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Desmurget C, Perilleux A, Souquet J, Borth N, Douet J. Molecular biomarkers identification and applications in CHO bioprocessing. J Biotechnol 2024:S0168-1656(24)00164-0. [PMID: 38852681 DOI: 10.1016/j.jbiotec.2024.06.005] [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: 12/18/2023] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Biomarkers are valuable tools in clinical research where they allow to predict susceptibility to diseases, or response to specific treatments. Likewise, biomarkers can be extremely useful in the biomanufacturing of therapeutic proteins. Indeed, constraints such as short timelines and the need to find hyper-productive cells could benefit from a data-driven approach during cell line and process development. Many companies still rely on large screening capacities to develop productive cell lines, but as they reach a limit of production, there is a need to go from empirical to rationale procedures. Similarly, during bioprocessing runs, substrate consumption and metabolism wastes are commonly monitored. None of them possess the ability to predict the culture behavior in the bioreactor. Big data driven approaches are being adapted to the study of industrial mammalian cell lines, enabled by the publication of Chinese hamster and CHO genome assemblies which allowed the use of next-generation sequencing with these cells, as well as continuous proteome and metabolome annotation. However, if these different -omics technologies contributed to the characterization of CHO cells, there is a significant effort remaining to apply this knowledge to biomanufacturing methods. The correlation of a complex phenotype such as high productivity or rapid growth to the presence or expression level of a specific biomarker could save time and effort in the screening of manufacturing cell lines or culture conditions. In this review we will first discuss the different biological molecules that can be identified and quantified in cells, their detection techniques, and associated challenges. We will then review how these markers are used during the different steps of cell line and bioprocess development, and the inherent limitations of this strategy.
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Affiliation(s)
- Caroline Desmurget
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Arnaud Perilleux
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Jonathan Souquet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julien Douet
- Merck Biotech Development Center, Ares Trading SA (an affiliate of Merck KGaA, Darmstadt, Germany), Fenil-sur-Corsier, Switzerland.
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2
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Banerjee S, Daetwyler S, Bai X, Michaud M, Jouhet J, Madhugiri S, Johnson E, Wang CW, Fiolka R, Toulmay A, Prinz WA. The Vps13-like protein BLTP2 is pro-survival and regulates phosphatidylethanolamine levels in the plasma membrane to maintain its fluidity and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578804. [PMID: 38370643 PMCID: PMC10871178 DOI: 10.1101/2024.02.04.578804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lipid transport proteins (LTPs) facilitate nonvesicular lipid exchange between cellular compartments and have critical roles in lipid homeostasis1. A new family of bridge-like LTPs (BLTPs) is thought to form lipid-transporting conduits between organelles2. One, BLTP2, is conserved across species but its function is not known. Here, we show that BLTP2 and its homolog directly regulate plasma membrane (PM) fluidity by increasing the phosphatidylethanolamine (PE) level in the PM. BLTP2 localizes to endoplasmic reticulum (ER)-PM contact sites34, 5, suggesting it transports PE from the ER to the PM. We find BLTP2 works in parallel with another pathway that regulates intracellular PE distribution and PM fluidity6, 7. BLTP2 expression correlates with breast cancer aggressiveness8-10. We found BLTP2 facilitates growth of a human cancer cell line and sustains its aggressiveness in an in vivo model of metastasis, suggesting maintenance of PM fluidity by BLTP2 may be critical for tumorigenesis in humans.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofei Bai
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Juliette Jouhet
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Shruthi Madhugiri
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emma Johnson
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao-Wen Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexandre Toulmay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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3
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Need for more focus on lipid species in studies of biological and model membranes. Prog Lipid Res 2022; 86:101160. [DOI: 10.1016/j.plipres.2022.101160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/06/2022] [Indexed: 11/23/2022]
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4
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Rems L, Tang X, Zhao F, Pérez-Conesa S, Testa I, Delemotte L. Identification of electroporation sites in the complex lipid organization of the plasma membrane. eLife 2022; 11:e74773. [PMID: 35195069 PMCID: PMC8912918 DOI: 10.7554/elife.74773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon termed electroporation is already utilized in many rapidly developing applications in medicine including gene therapy, cancer treatment, and treatment of cardiac arrhythmias. However, the molecular mechanisms of electroporation are not yet sufficiently well understood; in particular, it is unclear where exactly pores form in the complex organization of the plasma membrane. In this study, we combine coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis to identify how formation of pores depends on the local lipid organization. We show that pores do not form homogeneously across the membrane, but colocalize with domains that have specific features, the most important being high density of polyunsaturated lipids. We further show that knowing the lipid organization is sufficient to reliably predict poration sites with machine learning. Additionally, by analysing poration kinetics with Bayesian survival analysis we show that poration does not depend solely on local lipid arrangement, but also on membrane mechanical properties and the polarity of the electric field. Finally, we discuss how the combination of atomistic and coarse-grained molecular dynamics simulations, machine learning methods, and Bayesian survival analysis can guide the design of future experiments and help us to develop an accurate description of plasma membrane electroporation on the whole-cell level. Achieving this will allow us to shift the optimization of electroporation applications from blind trial-and-error approaches to mechanistic-driven design.
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Affiliation(s)
- Lea Rems
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Ljubljana, Faculty of Electrical EngineeringLjubljanaSlovenia
| | - Xinru Tang
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Fangwei Zhao
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
- University of Chinese Academy of SciencesBeijingChina
| | - Sergio Pérez-Conesa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Ilaria Testa
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
| | - Lucie Delemotte
- KTH Royal Institute of Technology, Dept. Applied Physics, Science for Life LaboratorySolnaSweden
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5
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Nikyar A, Bolhassani A, Rouhollah F, Heshmati M. In Vitro Delivery of HIV-1 Nef-Vpr DNA Construct Using the Human Antimicrobial Peptide LL-37. Curr Drug Deliv 2022; 19:1083-1092. [PMID: 35176981 DOI: 10.2174/1567201819666220217164055] [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: 07/25/2021] [Revised: 11/05/2021] [Accepted: 01/02/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND OBJECTIVES DNA-based therapeutic vaccines have been proposed as promising strategy for treatment of established HIV infections. However, these vaccines are often associated with certain shortcomings, such as poor immunogenicity and low transfection efficiency. In this study, we investigated ability of LL-37 to deliver a potential immunogenic fusion construct comprising HIV-1 nef and vpr genes into a mammalian cell line. METHODS First, the pEGFP-N1 eukaryotic expression vector harboring the HIV-1 nef-vpr fusion was produced free of endotoxin on large scale. Then, DNA/LL-37 complexes were prepared by co-incubation of pEGFP-nef-vpr with LL-37 for 45 minutes at different nitrogen to phosphate (N/P) ratios. Formation of DNA/peptide complexes was investigated by gel retardation assay. Next, stability and morphological characteristics of the nanoparticles were evaluated. Toxicity of LL-37 and the nanoparticles in HEK-293T cells was assessed by MTT assay. Transfection efficiency of the DNA/LL-37 complexes was studied by fluorescence microscopy, flow cytometry, and western blot analysis. RESULTS LL-37 formed stable complexes with pEGFP-nef-vpr (diameter of 150-200 nm) while providing good protection against nucleolytic and proteolytic degradation. The peptide significantly affected cell viability even at low concentrations. However, the LL-37/DNA complexes had no significant cytotoxic effect. Treatment of cells with pEGFP-N1/LL-37 and pEGFP-nef-vpr/LL-37 resulted in transfection of 36.32% ± 1.13 and 25.55% ± 2.07 of cells, respectively. CONCLUSION Given these findings and the important immunomodulatory and antiviral activities of LL-37, the use of this peptide can be further exploited in the development of novel gene delivery strategies and vaccine design.
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Affiliation(s)
- Arash Nikyar
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDs, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rouhollah
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Masoumeh Heshmati
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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6
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Casey AB, Mukherjee M, McGlynn RP, Cui M, Kohut SJ, Booth RG. A new class of serotonin 5-HT 2A /5-HT 2C receptor inverse agonists: Synthesis, molecular modeling, in vitro and in vivo pharmacology of novel 2-aminotetralins. Br J Pharmacol 2021; 179:2610-2630. [PMID: 34837227 DOI: 10.1111/bph.15756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE The 5-HT receptor (5-HTR) subtypes 5-HT2A and 5-HT2C are important neurotherapeutic targets, though, obtaining selectivity over 5-HT2B and closely related histamine H1 Rs is challenging. Here, we delineated molecular determinants of selective binding to 5-HT2A and 5-HT2C Rs for novel 4-phenyl-2-dimethylaminotetralins (4-PATs). EXPERIMENTAL APPROACH We synthesized 42 novel 4-PATs with halogen or aryl moieties at the C(4)-phenyl meta position. Affinity, function, molecular modeling, and 5-HT2A R mutagenesis studies were undertaken to understand structure-activity relationships at 5-HT2 -type and H1 Rs. Lead 4-PAT-type selective 5-HT2A /5-HT2C R inverse agonists were compared to pimavanserin, a selective 5-HT2A /5-HT2C R inverse agonist approved to treat psychoses, in the mouse head twitch response, and locomotor activity assays, as models relevant to antipsychotic drug development. KEY RESULTS Most 4-PAT diastereomers in the (2S,4R)-configuration bound non-selectively to 5-HT2A , 5-HT2C, and H1 Rs, with >100-fold selectivity over 5-HT2B Rs, whereas, diastereomers in the (2R,4R)-configuration bound preferentially to 5-HT2A over 5-HT2C Rs and had >100-fold selectivity over 5-HT2B and H1 Rs. Results suggest that G2385.42 and V2355.39 in 5-HT2A Rs (conserved in 5-HT2C Rs) are important for high affinity binding, whereas, interactions with T1945.42 and W1584.56 determine H1 R affinity. The 4-PAT (2S,4R)-2k, a potent and selective 5-HT2A /5-HT2C R inverse agonist, had activity like pimavanserin in the mouse head-twitch response assay, but was distinct in not suppressing locomotor activity. CONCLUSIONS AND IMPLICATIONS We provide evidence that the novel 4-PAT chemotype can yield selective 5-HT2A /5-HT2C R inverse agonists for antipsychotic drug development by optimizing ligand-receptor interactions in transmembrane domain 5. We also show that chirality can be exploited to attain selectivity over H1 Rs which may circumvent sedative effects.
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Affiliation(s)
- Austen B Casey
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, United States
| | - Munmun Mukherjee
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, United States
| | - Ryan P McGlynn
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, United States
| | - Meng Cui
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States
| | - Stephen J Kohut
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States.,Behavioral Neuroimaging Laboratory, McLean Hospital and Department of Psychiatry, Harvard Medical School, Belmont, Massachusetts, United States
| | - Raymond G Booth
- Center for Drug Discovery, Northeastern University, Boston, Massachusetts, United States.,Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States.,Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, United States
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7
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Ikhlef S, Lipp NF, Delfosse V, Fuggetta N, Bourguet W, Magdeleine M, Drin G. Functional analyses of phosphatidylserine/PI(4)P exchangers with diverse lipid species and membrane contexts reveal unanticipated rules on lipid transfer. BMC Biol 2021; 19:248. [PMID: 34801011 PMCID: PMC8606082 DOI: 10.1186/s12915-021-01183-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/04/2021] [Indexed: 11/14/2022] Open
Abstract
Background Lipid species are accurately distributed in the eukaryotic cell so that organelle and plasma membranes have an adequate lipid composition to support numerous cellular functions. In the plasma membrane, a precise regulation of the level of lipids such as phosphatidylserine, PI(4)P, and PI(4,5)P2, is critical for maintaining the signaling competence of the cell. Several lipid transfer proteins of the ORP/Osh family contribute to this fine-tuning by delivering PS, synthesized in the endoplasmic reticulum, to the plasma membrane in exchange for PI(4)P. To get insights into the role of these PS/PI(4)P exchangers in regulating plasma membrane features, we question how they selectively recognize and transfer lipid ligands with different acyl chains, whether these proteins exchange PS exclusively for PI(4)P or additionally for PI(4,5)P2, and how sterol abundance in the plasma membrane impacts their activity. Results We measured in vitro how the yeast Osh6p and human ORP8 transported PS and PI(4)P subspecies of diverse length and unsaturation degree between membranes by fluorescence-based assays. We established that the exchange activity of Osh6p and ORP8 strongly depends on whether these ligands are saturated or not, and is high with representative cellular PS and PI(4)P subspecies. Unexpectedly, we found that the speed at which these proteins individually transfer lipid ligands between membranes is inversely related to their affinity for them and that high-affinity ligands must be exchanged to be transferred more rapidly. Next we determined that Osh6p and ORP8 cannot use PI(4,5)P2 for exchange processes, because it is a low-affinity ligand, and do not transfer more PS into sterol-rich membranes. Conclusions Our study provides new insights into PS/PI(4)P exchangers by indicating the degree to which they can regulate the acyl chain composition of the PM, and how they control PM phosphoinositide levels. Moreover, we establish general rules on how the activity of lipid transfer proteins relates to their affinity for ligands. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01183-1.
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Affiliation(s)
- Souade Ikhlef
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560, Valbonne, France
| | - Nicolas-Frédéric Lipp
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560, Valbonne, France.,Current position: Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Vanessa Delfosse
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Nicolas Fuggetta
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560, Valbonne, France
| | - William Bourguet
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Maud Magdeleine
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560, Valbonne, France
| | - Guillaume Drin
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560, Valbonne, France.
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8
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Samoudi M, Masson HO, Kuo CC, Robinson CM, Lewis NE. From omics to Cellular mechanisms in mammalian cell factory development. Curr Opin Chem Eng 2021; 32:100688. [PMID: 37475722 PMCID: PMC10357924 DOI: 10.1016/j.coche.2021.100688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mammalian cells have been used widely as biopharmaceutical cell factories due to their ability to make complex biotherapeutic proteins with human-compatible modifications. However, their application for some products has been hampered by low protein yields. Numerous studies have aimed to characterize cellular bottlenecks in the hope of boosting protein productivity, but the complexity of the underlying pathways and the diversity of the modifications have complicated cell engineering when relying solely on traditional methodologies. Incorporating omics-based and systems approaches into cell engineering can provide valuable insights into desirable phenotypes of cell factories. Here, we discuss cell engineering strategies for enhancing protein productivity in mammalian cell factories, particularly CHO and HEK293, and the opportunities and limitations of the genome-wide screening and multi-omics approaches for guiding cell engineering. Systems biology strategies will also be discussed to show how they refine our understanding of the cellular mechanisms which will aid in effective engineering strategies.
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Affiliation(s)
- Mojtaba Samoudi
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Helen O. Masson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Chih-Chung Kuo
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Caressa M Robinson
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- National Biologics Facility, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Pulix M, Lukashchuk V, Smith DC, Dickson AJ. Molecular characterization of HEK293 cells as emerging versatile cell factories. Curr Opin Biotechnol 2021; 71:18-24. [PMID: 34058525 DOI: 10.1016/j.copbio.2021.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 01/27/2023]
Abstract
HEK293 cell lines are used for the production of recombinant proteins, virus-like particles and viral vectors. Recent work has generated molecular (systems level) characterisation of HEK293 variants that has enabled re-engineering of the cells towards enhanced use for manufacture-scale production of recombinant biopharmaceuticals (assessment of 'safe harbours' for gene insertion, engineering of new variants for stable, amplifiable expression). In parallel, there have been notable advances in the bioprocessing conditions (suspension adaptation, development of defined serum-free media) that offer the potential for large-scale manufacture, a feature especially important in the drive to produce viral vectors at large-scale and at commercially viable costs for gene therapy. The combination of cell-based and bioprocess-based modification of existing HEK293 cell processes, frequently informed by understandings transferred from developments with Chinese hamster ovary cell lines, seems destined to place the HEK293 cell systems firmly as a critical platform for production of future biologically based therapeutics.
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Affiliation(s)
- Michela Pulix
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, Department of Chemical Engineering & Analytical Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Cobra Biologics, Stephenson Building, Keele Science Park, Keele ST5 5SP, UK
| | - Vera Lukashchuk
- Cobra Biologics, Stephenson Building, Keele Science Park, Keele ST5 5SP, UK
| | - Daniel C Smith
- Cobra Biologics, Stephenson Building, Keele Science Park, Keele ST5 5SP, UK
| | - Alan J Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, Department of Chemical Engineering & Analytical Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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10
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Cebolla VL, Jarne C, Vela J, Garriga R, Membrado L, Galbán J. Scanning densitometry and mass spectrometry for HPTLC analysis of lipids: The last 10 years. J LIQ CHROMATOGR R T 2021. [DOI: 10.1080/10826076.2020.1866600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Carmen Jarne
- Instituto de Carboquímica, ICB-CSIC, Zaragoza, Spain
| | - Jesús Vela
- Departamento de Química Analítica, EINA, Universidad de Zaragoza, Zaragoza, Spain
| | - Rosa Garriga
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Luis Membrado
- Instituto de Carboquímica, ICB-CSIC, Zaragoza, Spain
| | - Javier Galbán
- Departamento de Química Analítica, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
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11
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Krokidis MG, Louka M, Efthimiadou EK, Ferreri C, Chatgilialoglu C. Fatty Acid Remodeling of Membrane Glycerophospholipids Induced by Bleomycin and Iron Oxide Nanoparticles in Human Embryonic Kidney Cells. Chem Res Toxicol 2020; 33:2565-2572. [PMID: 32865980 DOI: 10.1021/acs.chemrestox.0c00162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bleomycin has a long-studied mechanism of action through the formation of a complex with metals, such as iron. The bleomycin-iron complex was recently shown to induce membrane damage by free radical reactivity. Because the use of Fe nanoparticles is spreading for drug delivery strategies, molecular mechanisms of cell damage must include different compartments in order to observe the progression of the cell reactivity. In this study, human embryonic kidney (HEK-293) cells were exposed for 24 h to bleomycin and polymeric iron oxide nanoparticles (Fe-NPs), alone or in combination. The fatty acid-based membrane lipidomic analysis evidenced the fatty acid remodeling in response to the treatments. Bleomycin alone caused the increase of saturated fatty acid (SFA) moieties in cell membrane glycerophospholipids with concomitant diminution of monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acid levels. Under Fe-NPs treatment, omega-6 PUFA decreased and trans fatty acid isomers increased. Under coadministration bleomycin and Fe-NPs, all membrane remodeling changes disappeared compared to those of the controls, with only an increase of omega-6 PUFA that elevates peroxidation index remaining. Our results highlight the important role of fatty-acid-based membrane lipidome monitoring to follow up the fatty acid reorganization induced by the drug, to be considered as a side effect of the pharmacological activity, suggesting the need of an integrated approach for the investigation of drug and carrier molecular mechanisms.
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Affiliation(s)
- Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece
| | - Maria Louka
- Lipidomics Laboratory, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Eleni K Efthimiadou
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece.,Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Carla Ferreri
- Lipidomics Laboratory, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy.,ISOF, Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Lipidomics Laboratory, Lipinutragen Srl, Via Piero Gobetti 101, 40129 Bologna, Italy.,ISOF, Consiglio Nazionale delle Ricerche, Via Piero Gobetti 101, 40129 Bologna, Italy.,Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
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12
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Széliová D, Ruckerbauer DE, Galleguillos SN, Petersen LB, Natter K, Hanscho M, Troyer C, Causon T, Schoeny H, Christensen HB, Lee DY, Lewis NE, Koellensperger G, Hann S, Nielsen LK, Borth N, Zanghellini J. What CHO is made of: Variations in the biomass composition of Chinese hamster ovary cell lines. Metab Eng 2020; 61:288-300. [DOI: 10.1016/j.ymben.2020.06.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Kovtun O, Torres R, Ferguson RS, Josephs T, Rosenthal SJ. Single Quantum Dot Tracking Unravels Agonist Effects on the Dopamine Receptor Dynamics. Biochemistry 2020; 60:1031-1043. [PMID: 32584548 DOI: 10.1021/acs.biochem.0c00360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
D2 dopamine receptors (DRD2s) belong to a family of G protein-coupled receptors that modulate synaptic dopaminergic tone via regulation of dopamine synthesis, storage, and synaptic release. DRD2s are the primary target for traditional antipsychotic medications; dysfunctional DRD2 signaling has been linked to major depressive disorder, attention-deficit hyperactivity disorder, addiction, Parkinson's, and schizophrenia. DRD2 lateral diffusion appears to be an important post-translational regulatory mechanism; however, the dynamic response of DRD2s to ligand-induced activation is poorly understood. Dynamic imaging of the long isoform of DRD2 (D2L) fused to an N-terminal antihemagglutinin (HA) epitope and transiently expressed in HEK-293 cells was achieved through a combination of a high-affinity biotinylated anti-HA antigen-binding fragment (Fab) and streptavidin-conjugated quantum dots (QD). Significant reduction (∼40%) in the rate of lateral diffusion of QD-tagged D2L proteins was observed under agonist (quinpirole; QN)-stimulated conditions compared to basal conditions. QN-induced diffusional slowing was accompanied by an increase in frequency, lifetime, and confinement of temporary arrest of lateral diffusion (TALL), an intrinsic property of single receptor lateral motion. The role of the actin cytoskeleton in QN-induced diffusional slowing of D2L was also explored. The observed dynamic changes appear to be a sensitive indicator of the receptor activity status and might also spatially and temporally shape the receptor-mediated downstream signaling. This dynamic information could potentially be useful in informing drug discovery efforts based on single-molecule pharmacology.
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Affiliation(s)
- Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Ruben Torres
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Riley S Ferguson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Travis Josephs
- Neuroscience Program, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Sandra J Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37240, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
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14
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Yi DD, Wang XY, Zhang WL, Wang M, Zhang JH, Wang TY. Construction of an expression vector mediated by the dual promoter for prokaryotic and mammalian cell expression system. Mol Biol Rep 2020; 47:5185-5190. [PMID: 32564228 DOI: 10.1007/s11033-020-05593-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022]
Abstract
The aim of this study was to construct an expression vector mediated by the dual promoter that can simultaneously drive the recombinant protein production in eukaryotic and prokaryotic cells. The prokaryotic T7 promoter and ribosome binding site (RBS) was cloned downstream of CMV promoter in the eukaryotic expression vector pIRES-neo, and T7 termination sequence was inserted upstream of neomycin phosphotransferase gene to generate the dual promoter vector. The enhanced green fluorescent protein (eGFP) gene was used as reporter gene. Then, the resultant vector was transfected into Chinese hamster ovary (CHO) cells and transformed into Escherichia coli (E. coli) BL21, and the eGFP expression levels were analyzed by fluorescence microscopy, flow cytometry and Western blot, respectively. Fluorescence microscopy revealed that the eGFP was expressed in both CHO cells and E. coli BL21. Flow cytometry showed that the eGFP expression level had no significant difference between the dual promoter vector and control vector in transfected CHO cells. Western blot analysis indicated the eGFP expressed in transformed E. coli. In conclusion, a prokaryotic-eukaryotic double expression vector was successfully constructed, which has potential applications in rapid cloning and expression of recombinant proteins in both prokaryotic and eukaryotic expression systems.
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Affiliation(s)
- Dan-Dan Yi
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Wei-Li Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Meng Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Jun-He Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Jinsui Road, Xinxiang, 453003, Henan, China.
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
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15
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Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc Natl Acad Sci U S A 2020; 117:1788-1798. [PMID: 31911476 PMCID: PMC6983364 DOI: 10.1073/pnas.1906823117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The lipid dependence of the nicotinic acetylcholine receptor from the Torpedo electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity. More recently, it has been suggested that the bacterial homolog ELIC (Erwinia chrysanthemi ligand-gated ion channel) has a similar lipid sensitivity. As a first step toward the elucidation of the structural basis of this phenomenon, we solved the structures of ELIC embedded in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoelectron microscopy. Comparison of the two structural models revealed that the largest differences occur at the level of loop C-at the agonist-binding sites-and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). On the other hand, the transmembrane pore is occluded in a remarkably similar manner in both structures. A straightforward interpretation of these findings is that POPC-only membranes frustrate the ECD-TMD coupling in such a way that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker but fails to penetrate the membrane and propagate into the TMD. Furthermore, analysis of the structural models and molecular simulations suggested that the higher affinity for agonists characteristic of the open- and desensitized-channel conformations results, at least in part, from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent.
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16
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Széliová D, Schoeny H, Knez Š, Troyer C, Coman C, Rampler E, Koellensperger G, Ahrends R, Hann S, Borth N, Zanghellini J, Ruckerbauer DE. Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells. Methods Mol Biol 2020; 2088:119-160. [PMID: 31893373 DOI: 10.1007/978-1-0716-0159-4_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biomass composition is an important input for genome-scale metabolic models and has a big impact on their predictive capabilities. However, researchers often rely on generic data for biomass composition, e.g. collected from similar organisms. This leads to inaccurate predictions, because biomass composition varies between different cell lines, conditions, and growth phases. In this chapter we present protocols for the determination of the biomass composition of Chinese Hamster Ovary (CHO) cells. These methods can easily be adapted to other types of mammalian cells. The protocols include the quantification of cell dry mass and of the main biomass components, namely protein, lipid, DNA, RNA, and carbohydrates. Cell dry mass is determined gravimetrically by weighing a defined number of cells. Amino acid composition and protein content are measured by gas chromatography mass spectrometry. Lipids are quantified by shotgun mass spectrometry, which provides quantities for the different lipid classes and also the distribution of fatty acids. RNA is purified and then quantified spectrophotometrically. The methods for DNA and carbohydrates are simple fluorometric and colorimetric assays adapted to a 96-well plate format. To ensure quantitative results, internal standards or spike-in controls are used in all methods, e.g. to account for possible matrix effects or loss of material. Finally, the last section provides a guide on how to convert the measured data into biomass equations, which can then be integrated into a metabolic model.
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Affiliation(s)
- Diana Széliová
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Špela Knez
- University of Ljubljana, Ljubljana, Slovenia
| | - Christina Troyer
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cristina Coman
- Leibniz Institut für Analytische Wissenschaften - e.V., Dortmund, Germany
| | | | | | - Robert Ahrends
- Leibniz Institut für Analytische Wissenschaften - e.V., Dortmund, Germany
| | - Stephen Hann
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jürgen Zanghellini
- University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Biotech University of Applied Sciences, Tulln, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - David E Ruckerbauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.
- University of Natural Resources and Life Sciences, Vienna, Austria.
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17
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Budge JD, Knight TJ, Povey J, Roobol J, Brown IR, Singh G, Dean A, Turner S, Jaques CM, Young RJ, Racher AJ, Smales CM. Engineering of Chinese hamster ovary cell lipid metabolism results in an expanded ER and enhanced recombinant biotherapeutic protein production. Metab Eng 2020; 57:203-216. [PMID: 31805379 PMCID: PMC6975165 DOI: 10.1016/j.ymben.2019.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/18/2019] [Accepted: 11/23/2019] [Indexed: 01/02/2023]
Abstract
Chinese hamster ovary (CHO) cell expression systems have been exquisitely developed for the production of recombinant biotherapeutics (e.g. standard monoclonal antibodies, mAbs) and are able to generate efficacious, multi-domain proteins with human-like post translational modifications at high concentration with appropriate product quality attributes. However, there remains a need for development of new CHO cell expression systems able to produce more challenging secretory recombinant biotherapeutics at higher yield with improved product quality attributes. Amazingly, the engineering of lipid metabolism to enhance such properties has not been investigated even though the biosynthesis of recombinant proteins is at least partially controlled by cellular processes that are highly dependent on lipid metabolism. Here we show that the global transcriptional activator of genes involved in lipid biosynthesis, sterol regulatory element binding factor 1 (SREBF1), and stearoyl CoA desaturase 1 (SCD1), an enzyme which catalyzes the conversion of saturated fatty acids into monounsaturated fatty acids, can be overexpressed in CHO cells to different degrees. The amount of overexpression obtained of each of these lipid metabolism modifying (LMM) genes was related to the subsequent phenotypes observed. Expression of a number of model secretory biopharmaceuticals was enhanced between 1.5-9 fold in either SREBF1 or SCD1 engineered CHO host cells as assessed under batch and fed-batch culture. The SCD1 overexpressing polyclonal pool consistently showed increased concentration of a range of products. For the SREBF1 engineered cells, the level of SREBF1 expression that gave the greatest enhancement in yield was dependent upon the model protein tested. Overexpression of both SCD1 and SREBF1 modified the lipid profile of CHO cells and the cellular structure. Mechanistically, overexpression of SCD1 and SREBF1 resulted in an expanded endoplasmic reticulum (ER) that was dependent upon the level of LMM overexpression. We conclude that manipulation of lipid metabolism in CHO cells via genetic engineering is an exciting new approach to enhance the ability of CHO cells to produce a range of different types of secretory recombinant protein products via modulation of the cellular lipid profile and expansion of the ER.
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Affiliation(s)
- James D Budge
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Tanya J Knight
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Jane Povey
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Joanne Roobol
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Ian R Brown
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Gurdeep Singh
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Andrew Dean
- Lonza Biologics, 228 Bath Road, Slough, SL1 4DX, UK
| | - Sarah Turner
- Lonza Biologics, 228 Bath Road, Slough, SL1 4DX, UK
| | | | - Robert J Young
- Cell Engineering Group, Lonza Biologics, Granta Park, Cambridge, CB21 6GS, UK
| | | | - C Mark Smales
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
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18
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Yeo HC, Chen S, Ho YS, Lee DY. An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology. Metabolomics 2018; 14:98. [PMID: 30830409 DOI: 10.1007/s11306-018-1394-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/06/2018] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Given a raw LC-MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other 'omics' datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhaustive confirmatory analyses. In other cases, samples for validation may be difficult to obtain, replicate or maintain. Thus, it is critical that the computational identification of lipids is of appropriate accuracy, coverage, and unbiased by a researcher's experience and prior knowledge. OBJECTIVES We aim to prescribe a systematic framework for lipid identifications, without usage of their characteristic retention-time by fully exploiting their underlying mass features. RESULTS Initially, a hybrid technique, for deducing both common and distinctive daughter ions, is used to infer parent lipids from deconvoluted spectra. This is followed by parent confirmation using basic knowledge of their preferred product ions. Using the framework, we could achieve an accuracy of ~ 80% by correctly identified 101 species from 18 classes in Chinese hamster ovary (CHO) cells. The resulting inferences could explain the recombinant-producing capability of CHO-SH87 cells, compared to non-producing CHO-K1 cells. For comparison, a XCMS-based study of the same dataset, guided by a user's ad-hoc knowledge, identified less than 60 species of 12 classes from thousands of possibilities. CONCLUSION We describe a systematic LC-MS-based framework that identifies lipids for rapid hypothesis generation.
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Affiliation(s)
- Hock Chuan Yeo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore.
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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19
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Tamošaitis L, Smales CM. Meta-Analysis of Publicly Available Chinese Hamster Ovary (CHO) Cell Transcriptomic Datasets for Identifying Engineering Targets to Enhance Recombinant Protein Yields. Biotechnol J 2018; 13:e1800066. [DOI: 10.1002/biot.201800066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/23/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Linas Tamošaitis
- Industrial Biotechnology Centre and School of Biosciences; University of Kent; Canterbury Kent CT2 7NJ UK
| | - Christopher Mark Smales
- Industrial Biotechnology Centre and School of Biosciences; University of Kent; Canterbury Kent CT2 7NJ UK
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20
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A complicated complex: Ion channels, voltage sensing, cell membranes and peptide inhibitors. Neurosci Lett 2018; 679:35-47. [DOI: 10.1016/j.neulet.2018.04.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 01/04/2023]
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21
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Treyer A, Mateus A, Wiśniewski JR, Boriss H, Matsson P, Artursson P. Intracellular Drug Bioavailability: Effect of Neutral Lipids and Phospholipids. Mol Pharm 2018; 15:2224-2233. [DOI: 10.1021/acs.molpharmaceut.8b00064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andrea Treyer
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden
| | - André Mateus
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | - Pär Matsson
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala 75123, Sweden
- Science for Life Laboratory Drug Discovery and Development Platform (SciLifelab DDD-P), Uppsala 75123, Sweden
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala 75123, Sweden
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22
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Ali AS, Raju R, Ray S, Kshirsagar R, Gilbert A, Zang L, Karger BL. Lipidomics of CHO Cell Bioprocessing: Relation to Cell Growth and Specific Productivity of a Monoclonal Antibody. Biotechnol J 2018. [PMID: 29521466 DOI: 10.1002/biot.201700745] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As the demand for biological therapeutic proteins rises, there is an increasing need for robust and highly efficient bioprocesses, specifically, maximizing protein production by controlling the cellular nutritional and metabolic needs. A comprehensive lipidomics analysis has been performed, for the first time, over the time course of CHO cells producing an IgG1 monoclonal antibody (mAb) with fed batch 5 L bioreactors. The dynamic nature and importance of the CHO lipidome, especially on cellular growth and specific productivity, is demonstrated. A robust LC-MS method using positive and negative mode ESI was developed for lipid identification and quantitation of 377 unique lipids. The analysis revealed large changes in lipid features between the different days in bioprocessing including accumulation of triacylglycerol (TG) and lysophospholipid species with depletion of diacylglycerol (DG) species. Exploring pathway analysis where the lipid data was combined with polar metabolites and transcriptomics (RNA sequencing) revealed differences in lipid metabolism between the various stages of cellular growth and highlighted the role of key features of lipid metabolism on cell growth and specific productivity. The study demonstrates the importance of lipidomics in the expanding role of 'Omics methodologies in gaining insight into cellular behavior during protein production in a fed batch bioprocess.
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Affiliation(s)
- Amr S Ali
- Cell Culture Development, Biogen, Inc., Cambridge, MA 02142, USA.,Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Ravali Raju
- Cell Culture Development, Biogen, Inc., Cambridge, MA 02142, USA
| | - Somak Ray
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Alan Gilbert
- Cell Culture Development, Biogen, Inc., Cambridge, MA 02142, USA
| | - Li Zang
- Analytical Development, Biogen, Inc., Cambridge, MA 02142, USA
| | - Barry L Karger
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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23
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Stolfa G, Smonskey MT, Boniface R, Hachmann AB, Gulde P, Joshi AD, Pierce AP, Jacobia SJ, Campbell A. CHO-Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction. Biotechnol J 2017; 13:e1700227. [PMID: 29072373 DOI: 10.1002/biot.201700227] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 01/07/2023]
Abstract
CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.
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Affiliation(s)
- Gino Stolfa
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Ryan Boniface
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | | | - Paul Gulde
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Atul D Joshi
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Anson P Pierce
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Scott J Jacobia
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
| | - Andrew Campbell
- Bioproduction R&D, Thermo Fisher Scientific, Grand Island, USA
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24
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Heffner KM, Hizal DB, Yerganian GS, Kumar A, Can Ö, O’Meally R, Cole R, Chaerkady R, Wu H, Bowen MA, Betenbaugh MJ. Lessons from the Hamster: Cricetulus griseus Tissue and CHO Cell Line Proteome Comparison. J Proteome Res 2017; 16:3672-3687. [DOI: 10.1021/acs.jproteome.7b00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Amit Kumar
- Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Özge Can
- Acibadem University, Medical Biochemistry, Istanbul, Maltepe, Turkey
| | - Robert O’Meally
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | - Robert Cole
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | | | - Herren Wu
- MedImmune, Gaithersburg, Maryland 20878, United States
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