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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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O’Neill P, Mistry RK, Brown AJ, James DC. Protein-Specific Signal Peptides for Mammalian Vector Engineering. ACS Synth Biol 2023; 12:2339-2352. [PMID: 37487508 PMCID: PMC10443038 DOI: 10.1021/acssynbio.3c00157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 07/26/2023]
Abstract
Expression of recombinant proteins in mammalian cell factories relies on synthetic assemblies of genetic parts to optimally control flux through the product biosynthetic pathway. In comparison to other genetic part-types, there is a relative paucity of characterized signal peptide components, particularly for mammalian cell contexts. In this study, we describe a toolkit of signal peptide elements, created using bioinformatics-led and synthetic design approaches, that can be utilized to enhance production of biopharmaceutical proteins in Chinese hamster ovary cell factories. We demonstrate, for the first time in a mammalian cell context, that machine learning can be used to predict how discrete signal peptide elements will perform when utilized to drive endoplasmic reticulum (ER) translocation of specific single chain protein products. For more complex molecular formats, such as multichain monoclonal antibodies, we describe how a combination of in silico and targeted design rule-based in vitro testing can be employed to rapidly identify product-specific signal peptide solutions from minimal screening spaces. The utility of this technology is validated by deriving vector designs that increase product titers ≥1.8×, compared to standard industry systems, for a range of products, including a difficult-to-express monoclonal antibody. The availability of a vastly expanded toolbox of characterized signal peptide parts, combined with streamlined in silico/in vitro testing processes, will permit efficient expression vector re-design to maximize titers of both simple and complex protein products.
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Affiliation(s)
- Pamela O’Neill
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
| | - Rajesh K. Mistry
- AstraZeneca, BioPharmaceutical Development, Cell Culture and Fermentation
Sciences, Aaron Klugg Building, Granta
Park, Cambridge CB21 6GH, U.K.
| | - Adam J. Brown
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
- SynGenSys
Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K.
| | - David C. James
- Department
of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K.
- SynGenSys
Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K.
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Chen H, Chen JS, Paerhati P, Jakos T, Bai SY, Zhu JW, Yuan YS. Strategies and Applications of Antigen-Binding Fragment (Fab) Production in Escherichia coli. PHARMACEUTICAL FRONTS 2021. [DOI: 10.1055/s-0041-1735145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AbstractWith the advancement of genetic engineering, monoclonal antibodies (mAbs) have made far-reaching progress in the treatment of various human diseases. However, due to the high cost of production, the increasing demands for antibody-based therapies have not been fully met. Currently, mAb-derived alternatives, such as antigen-binding fragments (Fab), single-chain variable fragments, bispecifics, nanobodies, and conjugated mAbs have emerged as promising new therapeutic modalities. They can be readily prepared in bacterial systems with well-established fermentation technology and ease of manipulation, leading to the reduction of overall cost. This review aims to shed light on the strategies to improve the expression, purification, and yield of Fab fragments in Escherichia coli expression systems, as well as current advances in the applications of Fab fragments.
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Affiliation(s)
- Hui Chen
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Jun-Sheng Chen
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Pameila Paerhati
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Tanja Jakos
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Si-Yi Bai
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Jian-Wei Zhu
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
| | - Yun-Sheng Yuan
- Engineering Research Center of Cell & Therapeutic Antibody, Shanghai Jiao Tong University College of Pharmacy, Ministry of Education, Shanghai, People's Republic of China
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Gupta K, Parasnis M, Jain R, Dandekar P. Vector-related stratagems for enhanced monoclonal antibody production in mammalian cells. Biotechnol Adv 2019; 37:107415. [DOI: 10.1016/j.biotechadv.2019.107415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
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Han S, Machhi S, Berge M, Xi G, Linke T, Schoner R. Novel signal peptides improve the secretion of recombinant Staphylococcus aureus Alpha toxin H35L in Escherichia coli. AMB Express 2017; 7:93. [PMID: 28497288 PMCID: PMC5427057 DOI: 10.1186/s13568-017-0394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/26/2017] [Indexed: 11/10/2022] Open
Abstract
Secretion of heterologous proteins into Escherichia coli cell culture medium offers significant advantages for downstream processing over production as inclusion bodies; including cost and time savings, and reduction of endotoxin. Signal peptides play an important role in targeting proteins for translocation across the cytoplasmic membrane to the periplasmic space and release into culture medium during the secretion process. Alpha toxinH35L (ATH35L) was selected as an antigen for vaccine development against Staphylococcus aureus infections. It was successfully secreted into culture medium of E. coli by using bacterial signal peptides linked to the N-terminus of the protein. In order to improve the level of secreted ATH35L, we designed a series of novel signal peptides by swapping individual domains of modifying dsbA and pelB signal peptides and tested them in a fed-batch fermentation process. The data showed that some of the modified signal peptides improved the secretion efficiency of ATH35L compared with E. coli signal peptides from dsbA, pelB and phoA proteins. Indeed, one of the novel signal peptides improved the yield of secreted ATH35L by 3.5-fold in a fed-batch fermentation process and at the same time maintained processing at the expected site for signal peptide cleavage. Potentially, these new novel signal peptides can be used to improve the secretion efficiency of other heterologous proteins in E. coli. Furthermore, analysis of the synthetic signal peptide amino acid sequences provides some insight into the sequence features within the signal peptide that influence secretion efficiency.
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Huang Y, Fu J, Ludwig R, Tao L, Bongers J, Ma L, Yao M, Zhu M, Das T, Russell R. Identification and quantification of signal peptide variants in an IgG1 monoclonal antibody produced in mammalian cell lines. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:193-200. [PMID: 29078145 DOI: 10.1016/j.jchromb.2017.08.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/03/2017] [Accepted: 08/19/2017] [Indexed: 10/18/2022]
Abstract
Sequence variants of a monoclonal antibody resulting from incomplete processing of signal peptide were identified and characterized using multiple mass spectrometry platforms and reverse phase chromatography. Detection and quantification of these variants by three LC/MS platforms were assessed. Quantification was also performed by mass spectrometric analysis of the subunits of the antibody generated by reduction and IdeS proteolysis. Peptide mapping with LC/MS/MS detection was used to quantify and confirm the identities of signal peptide sequence variants. Although quantification of the signal peptide variants thru mass spectrometry approaches is system dependent, our data revealed the results are close to the values determined by chromatographic separation with UV detection. Each of the methods have proven effective in demonstrating the consistency of signal peptide variants levels across the manufacture history of the antibody.
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Affiliation(s)
- Yunping Huang
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States.
| | - Jinmei Fu
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
| | - Richard Ludwig
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
| | - Li Tao
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
| | - Jacob Bongers
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
| | - Li Ma
- MAP Discovery Support, Bristol-Myers Squibb Co., P.O. Box 5400, Princeton, NJ 08543, United States
| | - Ming Yao
- MAP Discovery Support, Bristol-Myers Squibb Co., P.O. Box 5400, Princeton, NJ 08543, United States
| | - Mingshe Zhu
- MAP Discovery Support, Bristol-Myers Squibb Co., P.O. Box 5400, Princeton, NJ 08543, United States
| | - Tapan Das
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
| | - Reb Russell
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Co., Pennington, NJ 08534, United States
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Gibson SJ, Bond NJ, Milne S, Lewis A, Sheriff A, Pettman G, Pradhan R, Higazi DR, Hatton D. N-terminal or signal peptide sequence engineering prevents truncation of human monoclonal antibody light chains. Biotechnol Bioeng 2017; 114:1970-1977. [DOI: 10.1002/bit.26301] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/01/2017] [Accepted: 03/24/2017] [Indexed: 01/02/2023]
Affiliation(s)
- S. J. Gibson
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - N. J. Bond
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - S. Milne
- Lonza Biologics Plc; Slough Berkshire United Kingdom
| | - A. Lewis
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | | | - G. Pettman
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | - R. Pradhan
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
| | | | - D. Hatton
- Department of Biopharmaceutical Development; MedImmune; Milstein Building, Granta Park Cambridge CB21 6GH United Kingdom
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Peng L, Yu X, Li C, Cai Y, Chen Y, He Y, Yang J, Jin J, Li H. Enhanced recombinant factor VII expression in Chinese hamster ovary cells by optimizing signal peptides and fed-batch medium. Bioengineered 2016; 7:189-97. [PMID: 27116572 DOI: 10.1080/21655979.2016.1176656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Signal peptides play an important role in directing and efficiently transporting secretory proteins to their proper locations in the endoplasmic reticulum of mammalian cells. The aim of this study was to enhance the expression of recombinant coagulation factor VII (rFVII) in CHO cells by optimizing the signal peptides and type of fed-batch culture medium used. Five sub-clones (O2, I3, H3, G2 and M3) with different signal peptide were selected by western blot (WB) analysis and used for suspension culture. We compared rFVII expression levels of 5 sub-clones and found that the highest rFVII expression level was obtained with the IgK signal peptide instead of Ori, the native signal peptide of rFVII. The high protein expression of rFVII with signal peptide IgK was mirrored by a high transcription level during suspension culture. After analyzing culture and feed media, the combination of M4 and F4 media yielded the highest rFVII expression of 20 mg/L during a 10-day suspension culture. After analyzing cell density and cell cycle, CHO cells feeding by F4 had a similar percentage of cells in G0/G1 and a higher cell density compared to F2 and F3. This may be the reason for high rFVII expression in M4+F4. In summary, rFVII expression was successfully enhanced by optimizing the signal peptide and fed-batch medium used in CHO suspension culture. Our data may be used to improve the production of other therapeutic proteins in fed-batch culture.
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Affiliation(s)
- Lin Peng
- a The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xiao Yu
- b Laboratory of Molecular Pharmacology , School of Pharmaceutical Sciences, Jiangnan University , Wuxi , China
| | - Chengyuan Li
- b Laboratory of Molecular Pharmacology , School of Pharmaceutical Sciences, Jiangnan University , Wuxi , China
| | - Yanfei Cai
- b Laboratory of Molecular Pharmacology , School of Pharmaceutical Sciences, Jiangnan University , Wuxi , China
| | - Yun Chen
- b Laboratory of Molecular Pharmacology , School of Pharmaceutical Sciences, Jiangnan University , Wuxi , China
| | - Yang He
- c Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University , Suzhou , China
| | - Jianfeng Yang
- d Cyrus Tang Hematology Center and Ministry of Education Engineering Center of Hematological Disease , Soochow University , Suzhou , China
| | - Jian Jin
- b Laboratory of Molecular Pharmacology , School of Pharmaceutical Sciences, Jiangnan University , Wuxi , China
| | - Huazhong Li
- a The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
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Liu H, Zou X, Li T, Wang X, Yuan W, Chen Y, Han W. Enhanced production of secretory glycoprotein VSTM1-v2 with mouse IgGκ signal peptide in optimized HEK293F transient transfection. J Biosci Bioeng 2015; 121:133-9. [PMID: 26140918 DOI: 10.1016/j.jbiosc.2015.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/14/2015] [Accepted: 05/25/2015] [Indexed: 01/28/2023]
Abstract
VSTM1-v2 is a secretory glycoprotein identified by our laboratory. Our previous study revealed that VSTM1-v2 could promote differentiation and activation of Th17 cells. To explore the role of VSTM1-v2 in the immune system further, a source of abundant high-quality recombinant protein is warranted. However, high-level expression of bioactive VSTM1-v2 is difficult due to its weak secretion capacity. To obtain sufficient recombinant VSTM1-v2, we developed an improved expression and purification system by replacing the native signal peptide with a mouse IgGκ signal peptide that did not alter the protein cleavage site. We also optimized parameters for a transient gene expression system in HEK293F cells suspended in serum-free media with polyethyleneimine. Finally, 3.6 mg/L recombinant VSTM1-v2 protein with N-glycosylation and no less than 95% purity was obtained through one-step purification with Ni affinity chromatography. The final yield after purification was increased by more than 7-fold compared to the yield from our previously reported HEK293T system (from 0.5 mg/L to 3.6 mg/L). More importantly, VSTM1-v2 protein exhibited excellent bioactivity. In conclusion, the improved system is not only a dependable source of abundant bioactive VSTM1-v2 for functional studies but also demonstrates a highly efficient approach for enhancing the production of proteins in a short time period, especially for secretory proteins with poor yields.
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Affiliation(s)
- Huihui Liu
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Xiajuan Zou
- Proteomics Laboratory, Medical and Healthy Analytical Center, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Ting Li
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Xiaolin Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wanqiong Yuan
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Yingyu Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China
| | - Wenling Han
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health, 38 Xueyuan Road, Beijing 100191, China; Peking University Center for Human Disease Genomics, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China.
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