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Toustou C, Boulogne I, Gonzalez AA, Bardor M. Comparative RNA-Seq of Ten Phaeodactylum tricornutum Accessions: Unravelling Criteria for Robust Strain Selection from a Bioproduction Point of View. Mar Drugs 2024; 22:353. [PMID: 39195469 DOI: 10.3390/md22080353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
The production of biologics in mammalian cells is hindered by some limitations including high production costs, prompting the exploration of other alternative expression systems that are cheaper and sustainable like microalgae. Successful productions of biologics such as monoclonal antibodies have already been demonstrated in the diatom Phaeodactylum tricornutum; however, limited production yields still remain compared to mammalian cells. Therefore, efforts are needed to make this microalga more competitive as a cell biofactory. Among the seventeen reported accessions of P. tricornutum, ten have been mainly studied so far. Among them, some have already been used to produce high-value-added molecules such as biologics. The use of "omics" is increasingly being described as useful for the improvement of both upstream and downstream steps in bioprocesses using mammalian cells. Therefore, in this context, we performed an RNA-Seq analysis of the ten most used P. tricornutum accessions (Pt1 to Pt10) and deciphered the differential gene expression in pathways that could affect bioproduction of biologics in P. tricornutum. Our results highlighted the benefits of certain accessions such as Pt9 or Pt4 for the production of biologics. Indeed, these accessions seem to be more advantageous. Moreover, these results contribute to a better understanding of the molecular and cellular biology of P. tricornutum.
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Affiliation(s)
- Charlotte Toustou
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Isabelle Boulogne
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Anne-Alicia Gonzalez
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Muriel Bardor
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
- ALGA BIOLOGICS, CURIB, 25 rue Tesnières, 76821 Mont-Saint-Aignan, France
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Vitharana S, Stillahn JM, Katayama DS, Henry CS, Manning MC. Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics. J Pharm Sci 2023; 112:2724-2751. [PMID: 37572779 DOI: 10.1016/j.xphs.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.
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Affiliation(s)
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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Jin X, He B. Combination of On-Line and Off-Line Two-Dimensional Liquid Chromatography-Mass Spectrometry for Comprehensive Characterization of mAb Charge Variants and Precise Instructions for Rapid Process Development. Int J Mol Sci 2023; 24:15184. [PMID: 37894864 PMCID: PMC10607358 DOI: 10.3390/ijms242015184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Charge variants, as an important quality attribute of mAbs, must be comprehensively characterized and monitored during development. However, due to their complex structure, the characterization of charge variants is challenging, labor-intensive, and time-consuming when using traditional approaches. This work combines on-line and off-line 2D-LC-MS to comprehensively characterize mAb charge variants and quickly offer precise instructions for process development. Six charge variant peaks of mAb 1 were identified using the developed platform. Off-line 2D-LC-MS analysis at the peptide level showed that the acidic peak P1 and the basic peaks P4 and P5 were caused by the deamidation of asparagine, the oxidation of methionine, and incomplete C-terminal K loss, respectively. On-line 2D-LC-MS at the intact protein level was used to identify the root causes, and it was found that the acidic peak P2 and the basic peak P6 were due to the glutathionylation of cysteine and succinimidation of aspartic acid, respectively, which were not found in off-line 2D-LC-MS because of the loss occurring during pre-treatment. These results suggest that process development could focus on cell culture for adjustment of glutathionylation. In this paper, we propose the concept of precision process development based on on-line 2D-LC-MS, which could quickly offer useful data with only 0.6 mg mAb within 6 h for precise instructions for process development. Overall, the combination of on-line and off-line 2D-LC-MS can characterize mAb charge variants more comprehensively, precisely, and quickly than other approaches. This is a very effective platform with routine operations that provides precise instructions for process development within hours, and will help to accelerate the development of innovative therapeutics.
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Affiliation(s)
- Xiaoqing Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, China
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Krumm TL, Ehsani A, Schaub J, Stiefel F. An Investigation into the Metabolic Differences between Conventional and High Seeding Density Fed-Batch Cell Cultures by Applying a Segmented Modeling Approach. Processes (Basel) 2023. [DOI: 10.3390/pr11041094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
The conventional fed-batch process characterized by a low titer currently challenges pharmaceutical development. Process optimization by applying a perfusion process in the pre-stage and subsequent production phase at a high seeding density (HSD) can meet this challenge. In this study, we employed a simplified approach based on measured experiments, namely segmented modeling, to systematically analyze an HSD fed-batch process compared to a standard process. A comparison indicated that the metabolic phases of HSD processes are not only shifted in time, but metabolite trends show an altered metabolism. In an extended study, we integrated the intracellular fluxes determined by a metabolic flux analysis into the segmented modeling approach. Compared to using only extracellular rates, similar phases are identified, and this highlights the reliability of phase identification modeling using extracellular rates only. Furthermore, the segmented linear regression approach is used to create a model that describes cellular behavior and that can be used to predict potential improvements in the feeding strategy and in harvest viability. Here, overfeeding was eliminated and a significantly higher titer was achieved. This work provides insights into the overall metabolic changes in the HSD process and paves the way towards the optimization of the feeding regime.
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Affiliation(s)
- Teresa Laura Krumm
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Alireza Ehsani
- Boehringer Ingelheim Pharma GmbH & Co.KG, Biopharmaceuticals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Jochen Schaub
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Fabian Stiefel
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
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Brunner M, Kolb K, Keitel A, Stiefel F, Wucherpfennig T, Bechmann J, Unsoeld A, Schaub J. Application of metabolic modeling for targeted optimization of high seeding density processes. Biotechnol Bioeng 2021; 118:1793-1804. [PMID: 33491766 PMCID: PMC8248150 DOI: 10.1002/bit.27693] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 01/09/2023]
Abstract
Process intensification by application of perfusion mode in pre‐stage bioreactors and subsequent inoculation of cell cultures at high seeding densities (HSD) has the potential to meet the increasing requirements of future manufacturing demands. However, process development is currently restrained by a limited understanding of the cell's requirements under these process conditions. The goal of this study was to use extended metabolite analysis and metabolic modeling for targeted optimization of HSD cultivations. The metabolite analysis of HSD N‐stage cultures revealed accumulation of inhibiting metabolites early in the process and flux balance analysis led to the assumption that reactive oxygen species (ROS) were contributing to the fast decrease in cell viability. Based on the metabolic analysis an optimized feeding strategy with lactate and cysteine supplementation was applied, resulting in an increase in antibody titer of up to 47%. Flux balance analysis was further used to elucidate the surprisingly strong synergistic effect of lactate and cysteine, indicating that increased lactate uptake led to reduced ROS formation under these conditions whilst additional cysteine actively reduced ROS via the glutathione pathway. The presented results finally demonstrate the benefit of modeling approaches for process intensification as well as the potential of HSD cultivations for biopharmaceutical manufacturing.
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Affiliation(s)
- Matthias Brunner
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Klara Kolb
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Alena Keitel
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Fabian Stiefel
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Wucherpfennig
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan Bechmann
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Andreas Unsoeld
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jochen Schaub
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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Prade E, Zeck A, Stiefel F, Unsoeld A, Mentrup D, Arango Gutierrez E, Gorr IH. Cysteine in cell culture media induces acidic IgG1 species by disrupting the disulfide bond network. Biotechnol Bioeng 2020; 118:1091-1104. [PMID: 33200817 PMCID: PMC7986432 DOI: 10.1002/bit.27628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/29/2020] [Accepted: 11/11/2020] [Indexed: 01/16/2023]
Abstract
A high degree of charge heterogeneity is an unfavorable phenomenon commonly observed for therapeutic monoclonal antibodies (mAbs). Removal of these impurities during manufacturing often comes at the cost of impaired step yields. A wide spectrum of posttranslational and chemical modifications is known to modify mAb charge. However, a deeper understanding of underlying mechanisms triggering charged species would be beneficial for the control of mAb charge variants during bioprocessing. In this study, a comprehensive analytical investigation was carried out to define the root causes and mechanisms inducing acidic variants of an immunoglobulin G1‐derived mAb. Characterization of differently charged species by liquid chromatography–mass spectrometry revealed the reduction of disulfide bonds in acidic variants, which is followed by cysteinylation and glutathionylation of cysteines. Importantly, biophysical stability and integrity of the mAb are not affected. By in vitro incubation of the mAb with the reducing agent cysteine, disulfide bond degradation was directly linked to an increase of numerous acidic species. Modifying the concentrations of cysteine during the fermentation of various mAbs illustrated that redox potential is a critical aspect to consider during bioprocess development with respect to charge variant control.
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Affiliation(s)
- Elke Prade
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anne Zeck
- Pharma and Biotech, NMI Natural and Medical Sciences Institute, University of Tübingen, Reutlingen, Germany
| | - Fabian Stiefel
- Late Stage USP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Andreas Unsoeld
- Late Stage USP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Mentrup
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Erik Arango Gutierrez
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ingo H Gorr
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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