL). This corresponded to an 11-fold increase relative to the initial process. Next, this process was transferred to a stirred tank bioreactor resulting in comparable yields. Moreover, DIP harvests purified and concentrated by steric exclusion chromatography displayed an increased interfering efficacy in vitro. Finally, a perfusion process with perfusion rate control was established, resulting in a 79-fold increase in total virus yields compared to the original batch process in shake flasks. Again, a very high purity of OP7 chimera DIPs was obtained. This process could thus be an excellent starting point for good manufacturing practice production of DIPs for use as antivirals. KEY POINTS: • Scalable cell culture-based process for highly effective antiviral OP7 chimera DIPs • Production of almost pure OP7 chimera DIPs in the absence of infectious virus • Perfusion mode production and purification train results in very high titers.
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Affiliation(s)
- Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Marc Dominique Hein
- Otto Von Guericke University Magdeburg, Bioprocess Engineering, Magdeburg, Germany
| | - Ghada Hemissi
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Sascha Young Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Otto Von Guericke University Magdeburg, Bioprocess Engineering, Magdeburg, Germany
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2
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Rüdiger D, Piasecka J, Küchler J, Pontes C, Laske T, Kupke SY, Reichl U. Mathematical model calibrated to in vitro data predicts mechanisms of antiviral action of the influenza defective interfering particle "OP7". iScience 2024; 27:109421. [PMID: 38523782 PMCID: PMC10959662 DOI: 10.1016/j.isci.2024.109421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Defective interfering particles (DIPs) are regarded as potent broad-spectrum antivirals. We developed a mathematical model that describes intracellular co-infection dynamics of influenza standard virus (STV) and "OP7", a new type of influenza DIP discovered recently. Based on experimental data from in vitro studies to calibrate the model and confirm its predictions, we deduce OP7's mechanisms of interference, which were yet unknown. Simulations suggest that the "superpromoter" on OP7 genomic viral RNA enhances its replication and results in a depletion of viral proteins. This reduces STV genomic RNA replication, which appears to constitute an antiviral effect. Further, a defective viral protein (M1-OP7) likely causes the deficiency of OP7's replication. It appears unable to bind to genomic viral RNAs to facilitate their nuclear export, a critical step in the viral life cycle. An improved understanding of OP7's antiviral mechanism is crucial toward application in humans as a prospective antiviral treatment strategy.
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Affiliation(s)
- Daniel Rüdiger
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Julita Piasecka
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Jan Küchler
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Carolina Pontes
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Tanja Laske
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Institute for Computational Systems Biology, University of Hamburg, 20148 Hamburg, Germany
| | - Sascha Y. Kupke
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
| | - Udo Reichl
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Saxony-Anhalt, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106 Magdeburg, Saxony-Anhalt, Germany
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3
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Zinnecker T, Badri N, Araujo D, Thiele K, Reichl U, Genzel Y. From single-cell cloning to high-yield influenza virus production - implementing advanced technologies in vaccine process development. Eng Life Sci 2024; 24:2300245. [PMID: 38584687 PMCID: PMC10991716 DOI: 10.1002/elsc.202300245] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 09/29/2023] [Revised: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 04/09/2024] Open
Abstract
Innovations in viral vaccine manufacturing are crucial for pandemic preparedness and to meet ever-rising global demands. For influenza, however, production still mainly relies on technologies established decades ago. Although modern production shifts from egg-based towards cell culture technologies, the full potential has not yet been fully exploited. Here, we evaluate whether implementation of state-of-the-art technologies for cell culture-based recombinant protein production are capable to challenge outdated approaches in viral vaccine process development. For this, a fully automated single-cell cloning strategy was established to generate monoclonal suspension Madin-Darby canine kidney (MDCK) cells. Among selected cell clones, we could observe distinct metabolic and growth characteristics, with C59 reaching a maximum viable cell concentration of 17.3 × 106 cells/mL and low doubling times in batch mode. Screening for virus production using a panel of human vaccine-relevant influenza A and B viruses in an ambr15 system revealed high titers with yields competing or even outperforming available MDCK cell lines. With C113, we achieved cell-specific virus yields of up to 25,000 virions/cell, making this cell clone highly attractive for vaccine production. Finally, we confirmed process performance at a 50-fold higher working volume. In summary, we present a scalable and powerful approach for accelerated development of high-yield influenza virus production in chemically defined medium starting from a single cell.
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Affiliation(s)
- Tilia Zinnecker
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | | | - Diogo Araujo
- Sartorius Stedim Biotech S.A.Aubagne CedexFrance
| | | | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
- Bioprocess EngineeringOtto‐von‐Guericke UniversityMagdeburgGermany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
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4
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Göbel S, Pelz L, Silva CAT, Brühlmann B, Hill C, Altomonte J, Kamen A, Reichl U, Genzel Y. Production of recombinant vesicular stomatitis virus-based vectors by tangential flow depth filtration. Appl Microbiol Biotechnol 2024; 108:240. [PMID: 38413399 PMCID: PMC10899354 DOI: 10.1007/s00253-024-13078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/17/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Cell culture-based production of vector-based vaccines and virotherapeutics is of increasing interest. The vectors used not only retain their ability to infect cells but also induce robust immune responses. Using two recombinant vesicular stomatitis virus (rVSV)-based constructs, we performed a proof-of-concept study regarding an integrated closed single-use perfusion system that allows continuous virus harvesting and clarification. Using suspension BHK-21 cells and a fusogenic oncolytic hybrid of vesicular stomatitis virus and Newcastle disease virus (rVSV-NDV), a modified alternating tangential flow device (mATF) or tangential flow depth filtration (TFDF) systems were used for cell retention. As the hollow fibers of the former are characterized by a large internal lumen (0.75 mm; pore size 0.65 μm), membrane blocking by the multi-nucleated syncytia formed during infection could be prevented. However, virus particles were completely retained. In contrast, the TFDF filter unit (lumen 3.15 mm, pore size 2-5 μm) allowed not only to achieve high viable cell concentrations (VCC, 16.4-20.6×106 cells/mL) but also continuous vector harvesting and clarification. Compared to an optimized batch process, 11-fold higher infectious virus titers were obtained in the clarified permeate (maximum 7.5×109 TCID50/mL). Using HEK293-SF cells and a rVSV vector expressing a green fluorescent protein, perfusion cultivations resulted in a maximum VCC of 11.3×106 cells/mL and infectious virus titers up to 7.1×1010 TCID50/mL in the permeate. Not only continuous harvesting but also clarification was possible. Although the cell-specific virus yield decreased relative to a batch process established as a control, an increased space-time yield was obtained. KEY POINTS: • Viral vector production using a TFDF perfusion system resulted in a 460% increase in space-time yield • Use of a TFDF system allowed continuous virus harvesting and clarification • TFDF perfusion system has great potential towards the establishment of an intensified vector production.
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Affiliation(s)
- Sven Göbel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Lars Pelz
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Cristina A T Silva
- Department of Chemical Engineering, Polytechnique Montréal, Montréal, Québec, Canada
| | | | | | - Jennifer Altomonte
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montréal, Québec, Canada
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
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5
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Heyer R, Hellwig P, Maus I, Walke D, Schlüter A, Hassa J, Sczyrba A, Tubbesing T, Klocke M, Mächtig T, Schallert K, Seick I, Reichl U, Benndorf D. Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. Water Res 2024; 250:121020. [PMID: 38128305 DOI: 10.1016/j.watres.2023.121020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/23/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics. Technical and chemical parameters indicated stable operation of the main fermenter but varying conditions for the open hydrolysis fermenter. Matching this, the microbiome in the hydrolysis fermenter has a higher dynamic than in the main fermenter. Metaproteomics-based microbiome analysis revealed a partial separation between early and common steps in carbohydrate degradation and primary fermentation in the hydrolysis fermenter but complex carbohydrate degradation, secondary fermentation, and methanogenesis in the main fermenter. Detailed metagenomics and metaproteomics characterization of the single metagenome-assembled genomes showed that the species focus on specific substrate niches and do not utilize their full genetic potential to degrade, for example, LCB. Overall, it seems that a separation of AD in a hydrolysis and a main fermenter does not improve the cleavage of complex substrates but significantly improves the overall process performance. In contrast, the remaining methanogenic activity in the hydrolysis fermenter may cause methane losses.
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Affiliation(s)
- Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Multidimensional Omics Analyses Group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany; Multidimensional Omics Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Patrick Hellwig
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany.
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Research Center Jülich GmbH, Institute of Bio- and Geosciences (IBG), IBG-5: Computational Metagenomics, Leo-Brandt-Str., 52428 Jülich, Germany.
| | - Daniel Walke
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Otto von Guericke University, Database and Software Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Research Center Jülich GmbH, Institute of Bio- and Geosciences (IBG), IBG-5: Computational Metagenomics, Leo-Brandt-Str., 52428 Jülich, Germany; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Tom Tubbesing
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany; Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany.
| | - Torsten Mächtig
- Christian-Albrechts-Universität Kiel, Institute of Agricultural Engineering, Olshausenstr. 40, 24098 Kiel, Germany.
| | - Kay Schallert
- Multidimensional Omics Analyses Group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany.
| | - Ingolf Seick
- Urban Water Management/Wastewater, Hochschule Magdeburg-Stendal, Breitscheidstrasse 2, 39114 Magdeburg, Germany.
| | - Udo Reichl
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany.
| | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany; Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany.
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6
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Dogra T, Pelz L, Boehme JD, Kuechler J, Kershaw O, Marichal-Gallardo P, Baelkner M, Hein MD, Gruber AD, Benndorf D, Genzel Y, Bruder D, Kupke SY, Reichl U. Generation of "OP7 chimera" defective interfering influenza A particle preparations free of infectious virus that show antiviral efficacy in mice. Sci Rep 2023; 13:20936. [PMID: 38017026 PMCID: PMC10684881 DOI: 10.1038/s41598-023-47547-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023] Open
Abstract
Influenza A virus (IAV) defective interfering particles (DIPs) are considered as new promising antiviral agents. Conventional DIPs (cDIPs) contain a deletion in the genome and can only replicate upon co-infection with infectious standard virus (STV), during which they suppress STV replication. We previously discovered a new type of IAV DIP "OP7" that entails genomic point mutations and displays higher antiviral efficacy than cDIPs. To avoid safety concerns for the medical use of OP7 preparations, we developed a production system that does not depend on infectious IAV. We reconstituted a mixture of DIPs consisting of cDIPs and OP7 chimera DIPs, in which both harbor a deletion in their genome. To complement the defect, the deleted viral protein is expressed by the suspension cell line used for production in shake flasks. Here, DIP preparations harvested are not contaminated with infectious virions, and the fraction of OP7 chimera DIPs depended on the multiplicity of infection. Intranasal administration of OP7 chimera DIP material was well tolerated in mice. A rescue from an otherwise lethal IAV infection and no signs of disease upon OP7 chimera DIP co-infection demonstrated the remarkable antiviral efficacy. The clinical development of this new class of broad-spectrum antiviral may contribute to pandemic preparedness.
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Affiliation(s)
- Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Julia D Boehme
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jan Kuechler
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Olivia Kershaw
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Maike Baelkner
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc D Hein
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Achim D Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Dirk Benndorf
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto Von Guericke University Magdeburg, Magdeburg, Germany
- Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sascha Y Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Magdeburg, Germany
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7
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Alberto Alcalá-Orozco E, Grote V, Fiebig T, Klamt S, Reichl U, Rexer T. A Cell-Free Multi-enzyme Cascade Reaction for the Synthesis of CDP-Glycerol. Chembiochem 2023; 24:e202300463. [PMID: 37578628 DOI: 10.1002/cbic.202300463] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023]
Abstract
CDP-glycerol is a nucleotide-diphosphate-activated version of glycerol. In nature, it is required for the biosynthesis of teichoic acid in Gram-positive bacteria, which is an appealing target epitope for the development of new vaccines. Here, a cell-free multi-enzyme cascade was developed to synthetize nucleotide-activated glycerol from the inexpensive and readily available substrates cytidine and glycerol. The cascade comprises five recombinant enzymes expressed in Escherichia coli that were purified by immobilized metal affinity chromatography. As part of the cascade, ATP is regenerated in situ from polyphosphate to reduce synthesis costs. The enzymatic cascade was characterized at the laboratory scale, and the products were analyzed by high-performance anion-exchange chromatography (HPAEC)-UV and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). After the successful synthesis had been confirmed, a design-of-experiments approach was used to screen for optimal operation conditions (temperature, pH value and MgCl2 concentration). Overall, a substrate conversion of 89 % was achieved with respect to the substrate cytidine.
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Affiliation(s)
- E Alberto Alcalá-Orozco
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Valerian Grote
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University Magdeburg, 39104, Magdeburg, Germany
| | - Thomas Rexer
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
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8
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Göbel S, Jaén KE, Fernandes RP, Reiter M, Altomonte J, Reichl U, Genzel Y. Characterization of a quail suspension cell line for production of a fusogenic oncolytic virus. Biotechnol Bioeng 2023; 120:3335-3346. [PMID: 37584190 DOI: 10.1002/bit.28530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/11/2023] [Accepted: 08/06/2023] [Indexed: 08/17/2023]
Abstract
The development of efficient processes for the production of oncolytic viruses (OV) plays a crucial role regarding the clinical success of virotherapy. Although many different OV platforms are currently under investigation, manufacturing of such viruses still mainly relies on static adherent cell cultures, which bear many challenges, particularly for fusogenic OVs. Availability of GMP-compliant continuous cell lines is limited, further complicating the development of commercially viable products. BHK21, AGE1. CR and HEK293 cells were previously identified as possible cell substrates for the recombinant vesicular stomatitis virus (rVSV)-based fusogenic OV, rVSV-NDV. Now, another promising cell substrate was identified, the CCX.E10 cell line, developed by Nuvonis Technologies. This suspension cell line is considered non-GMO as no foreign genes or viral sequences were used for its development. The CCX.E10 cells were thus thoroughly investigated as a potential candidate for OV production. Cell growth in the chemically defined medium in suspension resulted in concentrations up to 8.9 × 106 cells/mL with a doubling time of 26.6 h in batch mode. Cultivation and production of rVSV-NDV, was demonstrated successfully for various cultivation systems (ambr15, shake flask, stirred tank reactor, and orbitally shaken bioreactor) at vessel scales ranging from 15 mL to 10 L. High infectious virus titers of up to 4.2 × 108 TCID50 /mL were reached in orbitally shaken bioreactors and stirred tank reactors in batch mode, respectively. Our results suggest that CCX.E10 cells are a very promising option for industrial production of OVs, particularly for fusogenic VSV-based constructs.
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Affiliation(s)
- Sven Göbel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Karim E Jaén
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Rita P Fernandes
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | | | - Jennifer Altomonte
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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9
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Hein MD, Kazenmaier D, van Heuvel Y, Dogra T, Cattaneo M, Kupke SY, Stitz J, Genzel Y, Reichl U. Production of retroviral vectors in continuous high cell density culture. Appl Microbiol Biotechnol 2023; 107:5947-5961. [PMID: 37542575 PMCID: PMC10485120 DOI: 10.1007/s00253-023-12689-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/07/2023]
Abstract
Retroviral vectors derived from murine leukemia virus (MLV) are used in somatic gene therapy applications e.g. for genetic modification of hematopoietic stem cells. Recently, we reported on the establishment of a suspension viral packaging cell line (VPC) for the production of MLV vectors. Human embryonic kidney 293-F (HEK293-F) cells were genetically modified for this purpose using transposon vector technology. Here, we demonstrate the establishment of a continuous high cell density (HCD) process using this cell line. First, we compared different media regarding the maximum achievable viable cell concentration (VCC) in small scale. Next, we transferred this process to a stirred tank bioreactor before we applied intensification strategies. Specifically, we established a perfusion process using an alternating tangential flow filtration system. Here, VCCs up to 27.4E + 06 cells/mL and MLV vector titers up to 8.6E + 06 transducing units/mL were achieved. Finally, we established a continuous HCD process using a tubular membrane for cell retention and continuous viral vector harvesting. Here, the space-time yield was 18-fold higher compared to the respective batch cultivations. Overall, our results clearly demonstrate the feasibility of HCD cultivations for high yield production of viral vectors, especially when combined with continuous viral vector harvesting. KEY POINTS: • A continuous high cell density process for MLV vector production was established • The tubular cell retention membrane allowed for continuous vector harvesting • The established process had a 18-fold higher space time yield compared to a batch.
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Affiliation(s)
- Marc D Hein
- Chair of Bioprocess Engineering, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Daniel Kazenmaier
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Faculty of Biotechnology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Yasemin van Heuvel
- Faculty of Applied Natural Sciences, University of Applied Sciences Cologne, Leverkusen, Germany
- Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Tanya Dogra
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | | | - Sascha Y Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Jörn Stitz
- Faculty of Applied Natural Sciences, University of Applied Sciences Cologne, Leverkusen, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Udo Reichl
- Chair of Bioprocess Engineering, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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10
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Wenzel L, Hoffmann M, Rapp E, Rexer TFT, Reichl U. Cell-free N-glycosylation of peptides using synthetic lipid-linked hybrid and complex N-glycans. Front Mol Biosci 2023; 10:1266431. [PMID: 37767159 PMCID: PMC10520871 DOI: 10.3389/fmolb.2023.1266431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free, chemoenzymatic platforms are emerging technologies towards generating glycoconjugates with defined and homogeneous glycoforms. Recombinant oligosaccharyltransferases can be applied to glycosylate "empty," i.e., aglycosyalted, peptides and proteins. While bacterial oligosaccharlytransferases have been extensively investigated, only recently a recombinant eukaryotic single-subunit oligosaccharyltransferase has been successfully used to in vitro N-glycosylate peptides. However, its applicability towards synthesizing full-length glycoproteins and utilizing glycans beyond mannose-type glycans for the transfer have not be determined. Here, we show for the first time the synthesis of hybrid- and complex-type glycans using synthetic lipid carriers as substrates for in vitro N-glycosylation reactions. For this purpose, transmembrane-deleted human β-1,2 N-acetylglucosamintransferase I and II (MGAT1ΔTM and MGAT2ΔTM) and β-1,4-galactosyltransferase (GalTΔTM) have been expressed in Escherichia coli and used to extend an existing multi-enzyme cascade. Both hybrid and agalactosylated complex structures were transferred to the N-glycosylation consensus sequence of peptides (10 amino acids: G-S-D-A-N-Y-T-Y-T-Q) by the recombinant oligosaccharyltransferase STT3A from Trypanosoma brucei.
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Affiliation(s)
- Lisa Wenzel
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Thomas F. T. Rexer
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
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11
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Pelz L, Piagnani E, Marsall P, Wynserski N, Hein MD, Marichal-Gallardo P, Kupke SY, Reichl U. Broad-Spectrum Antiviral Activity of Influenza A Defective Interfering Particles against Respiratory Syncytial, Yellow Fever, and Zika Virus Replication In Vitro. Viruses 2023; 15:1872. [PMID: 37766278 PMCID: PMC10537524 DOI: 10.3390/v15091872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/08/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
New broadly acting and readily available antiviral agents are needed to combat existing and emerging viruses. Defective interfering particles (DIPs) of influenza A virus (IAV) are regarded as promising options for the prevention and treatment of IAV infections. Interestingly, IAV DIPs also inhibit unrelated viral infections by stimulating antiviral innate immunity. Here, we tested the ability of IAV DIPs to suppress respiratory syncytial, yellow fever and Zika virus infections in vitro. In human lung (A549) cells, IAV DIP co-infection inhibited the replication and spread of all three viruses. In contrast, we observed no antiviral activity in Vero cells, which are deficient in the production of interferon (IFN), demonstrating its importance for the antiviral effect. Further, in A549 cells, we observed an enhanced type-I and type-III IFN response upon co-infection that appears to explain the antiviral potential of IAV DIPs. Finally, a lack of antiviral activity in the presence of the Janus kinase 1/2 (JAK1/2) inhibitor ruxolitinib was detected. This revealed a dependency of the antiviral activity on the JAK/signal transducers and activators of transcription (STAT) signaling pathway. Overall, this study supports the notion that IAV DIPs may be used as broad-spectrum antivirals to treat infections with a variety of IFN-sensitive viruses, particularly respiratory viruses.
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Affiliation(s)
- Lars Pelz
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Elena Piagnani
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Patrick Marsall
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Nancy Wynserski
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Marc Dominique Hein
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Sascha Young Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
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12
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Göbel S, Jaén KE, Dorn M, Neumeyer V, Jordan I, Sandig V, Reichl U, Altomonte J, Genzel Y. Process intensification strategies toward cell culture-based high-yield production of a fusogenic oncolytic virus. Biotechnol Bioeng 2023; 120:2639-2657. [PMID: 36779302 DOI: 10.1002/bit.28353] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 11/22/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
We present a proof-of-concept study for production of a recombinant vesicular stomatitis virus (rVSV)-based fusogenic oncolytic virus (OV), rVSV-Newcastle disease virus (NDV), at high cell densities (HCD). Based on comprehensive experiments in 1 L stirred tank reactors (STRs) in batch mode, first optimization studies at HCD were carried out in semi-perfusion in small-scale cultivations using shake flasks. Further, a perfusion process was established using an acoustic settler for cell retention. Growth, production yields, and process-related impurities were evaluated for three candidate cell lines (AGE1.CR, BHK-21, HEK293SF)infected at densities ranging from 15 to 30 × 106 cells/mL. The acoustic settler allowed continuous harvesting of rVSV-NDV with high cell retention efficiencies (above 97%) and infectious virus titers (up to 2.4 × 109 TCID50 /mL), more than 4-100 times higher than for optimized batch processes. No decrease in cell-specific virus yield (CSVY) was observed at HCD, regardless of the cell substrate. Taking into account the accumulated number of virions both from the harvest and bioreactor, a 15-30 fold increased volumetric virus productivity for AGE1.CR and HEK293SF was obtained compared to batch processes performed at the same scale. In contrast to all previous findings, formation of syncytia was observed at HCD for the suspension cells BHK 21 and HEK293SF. Oncolytic potency was not affected compared to production in batch mode. Overall, our study describes promising options for the establishment of perfusion processes for efficient large-scale manufacturing of fusogenic rVSV-NDV at HCD for all three candidate cell lines.
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Affiliation(s)
- Sven Göbel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Karim E Jaén
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munchen, Germany
| | - Marie Dorn
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Faculty of Process and Systems Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Victoria Neumeyer
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munchen, Germany
| | | | | | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Jennifer Altomonte
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munchen, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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13
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Burock R, Cajic S, Hennig R, Buettner FFR, Reichl U, Rapp E. Reliable N-Glycan Analysis-Removal of Frequently Occurring Oligosaccharide Impurities by Enzymatic Degradation. Molecules 2023; 28:molecules28041843. [PMID: 36838829 PMCID: PMC9967028 DOI: 10.3390/molecules28041843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Glycosylation, especially N-glycosylation, is one of the most common protein modifications, with immense importance at the molecular, cellular, and organismal level. Thus, accurate and reliable N-glycan analysis is essential in many areas of pharmaceutical and food industry, medicine, and science. However, due to the complexity of the cellular glycosylation process, in-depth glycoanalysis is still a highly challenging endeavor. Contamination of samples with oligosaccharide impurities (OSIs), typically linear glucose homo-oligomers, can cause further complications. Due to their physicochemical similarity to N-glycans, OSIs produce potentially overlapping signals, which can remain unnoticed. If recognized, suspected OSI signals are usually excluded in data evaluation. However, in both cases, interpretation of results can be impaired. Alternatively, sample preparation can be repeated to include an OSI removal step from samples. However, this significantly increases sample amount, time, and effort necessary. To overcome these issues, we investigated the option to enzymatically degrade and thereby remove interfering OSIs as a final sample preparation step. Therefore, we screened ten commercially available enzymes concerning their potential to efficiently degrade maltodextrins and dextrans as most frequently found OSIs. Of these enzymes, only dextranase from Chaetomium erraticum and glucoamylase P from Hormoconis resinae enabled a degradation of OSIs within only 30 min that is free of side reactions with N-glycans. Finally, we applied the straightforward enzymatic degradation of OSIs to N-glycan samples derived from different standard glycoproteins and various stem cell lysates.
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Affiliation(s)
- Robert Burock
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - Samanta Cajic
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
| | - René Hennig
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
- Correspondence:
| | - Falk F. R. Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Udo Reichl
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Bioprocess Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- MPI for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestraße 20, 39120 Magdeburg, Germany
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14
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Khesali Aghtaei H, Püttker S, Maus I, Heyer R, Huang L, Sczyrba A, Reichl U, Benndorf D. Adaptation of a microbial community to demand-oriented biological methanation. Biotechnol Biofuels Bioprod 2022; 15:125. [PMID: 36384582 PMCID: PMC9670408 DOI: 10.1186/s13068-022-02207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Biological conversion of the surplus of renewable electricity and carbon dioxide (CO2) from biogas plants to biomethane (CH4) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producing Bacteria and methanogenic Archaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH4 production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H2)-feeding regimes lasting several days. RESULTS Applying various "on-off" H2-feeding regimes, the CH4 production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phyla Firmicutes, Bacteroidota and Thermotogota followed by hydrogenotrophic Archaea of the phylum Methanobacteriota. Homo-acetogenic and heterotrophic fermenting Bacteria formed a complex food web with methanogens. The abundance of the methanogenic Archaea roughly doubled during discontinuous H2-feeding, which was related mainly to an increase in acetoclastic Methanothrix species. Results also suggested that Bacteria feeding on methanogens could reduce overall CH4 production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenic Archaea. During the BM process, the additional production of H2 by fermenting Bacteria seemed to support the maintenance of hydrogenotrophic methanogens at non-H2-feeding phases. Besides the elusive role of Methanothrix during the H2-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species. CONCLUSIONS Taken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H2-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenic Archaea during the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale.
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Affiliation(s)
- Hoda Khesali Aghtaei
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Sebastian Püttker
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Robert Heyer
- Database and Software Engineering Group, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
- Multidimensional Omics Analyses group, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - Liren Huang
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alexander Sczyrba
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany.
- Bioprocess Engineering, Otto Von Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366, Köthen, Germany.
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15
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Möckel M, Baldok N, Walles T, Hartig R, Müller AJ, Reichl U, Genzel Y, Walles H, Wiese-Rischke C. Human 3D Airway Tissue Models for Real-Time Microscopy: Visualizing Respiratory Virus Spreading. Cells 2022; 11:cells11223634. [PMID: 36429061 PMCID: PMC9688616 DOI: 10.3390/cells11223634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/04/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
Abstract
Our knowledge about respiratory virus spreading is mostly based on monolayer cultures that hardly reflect the complex organization of the airway epithelium. Thus, there is a strong demand for biologically relevant models. One possibility to study virus spreading at the cellular level is real-time imaging. In an attempt to visualize virus spreading under somewhat more physiological conditions, Calu-3 cells and human primary fibroblasts were co-cultured submerged or as air-liquid interface (ALI). An influenza A virus (IAV) replicating well in cell culture, and carrying a red fluorescent protein (RFP) reporter gene was used for real-time imaging. Our three-dimensional (3D) models exhibited important characteristics of native airway epithelium including a basement membrane, tight junctions and, in ALI models, strong mucus production. In submerged models, first fluorescence signals appeared between 9 and 12 h post infection (hpi) with a low multiplicity of infection of 0.01. Virus spreading further proceeded in the immediate vicinity of infected cells. In ALI models, RFP was found at 22 hpi and later. Consequently, the progression of infection was delayed, in contrast to the submerged model. With these features, we believe that our 3D airway models can deliver new insights in the spreading of IAV and other respiratory viruses.
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Affiliation(s)
- Marion Möckel
- University Clinic for Cardiac and Thoracic Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
| | - Nino Baldok
- University Clinic for Cardiac and Thoracic Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, D-39106 Magdeburg, Germany
| | - Thorsten Walles
- University Clinic for Cardiac and Thoracic Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
| | - Roland Hartig
- Institute for Molecular and Clinical Immunology, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
| | - Andreas J. Müller
- Institute for Molecular and Clinical Immunology, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
- Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Udo Reichl
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, D-39106 Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, D-39106 Magdeburg, Germany
| | - Heike Walles
- Core Facility Tissue Engineering, Otto-von-Guericke-University Magdeburg, D-39106 Magdeburg, Germany
| | - Cornelia Wiese-Rischke
- University Clinic for Cardiac and Thoracic Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany
- Correspondence:
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16
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Rexer T, Son T, Alcala A, Mahour R, Reichl U. Cell‐free biocatalytic synthesis of nucleotide sugars. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202255124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- T. Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems Bioprocess Engineering Sandtorstr. 1 39106 Magdeburg Germany
| | - T. H. Son
- Max Planck Institute for Dynamics of Complex Technical Systems Bioprocess Engineering Sandtorstr. 1 39106 Magdeburg Germany
| | - A. Alcala
- Max Planck Institute for Dynamics of Complex Technical Systems Bioprocess Engineering Sandtorstr. 1 39106 Magdeburg Germany
| | - R. Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems Bioprocess Engineering Sandtorstr. 1 39106 Magdeburg Germany
| | - U. Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems Bioprocess Engineering Sandtorstr. 1 39106 Magdeburg Germany
- Otto-von-Guericke University Magdeburg Chair of Bioprocess Engineering Universitätsplatz 2 39106 Magdeburg Germany
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17
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Göbel S, Kortum F, Chavez KJ, Jordan I, Sandig V, Reichl U, Altomonte J, Genzel Y. Cell-line screening and process development for a fusogenic oncolytic virus in small-scale suspension cultures. Appl Microbiol Biotechnol 2022; 106:4945-4961. [PMID: 35767011 PMCID: PMC9329169 DOI: 10.1007/s00253-022-12027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/09/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
Abstract
Oncolytic viruses (OVs) represent a novel class of immunotherapeutics under development for the treatment of cancers. OVs that express a cognate or transgenic fusion protein is particularly promising as their enhanced intratumoral spread via syncytia formation can be a potent mechanism for tumor lysis and induction of antitumor immune responses. Rapid and efficient fusion of infected cells results in cell death before high titers are reached. Although this is an attractive safety feature, it also presents unique challenges for large-scale clinical-grade manufacture of OVs. Here we evaluate the use of four different suspension cell lines for the production of a novel fusogenic hybrid of vesicular stomatitis virus and Newcastle disease virus (rVSV-NDV). The candidate cell lines were screened for growth, metabolism, and virus productivity. Permissivity was evaluated based on extracellular infectious virus titers and cell-specific virus yields (CSVYs). For additional process optimizations, virus adaptation and multiplicity of infection (MOI) screenings were performed and confirmed in a 1 L bioreactor. BHK-21 and HEK293SF cells infected at concentrations of 2 × 106 cells/mL were identified as promising candidates for rVSV-NDV production, leading to infectious titers of 3.0 × 108 TCID50/mL and 7.5 × 107 TCID50/mL, and CSVYs of 153 and 9, respectively. Compared to the AGE1.CR.pIX reference produced in adherent cultures, oncolytic potency was not affected by production in suspension cultures and possibly even increased in cultures of HEK293SF and AGE1.CR.pIX. Our study describes promising suspension cell-based processes for efficient large-scale manufacturing of rVSV-NDV. Key points • Cell contact-dependent oncolytic virus (OV) replicates in suspension cells. • Oncolytic potency is not encompassed during suspension cultivation. • Media composition, cell line, and MOI are critical process parameters for OV production. • The designed process is scalable and shows great promise for manufacturing clinical-grade material. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12027-5.
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Affiliation(s)
- Sven Göbel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Fabian Kortum
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Karim Jaén Chavez
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Ingo Jordan
- ProBioGen AG, Herbert-Bayer-Str. 8, 13086, Berlin, Germany
| | - Volker Sandig
- ProBioGen AG, Herbert-Bayer-Str. 8, 13086, Berlin, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany
- Chair for Bioprocess Engineering, Otto-Von-Guericke-University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Jennifer Altomonte
- Department of Internal Medicine II, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106, Magdeburg, Germany.
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18
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Ramos JRC, Bissinger T, Genzel Y, Reichl U. Impact of Influenza A Virus Infection on Growth and Metabolism of Suspension MDCK Cells Using a Dynamic Model. Metabolites 2022; 12:metabo12030239. [PMID: 35323683 PMCID: PMC8950586 DOI: 10.3390/metabo12030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Cell cultured-based influenza virus production is a viable option for vaccine manufacturing. In order to achieve a high concentration of viable cells, is requirement to have not only optimal process conditions, but also an active metabolism capable of intracellular synthesis of viral components. Experimental metabolic data collected in such processes are complex and difficult to interpret, for which mathematical models are an appropriate way to simulate and analyze the complex and dynamic interaction between the virus and its host cell. A dynamic model with 35 states was developed in this study to describe growth, metabolism, and influenza A virus production in shake flask cultivations of suspension Madin-Darby Canine Kidney (MDCK) cells. It considers cell growth (concentration of viable cells, mean cell diameters, volume of viable cells), concentrations of key metabolites both at the intracellular and extracellular level and virus titers. Using one set of parameters, the model accurately simulates the dynamics of mock-infected cells and correctly predicts the overall dynamics of virus-infected cells for up to 60 h post infection (hpi). The model clearly suggests that most changes observed after infection are related to cessation of cell growth and the subsequent transition to apoptosis and cell death. However, predictions do not cover late phases of infection, particularly for the extracellular concentrations of glutamate and ammonium after about 12 hpi. Results obtained from additional in silico studies performed indicated that amino acid degradation by extracellular enzymes resulting from cell lysis during late infection stages may contribute to this observed discrepancy.
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Affiliation(s)
- João Rodrigues Correia Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Correspondence:
| | - Thomas Bissinger
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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19
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Küchler J, Püttker S, Lahmann P, Genzel Y, Kupke S, Benndorf D, Reichl U. Absolute quantification of viral proteins during single-round replication of MDCK suspension cells. J Proteomics 2022; 259:104544. [PMID: 35240312 DOI: 10.1016/j.jprot.2022.104544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/10/2021] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/17/2022]
Abstract
Madin-Darby canine kidney (MDCK) cells are widely used in basic research and for the propagation of influenza A viruses (IAV) for vaccine production. To identify targets for antiviral therapies and to optimize vaccine manufacturing, a detailed understanding of the viral life cycle is important. This includes the characterization of virus entry, the synthesis of the various viral RNAs and proteins, the transfer of viral compounds in the cell and virus budding. In case quantitative information is available, the analysis can be complemented by mathematical modelling approaches. While comprehensive studies focusing on IAV entry as well as viral mRNA, vRNA and cRNA accumulation in the nucleus of cells have been performed, quantitative data regarding IAV protein synthesis and accumulation was mostly lacking. In this study, we present a mass spectrometry (MS)-based method to evaluate whether an absolute quantification of viral proteins is possible for single-round replication in suspension MDCK cells. Using influenza A/PR/8/34 (H1N1, RKI) as a model strain at a multiplicity of infection of ten, defined amounts of isotopically labelled peptides of synthetic origin of four IAV proteins (hemagglutinin, neuraminidase, nucleoprotein, matrix protein 1) were added as an internal standard before tryptic digestion of samples for absolute quantification (AQUA). The first intracellular protein detected was NP at 1 h post infection (hpi). A maximum extracellular concentration of 7.7E+12 copies/mL was achieved. This was followed by hemagglutinin (3 hpi, maximum 4.1E+12 copies/mL at 13 hpi), matrix protein 1 (5 hpi, maximum 2.2E+12 copies/mL at 13 hpi) and neuraminidase (5 hpi, 6.0E+11 copies/mL at 13 hpi). In sum, for the first time absolute IAV protein copy numbers were quantified by a MS-based method for infected MDCK cells providing important insights into viral protein dynamics during single-round virus replication. SIGNIFICANCE: Influenza A virus is a significant human pathogen worldwide. To improve therapies against influenza and overcome bottlenecks in vaccine production in cell culture, it is critical to gain a detailed understanding of the viral life cycle. In addition to qPCR-based models, this study will examine the dynamics of influenza virus proteins during infection of producer cells to gain initial insights into changes in absolute copy numbers.
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Affiliation(s)
- Jan Küchler
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Patrick Lahmann
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Sascha Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
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20
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 PMCID: PMC8674281 DOI: 10.1038/s41467-021-27542-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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21
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 DOI: 10.1101/2021.03.05.433915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 05/21/2023] Open
Abstract
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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22
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Pelz L, Rüdiger D, Dogra T, Alnaji FG, Genzel Y, Brooke CB, Kupke SY, Reichl U. Semi-continuous Propagation of Influenza A Virus and Its Defective Interfering Particles: Analyzing the Dynamic Competition To Select Candidates for Antiviral Therapy. J Virol 2021; 95:e0117421. [PMID: 34550771 PMCID: PMC8610589 DOI: 10.1128/jvi.01174-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/19/2021] [Indexed: 12/26/2022] Open
Abstract
Defective interfering particles (DIPs) of influenza A virus (IAV) are naturally occurring mutants that have an internal deletion in one of their eight viral RNA (vRNA) segments, rendering them propagation-incompetent. Upon coinfection with infectious standard virus (STV), DIPs interfere with STV replication through competitive inhibition. Thus, DIPs are proposed as potent antivirals for treatment of the influenza disease. To select corresponding candidates, we studied de novo generation of DIPs and propagation competition between different defective interfering (DI) vRNAs in an STV coinfection scenario in cell culture. A small-scale two-stage cultivation system that allows long-term semi-continuous propagation of IAV and its DIPs was used. Strong periodic oscillations in virus titers were observed due to the dynamic interaction of DIPs and STVs. Using next-generation sequencing, we detected a predominant formation and accumulation of DI vRNAs on the polymerase-encoding segments. Short DI vRNAs accumulated to higher fractions than longer ones, indicating a replication advantage, yet an optimum fragment length was observed. Some DI vRNAs showed breaking points in a specific part of their bundling signal (belonging to the packaging signal), suggesting its dispensability for DI vRNA propagation. Over a total cultivation time of 21 days, several individual DI vRNAs accumulated to high fractions, while others decreased. Using reverse genetics for IAV, purely clonal DIPs derived from highly replicating DI vRNAs were generated. We confirm that these DIPs exhibit a superior in vitro interfering efficacy compared to DIPs derived from lowly accumulated DI vRNAs and suggest promising candidates for efficacious antiviral treatment. IMPORTANCE Defective interfering particles (DIPs) emerge naturally during viral infection and typically show an internal deletion in the viral genome. Thus, DIPs are propagation-incompetent. Previous research suggests DIPs as potent antiviral compounds for many different virus families due to their ability to interfere with virus replication by competitive inhibition. For instance, the administration of influenza A virus (IAV) DIPs resulted in a rescue of mice from an otherwise lethal IAV dose. Moreover, no apparent toxic effects were observed when only DIPs were administered to mice and ferrets. IAV DIPs show antiviral activity against many different IAV strains, including pandemic and highly pathogenic avian strains, and even against nonhomologous viruses, such as SARS-CoV-2, by stimulation of innate immunity. Here, we used a cultivation/infection system, which exerted selection pressure toward accumulation of highly competitive IAV DIPs. These DIPs showed a superior interfering efficacy in vitro, and we suggest them for effective antiviral therapy.
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Affiliation(s)
- Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Daniel Rüdiger
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Tanya Dogra
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Fadi G. Alnaji
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Christopher B. Brooke
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, Illinois, USA
| | - Sascha Y. Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- Otto-von-Guericke-University Magdeburg, Bioprocess Engineering, Magdeburg, Germany
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23
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Walke D, Schallert K, Ramesh P, Benndorf D, Lange E, Reichl U, Heyer R. MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. Int J Mol Sci 2021; 22:ijms222010992. [PMID: 34681649 PMCID: PMC8539661 DOI: 10.3390/ijms222010992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called 'Pathway-Creator' and 'Pathway-Calculator'. The 'Pathway-Creator' enables an easy set-up of user-defined pathways with specific taxonomic constraints. The 'Pathway-Calculator' automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS.
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Affiliation(s)
- Daniel Walke
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Correspondence: (D.W.); (R.H.)
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Prasanna Ramesh
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Emanuel Lange
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Correspondence: (D.W.); (R.H.)
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24
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Mahour R, Lee JW, Grimpe P, Boecker S, Grote V, Klamt S, Seidel-Morgenstern A, Rexer TFT, Reichl U. Cell-free multi-enzyme synthesis and purification of uridine diphosphate galactose. Chembiochem 2021; 23:e202100361. [PMID: 34637168 PMCID: PMC9299652 DOI: 10.1002/cbic.202100361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 07/22/2021] [Revised: 10/10/2021] [Indexed: 11/26/2022]
Abstract
High costs and low availability of UDP‐galactose hampers the enzymatic synthesis of valuable oligosaccharides such as human milk oligosaccharides. Here, we report the development of a platform for the scalable, biocatalytic synthesis and purification of UDP‐galactose. UDP‐galactose was produced with a titer of 48 mM (27.2 g/L) in a small‐scale batch process (200 μL) within 24 h using 0.02 genzyme/gproduct. Through in‐situ ATP regeneration, the amount of ATP (0.6 mM) supplemented was around 240‐fold lower than the stoichiometric equivalent required to achieve the final product yield. Chromatographic purification using porous graphic carbon adsorbent yielded UDP‐galactose with a purity of 92 %. The synthesis was transferred to 1 L preparative scale production in a stirred tank bioreactor. To further reduce the synthesis costs here, the supernatant of cell lysates was used bypassing expensive purification of enzymes. Here, 23.4 g/L UDP‐galactose were produced within 23 h with a synthesis yield of 71 % and a biocatalyst load of 0.05 gtotal_protein/gproduct. The costs for substrates per gram of UDP‐galactose synthesized were around 0.26 €/g.
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Affiliation(s)
- Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Bioprocess Engineering, GERMANY
| | - Ju Weon Lee
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Physical and Chemical Foundations of Process Engineering, GERMANY
| | - Pia Grimpe
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Bioprocess Engineering, GERMANY
| | - Simon Boecker
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Anaylsis and Redesign of Biological Networks, GERMANY
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Bioprocess Engineering, GERMANY
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Analysis and Redesing of Biological Networks, GERMANY
| | - Andreas Seidel-Morgenstern
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Physical and Chemical Foundations of Process Engineering, GERMANY
| | - Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Bioprocess Engineering, Sandtorstrasse 1, 39106, Magdeburg, GERMANY
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems: Max-Planck-Institut fur Dynamik komplexer technischer Systeme, Bioprocess Engineering, GERMANY
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25
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Gränicher G, Babakhani M, Göbel S, Jordan I, Marichal-Gallardo P, Genzel Y, Reichl U. A high cell density perfusion process for Modified Vaccinia virus Ankara production: Process integration with inline DNA digestion and cost analysis. Biotechnol Bioeng 2021; 118:4720-4734. [PMID: 34506646 DOI: 10.1002/bit.27937] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/22/2021] [Revised: 07/10/2021] [Accepted: 09/01/2021] [Indexed: 12/21/2022]
Abstract
By integrating continuous cell cultures with continuous purification methods, process yields and product quality attributes have been improved over the last 10 years for recombinant protein production. However, for the production of viral vectors such as Modified Vaccinia virus Ankara (MVA), no such studies have been reported although there is an increasing need to meet the requirements for a rising number of clinical trials against infectious or neoplastic diseases. Here, we present for the first time a scalable suspension cell (AGE1.CR.pIX cells) culture-based perfusion process in bioreactors integrating continuous virus harvesting through an acoustic settler with semi-continuous chromatographic purification. This allowed obtaining purified MVA particles with a space-time yield more than 600% higher for the integrated perfusion process (1.05 × 1011 TCID50 /Lbioreactor /day) compared to the integrated batch process. Without further optimization, purification by membrane-based steric exclusion chromatography resulted in an overall product recovery of 50.5%. To decrease the level of host cell DNA before chromatography, a novel inline continuous DNA digestion step was integrated into the process train. A detailed cost analysis comparing integrated production in batch versus production in perfusion mode showed that the cost per dose for MVA was reduced by nearly one-third using this intensified small-scale process.
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Affiliation(s)
- Gwendal Gränicher
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Masoud Babakhani
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair for Bioprocess Engineering, Faculty of Process- and Systems Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Sven Göbel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Institute of Biochemical Engineering, Faculty 4 - Energy-, Process- and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | | | - Pavel Marichal-Gallardo
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair for Bioprocess Engineering, Faculty of Process- and Systems Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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26
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Ruhnau J, Grote V, Juarez-Osorio M, Bruder D, Mahour R, Rapp E, Rexer TFT, Reichl U. Cell-Free Glycoengineering of the Recombinant SARS-CoV-2 Spike Glycoprotein. Front Bioeng Biotechnol 2021; 9:699025. [PMID: 34485255 PMCID: PMC8415157 DOI: 10.3389/fbioe.2021.699025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 04/22/2021] [Accepted: 07/15/2021] [Indexed: 01/23/2023] Open
Abstract
The baculovirus-insect cell expression system is readily utilized to produce viral glycoproteins for research as well as for subunit vaccines and vaccine candidates, for instance against SARS-CoV-2 infections. However, the glycoforms of recombinant proteins derived from this expression system are inherently different from mammalian cell-derived glycoforms with mainly complex-type N-glycans attached, and the impact of these differences in protein glycosylation on the immunogenicity is severely under investigated. This applies also to the SARS-CoV-2 spike glycoprotein, which is the antigen target of all licensed vaccines and vaccine candidates including virus like particles and subunit vaccines that are variants of the spike protein. Here, we expressed the transmembrane-deleted human β-1,2 N-acetlyglucosamintransferases I and II (MGAT1ΔTM and MGAT2ΔTM) and the β-1,4-galactosyltransferase (GalTΔTM) in E. coli to in-vitro remodel the N-glycans of a recombinant SARS-CoV-2 spike glycoprotein derived from insect cells. In a cell-free sequential one-pot reaction, fucosylated and afucosylated paucimannose-type N-glycans were converted to complex-type galactosylated N-glycans. In the future, this in-vitro glycoengineering approach can be used to efficiently generate a wide range of N-glycans on antigens considered as vaccine candidates for animal trials and preclinical testing to better characterize the impact of N-glycosylation on immunity and to improve the efficacy of protein subunit vaccines.
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Affiliation(s)
- Johannes Ruhnau
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Mariana Juarez-Osorio
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Dunja Bruder
- Infection Immunology, Institute of Medical Microbiology, Infection Prevention and Control, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.,Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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27
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Rüdiger D, Pelz L, Hein MD, Kupke SY, Reichl U. Multiscale model of defective interfering particle replication for influenza A virus infection in animal cell culture. PLoS Comput Biol 2021; 17:e1009357. [PMID: 34491996 PMCID: PMC8448327 DOI: 10.1371/journal.pcbi.1009357] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/17/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Cell culture-derived defective interfering particles (DIPs) are considered for antiviral therapy due to their ability to inhibit influenza A virus (IAV) production. DIPs contain a large internal deletion in one of their eight viral RNAs (vRNAs) rendering them replication-incompetent. However, they can propagate alongside their homologous standard virus (STV) during infection in a competition for cellular and viral resources. So far, experimental and modeling studies for IAV have focused on either the intracellular or the cell population level when investigating the interaction of STVs and DIPs. To examine these levels simultaneously, we conducted a series of experiments using highly different multiplicities of infections for STVs and DIPs to characterize virus replication in Madin-Darby Canine Kidney suspension cells. At several time points post infection, we quantified virus titers, viable cell concentration, virus-induced apoptosis using imaging flow cytometry, and intracellular levels of vRNA and viral mRNA using real-time reverse transcription qPCR. Based on the obtained data, we developed a mathematical multiscale model of STV and DIP co-infection that describes dynamics closely for all scenarios with a single set of parameters. We show that applying high DIP concentrations can shut down STV propagation completely and prevent virus-induced apoptosis. Interestingly, the three observed viral mRNAs (full-length segment 1 and 5, defective interfering segment 1) accumulated to vastly different levels suggesting the interplay between an internal regulation mechanism and a growth advantage for shorter viral RNAs. Furthermore, model simulations predict that the concentration of DIPs should be at least 10000 times higher than that of STVs to prevent the spread of IAV. Ultimately, the model presented here supports a comprehensive understanding of the interactions between STVs and DIPs during co-infection providing an ideal platform for the prediction and optimization of vaccine manufacturing as well as DIP production for therapeutic use.
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Affiliation(s)
- Daniel Rüdiger
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Lars Pelz
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marc D. Hein
- Chair of Bioprocess Engineering, Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Y. Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Chair of Bioprocess Engineering, Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Magdeburg, Germany
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28
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Chuzel L, Fossa SL, Boisvert ML, Cajic S, Hennig R, Ganatra MB, Reichl U, Rapp E, Taron CH. Combining functional metagenomics and glycoanalytics to identify enzymes that facilitate structural characterization of sulfated N-glycans. Microb Cell Fact 2021; 20:162. [PMID: 34419057 PMCID: PMC8379841 DOI: 10.1186/s12934-021-01652-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sulfate modification of N-glycans is important for several biological functions such as clearance of pituitary hormones or immunoregulation. Yet, the prevalence of this N-glycan modification and its functions remain largely unexplored. Characterization of N-glycans bearing sulfate modifications is hampered in part by a lack of enzymes that enable site-specific detection of N-glycan sulfation. In this study, we used functional metagenomic screening to identify enzymes that act upon sulfated N-acetylglucosamine (GlcNAc). Using multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) -based glycoanalysis we proved their ability to act upon GlcNAc-6-SO4 on N-glycans. RESULTS Our screen identified a sugar-specific sulfatase that specifically removes sulfate from GlcNAc-6-SO4 when it is in a terminal position on an N-glycan. Additionally, in the absence of calcium, this sulfatase binds to the sulfated glycan but does not remove the sulfate group, suggesting it could be used for selective isolation of sulfated N-glycans. Further, we describe isolation of a sulfate-dependent hexosaminidase that removes intact GlcNAc-6-SO4 (but not asulfated GlcNAc) from a terminal position on N-glycans. Finally, the use of these enzymes to detect the presence of sulfated N-glycans by xCGE-LIF is demonstrated. CONCLUSION The present study demonstrates the feasibility of using functional metagenomic screening combined with glycoanalytics to discover enzymes that act upon chemical modifications of glycans. The discovered enzymes represent new specificities that can help resolve the presence of GlcNAc-6-SO4 in N-glycan structural analyses.
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Affiliation(s)
- Léa Chuzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | - Samanta Cajic
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | | | | | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106, Magdeburg, Germany
| | - Erdmann Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- glyXera GmbH, 39120, Magdeburg, Germany
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29
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Rand U, Kupke SY, Shkarlet H, Hein MD, Hirsch T, Marichal-Gallardo P, Cicin-Sain L, Reichl U, Bruder D. Antiviral Activity of Influenza A Virus Defective Interfering Particles against SARS-CoV-2 Replication In Vitro through Stimulation of Innate Immunity. Cells 2021; 10:1756. [PMID: 34359926 PMCID: PMC8303422 DOI: 10.3390/cells10071756] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, worldwide vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 show only limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19, we conducted in vitro co-infection experiments with cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2 in human lung cells. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. Further, our results suggest boosting of IFN-induced antiviral activity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19, and potentially also for suppressing the replication of new variants of SARS-CoV-2.
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Affiliation(s)
- Ulfert Rand
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (U.R.); (L.C.-S.)
| | - Sascha Young Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
| | - Hanna Shkarlet
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Marc Dominique Hein
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany;
| | - Tatjana Hirsch
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
| | - Luka Cicin-Sain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (U.R.); (L.C.-S.)
- German Centre for Infection Research, Hannover-Braunschweig Site, 38124 Braunschweig, Germany
- Centre for Individualized Infection Medicine, a Joint Venture of Helmholtz Centre for Infection Research and Medical School Hannover, 38124 Braunschweig, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (P.M.-G.); (U.R.)
- Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany;
| | - Dunja Bruder
- Immune Regulation Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (H.S.); (T.H.); (D.B.)
- Institute of Medical Microbiology, Infection Prevention and Control, Infection Immunology Group, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
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30
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Bissinger T, Wu Y, Marichal-Gallardo P, Riedel D, Liu X, Genzel Y, Tan WS, Reichl U. Towards integrated production of an influenza A vaccine candidate with MDCK suspension cells. Biotechnol Bioeng 2021; 118:3996-4013. [PMID: 34219217 DOI: 10.1002/bit.27876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/15/2021] [Revised: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022]
Abstract
Seasonal influenza epidemics occur both in northern and southern hemispheres every year. Despite the differences in influenza virus surface antigens and virulence of seasonal subtypes, manufacturers are well-adapted to respond to this periodical vaccine demand. Due to decades of influenza virus research, the development of new influenza vaccines is relatively straight forward. In similarity with the ongoing coronavirus disease 2019 pandemic, vaccine manufacturing is a major bottleneck for a rapid supply of the billions of doses required worldwide. In particular, egg-based vaccine production would be difficult to schedule and shortages of other egg-based vaccines with high demands also have to be anticipated. Cell culture-based production systems enable the manufacturing of large amounts of vaccines within a short time frame and expand significantly our options to respond to pandemics and emerging viral diseases. In this study, we present an integrated process for the production of inactivated influenza A virus vaccines based on a Madin-Darby Canine Kidney (MDCK) suspension cell line cultivated in a chemically defined medium. Very high titers of 3.6 log10 (HAU/100 µl) were achieved using fast-growing MDCK cells at concentrations up to 9.5 × 106 cells/ml infected with influenza A/PR/8/34 H1N1 virus in 1 L stirred tank bioreactors. A combination of membrane-based steric-exclusion chromatography followed by pseudo-affinity chromatography with a sulfated cellulose membrane adsorber enabled full recovery for the virus capture step and up to 80% recovery for the virus polishing step. Purified virus particles showed a homogenous size distribution with a mean diameter of 80 nm. Based on a monovalent dose of 15 µg hemagglutinin (single-radial immunodiffusion assay), the level of total protein and host cell DNA was 58 µg and 10 ng, respectively. Furthermore, all process steps can be fully scaled up to industrial quantities for commercial manufacturing of either seasonal or pandemic influenza virus vaccines. Fast production of up to 300 vaccine doses per liter within 4-5 days makes this process competitive not only to other cell-based processes but to egg-based processes as well.
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Affiliation(s)
- Thomas Bissinger
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yixiao Wu
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dietmar Riedel
- Facility for Transmission Electron Microscopy, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Xuping Liu
- Shanghai BioEngine Sci-Tech Co., Shanghai, China
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Wen-Song Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Shanghai BioEngine Sci-Tech Co., Shanghai, China
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
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31
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Offersgaard A, Duarte Hernandez CR, Pihl AF, Costa R, Venkatesan NP, Lin X, Van Pham L, Feng S, Fahnøe U, Scheel TKH, Ramirez S, Reichl U, Bukh J, Genzel Y, Gottwein JM. SARS-CoV-2 Production in a Scalable High Cell Density Bioreactor. Vaccines (Basel) 2021; 9:706. [PMID: 34209694 PMCID: PMC8310283 DOI: 10.3390/vaccines9070706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has demonstrated the value of pursuing different vaccine strategies. Vaccines based on whole viruses, a widely used vaccine technology, depend on efficient virus production. This study aimed to establish SARS-CoV-2 production in the scalable packed-bed CelCradleTM 500-AP bioreactor. CelCradleTM 500-AP bottles with 0.5 L working volume and 5.5 g BioNOC™ II carriers were seeded with 1.5 × 108 Vero (WHO) cells, approved for vaccine production, in animal component-free medium and infected at a multiplicity of infection of 0.006 at a total cell number of 2.2-2.5 × 109 cells/bottle seven days post cell seeding. Among several tested conditions, two harvests per day and a virus production temperature of 33 °C resulted in the highest virus yield with a peak SARS-CoV-2 infectivity titer of 7.3 log10 50% tissue culture infectious dose (TCID50)/mL at 72 h post-infection. Six harvests had titers of ≥6.5 log10 TCID50/mL, and a total of 10.5 log10 TCID50 were produced in ~5 L. While trypsin was reported to enhance virus spread in cell culture, addition of 0.5% recombinant trypsin after infection did not improve virus yields. Overall, we demonstrated successful animal component-free production of SARS-CoV-2 in well-characterized Vero (WHO) cells in a scalable packed-bed bioreactor.
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Affiliation(s)
- Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Carlos Rene Duarte Hernandez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Finne Pihl
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rui Costa
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Xiangliang Lin
- Esco Aster Pte Ltd., Singapore 486 777, Singapore; (N.P.V.); (X.L.)
| | - Long Van Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shan Feng
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Troels Kasper Høyer Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (U.R.); (Y.G.)
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; (U.R.); (Y.G.)
| | - Judith Margarete Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark; (A.O.); (C.R.D.H.); (A.F.P.); (R.C.); (L.V.P.); (S.F.); (U.F.); (T.K.H.S.); (S.R.); (J.B.)
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Biemann R, Buß E, Benndorf D, Lehmann T, Schallert K, Püttker S, Reichl U, Isermann B, Schneider JG, Saake G, Heyer R. Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss. Biomolecules 2021; 11:biom11050726. [PMID: 34066026 PMCID: PMC8150863 DOI: 10.3390/biom11050726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (-13.7%), improved insulin sensitivity (HOMA-IR, -46.1%), and reduced levels of circulating hsCRP (-39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome.
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Affiliation(s)
- Ronald Biemann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Paul-List-Str. 13/15, 04103 Leipzig, Germany;
- Correspondence: (R.B.); (D.B.); (R.H.)
| | - Enrico Buß
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Correspondence: (R.B.); (D.B.); (R.H.)
| | - Theresa Lehmann
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Paul-List-Str. 13/15, 04103 Leipzig, Germany;
- Institute of Clinical Chemistry and Pathobiochemistry, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Jochen G. Schneider
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg;
- Department of Internal Medicine II, Saarland University Medical Center, Kirrberger Str., 66424 Homburg Saar, Germany
| | - Gunter Saake
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Correspondence: (R.B.); (D.B.); (R.H.)
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Hein MD, Arora P, Marichal-Gallardo P, Winkler M, Genzel Y, Pöhlmann S, Schughart K, Kupke SY, Reichl U. Cell culture-based production and in vivo characterization of purely clonal defective interfering influenza virus particles. BMC Biol 2021; 19:91. [PMID: 33941189 PMCID: PMC8091782 DOI: 10.1186/s12915-021-01020-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Received: 08/20/2020] [Accepted: 04/01/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Infections with influenza A virus (IAV) cause high morbidity and mortality in humans. Additional to vaccination, antiviral drugs are a treatment option. Besides FDA-approved drugs such as oseltamivir or zanamivir, virus-derived defective interfering (DI) particles (DIPs) are considered promising new agents. IAV DIPs typically contain a large internal deletion in one of their eight genomic viral RNA (vRNA) segments. Consequently, DIPs miss the genetic information necessary for replication and can usually only propagate by co-infection with infectious standard virus (STV), compensating for their defect. In such a co-infection scenario, DIPs interfere with and suppress STV replication, which constitutes their antiviral potential. RESULTS In the present study, we generated a genetically engineered MDCK suspension cell line for production of a purely clonal DIP preparation that has a large deletion in its segment 1 (DI244) and is not contaminated with infectious STV as egg-derived material. First, the impact of the multiplicity of DIP (MODIP) per cell on DI244 yield was investigated in batch cultivations in shake flasks. Here, the highest interfering efficacy was observed for material produced at a MODIP of 1E-2 using an in vitro interference assay. Results of RT-PCR suggested that DI244 material produced was hardly contaminated with other defective particles. Next, the process was successfully transferred to a stirred tank bioreactor (500 mL working volume) with a yield of 6.0E+8 PFU/mL determined in genetically modified adherent MDCK cells. The produced material was purified and concentrated about 40-fold by membrane-based steric exclusion chromatography (SXC). The DI244 yield was 92.3% with a host cell DNA clearance of 97.1% (99.95% with nuclease digestion prior to SXC) and a total protein reduction of 97.2%. Finally, the DIP material was tested in animal experiments in D2(B6).A2G-Mx1r/r mice. Mice infected with a lethal dose of IAV and treated with DIP material showed a reduced body weight loss and all animals survived. CONCLUSION In summary, experiments not only demonstrated that purely clonal influenza virus DIP preparations can be obtained with high titers from animal cell cultures but confirmed the potential of cell culture-derived DIPs as an antiviral agent.
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Affiliation(s)
- Marc D Hein
- Otto-von-Guericke-University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
| | - Prerna Arora
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Michael Winkler
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Stefan Pöhlmann
- German Primate Center-Leibniz Institute for Primate Research, Infection Biology Unit, Göttingen, Germany.,University Göttingen, Faculty of Biology and Psychology, Göttingen, Germany
| | - Klaus Schughart
- Helmholtz Centre for Infection Research, Department of Infection Genetics, Braunschweig, Germany.,University of Veterinary Medicine Hannover, Hannover, Germany.,University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, TN, USA
| | - Sascha Y Kupke
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Otto-von-Guericke-University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
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Marichal-Gallardo P, Börner K, Pieler MM, Sonntag-Buck V, Obr M, Bejarano D, Wolff MW, Kräusslich HG, Reichl U, Grimm D. Single-Use Capture Purification of Adeno-Associated Viral Gene Transfer Vectors by Membrane-Based Steric Exclusion Chromatography. Hum Gene Ther 2021; 32:959-974. [PMID: 33554722 PMCID: PMC10116406 DOI: 10.1089/hum.2019.284] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present membrane-based steric exclusion chromatography (SXC) as a universal capture step for purification of adeno-associated virus (AAV) gene transfer vectors independent of their serotype and surface characteristics. SXC is performed by mixing an unpurified cell culture supernatant containing AAV particles with polyethylene glycol (PEG) and feeding the mixture onto a chromatography filter unit. The purified AAV particles are recovered by flushing the unit with a solution lacking PEG. SXC is an inexpensive single-use method that permits to concentrate, purify, and re-buffer AAV particles with yields >95% and >80% impurity clearance. SXC could theoretically be employed at industrial scales with units of nearly 20 m2.
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Affiliation(s)
- Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kathleen Börner
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant, Heidelberg University, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Michael M Pieler
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Vera Sonntag-Buck
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Obr
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Bejarano
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael W Wolff
- Institute of Bioprocess Engineering and Pharmaceutical Technology, Technische Hochschule Mittelhessen, Gießen, Germany
| | - Hans-Georg Kräusslich
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant, Heidelberg University, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Dirk Grimm
- Center for Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,BioQuant, Heidelberg University, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
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Pralow A, Nikolay A, Leon A, Genzel Y, Rapp E, Reichl U. Site-specific N-glycosylation analysis of animal cell culture-derived Zika virus proteins. Sci Rep 2021; 11:5147. [PMID: 33664361 PMCID: PMC7933209 DOI: 10.1038/s41598-021-84682-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
Here, we present for the first time, a site-specific N-glycosylation analysis of proteins from a Brazilian Zika virus (ZIKV) strain. The virus was propagated with high yield in an embryo-derived stem cell line (EB66, Valneva SE), and concentrated by g-force step-gradient centrifugation. Subsequently, the sample was proteolytically digested with different enzymes, measured via a LC–MS/MS-based workflow, and analyzed in a semi-automated way using the in-house developed glyXtoolMS software. The viral non-structural protein 1 (NS1) was glycosylated exclusively with high-mannose structures on both potential N-glycosylation sites. In case of the viral envelope (E) protein, no specific N-glycans could be identified with this method. Nevertheless, N-glycosylation could be proved by enzymatic de-N-glycosylation with PNGase F, resulting in a strong MS-signal of the former glycopeptide with deamidated asparagine at the potential N-glycosylation site N444. This confirmed that this site of the ZIKV E protein is highly N-glycosylated but with very high micro-heterogeneity. Our study clearly demonstrates the progress made towards site-specific N-glycosylation analysis of viral proteins, i.e. for Brazilian ZIKV. It allows to better characterize viral isolates, and to monitor glycosylation of major antigens. The method established can be applied for detailed studies regarding the impact of protein glycosylation on antigenicity and human pathogenicity of many viruses including influenza virus, HIV and corona virus.
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Affiliation(s)
- Alexander Pralow
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Alexander Nikolay
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | | | - Yvonne Genzel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany. .,glyXera GmbH, Magdeburg, Germany.
| | - Udo Reichl
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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Affiliation(s)
- Reza Mahour
- Department of Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Sandtorstrasse 1 39106 Magdeburg Germany
| | - Pavel A. Marichal‐Gallardo
- Department of Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Sandtorstrasse 1 39106 Magdeburg Germany
| | - Thomas F. T. Rexer
- Department of Bioprocess Engineering Max Planck Institute for Dynamics of Complex Technical Systems Sandtorstrasse 1 39106 Magdeburg Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems Sandtorstrasse 1 39106 Magdeburg
- Otto-von-Guericke-University Magdeburg Chair of Bioprocess Engineering Universitätsplatz 2 39106 Magdeburg Germany
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Reichl U, Seidel‐Morgenstern A, Sundmacher K, Tsotsas E, van Wachem B. Forschungsarbeiten am Institut für Verfahrenstechnik der Otto‐von‐Guericke‐Universität Magdeburg. CHEM-ING-TECH 2021. [DOI: 10.1002/cite.202100002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Udo Reichl
- Otto von-Guericke Universität Magdeburg Institut für Verfahrenstechnik Universitätsplatz 2 39106 Magdeburg Deutschland
| | - Andreas Seidel‐Morgenstern
- Otto von-Guericke Universität Magdeburg Institut für Verfahrenstechnik Universitätsplatz 2 39106 Magdeburg Deutschland
| | - Kai Sundmacher
- Otto von-Guericke Universität Magdeburg Institut für Verfahrenstechnik Universitätsplatz 2 39106 Magdeburg Deutschland
| | - Evangelos Tsotsas
- Otto von-Guericke Universität Magdeburg Institut für Verfahrenstechnik Universitätsplatz 2 39106 Magdeburg Deutschland
| | - Berend van Wachem
- Otto von-Guericke Universität Magdeburg Institut für Verfahrenstechnik Universitätsplatz 2 39106 Magdeburg Deutschland
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Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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Pech S, Rehberg M, Janke R, Benndorf D, Genzel Y, Muth T, Sickmann A, Rapp E, Reichl U. Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins. Appl Microbiol Biotechnol 2021; 105:1861-1874. [PMID: 33582836 PMCID: PMC7907048 DOI: 10.1007/s00253-021-11150-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 09/08/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022]
Abstract
Abstract Adaptations of animal cells to growth in suspension culture concern in particular viral vaccine production, where very specific aspects of virus-host cell interaction need to be taken into account to achieve high cell specific yields and overall process productivity. So far, the complexity of alterations on the metabolism, enzyme, and proteome level required for adaptation is only poorly understood. In this study, for the first time, we combined several complex analytical approaches with the aim to track cellular changes on different levels and to unravel interconnections and correlations. Therefore, a Madin-Darby canine kidney (MDCK) suspension cell line, adapted earlier to growth in suspension, was cultivated in a 1-L bioreactor. Cell concentrations and cell volumes, extracellular metabolite concentrations, and intracellular enzyme activities were determined. The experimental data set was used as the input for a segregated growth model that was already applied to describe the growth dynamics of the parental adherent cell line. In addition, the cellular proteome was analyzed by liquid chromatography coupled to tandem mass spectrometry using a label-free protein quantification method to unravel altered cellular processes for the suspension and the adherent cell line. Four regulatory mechanisms were identified as a response of the adaptation of adherent MDCK cells to growth in suspension. These regulatory mechanisms were linked to the proteins caveolin, cadherin-1, and pirin. Combining cell, metabolite, enzyme, and protein measurements with mathematical modeling generated a more holistic view on cellular processes involved in the adaptation of an adherent cell line to suspension growth. Key points • Less and more efficient glucose utilization for suspension cell growth • Concerted alteration of metabolic enzyme activity and protein expression • Protein candidates to interfere glycolytic activity in MDCK cells Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11150-z.
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Affiliation(s)
- Sabine Pech
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Markus Rehberg
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Robert Janke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Thilo Muth
- Section S.3 eScience, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Erdmann Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyxera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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40
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Wu Y, Bissinger T, Genzel Y, Liu X, Reichl U, Tan WS. High cell density perfusion process for high yield of influenza A virus production using MDCK suspension cells. Appl Microbiol Biotechnol 2021; 105:1421-1434. [PMID: 33515287 PMCID: PMC7847233 DOI: 10.1007/s00253-020-11050-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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] [Received: 06/30/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022]
Abstract
Similar to the recent COVID-19 pandemic, influenza A virus poses a constant threat to the global community. For the treatment of flu disease, both antivirals and vaccines are available with vaccines the most effective and safest approach. In order to overcome limitations in egg-based vaccine manufacturing, cell culture-based processes have been established. While this production method avoids egg-associated risks in face of pandemics, process intensification using animal suspension cells in high cell density perfusion cultures should allow to further increase manufacturing capacities worldwide. In this work, we demonstrate the development of a perfusion process using Madin-Darby canine kidney (MDCK) suspension cells for influenza A (H1N1) virus production from scale-down shake flask cultivations to laboratory scale stirred tank bioreactors. Shake flask cultivations using semi-perfusion mode enabled high-yield virus harvests (4.25 log10(HAU/100 μL)) from MDCK cells grown up to 41 × 106 cells/mL. Scale-up to bioreactors with an alternating tangential flow (ATF) perfusion system required optimization of pH control and implementation of a temperature shift during the infection phase. Use of a capacitance probe for on-line perfusion control allowed to minimize medium consumption. This contributed to a better process control and a more economical performance while maintaining a maximum virus titer of 4.37 log10(HAU/100 μL) and an infectious virus titer of 1.83 × 1010 virions/mL. Overall, this study clearly demonstrates recent advances in cell culture-based perfusion processes for next-generation high-yield influenza vaccine manufacturing for pandemic preparedness. KEY POINTS: • First MDCK suspension cell-based perfusion process for IAV produciton was established. • "Cell density effect" was overcome and process was intensified by reduction of medium use and automated process control. • The process achieved cell density over 40 × 106 cells/mL and virus yield over 4.37 log10(HAU/100 μL).
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Affiliation(s)
- Yixiao Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Thomas Bissinger
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Xuping Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China. .,Shanghai BioEngine Sci-Tech Co., Ltd, 781 Cailun Road, Shanghai, 201203, China.
| | - Udo Reichl
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.,Chair of Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Universitaetsplatz 2, 39106, Magdeburg, Germany
| | - Wen-Song Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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41
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Hein MD, Kollmus H, Marichal-Gallardo P, Püttker S, Benndorf D, Genzel Y, Schughart K, Kupke SY, Reichl U. OP7, a novel influenza A virus defective interfering particle: production, purification, and animal experiments demonstrating antiviral potential. Appl Microbiol Biotechnol 2020; 105:129-146. [PMID: 33275160 PMCID: PMC7778630 DOI: 10.1007/s00253-020-11029-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Received: 09/05/2020] [Revised: 11/14/2020] [Accepted: 11/22/2020] [Indexed: 11/24/2022]
Abstract
Abstract The novel influenza A virus (IAV) defective interfering particle “OP7” inhibits IAV replication in a co-infection and was previously suggested as a promising antiviral agent. Here, we report a batch-mode cell culture-based production process for OP7. In the present study, a seed virus containing standard virus (STV) and OP7 was used. The yield of OP7 strongly depended on the production multiplicity of infection. To inactivate infectious STV in the OP7 material, which may cause harm in a potential application, UV irradiation was used. The efficacy of OP7 in this material was preserved, as shown by an in vitro interference assay. Next, steric exclusion chromatography was used to purify and to concentrate (~ 13-fold) the UV-treated material. Finally, administration of produced OP7 material in mice did not show any toxic effects. Furthermore, all mice infected with a lethal dose of IAV survived the infection upon OP7 co-treatment. Thus, the feasibility of a production workflow for OP7 and its potential for antiviral treatment was demonstrated. Key points • OP7 efficacy strongly depended on the multiplicity of infection used for production • Purification by steric exclusion chromatography increased OP7 efficacy • OP7-treated mice were protected against a lethal infection with IAV Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-11029-5.
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Affiliation(s)
- Marc D Hein
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Pavel Marichal-Gallardo
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine Hannover, Hannover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Sascha Y Kupke
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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42
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Heyer R, Klang J, Hellwig P, Schallert K, Kress P, Huelsemann B, Theuerl S, Reichl U, Benndorf D. Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants. Bioresour Technol 2020; 314:123679. [PMID: 32629381 DOI: 10.1016/j.biortech.2020.123679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/15/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
In anaerobic digestion plants (ADs), homogenization of the feed, fermenter content and microbial communities is crucial for efficient and robust biogas production. However, mixing also requires a significant amount of energy. For an 850 m3 agricultural AD equipped with eight sampling ports, we investigated whether different feeding and stirring regimes enable a sufficient homogenization of the microbial community using metaproteomics and terminal restriction fragment length polymorphism (TRFLP) analysis. Systematic comparison of samples taken at the top and the bottom as well as at the rim and the center of the AD using scatter plots and students t-test revealed only a small number of differences in metaproteins, taxonomies and biological processes. Obviously, the applied stirring and feeding conditions were sufficient to largely homogenize the content of the AD.
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Affiliation(s)
- Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Johanna Klang
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
| | - Patrick Hellwig
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Kay Schallert
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Philipp Kress
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Garbenstraße 9, 70599 Stuttgart, Germany.
| | - Benedikt Huelsemann
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Garbenstraße 9, 70599 Stuttgart, Germany.
| | - Susanne Theuerl
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany; Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Dirk Benndorf
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106 Magdeburg, Germany.
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43
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Gränicher G, Tapia F, Behrendt I, Jordan I, Genzel Y, Reichl U. Production of Modified Vaccinia Ankara Virus by Intensified Cell Cultures: A Comparison of Platform Technologies for Viral Vector Production. Biotechnol J 2020; 16:e2000024. [PMID: 32762152 PMCID: PMC7435511 DOI: 10.1002/biot.202000024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/17/2020] [Indexed: 12/23/2022]
Abstract
Modified Vaccinia Ankara (MVA) virus is a promising vector for vaccination against various challenging pathogens or the treatment of some types of cancers, requiring a high amount of virions per dose for vaccination and gene therapy. Upstream process intensification combining perfusion technologies, the avian suspension cell line AGE1.CR.pIX and the virus strain MVA-CR19 is an option to obtain very high MVA yields. Here the authors compare different options for cell retention in perfusion mode using conventional stirred-tank bioreactors. Furthermore, the authors study hollow-fiber bioreactors and an orbital-shaken bioreactor in perfusion mode, both available for single-use. Productivity for the virus strain MVA-CR19 is compared to results from batch and continuous production reported in literature. The results demonstrate that cell retention devices are only required to maximize cell concentration but not for continuous harvesting. Using a stirred-tank bioreactor, a perfusion strategy with working volume expansion after virus infection results in the highest yields. Overall, infectious MVA virus titers of 2.1-16.5 × 109 virions/mL are achieved in these intensified processes. Taken together, the study shows a novel perspective on high-yield MVA virus production in conventional bioreactor systems linked to various cell retention devices and addresses options for process intensification including fully single-use perfusion platforms.
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Affiliation(s)
- Gwendal Gränicher
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, Magdeburg, 39106, Germany
| | - Felipe Tapia
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, Magdeburg, 39106, Germany
| | - Ilona Behrendt
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, Magdeburg, 39106, Germany
| | - Ingo Jordan
- ProBioGen AG, Goethestr. 54, Berlin, 13086, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, Magdeburg, 39106, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, Magdeburg, 39106, Germany.,Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, Magdeburg, 39106, Germany
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44
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Coronel J, Gränicher G, Sandig V, Noll T, Genzel Y, Reichl U. Application of an Inclined Settler for Cell Culture-Based Influenza A Virus Production in Perfusion Mode. Front Bioeng Biotechnol 2020; 8:672. [PMID: 32714908 PMCID: PMC7343718 DOI: 10.3389/fbioe.2020.00672] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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] [Received: 02/21/2020] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
Influenza viruses have been successfully propagated using a variety of animal cell lines in batch, fed-batch, and perfusion culture. For suspension cells, most studies reported on membrane-based cell retention devices typically leading to an accumulation of viruses in the bioreactor in perfusion mode. Aiming at continuous virus harvesting for improved productivities, an inclined settler was evaluated for influenza A virus (IAV) production using the avian suspension cell line AGE1.CR.pIX. Inclined settlers present many advantages as they are scalable, robust, and comply with cGMP regulations, e.g., for recombinant protein manufacturing. Perfusion rates up to 3000 L/day have been reported. In our study, successful growth of AGE1.CR.pIX cells up to 50 × 106 cells/mL and a cell retention efficiency exceeding 96% were obtained with the settler cooled to room temperature. No virus retention was observed. A total of 5.4-6.5 × 1013 virions were produced while a control experiment with an ATF system equaled to 1.9 × 1013 virions. For infection at 25 × 106 cells/mL, cell-specific virus yields up to 3474 virions/cell were obtained, about 5-fold higher than for an ATF based cultivation performed as a control (723 virions/cell). Trypsin activity was shown to have a large impact on cell growth dynamics after infection following the cell retention device, especially at a cell concentration of 50 × 106 cells/mL. Further control experiments performed with an acoustic settler showed that virus production was improved with a heat exchanger of the inclined settler operated at 27°C. In summary, cell culture-based production of viruses in perfusion mode with an inclined settler and continuous harvesting can drastically increase IAV yields and possibly the yield of other viruses. To our knowledge, this is the first report to show the potential of this device for viral vaccine production.
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Affiliation(s)
- Juliana Coronel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Gwendal Gränicher
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | | | - Thomas Noll
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
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45
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Nikolay A, de Grooth J, Genzel Y, Wood JA, Reichl U. Virus harvesting in perfusion culture: Choosing the right type of hollow fiber membrane. Biotechnol Bioeng 2020; 117:3040-3052. [PMID: 32568408 DOI: 10.1002/bit.27470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/13/2019] [Revised: 05/28/2020] [Accepted: 06/20/2020] [Indexed: 02/04/2023]
Abstract
The use of bioreactors coupled to membrane-based perfusion systems enables very high cell and product concentrations in vaccine and viral vector manufacturing. Many virus particles, however, are not stable and either lose their infectivity or physically degrade resulting in significant product losses if not harvested continuously. Even hollow fiber membranes with a nominal pore size of 0.2 µm can retain much smaller virions within a bioreactor. Here, we report on a systematic study to characterize structural and physicochemical membrane properties with respect to filter fouling and harvesting of yellow fever virus (YFV; ~50 nm). In tangential flow filtration perfusion experiments, we observed that YFV retention was only marginally determined by nominal but by effective pore sizes depending on filter fouling. Evaluation of scanning electron microscope images indicated that filter fouling can be reduced significantly by choosing membranes with (i) a flat inner surface (low boundary layer thickness), (ii) a smooth material structure (reduced deposition), (iii) a high porosity (high transmembrane flux), (iv) a distinct pore size distribution (well-defined pore selectivity), and (v) an increased fiber wall thickness (larger effective surface area). Lowest filter fouling was observed with polysulfone (PS) membranes. While the use of a small-pore PS membrane (0.08 µm) allowed to fully retain YFV within the bioreactor, continuous product harvesting was achieved with the large-pore PS membrane (0.34 µm). Due to the low protein rejection of the latter, this membrane type could also be of interest for other applications, that is, recombinant protein production in perfusion cultures.
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Affiliation(s)
- Alexander Nikolay
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Joris de Grooth
- Films in Fluids, University of Twente, Enschede, The Netherlands
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Jeffery A Wood
- Soft Matter, Fluidics and Interfaces, Faculty of Science and Technology, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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46
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Gränicher G, Coronel J, Trampler F, Jordan I, Genzel Y, Reichl U. Performance of an acoustic settler versus a hollow fiber-based ATF technology for influenza virus production in perfusion. Appl Microbiol Biotechnol 2020; 104:4877-4888. [PMID: 32291490 PMCID: PMC7228903 DOI: 10.1007/s00253-020-10596-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/10/2020] [Accepted: 03/31/2020] [Indexed: 12/24/2022]
Abstract
Process intensification and integration is crucial regarding an ever increasing pressure on manufacturing costs and capacities in biologics manufacturing. For virus production in perfusion mode, membrane-based alternating tangential flow filtration (ATF) and acoustic settler are the commonly described cell retention technologies. While acoustic settlers allow for continuous influenza virus harvesting, the use of commercially available membranes for ATF systems typically results in the accumulation of virus particles in the bioreactor vessel. Accordingly, with one single harvest at the end of a cultivation, this increases the risk of lowering the product quality. To assess which cell retention device would be most suitable for influenza A virus production, we compared various key performance figures using AGE1.CR.pIX cells at concentrations between 25 and 50 × 106 cells/mL at similar infection conditions using either an ATF system or an acoustic settler. Production yields, process-related impurities, and aggregation of viruses and other large molecules were evaluated. Taking into account the total number of virions from both the bioreactor and the harvest vessel, a 1.5-3.0-fold higher volumetric virus yield was obtained for the acoustic settler. In addition, fewer large-sized aggregates (virus particles and other molecules) were observed in the harvest taken directly from the bioreactor. In contrast, similar levels of process-related impurities (host cell dsDNA, total protein) were obtained in the harvest for both retention systems. Overall, a clear advantage was observed for continuous virus harvesting after the acoustic settler operation mode was optimized. This development may also allow direct integration of subsequent downstream processing steps. KEY POINTS: • High suspension cell density, immortalized avian cell line, influenza vaccine.
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Affiliation(s)
- Gwendal Gränicher
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| | - Juliana Coronel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Felix Trampler
- SonoSep Technologies, Waldgasse 7, 2371, Hinterbrühl, Austria
| | - Ingo Jordan
- ProBioGen AG, Goethestr 54, 13086, Berlin, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
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47
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Ramos JRC, Rath AG, Genzel Y, Sandig V, Reichl U. A dynamic model linking cell growth to intracellular metabolism and extracellular by-product accumulation. Biotechnol Bioeng 2020; 117:1533-1553. [PMID: 32022250 DOI: 10.1002/bit.27288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 05/26/2019] [Revised: 12/12/2019] [Accepted: 01/26/2020] [Indexed: 12/16/2022]
Abstract
Mathematical modeling of animal cell growth and metabolism is essential for the understanding and improvement of the production of biopharmaceuticals. Models can explain the dynamic behavior of cell growth and product formation, support the identification of the most relevant parameters for process design, and significantly reduce the number of experiments to be performed for process optimization. Few dynamic models have been established that describe both extracellular and intracellular dynamics of growth and metabolism of animal cells. In this study, a model was developed, which comprises a set of 33 ordinary differential equations to describe batch cultivations of suspension AGE1.HN.AAT cells considered for the production of α1-antitrypsin. This model combines a segregated cell growth model with a structured model of intracellular metabolism. Overall, it considers the viable cell concentration, mean cell diameter, viable cell volume, concentration of extracellular substrates, and intracellular concentrations of key metabolites from the central carbon metabolism. Furthermore, the release of metabolic by-products such as lactate and ammonium was estimated directly from the intracellular reactions. Based on the same set of parameters, this model simulates well the dynamics of four independent batch cultivations. Analysis of the simulated intracellular rates revealed at least two distinct cellular physiological states. The first physiological state was characterized by a high glycolytic rate and high lactate production. Whereas the second state was characterized by efficient adenosine triphosphate production, a low glycolytic rate, and reactions of the TCA cycle running in the reverse direction from α-ketoglutarate to citrate. Finally, we show possible applications of the model for cell line engineering and media optimization with two case studies.
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Affiliation(s)
- João R C Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Alexander G Rath
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, AMINO GmbH, Frellstedt, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Volker Sandig
- Bioprocess Engineering, ProBioGen AG, Berlin, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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48
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Abstract
The global demand for complex biopharmaceuticals like recombinant proteins, vaccines, or viral vectors is steadily rising. To further improve process productivity and to reduce production costs, process intensification can contribute significantly. The design and optimization of perfusion processes toward very high cell densities require careful selection of strategies for optimal perfusion rate control. In this chapter, various options are discussed to guarantee high cell-specific virus yields and to achieve virus concentrations up to 1010 virions/mL. This includes reactor volume exchange regimes and perfusion rate control based on process variables such as cell concentration and metabolite or by-product concentration. Strategies to achieve high cell densities by perfusion rate control and their experimental implementation are described in detail for pseudo-perfusion or small-scale perfusion bioreactor systems. Suspension cell lines such as MDCK, BHK-21, EB66®, and AGE1.CR.pIX® are used to exemplify production of influenza, yellow fever, Zika, and modified vaccinia Ankara virus.
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Affiliation(s)
- Alexander Nikolay
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Thomas Bissinger
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Gwendal Gränicher
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yixiao Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
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Bissinger T, Fritsch J, Mihut A, Wu Y, Liu X, Genzel Y, Tan WS, Reichl U. Semi-perfusion cultures of suspension MDCK cells enable high cell concentrations and efficient influenza A virus production. Vaccine 2019; 37:7003-7010. [DOI: 10.1016/j.vaccine.2019.04.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/10/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
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Tapia F, Laske T, Wasik MA, Rammhold M, Genzel Y, Reichl U. Production of Defective Interfering Particles of Influenza A Virus in Parallel Continuous Cultures at Two Residence Times-Insights From qPCR Measurements and Viral Dynamics Modeling. Front Bioeng Biotechnol 2019; 7:275. [PMID: 31681751 PMCID: PMC6813217 DOI: 10.3389/fbioe.2019.00275] [Citation(s) in RCA: 15] [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] [Received: 07/11/2019] [Accepted: 10/01/2019] [Indexed: 01/06/2023] Open
Abstract
Defective interfering particles (DIPs) are a natural byproduct of influenza A virus (IAV) replication. DIPs interfere with the propagation and spread of infectious standard virus (STV), reduce virus yields by competing for viral and cellular resources, and induce antiviral responses. These properties open exciting possibilities for the development of DIP-based antivirals. Exploring options for cell culture-based DIP production, we have established a fully continuous cultivation process, where one bioreactor is used to grow cells that are fed to two bioreactors operated in parallel for virus production. This system allows head-to-head comparisons of STV and DIP replication dynamics over extended time periods. Cultivations were performed at two residence times (RT, 22 and 36 h) using MDCK suspension cells grown in a fully defined medium. For infection, we used a virus seed generated by reverse genetics containing STVs and a known DIP carrying a deletion in segment 1 (delS1(1)). Four days post infection, DIPs achieved maximum concentrations of 7.0·109 virions/mL and 8.4·109 virions/mL for RTs of 22 and 36 h, respectively. Furthermore, oscillations in virus titers with two to three maxima were found for DIP accumulation at 36 and 22 h RT, respectively. To complement the study, a basic mathematical model using simple kinetics and a reasonable number of parameters to describe DIP-propagation in continuous cultures was established. Upon fitting the model individually to each of the two data sets, oscillations in the viral dynamics and the cell population dynamics were described well. Modeling suggests that both STV inactivation and virus degradation have to be taken into account to achieve good agreement of simulations and experimental data for longer RTs. Together, the high DIP titers obtained, and the successful simulation of the experimental data showed that the combination of continuous bioreactors and mathematical models can enable studies regarding DIP dynamics over extended time periods and allow large scale manufacturing of DIP-based antivirals.
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Affiliation(s)
- Felipe Tapia
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Tanja Laske
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Milena A Wasik
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Rammhold
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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