1
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Toustou C, Boulogne I, Gonzalez AA, Bardor M. Comparative RNA-Seq of Ten Phaeodactylum tricornutum Accessions: Unravelling Criteria for Robust Strain Selection from a Bioproduction Point of View. Mar Drugs 2024; 22:353. [PMID: 39195469 DOI: 10.3390/md22080353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
The production of biologics in mammalian cells is hindered by some limitations including high production costs, prompting the exploration of other alternative expression systems that are cheaper and sustainable like microalgae. Successful productions of biologics such as monoclonal antibodies have already been demonstrated in the diatom Phaeodactylum tricornutum; however, limited production yields still remain compared to mammalian cells. Therefore, efforts are needed to make this microalga more competitive as a cell biofactory. Among the seventeen reported accessions of P. tricornutum, ten have been mainly studied so far. Among them, some have already been used to produce high-value-added molecules such as biologics. The use of "omics" is increasingly being described as useful for the improvement of both upstream and downstream steps in bioprocesses using mammalian cells. Therefore, in this context, we performed an RNA-Seq analysis of the ten most used P. tricornutum accessions (Pt1 to Pt10) and deciphered the differential gene expression in pathways that could affect bioproduction of biologics in P. tricornutum. Our results highlighted the benefits of certain accessions such as Pt9 or Pt4 for the production of biologics. Indeed, these accessions seem to be more advantageous. Moreover, these results contribute to a better understanding of the molecular and cellular biology of P. tricornutum.
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Affiliation(s)
- Charlotte Toustou
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Isabelle Boulogne
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Anne-Alicia Gonzalez
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Muriel Bardor
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
- ALGA BIOLOGICS, CURIB, 25 rue Tesnières, 76821 Mont-Saint-Aignan, France
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2
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Dündar Orhan Y, Üstüntanır Dede AF, Duran Ş, Arslanyolu M. Use of E-64 cysteine protease inhibitor for the recombinant protein production in Tetrahymena thermophila. Eur J Protistol 2024; 94:126085. [PMID: 38703600 DOI: 10.1016/j.ejop.2024.126085] [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: 11/17/2023] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
Tetrahymena thermophila is an alternative organism for recombinant protein production. However, the production efficiency in T. thermophila is quite low mainly due to the rich cysteine proteases. In this study, we studied whether supplementation of the E-64 inhibitor to T. thermophila cultures increases the recombinant protein production efficiency without any toxic side effects. Our study showed that supplementation of E-64 had no lethal effects on T. thermophila cells in flask culture at 30 °C and 38 °C. In vitro protease activity analysis using secretome as protease enzyme source from E-64-supplemented cell cultures showed a reduced protein substrate degradation using bovine serum albumin, rituximab, and milk lactoglobulin proteins. E-64 also prevented proteolysis of the recombinantly produced and secreted TtmCherry2-sfGFP fusion protein at some level. This reduced inhibitory effect of E-64 could be due to genetic compensation of the inhibited proteases. As a result, the 5 µM concentration of E-64 was found to be a non-toxic protease inhibitory supplement to improve extracellular recombinant protein production efficiency in T. thermophila. This study suggests that the use of E-64 may increase the efficiency of extracellular recombinant protein production by continuously reducing extracellular cysteine protease activity during cultivation.
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Affiliation(s)
- Yeliz Dündar Orhan
- Department of Advanced Technologies, Institute of Graduate Programs, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Turkey.
| | - Ayça Fulya Üstüntanır Dede
- Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Turkey.
| | - Şeyma Duran
- Department of Molecular Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunus Emre Campus, Eskişehir 26470, Turkey.
| | - Muhittin Arslanyolu
- Department of Biology, Faculty of Sciences, Eskisehir Technical University, Yunusemre Campus, Eskişehir 26470, Turkey.
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3
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Yan G, Lu X, Sun R, Zhou W, Zhou H. Intensified perfusion culture (IPC) reduced recombinant protein fragmentation. Biotechnol Prog 2024; 40:e3405. [PMID: 37997628 DOI: 10.1002/btpr.3405] [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: 03/05/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Mammalian cells remain the mainstay of biological production host. In industry, cultivating and harvest strategies are sorted in batch mode (e.g., batch, fed-batch, concentrated fed-batch and intensified fed-batch) and continuous mode (e.g., perfusion). To retrieve greater productivity and better product quality, especially for the sensitive products prone to fragmentation, culture modes with various modifications are innovated (e.g., intensified perfusion culture [IPC]). In our study, we demonstrated that the fragmentation of Fc-fusion product (Molecule A) is time-dependent in traditional fed-batch (TFB) culture. The fragmentation proportion increased from 3.8% to 12.4% for Clone A, 0.8% to 1.7% for Clone B and 0.9% to 2.0% for Clone C from Day 10 to Day 14. By applying a novel bioprocess, IPC, which allows continuous feeding of the fresh medium and constant removal of the spent medium without bleeding cells to maintain a defined constant viable cell density, the fragmentation was reduced to 0.3% while the productivity was increased from 2.96 g/L to 15.51 g/L for Clone A. To validate whether the fragmentation reduction is product-sensitive, plasmids carrying the DNA sequences of two other Fc-fusion molecules (Molecule B and Molecule C) were transfected into the host. The results showed consistent fragmentation reducing effect by using IPC. Furthermore, the cultivation scale was expanded to 50 L and 1000 L. A minimum fragmentation level below 0.1% was observed for Molecule C. Our study revealed the capability of IPC in reducing Fc-fusion protein fragmentation and the reproducibility when scaling up while maintaining high productivity.
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Affiliation(s)
- Ge Yan
- Cell Culture Process Development, WuXi Biologics, Shanghai, China
| | - Xun Lu
- Cell Culture Process Development, WuXi Biologics, Shanghai, China
| | - Ruiqiang Sun
- Cell Culture Process Development, WuXi Biologics, Shanghai, China
| | - Weichang Zhou
- Biologics Development, WuXi Biologics, Shanghai, China
| | - Hang Zhou
- Bioprocess Research and Development, WuXi Biologics, Shanghai, China
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4
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Guadarrama-Pérez V, Aguilar C, Porras-Sanjuanico A, Merino E, Ramírez OT, Barona-Gómez F, Palomares LA. Expression in CHO cells of a bacterial biosynthetic pathway producing a small non-ribosomal peptide aldehyde prevents proteolysis of recombinant proteins. Metab Eng 2024; 82:79-88. [PMID: 38290598 DOI: 10.1016/j.ymben.2024.01.005] [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: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
A significant problem during recombinant protein production is proteolysis. One of the most common preventive strategies is the addition of protease inhibitors, which has drawbacks, such as their short half-life and high cost, and their limited prevention of extracellular proteolysis. Actinomycetes produce the most commonly used inhibitors, which are non-ribosomal small aldehydic peptides. Previously, an unprecedented biosynthetic route involving a condensation-minus non-ribosomal peptide synthetase (NRPSs) and a tRNA utilizing enzyme (tRUE) was shown to direct the synthesis of one of these inhibitor peptides, livipeptin. Here, we show that expression of the livipeptin biosynthetic pathway encoded by the lvp genes in CHO cells resulted in the production of this metabolite with cysteine protease inhibitory activity, implying that mammalian tRNAs were recruited by the lvp system. CHO cells transiently expressing the biosynthetic pathway produced livipeptin without affecting cell growth or viability. Expression of the lvp system in CHO cells producing two model proteins, secreted alkaline phosphatase (hSeAP) and a monoclonal antibody, resulted in higher specific productivity with reduced proteolysis. We show for the first time that the expression of a bacterial biosynthetic pathway is functional in CHO cells, resulting in the efficient, low-cost synthesis of a protease inhibitor without adverse effects on CHO cells. This expands the field of metabolic engineering of mammalian cells by expressing the overwhelming diversity of actinomycetes biosynthetic pathways and opens a new option for proteolysis inhibition in bioprocess engineering.
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Affiliation(s)
- Violeta Guadarrama-Pérez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - César Aguilar
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Cinvestav-IPN, Irapuato, Guanajuato, Mexico; Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Alberto Porras-Sanjuanico
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - Enrique Merino
- Departamento de Microbiología Molecular. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, 62210, Mexico.
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Cinvestav-IPN, Irapuato, Guanajuato, Mexico; Institute of Biology, Leiden University, Leiden, 2333, BE, the Netherlands.
| | - Laura A Palomares
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología. Universidad Nacional Autónoma de México. Cuernavaca, Mor, 62210, México.
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5
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Geng SL, Zhao XJ, Zhang X, Zhang JH, Mi CL, Wang TY. Recombinant therapeutic proteins degradation and overcoming strategies in CHO cells. Appl Microbiol Biotechnol 2024; 108:182. [PMID: 38285115 PMCID: PMC10824870 DOI: 10.1007/s00253-024-13008-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
Mammalian cell lines are frequently used as the preferred host cells for producing recombinant therapeutic proteins (RTPs) having post-translational modified modification similar to those observed in proteins produced by human cells. Nowadays, most RTPs approved for marketing are produced in Chinese hamster ovary (CHO) cells. Recombinant therapeutic antibodies are among the most important and promising RTPs for biomedical applications. One of the issues that occurs during development of RTPs is their degradation, which caused by a variety of factors and reducing quality of RTPs. RTP degradation is especially concerning as they could result in reduced biological functions (antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity) and generate potentially immunogenic species. Therefore, the mechanisms underlying RTP degradation and strategies for avoiding degradation have regained an interest from academia and industry. In this review, we outline recent progress in this field, with a focus on factors that cause degradation during RTP production and the development of strategies for overcoming RTP degradation. KEY POINTS: • The recombinant therapeutic protein degradation in CHO cell systems is reviewed. • Enzymatic factors and non-enzymatic methods influence recombinant therapeutic protein degradation. • Reducing the degradation can improve the quality of recombinant therapeutic proteins.
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Affiliation(s)
- Shao-Lei Geng
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- Henan Engineering Research Center for Biopharmaceutical Innovation, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Xiao-Jie Zhao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Xi Zhang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Ji-Hong Zhang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Chun-Liu Mi
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- Henan Engineering Research Center for Biopharmaceutical Innovation, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- Henan Engineering Research Center for Biopharmaceutical Innovation, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
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6
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Zhao Y, Li H, Fan Z, Wang T. Effect of Host Cell Protein on Chinese Hamster Ovary Recombinant Protein Production and its Removal Strategies: A Mini Review. Curr Pharm Biotechnol 2024; 25:665-675. [PMID: 37594091 DOI: 10.2174/1389201024666230818112633] [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: 04/05/2023] [Revised: 07/01/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Chinese hamster ovary cells are the main expression system for recombinant therapeutic proteins. During the production of these proteins, certain host cell proteins are secreted, broken down, and released by host cells in the culture along with the proteins of interest. These host cell proteins are often difficult to remove during the downstream purification process, and thus affect the quality, safety, and effectiveness of recombinant protein biopharmaceutical products and increase the production cost of recombinant therapeutic proteins. Therefore, host cell protein production must be reduced as much as possible during the production process and eliminated during purification. This article reviews the harm caused by host cell proteins in the production of recombinant protein drugs using Chinese hamster ovary cell, factors affecting host cell proteins, the monitoring and identification of these proteins, and methods to reduce their type and quantity in the final product.
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Affiliation(s)
- Yaru Zhao
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang, China
| | - He Li
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang, China
| | - Zhenlin Fan
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang, China
| | - Tianyun Wang
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
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7
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Reinders LMH, Klassen MD, Endres P, Krumm A, Jaeger M, Schmidt TC, Teutenberg T. Development of a Two-dimensional Liquid Chromatography High-Resolution Mass Spectrometry Method for the Characterization of Monoclonal Antibodies in Cell-Free Culture Supernatant via FcR Affinity Chromatography. Chromatographia 2022. [DOI: 10.1007/s10337-022-04228-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Hu L, Liu S, Xia L, Cong X, Xu C, Wang L, Li Y. CHO cathepsin B identified as the protease responsible for a target bispecific antibody fragmentation. Protein Expr Purif 2022; 199:106144. [PMID: 35839975 DOI: 10.1016/j.pep.2022.106144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022]
Abstract
In a previous work we demonstrated that CHO protease caused fragmentation of an expressed bispecific antibody (bsAb) and this detrimental host cell protein (HCP) can be effectively removed through an optimized Protein A wash step. In addition, preliminary evidence suggested that the responsible protease belongs to the threonine or cysteine protease family. In the current study, this protease was further identified as cathepsin B. First, we identified several CHO proteases in the further fractionated Protein A wash using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and this allowed us to select four candidate proteases. Next, by examining the cleavage pattern of each individual protease and comparing it with that observed during purification, cathepsin B was identified as the protease responsible for the observed bsAb fragmentation.
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Affiliation(s)
- Lixia Hu
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Shanshan Liu
- ,Analytical Sciences (AS), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Lisha Xia
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Xiaoji Cong
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Chu Xu
- ,Analytical Sciences (AS), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Li Wang
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China
| | - Yifeng Li
- Technology and Process Development (TPD), WuXi Biologics, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai, 200131, China.
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9
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The potential of emerging sub-omics technologies for CHO cell engineering. Biotechnol Adv 2022; 59:107978. [DOI: 10.1016/j.biotechadv.2022.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 11/23/2022]
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10
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Carver J, Kern M, Ko P, Greenwood-Goodwin M, Yu XC, Duan D, Tang D, Misaghi S, Auslaender S, Haley B, Yuk IH, Shen A. A ribonucleoprotein-based decaplex CRISPR/Cas9 knockout strategy for CHO host engineering. Biotechnol Prog 2022; 38:e3212. [PMID: 34538022 DOI: 10.1002/btpr.3212] [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: 07/11/2021] [Revised: 08/24/2021] [Accepted: 09/16/2021] [Indexed: 11/08/2022]
Abstract
Chinese hamster ovary (CHO) cell engineering based on CRISPR/Cas9 knockout (KO) technology requires the delivery of guide RNA (gRNA) and Cas9 enzyme for efficient gene targeting. With an ever-increasing list of promising gene targets, developing, and optimizing a multiplex gene KO protocol is crucial for rapid CHO cell engineering. Here, we describe a method that can support efficient targeting and KO of up to 10 genes through sequential transfections. This method utilizes Cas9 protein to first screen multiple synthetic gRNAs per gene, followed by Sanger sequencing indel analysis, to identify effective gRNA sequences. Using sequential transfections of these potent gRNAs led to the isolation of single cell clones with the targeted deletion of all 10 genes (as confirmed by Sanger sequencing at the DNA level and mass spectrometry at the protein level). Screening 704 single cell clones yielded 6 clones in which all 10 genes were deleted through sequential transfections, demonstrating the success of this decaplex gene editing strategy. This pragmatic approach substantially reduces the time and effort required to generate multiple gene knockouts in CHO cells.
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Affiliation(s)
- Joseph Carver
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Marie Kern
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Peggy Ko
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | | | - X Christopher Yu
- Analytical Development Quality Control, Genentech, Inc., South San Francisco, California, USA
| | - Dana Duan
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Danming Tang
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Simon Auslaender
- Large Molecule Research, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Ben Haley
- Research Biology, Genentech, Inc., South San Francisco, California, USA
| | - Inn H Yuk
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
| | - Amy Shen
- Cell Culture and Bioprocess Operations, Genentech, Inc., South San Francisco, California, USA
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11
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Zeh N, Schlossbauer P, Raab N, Klingler F, Handrick R, Otte K. Cell line development for continuous high cell density biomanufacturing: Exploiting hypoxia for improved productivity. Metab Eng Commun 2021; 13:e00181. [PMID: 34401326 PMCID: PMC8348152 DOI: 10.1016/j.mec.2021.e00181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 01/18/2023] Open
Abstract
Oxygen deficiency (hypoxia) induces adverse effects during biotherapeutic protein production leading to reduced productivity and cell growth. Hypoxic conditions occur during classical batch fermentations using high cell densities or perfusion processes. Here we present an effort to create novel engineered Chinese hamster ovary (CHO) cell lines by exploiting encountered hypoxic bioprocess conditions to reinforce cellular production capacities. After verifying the conservation of the hypoxia-responsive pathway in CHO cell lines by analyzing oxygen sensing proteins HIF1a, HIF1β and VDL, hypoxia-response-elements (HREs) were functionally analyzed and used to create hypoxia-responsive expression vectors. Subsequently engineered hypoxia sensitive CHO cell lines significantly induced protein expression (SEAP) during adverse oxygen limitation encountered during batch fermentations as well as high cell density perfusion processes (2.7 fold). We also exploited this novel cell system to establish a highly effective oxygen shift as innovative bioprocessing strategy using hypoxia induction to improve production titers. Thus, substantial improvements can be made to optimize CHO cell productivity for novel bioprocessing challenges as oxygen limitation, providing an avenue to establish better cell systems by exploiting adverse process conditions for optimized biotherapeutic production.
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Affiliation(s)
- Nikolas Zeh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Patrick Schlossbauer
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Florian Klingler
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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12
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Gao ZZ, Li C, Chen G, Yuan JJ, Zhou YQ, Jiao JY, Nie L, Qi J, Yang Y, Chen SQ, Wang HB. Optimization strategies for expression of a novel bifunctional anti-PD-L1/TGFBR2-ECD fusion protein. Protein Expr Purif 2021; 189:105973. [PMID: 34560256 DOI: 10.1016/j.pep.2021.105973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 01/10/2023]
Abstract
The novel anti-PD-L1/TGFBR2-ECD fusion protein (BR102) comprises an anti-PD-L1 antibody (HS636) which is fused at the C terminus of the heavy chain to a TGF-β1 receptor Ⅱ ectodomain (TGFBR2-ECD), and which can sequester the PD-1/PD-L1 pathway and TGF-β bioactivity in the immunosuppressive tumor microenvironment. In the expression of TGFBR2-ECD wild-type fused protein (BR102-WT), a 50 kDa clipped species was confirmed to be induced by proteolytic cleavage at a "QKS" site located in the N-terminus of the ectodomain, which resulted in the formation of IgG-like clipping. The matrix metalloproteinase-9 was determined to be associated with BR102-WT digestion. In addition, it was observed that the N-glycosylation modifications of the fusion protein were tightly involved in regulating proteolytic activity and the levels of cleavage could be significantly suppressed by MMP-inhibitors. To avoid proteolytic degradation, eliminating protease-sensitive amino acid motifs and introducing potential glycosylation were performed. Three sensitive motifs were mutated, and the levels of clipping were strongly restrained. The mutant candidates exhibited similar binding affinities to hPD-L1 and hTGF-β1 as well as highly purified BR102-WT2. Furthermore, the mutants displayed more significant proteolytic resistance than that of BR102-WT2 in the lysate incubation reaction and the plasma stability test. Moreover, the bifunctional candidate Mu3 showed an additive antitumor effect in MC38/hPD-L1 bearing models as compared to that of with anti-PD-L1 antibody alone. In conclusion, in this study, the protease-sensitive features of BR102-WT were well characterized and efficient optimization was performed. The candidate BR102-Mutants exhibited advanced druggability in drug stability and displayed desirable antitumor activity.
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Affiliation(s)
- Zhang-Zhao Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310006, China; Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Cui Li
- Department of Pharmacy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Gang Chen
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Jun-Jie Yuan
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Ya-Qiong Zhou
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Jing-Yu Jiao
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Lei Nie
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Jian Qi
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Yong Yang
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China
| | - Shu-Qing Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310006, China.
| | - Hai-Bin Wang
- Hisun Biopharmaceutical Co., Ltd., Hangzhou, Zhejiang, 311404, China.
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13
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Cid R, Bolívar J. Platforms for Production of Protein-Based Vaccines: From Classical to Next-Generation Strategies. Biomolecules 2021; 11:1072. [PMID: 34439738 PMCID: PMC8394948 DOI: 10.3390/biom11081072] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
To date, vaccination has become one of the most effective strategies to control and reduce infectious diseases, preventing millions of deaths worldwide. The earliest vaccines were developed as live-attenuated or inactivated pathogens, and, although they still represent the most extended human vaccine types, they also face some issues, such as the potential to revert to a pathogenic form of live-attenuated formulations or the weaker immune response associated with inactivated vaccines. Advances in genetic engineering have enabled improvements in vaccine design and strategies, such as recombinant subunit vaccines, have emerged, expanding the number of diseases that can be prevented. Moreover, antigen display systems such as VLPs or those designed by nanotechnology have improved the efficacy of subunit vaccines. Platforms for the production of recombinant vaccines have also evolved from the first hosts, Escherichia coli and Saccharomyces cerevisiae, to insect or mammalian cells. Traditional bacterial and yeast systems have been improved by engineering and new systems based on plants or insect larvae have emerged as alternative, low-cost platforms. Vaccine development is still time-consuming and costly, and alternative systems that can offer cost-effective and faster processes are demanding to address infectious diseases that still do not have a treatment and to face possible future pandemics.
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Affiliation(s)
- Raquel Cid
- ADL Bionatur Solutions S.A., Av. del Desarrollo Tecnológico 11, 11591 Jerez de la Frontera, Spain
| | - Jorge Bolívar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus Universitario de Puerto Real, University of Cadiz, 11510 Puerto Real, Spain
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14
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Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021; 3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
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Affiliation(s)
- Isaac Shamie
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego 92093, USA
| | - Karen J la Cour Karottki
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Anders H Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Hooman Hefzi
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Shangzhong Li
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Samuel J Roth
- Department of Medicine, University of California, San Diego 92093, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | | | | | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
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15
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Dovgan T, Golghalyani V, Zurlo F, Hatton D, Lindo V, Turner R, Harris C, Cui T. Targeted CHO cell engineering approaches can reduce HCP-related enzymatic degradation and improve mAb product quality. Biotechnol Bioeng 2021; 118:3821-3831. [PMID: 34125434 DOI: 10.1002/bit.27857] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/16/2021] [Accepted: 06/05/2021] [Indexed: 12/11/2022]
Abstract
Host cell proteins (HCP) that co-purify with biologics produced in Chinese hamster ovary cells have been shown to impact product quality through proteolytic degradation of recombinant proteins, leading to potential product losses. Several problematic HCPs can remain in the final product even after extensive purification. Each recombinant cell line has a unique HCP profile that can be determined by numerous upstream and downstream factors, including clonal variation and the protein sequence of the expressed therapeutic molecule. Here, we worked with recombinant cell lines with high levels of copurifying HCPs, and showed that in those cell lines even modest downregulation (≤50%) of the difficult to remove HCP Cathepsin D, through stable short hairpin RNA interference or monoallelic deletion of the target gene using CRISPR-Cas9, is sufficient to greatly reduce levels of co-purifying HCP as measured by high throughput targeted LC-MS. This reduction led to improved product quality by reducing fragmentation of the drug product in forced degradation studies to negligible levels. We also show the potential of cell engineering to target other undesired HCPs and relieve the burden on downstream purification.
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Affiliation(s)
- Tatiana Dovgan
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK.,Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Vahid Golghalyani
- Analytical Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Fabio Zurlo
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Diane Hatton
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Viv Lindo
- Analytical Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Richard Turner
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Claire Harris
- Cell Culture and Fermentation Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
| | - Tingting Cui
- Purification Process Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, Cambridge, AstraZeneca, UK
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16
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Schweickert PG, Wang N, Sandefur SL, Lloyd ME, Konieczny SF, Frye CC, Cheng Z. CRISPR/Cas12a-mediated CHO genome engineering can be effectively integrated at multiple stages of the cell line generation process for bioproduction. Biotechnol J 2021; 16:e2000308. [PMID: 33369118 DOI: 10.1002/biot.202000308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022]
Abstract
Most biopharmaceuticals produced today are generated using Chinese hamster ovary (CHO) cells, therefore significant attention is focused on methods to improve CHO cell productivity and product quality. The discovery of gene-editing tools, such as CRISPR/Cas9, offers new opportunities to improve CHO cell bioproduction through cell line engineering. Recently an additional CRISPR-associated protein, Cas12a (Cpf1), was shown to be effective for gene editing in eukaryotic cells, including CHO. In this study, we demonstrate the successful application of CRISPR/Cas12a for the generation of clonally derived CHO knockout (KO) cell lines with improved product quality attributes. While we found Cas12a efficiency to be highly dependent on the targeting RNA used, we were able to generate CHO KO cell lines using small screens of only 96-320 clonally derived cell lines. Additionally, we present a novel bulk culture analysis approach that can be used to quickly assess CRISPR RNA efficiency and determine ideal screen sizes for generating genetic KO cell lines. Most critically, we find that Cas12a can be directly integrated into the cell line generation process through cotransfection with no negative impact on titer or screen size. Overall, our results show CRISPR/Cas12a to be an efficient and effective CHO genome editing tool.
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Affiliation(s)
- Patrick G Schweickert
- Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Ning Wang
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Stephanie L Sandefur
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Michael E Lloyd
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Stephen F Konieczny
- Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Christopher C Frye
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Zhuo Cheng
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
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17
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Huang Z, Xu J, Yongky A, Morris CS, Polanco AL, Reily M, Borys MC, Li ZJ, Yoon S. CHO cell productivity improvement by genome-scale modeling and pathway analysis: Application to feed supplements. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Li SW, Wright M, Healey JF, Hutchinson JM, O’Rourke S, Mesa KA, Lollar P, Berman PW. Gene editing in CHO cells to prevent proteolysis and enhance glycosylation: Production of HIV envelope proteins as vaccine immunogens. PLoS One 2020; 15:e0233866. [PMID: 32470085 PMCID: PMC7259603 DOI: 10.1371/journal.pone.0233866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/13/2020] [Indexed: 01/12/2023] Open
Abstract
Several candidate HIV subunit vaccines based on recombinant envelope (Env) glycoproteins have been advanced into human clinical trials. To facilitate biopharmaceutical production, it is necessary to produce these in CHO (Chinese Hamster Ovary) cells, the cellular substrate used for the manufacturing of most recombinant protein therapeutics. However, previous studies have shown that when recombinant Env proteins from clade B viruses, the major subtype represented in North America, Europe, and other parts of the world, are expressed in CHO cells, they are proteolyzed and lack important glycan-dependent epitopes present on virions. Previously, we identified C1s, a serine protease in the complement pathway, as the endogenous CHO protease responsible for the cleavage of clade B laboratory isolates of -recombinant gp120s (rgp120s) expressed in stable CHO-S cell lines. In this paper, we describe the development of two novel CHOK1 cell lines with the C1s gene inactivated by gene editing, that are suitable for the production of any protein susceptible to C1s proteolysis. One cell line, C1s-/- CHOK1 2.E7, contains a deletion in the C1s gene. The other cell line, C1s-/- MGAT1- CHOK1 1.A1, contains a deletion in both the C1s gene and the MGAT1 gene, which limits glycosylation to mannose-5 or earlier intermediates in the N-linked glycosylation pathway. In addition, we compare the substrate specificity of C1s with thrombin on the cleavage of both rgp120 and human Factor VIII, two recombinant proteins known to undergo unintended proteolysis (clipping) when expressed in CHO cells. Finally, we demonstrate the utility and practicality of the C1s-/- MGAT1- CHOK1 1.A1 cell line for the expression of clinical isolates of clade B Envs from rare individuals that possess broadly neutralizing antibodies and are able to control virus replication without anti-retroviral drugs (elite neutralizer/controller phenotypes). The Envs represent unique HIV vaccine immunogens suitable for further immunogenicity and efficacy studies.
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Affiliation(s)
- Sophia W. Li
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Meredith Wright
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - John F. Healey
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Jennie M. Hutchinson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sara O’Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kathryn A. Mesa
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Pete Lollar
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Phillip W. Berman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
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19
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Multiplex secretome engineering enhances recombinant protein production and purity. Nat Commun 2020; 11:1908. [PMID: 32313013 PMCID: PMC7170862 DOI: 10.1038/s41467-020-15866-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/31/2020] [Indexed: 01/20/2023] Open
Abstract
Host cell proteins (HCPs) are process-related impurities generated during biotherapeutic protein production. HCPs can be problematic if they pose a significant metabolic demand, degrade product quality, or contaminate the final product. Here, we present an effort to create a "clean" Chinese hamster ovary (CHO) cell by disrupting multiple genes to eliminate HCPs. Using a model of CHO cell protein secretion, we predict that the elimination of unnecessary HCPs could have a non-negligible impact on protein production. We analyze the HCP content of 6-protein, 11-protein, and 14-protein knockout clones. These cell lines exhibit a substantial reduction in total HCP content (40%-70%). We also observe higher productivity and improved growth characteristics in specific clones. The reduced HCP content facilitates purification of a monoclonal antibody. Thus, substantial improvements can be made in protein titer and purity through large-scale HCP deletion, providing an avenue to increased quality and affordability of high-value biopharmaceuticals.
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20
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Schweickert PG, Cheng Z. Application of Genetic Engineering in Biotherapeutics Development. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Barredo GR, Giudicessi SL, Martínez Ceron MC, Saavedra SL, Rodriguez S, Filgueira Risso L, Erra-Balsells R, Mahler G, Albericio F, Cascone O, Camperi SA. A short peptide fragment of the vascular endothelial growth factor as a novel ligand for bevacizumab purification. Protein Expr Purif 2019; 165:105500. [PMID: 31542564 DOI: 10.1016/j.pep.2019.105500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 11/18/2022]
Abstract
Bevacizumab is a vascular endothelial growth factor (VEGF)-directed monoclonal antibody (mAb) used for the treatment of several human cancers. Given that bevacizumab is administered intravenously, it must have extremely high purity, which is achieved by purification with protein A affinity chromatography (AC). However, protein A is a very expensive ligand, thereby increasing the cost of purification. Furthermore, the harsh elution conditions required to recover bevacizumab from the AC column can damage both the mAb and protein A. In contrast, short peptides show higher stability, easier synthesis and lower cost and are therefore ideal ligands for AC. In the present study, the peptide Ac-PHQGQHIGVSK contained in the VEGF fragment that binds bevacizumab, was synthesized and immobilized on agarose. The peptidyl-agarose showed affinity for bevacizumab, with an equilibrium dissociation constant value of 2.2±0.5 x 10-7 M under optimal conditions. Samples of CHO cell filtrate producing bevacizumab were loaded on the peptidyl-agarose chromatography column. Bevacizumab was recovered from the elution fraction with a yield of 94% and a purity of 98%. The maximum capacity (qm) 38±2 mg of bevacizumab per mL of matrix was comparable to that of commercial protein A matrices. Moreover, the peptide ligand showed greater stability and a lower cost than protein A. Unlike peptides previously reported for IgG purification, the ligand described herein allows mAb elution under mild conditions, thereby favoring the integrity of bevacizumab. The lack of Trp, Met or Cys in the peptide prevents its oxidation and extends the useful life of the chromatographic matrix.
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Affiliation(s)
- Gabriela R Barredo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina
| | - Silvana L Giudicessi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina
| | - María C Martínez Ceron
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina
| | - Soledad L Saavedra
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina
| | - Santiago Rodriguez
- MAbxience SAU, Carlos Villate 5148, 1605, Munro, Buenos Aires, Argentina
| | | | - Rosa Erra-Balsells
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Pabellón II. Ciudad Universitaria, 1428, Buenos Aires, Argentina; CONICET, Universidad de Buenos Aires, Centro de Investigación en Hidratos de Carbono (CIHIDECAR), Facultad de Ciencias Exactas y Naturales, Pabellón II Ciudad Universitaria, 1428, Buenos Aires, Argentina
| | - Gustavo Mahler
- AGC Biologics, 22021 20th Avenue SE, Bothell, WA, 98021, USA
| | - Fernando Albericio
- School of Chemistry & Physics, University of KwaZulu-Natal, Durban, 4001, South Africa; CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Department of Organic Chemistry, University of Barcelona, Barcelona, 08028, Spain
| | - Osvaldo Cascone
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina
| | - Silvia A Camperi
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Biotecnología, Junín 956, 1113, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, Junín 956, 1113, Buenos Aires, Argentina.
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22
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Li SW, Yu B, Byrne G, Wright M, O'Rourke S, Mesa K, Berman PW. Identification and CRISPR/Cas9 Inactivation of the C1s Protease Responsible for Proteolysis of Recombinant Proteins Produced in CHO Cells. Biotechnol Bioeng 2019; 116:2130-2145. [PMID: 31087560 DOI: 10.1002/bit.27016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/12/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
Proteolysis associated with recombinant protein expression in Chinese Hamster Ovary (CHO) cells has hindered the development of biologics including HIV vaccines. When expressed in CHO cells, the recombinant HIV envelope protein, gp120, undergoes proteolytic clipping by a serine protease at a key epitope recognized by neutralizing antibodies. The problem is particularly acute for envelope proteins from clade B viruses that represent the major genetic subtype circulating in much of the developed world, including the US and Europe. In this paper, we have identified complement Component 1's (C1s), a serine protease from the complement cascade, as the protease responsible for the proteolysis of gp120 in CHO cells. CRISPR/Cas9 knockout of the C1s protease in a CHO cell line was shown to eliminate the proteolytic activity against the recombinantly expressed gp120. In addition, the C1s-/- MGAT1- CHO cell line, with the C1s protease and the MGAT1 glycosyltransferase knocked out, enabled the production of unclipped gp120 from a clade B isolate (BaL-rgp120) and enriched for mannose-5 glycans on gp120 that are required for the binding of multiple broadly neutralizing monoclonal antibodies (bN-mAbs). The availability of this technology will allow for the scale-up and testing of multiple vaccine concepts in regions of the world where clade B viruses are in circulation. Furthermore, the proteolysis issues caused by the C1s protease suggests a broader need for a C1s-deficient CHO cell line to express other recombinant proteins that are susceptible to serine protease activity in CHO cells. Similarly, the workflow described here to identify and knockout C1s in a CHO cell line can be applied to remedy the proteolysis of biologics by other CHO proteases.
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Affiliation(s)
- Sophia W Li
- Department of Chemistry, University of California Santa Cruz, California
| | - Bin Yu
- Department of Biomolecular Engineering, University of California Santa Cruz, California
| | - Gabriel Byrne
- Department of Biomolecular Engineering, University of California Santa Cruz, California
| | - Meredith Wright
- Department of Biomolecular Engineering, University of California Santa Cruz, California
| | - Sara O'Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, California
| | - Kathryn Mesa
- Department of Biomolecular Engineering, University of California Santa Cruz, California
| | - Phillip W Berman
- Department of Biomolecular Engineering, University of California Santa Cruz, California
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23
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Cai CX, Schneck NA, Harris D, Blackstock D, Ivleva VB, Cheng KC, Charlton A, Arnold FJ, Cooper JW, Lei QP. Quantification of residual AEBSF-related impurities by reversed-phase liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1116:19-23. [PMID: 30953918 DOI: 10.1016/j.jchromb.2019.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/19/2019] [Accepted: 03/19/2019] [Indexed: 01/10/2023]
Abstract
During research of a broadly neutralizing antibody (bNAb) for HIV-1 infection, site-specific clipping was observed during cell culture incubation. Protease inhibitor, 4-(2-aminoethyl) benzenesulfonyl fluoride (AEBSF), was supplemented to the cell culture feeding to mitigate clipping as one of the control strategies. It led to the need and development of a new assay to monitor the free AEBSF-related impurities during the purification process. In this work, a reversed-phase liquid chromatography (RPLC-UV) method was developed to measure the total concentration of AEBSF and its major degradant product, 4-(aminoethyl) benzenesulfonic acid (AEBS-OH). This quantitative approach involved hydrolysis pre-treatment to drive all AEBSF to AEBS-OH, a filtration step to remove large molecules, followed by RPLC-UV analysis. The method was qualified and shown to be capable of measuring AEBS-OH down to 0.5 μM with good accuracy and precision, which was then applied for process clearance studies. The results demonstrated that a Protein A purification step in conjunction with a mock ultrafiltration/diafiltration (UF/DF) step could remove AEBSF-related impurities below the detection level. Overall, this study is the first to provide a unique approach for monitoring the clearance of free AEBSF and its related degradant, AEBS-OH, in support of the bNAb research.
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Affiliation(s)
- Cindy X Cai
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Nicole A Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Doug Harris
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Daniel Blackstock
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Vera B Ivleva
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Kuang-Chuan Cheng
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Adam Charlton
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Frank J Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Gaithersburg, MD, USA.
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24
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Bojar D, Fuhrer T, Fussenegger M. Purity by design: Reducing impurities in bioproduction by stimulus-controlled global translational downregulation of non-product proteins. Metab Eng 2018; 52:110-123. [PMID: 30468874 DOI: 10.1016/j.ymben.2018.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/01/2018] [Accepted: 11/17/2018] [Indexed: 01/22/2023]
Abstract
Capitalizing on the ability of mammalian cells to conduct complex post-translational modifications, most protein therapeutics are currently produced in cell culture systems. Addition of a signal peptide to the product protein enables its accumulation in the cell culture supernatant, but separation of the product from endogenously secreted proteins remains costly and labor-intensive. We considered that global downregulation of translation of non-product proteins would be an efficient strategy to minimize downstream processing requirements. Therefore, taking advantage of the ability of mammalian protein kinase R (PKR) to switch off most cellular translation processes in response to infection by viruses, we fused a caffeine-inducible dimerization domain to the catalytic domain of PKR. Addition of caffeine to this construct results in homodimerization and activation of PKR, effectively rewiring rapid global translational downregulation to the addition of the stimulus in a dose-dependent manner. Then, to protect translation of the target therapeutic, we screened viral and cellular internal ribosomal entry sites (IRESes) known or suspected to be resistant to PKR-induced translational stress. After choosing the best-in-class Seneca valley virus (SVV) IRES, we additionally screened for IRES transactivation factors (ITAFs) as well as for supplementary small molecules to further boost the production titer of the product protein under conditions of global translational downregulation. Importantly, the residual global translation activity of roughly 10% under maximal downregulation is sufficient to maintain cellular viability during a production timeframe of at least five days. Standard industrially used adherent as well as suspension-adapted cell lines transfected with this synthetic biology-inspired Protein Kinase R-Enhanced Protein Production (PREPP) system could produce several medicinally relevant protein therapeutics, such as the blockbuster drug rituximab, in substantial quantities and with significantly higher purity than previous culture technologies. We believe incorporation of such purity-by-design technology in the production process will alleviate downstream processing bottlenecks in future biopharmaceutical manufacturing.
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Affiliation(s)
- Daniel Bojar
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tobias Fuhrer
- ETH Zurich, Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Martin Fussenegger
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.
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