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Lu YA, McCann MG, Hu WS, Zhang Q. Multi-cell-line learning for the data-driven construction of mechanistic metabolic models. Biotechnol Bioeng 2024. [PMID: 38831695 DOI: 10.1002/bit.28757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/25/2024] [Accepted: 05/19/2024] [Indexed: 06/05/2024]
Abstract
Mammalian cells are commonly used as hosts in cell culture for biologics production in the pharmaceutical industry. Structured mechanistic models of metabolism have been used to capture complex cellular mechanisms that contribute to varying metabolic shifts in different cell lines. However, little research has focused on the impact of temporal changes in enzyme abundance and activity on the modeling of cell metabolism. In this work, we present a framework for constructing mechanistic models of metabolism that integrate growth-signaling control of enzyme activity and transcript dynamics. The proposed approach is applied to build models for three Chinese hamster ovary (CHO) cell lines using fed-batch culture data and time-series transcript profiles. Leveraging information from the transcriptome data, we develop a parameter estimation approach based on multi-cell-line (MCL) learning, which combines data sets from different cell lines and trains the individual cell-line models jointly to improve model accuracy. The computational results demonstrate the important role of growth signaling and transcript variability in metabolic models as well as the virtue of the MCL approach for constructing cell-line models with a limited amount of data. The resulting models exhibit a high level of accuracy in predicting distinct metabolic behaviors in the different cell lines; these models can potentially be used to accelerate the process and cell-line development for the biomanufacturing of new protein therapeutics.
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Affiliation(s)
- Yen-An Lu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Meghan G McCann
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qi Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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2
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Bokelmann C, Ehsani A, Schaub J, Stiefel F. Deciphering Metabolic Pathways in High-Seeding-Density Fed-Batch Processes for Monoclonal Antibody Production: A Computational Modeling Perspective. Bioengineering (Basel) 2024; 11:331. [PMID: 38671753 PMCID: PMC11048072 DOI: 10.3390/bioengineering11040331] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Due to their high specificity, monoclonal antibodies (mAbs) have garnered significant attention in recent decades, with advancements in production processes, such as high-seeding-density (HSD) strategies, contributing to improved titers. This study provides a thorough investigation of high seeding processes for mAb production in Chinese hamster ovary (CHO) cells, focused on identifying significant metabolites and their interactions. We observed high glycolytic fluxes, the depletion of asparagine, and a shift from lactate production to consumption. Using a metabolic network and flux analysis, we compared the standard fed-batch (STD FB) with HSD cultivations, exploring supplementary lactate and cysteine, and a bolus medium enriched with amino acids. We reconstructed a metabolic network and kinetic models based on the observations and explored the effects of different feeding strategies on CHO cell metabolism. Our findings revealed that the addition of a bolus medium (BM) containing asparagine improved final titers. However, increasing the asparagine concentration in the feed further prevented the lactate shift, indicating a need to find a balance between increased asparagine to counteract limitations and lower asparagine to preserve the shift in lactate metabolism.
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Affiliation(s)
- Carolin Bokelmann
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alireza Ehsani
- Boehringer Ingelheim Pharma GmbH & Co.KG, Launch & Innovation, 88400 Biberach an der Riß, Germany
| | - Jochen Schaub
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, 88400 Biberach an der Riß, Germany
| | - Fabian Stiefel
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Sciences Germany, 88400 Biberach an der Riß, Germany
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3
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Bendig T, Ulmer A, Luzia L, Müller S, Sahle S, Bergmann FT, Lösch M, Erdemann F, Zeidan AA, Mendoza SN, Teusink B, Takors R, Kummer U, Figueiredo AS. The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. J Biotechnol 2023; 374:90-100. [PMID: 37572793 DOI: 10.1016/j.jbiotec.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is hallmarked by the breakdown of lactose to organic acids such as lactate. This leads to a substantial decrease in pH - both in the medium, as well as cytosolic. The latter impairs metabolic activities due to the pH-dependence of enzymes, which compromises microbial growth. To quantitatively elucidate the impact of the acidification on metabolism of L. bulgaricus in an integrated way, we have developed a proton-dependent computational model of lactose metabolism and casein degradation based on experimental data. The model accounts for the influence of pH on enzyme activities as well as cellular growth and proliferation of the bacterial population. We used a machine learning approach to quantify the cell volume throughout fermentation. Simulation results show a decrease in metabolic flux with acidification of the cytosol. Additionally, the validated model predicts a similar metabolic behaviour within a wide range of non-limiting substrate concentrations. This computational model provides a deeper understanding of the intricate relationships between metabolic activity and acidification and paves the way for further optimization of yoghurt production under industrial settings.
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Affiliation(s)
- Tamara Bendig
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Laura Luzia
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Susanne Müller
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Sven Sahle
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Frank T Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Maren Lösch
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Florian Erdemann
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ahmad A Zeidan
- Systems Biology, R&D Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | | | - Bas Teusink
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
| | - Ana Sofia Figueiredo
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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4
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Immobilization of mixed cells by Flaxseeds (Linum usitatissimum) extract as new nonconventional biocarrier for biodegradation of sodium dodecyl sulfate. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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5
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Li Y, Fu Y, Zhang Y, Duan B, Zhao Y, Shang M, Cheng Y, Zhang K, Yu Q, Wang T. Nuclear Fructose-1,6-Bisphosphate Inhibits Tumor Growth and Sensitizes Chemotherapy by Targeting HMGB1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203528. [PMID: 36642839 PMCID: PMC9982576 DOI: 10.1002/advs.202203528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Metabolites are important for cell fate determination. Fructose-1,6-bisphosphate (F1,6P) is the rate-limiting product in glycolysis and the rate-limiting substrate in gluconeogenesis. Here, it is discovered that the nuclear-accumulated F1,6P impairs cancer cell viability by directly binding to high mobility group box 1 (HMGB1), the most abundant non-histone chromosome structural protein with paradoxical roles in tumor development. F1,6P disrupts the association between the HMGB1 A-box and C-tail by targeting K43/K44 residues, inhibits HMGB1 oligomerization, and stabilizes P53 protein by increasing P53-HMGB1 interaction. Moreover, F1,6P lowers the affinity of HMGB1 for DNA and DNA adducts, which sensitizes cancer cells to chemotherapeutic drug(s)-induced DNA replication stress and DNA damage. Concordantly, F1,6P resensitizes cancer cells with chemotherapy resistance, impairs tumor growth and enhances chemosensitivity in mice, and impedes the growth of human tumor organoids. These findings reveal a novel role for nuclear-accumulated F1,6P and underscore the potential utility of F1,6P as a drug for cancer therapy.
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Affiliation(s)
- Yeyi Li
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Yuan Fu
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Yan Zhang
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Bilian Duan
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Yanli Zhao
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Man Shang
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
| | - Ying Cheng
- Center for Mitochondrial Biology & Medicinethe Key Laboratory of Biomedical Information Engineering of Ministry of EducationSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'an710049China
| | - Kai Zhang
- The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsTianjin Key Laboratory of Medical EpigeneticsKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of Biochemistry and Molecular BiologyTianjin Medical UniversityTianjin300070China
| | - Qiujing Yu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjin300070China
| | - Ting Wang
- National Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjin's Clinical Research Center for CancerTianjin Lung Cancer CenterDepartment of Thoracic OncologyTianjin Cancer Institute and HospitalTianjin Key Laboratory of Inflammatory BiologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsDepartment of PharmacologySchool of Basic Medical SciencesTianjin Medical University Cancer Institute and HospitalTianjin Medical UniversityTianjin300060China
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Lapin A, Perfahl H, Jain HV, Reuss M. Integrating a dynamic central metabolism model of cancer cells with a hybrid 3D multiscale model for vascular hepatocellular carcinoma growth. Sci Rep 2022; 12:12373. [PMID: 35858953 PMCID: PMC9300625 DOI: 10.1038/s41598-022-15767-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
We develop here a novel modelling approach with the aim of closing the conceptual gap between tumour-level metabolic processes and the metabolic processes occurring in individual cancer cells. In particular, the metabolism in hepatocellular carcinoma derived cell lines (HEPG2 cells) has been well characterized but implementations of multiscale models integrating this known metabolism have not been previously reported. We therefore extend a previously published multiscale model of vascular tumour growth, and integrate it with an experimentally verified network of central metabolism in HEPG2 cells. This resultant combined model links spatially heterogeneous vascular tumour growth with known metabolic networks within tumour cells and accounts for blood flow, angiogenesis, vascular remodelling and nutrient/growth factor transport within a growing tumour, as well as the movement of, and interactions between normal and cancer cells. Model simulations report for the first time, predictions of spatially resolved time courses of core metabolites in HEPG2 cells. These simulations can be performed at a sufficient scale to incorporate clinically relevant features of different tumour systems using reasonable computational resources. Our results predict larger than expected temporal and spatial heterogeneity in the intracellular concentrations of glucose, oxygen, lactate pyruvate, f16bp and Acetyl-CoA. The integrated multiscale model developed here provides an ideal quantitative framework in which to study the relationship between dosage, timing, and scheduling of anti-neoplastic agents and the physiological effects of tumour metabolism at the cellular level. Such models, therefore, have the potential to inform treatment decisions when drug response is dependent on the metabolic state of individual cancer cells.
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Affiliation(s)
- Alexey Lapin
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany.,Institute of Chemical Process Engineering, University Stuttgart, Stuttgart, Germany
| | - Holger Perfahl
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany
| | - Harsh Vardhan Jain
- Department of Mathematics and Statistics, University of Minnesota Duluth, Duluth, MN, USA
| | - Matthias Reuss
- Stuttgart Research Center Systems Biology, University Stuttgart, Stuttgart, Germany.
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7
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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] [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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8
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Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction. Nat Commun 2020; 11:5078. [PMID: 33033266 PMCID: PMC7544899 DOI: 10.1038/s41467-020-18960-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Metabolic engineering facilitates chemical biosynthesis by rewiring cellular resources to produce target compounds. However, an imbalance between cell growth and bioproduction often reduces production efficiency. Genetic code expansion (GCE)-based orthogonal translation systems incorporating non-canonical amino acids (ncAAs) into proteins by reassigning non-canonical codons to ncAAs qualify for balancing cellular metabolism. Here, GCE-based cell growth and biosynthesis balance engineering (GCE-CGBBE) is developed, which is based on titrating expression of cell growth and metabolic flux determinant genes by constructing ncAA-dependent expression patterns. We demonstrate GCE-CGBBE in genome-recoded Escherichia coli Δ321AM by precisely balancing glycolysis and N-acetylglucosamine production, resulting in a 4.54-fold increase in titer. GCE-CGBBE is further expanded to non-genome-recoded Bacillus subtilis to balance growth and N-acetylneuraminic acid bioproduction by titrating essential gene expression, yielding a 2.34-fold increase in titer. Moreover, the development of ncAA-dependent essential gene expression regulation shows efficient biocontainment of engineered B. subtilis to avoid unintended proliferation in nature. An imbalance between cell growth and bioproduction of engineered microbes often reduces production efficiency. Here, the authors report genetic code expansion-based cell growth and biosynthesis balance engineering to achieve high levels production of N-acetylglucosamine in E. coli and N-acetylneuraminic acid in B. subtilis.
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