1
|
Hoffmann MD, Sorensen RJ, Extross A, He Y, Schmidt D. Protein Carrier AAV. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607995. [PMID: 39185209 PMCID: PMC11343202 DOI: 10.1101/2024.08.14.607995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
AAV is widely used for efficient delivery of DNA payloads. The extent to which the AAV capsid can be used to deliver a protein payload is unexplored. Here, we report engineered AAV capsids that directly package proteins - Protein Carrier AAV (pcAAV). Nanobodies inserted into the interior of the capsid mediate packaging of a cognate protein, including Green Fluorescent Protein (GFP), Streptococcus pyogenes Cas9, Cre recombinase, and the engineered peroxidase APEX2. We show that protein packaging efficiency is affected by the nanobody insertion position, the capsid protein isoform into which the nanobody is inserted, and the subcellular localization of the packaged protein during recombinant AAV capsid production; each of these factors can be rationally engineered to optimize protein packaging efficiency. We demonstrate that proteins packaged within pcAAV retain their enzymatic activity and that pcAAV can bind and enter the cell to deliver the protein payload. Establishing pcAAV as a protein delivery platform may expand the utility of AAV as a therapeutic and research tool.
Collapse
|
2
|
Catalán-Tatjer D, Tzimou K, Nielsen LK, Lavado-García J. Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platforms. Biotechnol Adv 2024; 73:108370. [PMID: 38692443 DOI: 10.1016/j.biotechadv.2024.108370] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Recombinant adeno-associated viruses (rAAVs) stand at the forefront of gene therapy applications, holding immense significance for their safe and efficient gene delivery capabilities. The constantly increasing and unmet demand for rAAVs underscores the need for a more comprehensive understanding of AAV biology and its impact on rAAV production. In this literature review, we delved into AAV biology and rAAV manufacturing bioprocesses, unravelling the functions and essentiality of proteins involved in rAAV production. We discuss the interconnections between these proteins and how they affect the choice of rAAV production platform. By addressing existing inconsistencies, literature gaps and limitations, this review aims to define a minimal set of genes that are essential for rAAV production, providing the potential to advance rAAV biomanufacturing, with a focus on minimizing the genetic load within rAAV-producing cells.
Collapse
Affiliation(s)
- David Catalán-Tatjer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Konstantina Tzimou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Lars K Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Australia
| | - Jesús Lavado-García
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| |
Collapse
|
3
|
Hu Y, Hu M, Ye X, Wu Z, Kang J, Wong C, Palackal N, Qiu H, Li N. A simple and sensitive differential digestion method to analyze adeno-associated virus residual host cell proteins by LC-MS. J Pharm Biomed Anal 2024; 242:116009. [PMID: 38354541 DOI: 10.1016/j.jpba.2024.116009] [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: 11/15/2023] [Revised: 01/24/2024] [Accepted: 02/03/2024] [Indexed: 02/16/2024]
Abstract
Many methods using liquid chromatography-mass spectrometry (LC-MS) have been established for identifying residual host cell proteins (HCPs) to aid in the process development and quality control of therapeutic proteins. However, the use of MS-based techniques for adeno-associated virus (AAV) is still in its infancy, with few methods reported and minimal information available on potentially problematic HCPs. In this study, we developed a highly sensitive and effective differential digestion method to profile residual HCPs in AAV. Unlike direct digestion, which completely digests both AAV and HCPs, our differential digestion method takes advantage of AAV's unique characteristics to maintain the integrity of AAV while preferentially digesting HCPs under denaturing and reducing conditions. This differential digestion method requires only several micrograms of sample and significantly enhances the identification of HCPs. Furthermore, this method can be applied to all five different AAV serotypes for comprehensive HCP profiling. Our work fills a gap in AAV HCP analysis by providing a sensitive and robust strategy for detecting, monitoring, and measuring HCPs.
Collapse
Affiliation(s)
- Yunli Hu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA.
| | - Mengqi Hu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Xiang Ye
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Zhijie Wu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Jianming Kang
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Christina Wong
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Nisha Palackal
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| | - Haibo Qiu
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA.
| | - Ning Li
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591-6707, USA
| |
Collapse
|
4
|
Wang Y, Fu Q, Park SY, Lee YS, Park SY, Lee DY, Yoon S. Decoding cellular mechanism of recombinant adeno-associated virus (rAAV) and engineering host-cell factories toward intensified viral vector manufacturing. Biotechnol Adv 2024; 71:108322. [PMID: 38336188 DOI: 10.1016/j.biotechadv.2024.108322] [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: 06/11/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is one of the prominent gene delivery vehicles that has opened promising opportunities for novel gene therapeutic approaches. However, the current major viral vector production platform, triple transfection in mammalian cells, may not meet the increasing demand. Thus, it is highly required to understand production bottlenecks from the host cell perspective and engineer the cells to be more favorable and tolerant to viral vector production, thereby effectively enhancing rAAV manufacturing. In this review, we provided a comprehensive exploration of the intricate cellular process involved in rAAV production, encompassing various stages such as plasmid entry to the cytoplasm, plasmid trafficking and nuclear delivery, rAAV structural/non-structural protein expression, viral capsid assembly, genome replication, genome packaging, and rAAV release/secretion. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production is summarized for each stage. The control strategies from the perspectives of host cell and materials (e.g., AAV plasmids) are proposed as our insights based on the characterization of molecular features and our existing knowledge of the AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.
Collapse
Affiliation(s)
- Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America.
| |
Collapse
|
5
|
Ohba K, Sehara Y, Enoki T, Mineno J, Ozawa K, Mizukami H. Adeno-associated virus vector system controlling capsid expression improves viral quantity and quality. iScience 2023; 26:106487. [PMID: 37096037 PMCID: PMC10122016 DOI: 10.1016/j.isci.2023.106487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Adeno-associated virus (AAV) vectors are promising tools for gene therapy. The current AAV vector system produces an abundance of empty capsids that are eliminated before clinical use, leading to increased costs for gene therapy. In the present study, we established an AAV production system that regulates the timing of capsid expression using a tetracycline-dependent promoter. Tetracycline-regulating capsid expression increased viral yield and reduced empty capsids in various serotypes without altering AAV vector infectivity in vitro and in vivo. The replicase expression pattern change observed in the developed AAV vector system improved viral quantity and quality, whereas timing control of capsid expression reduced empty capsids. These findings provide a new perspective on the development of AAV vector production systems in gene therapy.
Collapse
Affiliation(s)
- Kenji Ohba
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
- Corresponding author
| | - Yoshihide Sehara
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Tatsuji Enoki
- CDM Center, TAKARA Bio Inc., Kusatsu, Shiga 525-0058, Japan
| | - Junichi Mineno
- CDM Center, TAKARA Bio Inc., Kusatsu, Shiga 525-0058, Japan
| | - Keiya Ozawa
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
- Department of Immuno-Gene & Cell Therapy (Takara Bio), Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| |
Collapse
|
6
|
Serrano MAC, Furman R, Chen G, Tao L. Mass spectrometry in gene therapy: Challenges and opportunities for AAV analysis. Drug Discov Today 2023; 28:103442. [PMID: 36396118 DOI: 10.1016/j.drudis.2022.103442] [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: 06/13/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
The characterization of adeno-associated virus (AAV)-based gene therapy products represents significant challenges owing to their extremely large molecular sizes, structural complexity and heterogeneity, and limited sample amounts. Mass spectrometry (MS) is one of the key analytical tools that can overcome these challenges and serve as an important technique for the analysis of multiple attributes. In this review, the current methodologies and emerging trends in MS analysis of AAV gene therapy products are presented, highlighting their advantages and unique capabilities in addressing key issues encountered in intact AAV vector analysis, capsid viral protein characterization and impurity analysis.
Collapse
Affiliation(s)
- Mahalia A C Serrano
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Ran Furman
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
| | - Guodong Chen
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA.
| | - Li Tao
- Analytical Development and Attribute Sciences, Biologics Development, Global Product Development and Supply, Bristol Myers Squibb, New Brunswick, NJ, USA
| |
Collapse
|
7
|
Guo J, Kufer R, Li D, Wohlrab S, Greenwood-Goodwin M, Yang F. Technical advancement and practical considerations of LC-MS/MS-based methods for host cell protein identification and quantitation to support process development. MAbs 2023; 15:2213365. [PMID: 37218066 PMCID: PMC10208169 DOI: 10.1080/19420862.2023.2213365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Host cell proteins (HCPs) are process-related impurities derived from the manufacturing of recombinant biotherapeutics. Residual HCP in drug products, ranging from 1 to 100 ppm (ng HCP/mg product) or even below sub-ppm level, may affect product quality, stability, efficacy, or safety. Therefore, removal of HCPs to appropriate levels is critical for the bioprocess development of biotherapeutics. Liquid chromatography-mass spectrometry (LC-MS) analysis has become an important tool to identify, quantify, and monitor the clearance of individual HCPs. This review covers the technical advancement of sample preparation strategies, new LC-MS-based techniques, and data analysis approaches to robustly and sensitively measure HCPs while overcoming the high dynamic range analytical challenges. We also discuss our strategy for LC-MS-based HCP workflows to enable fast support of process development throughout the product life cycle, and provide insights into developing specific analytical strategies leveraging LC-MS tools to control HCPs in process and mitigate their potential risks to drug quality, stability, and patient safety.
Collapse
Affiliation(s)
- Jia Guo
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, South San Francisco, CA, USA
| | - Regina Kufer
- Pharma Technical Development Analytics, Roche Diagnostics GmbH, Penzberg, Germany
| | - Delia Li
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, South San Francisco, CA, USA
| | - Stefanie Wohlrab
- Pharma Technical Development Analytics, Roche Diagnostics GmbH, Penzberg, Germany
| | | | - Feng Yang
- Protein Analytical Chemistry, Genentech, A Member of the Roche Group, South San Francisco, CA, USA
| |
Collapse
|
8
|
Dobrowsky T, Gianni D, Pieracci J, Suh J. AAV manufacturing for clinical use: Insights on current challenges from the upstream process perspective. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
9
|
Analytics of host cell proteins (HCPs): lessons from biopharmaceutical mAb analysis for Gene therapy products. Curr Opin Biotechnol 2021; 71:98-104. [PMID: 34311150 DOI: 10.1016/j.copbio.2021.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/18/2022]
Abstract
Analytics for host cell protein (HCP) analysis of therapeutic monoclonal antibody preparations have developed enormously. We consider how learnings from this can inform HCP analysis of gene therapy viral vector products. The application of mass spectrometry (MS) approaches for analysis of HCPs in viral vector preparations is being established, although such information remains limited and is yet to be widely applied into process or host cell line development to reduce HCP amounts or risk. As these MS approaches, and the data from them, are applied and become available, the process understanding created will speed process development activity. We describe technologies that have been, or can be, applied to viral vector HCP analysis to aid process development, reduce HCP amounts, identify critical HCPs and thus inform risk assessment and management based on a knowledge of specific HCPs, ultimately delivering safe and efficacious gene therapy products to the clinic.
Collapse
|
10
|
Tanaka T, Hanaoka H, Sakurai S. Optimization of the quality by design approach for gene therapy products: A case study for adeno-associated viral vectors. Eur J Pharm Biopharm 2020; 155:88-102. [PMID: 32784043 DOI: 10.1016/j.ejpb.2020.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/10/2020] [Accepted: 08/05/2020] [Indexed: 01/02/2023]
Abstract
The development of gene therapy products has been expanding globally, and among them, the recombinant adeno-associated virus (rAAV) vector is one of the most promising vectors for gene transfer. For efficient and rapid development of the manufacturing process and quality control strategy, the quality by design (QbD) approach can be as effective for gene therapy products as it is for gene recombinant proteins, which have been developed for decades. However, prior available knowledge required for the QbD approach is limited in the field of gene therapy. Here, we comprehensively review rAAV study results that can form the basis of QbD-based development and propose a critical quality attribute identification method suitable for gene therapy development. As a case study for rAAV, we propose a series of practical development steps, including a quality target product profile (QTPP) setting, identification of critical quality attributes (CQAs), repetitive risk assessment associated with process optimization, design space (DS) establishment, and control strategy using the QbD method. Our case study, which was based on publicly available literature, is a basic model that can be augmented by unique data pertaining to specific products. An improvement in rAAV development is expected using this model as the first step.
Collapse
Affiliation(s)
- Toshimitsu Tanaka
- Department of Regulatory Science of Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| | - Hideki Hanaoka
- Department of Regulatory Science of Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Research Center, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8766, Japan.
| | - Shingo Sakurai
- Department of Regulatory Science of Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Pharmaceuticals and Medical Devices Agency, Shin-Kasumigaseki Building, 3-3-2 Kasumigaseki, Chiyoda-ku, Tokyo 100-0013, Japan.
| |
Collapse
|
11
|
Buck TM, Wijnholds J. Recombinant Adeno-Associated Viral Vectors (rAAV)-Vector Elements in Ocular Gene Therapy Clinical Trials and Transgene Expression and Bioactivity Assays. Int J Mol Sci 2020; 21:E4197. [PMID: 32545533 PMCID: PMC7352801 DOI: 10.3390/ijms21124197] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal dystrophies and optic neuropathies cause chronic disabling loss of visual function. The development of recombinant adeno-associated viral vectors (rAAV) gene therapies in all disease fields have been promising, but the translation to the clinic has been slow. The safety and efficacy profiles of rAAV are linked to the dose of applied vectors. DNA changes in the rAAV gene cassette affect potency, the expression pattern (cell-specificity), and the production yield. Here, we present a library of rAAV vectors and elements that provide a workflow to design novel vectors. We first performed a meta-analysis on recombinant rAAV elements in clinical trials (2007-2020) for ocular gene therapies. We analyzed 33 unique rAAV gene cassettes used in 57 ocular clinical trials. The rAAV gene therapy vectors used six unique capsid variants, 16 different promoters, and six unique polyadenylation sequences. Further, we compiled a list of promoters, enhancers, and other sequences used in current rAAV gene cassettes in preclinical studies. Then, we give an update on pro-viral plasmid backbones used to produce the gene therapy vectors, inverted terminal repeats, production yield, and rAAV safety considerations. Finally, we assess rAAV transgene and bioactivity assays applied to cells or organoids in vitro, explants ex vivo, and clinical studies.
Collapse
Affiliation(s)
- Thilo M. Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
- Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands
| |
Collapse
|
12
|
Aponte-Ubillus JJ, Barajas D, Peltier J, Bardliving C, Shamlou P, Gold D. A rAAV2-producing yeast screening model to identify host proteins enhancing rAAV DNA replication and vector yield. Biotechnol Prog 2018; 35:e2725. [PMID: 30298993 DOI: 10.1002/btpr.2725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/01/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022]
Abstract
Recombinant adeno-associated viral vectors (rAAV) are promising therapies for genetic diseases. Although current platforms for recombinant vector production can generate drug material for pre-clinical and clinical studies, rAAV biomanufacturing will eventually face commercial supply challenges if per cell vector productivity and process scalability are not improved. Because considerable efforts have traditionally focused on optimizing rAAV plasmid design, herein we investigate the impact of host cell proteins on vector production to identify proteins that may enhance rAAV yield. Using a rAAV2-GFP-producing Saccharomyces cerevisiae model in combination with the yeast Tet Hughes Collection screening library, we identified 22 gene candidates that improved rAAV DNA replication (rAAV-GFP/18s rDNA ratio) and vector yield (benzonase-resistant rAAV DNA vector genome titer) as high as 6-fold and 15-fold relative to control, respectively. The candidate proteins participate in biological processes such as DNA replication, ribosome biogenesis, and RNA and protein processing. The best five candidates (PRE4, HEM4, TOP2, GPN3, and SDO1) were further screened by generating overexpression mutants in the YPH500 yeast strain. Subsequent clone evaluation was performed to confirm the rAAV-promoting activity of selected candidates under plate-based and bioreactor-controlled fermentation conditions. Digital droplet PCR analysis of cell lysate and AVB resin-purified material confirmed HEM4 and TOP2 overexpression mutants displayed the highest per cell total rAAV DNA productivity (1.6 and 1.7-fold increase over control, respectively) and per cell vector productivity (3 and 4-fold over control, respectively). This evaluation confirmed that overexpression of HEM4 and TOP2 proteins enhanced total and benzonase-resistant rAAV DNA yield. Further studies are needed to understand their mechanism of action and to assess their potential application in molecular strategies for rAAV production. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2725, 2019.
Collapse
Affiliation(s)
- Juan Jose Aponte-Ubillus
- Process Sciences Department, Biomarin Pharmaceutical Inc, Novato, CA, 94949.,Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, 91711
| | - Daniel Barajas
- Process Sciences Department, Biomarin Pharmaceutical Inc, Novato, CA, 94949
| | - Joseph Peltier
- Process Sciences Department, Biomarin Pharmaceutical Inc, Novato, CA, 94949
| | - Cameron Bardliving
- Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, 91711
| | - Parviz Shamlou
- Amgen Bioprocessing Center, Keck Graduate Institute, Claremont, CA, 91711
| | - Daniel Gold
- Process Sciences Department, Biomarin Pharmaceutical Inc, Novato CA, 94949
| |
Collapse
|
13
|
Penaud-Budloo M, François A, Clément N, Ayuso E. Pharmacology of Recombinant Adeno-associated Virus Production. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 8:166-180. [PMID: 29687035 PMCID: PMC5908265 DOI: 10.1016/j.omtm.2018.01.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recombinant adeno-associated viral (rAAV) vectors have been used in more than 150 clinical trials with a good safety profile and significant clinical benefit in many genetic diseases. In addition, due to their ability to infect non-dividing and dividing cells and to serve as efficient substrate for homologous recombination, rAAVs are being used as a tool for gene-editing approaches. However, manufacturing of these vectors at high quantities and fulfilling current good manufacturing practices (GMP) is still a challenge, and several technological platforms are competing for this niche. Herein, we will describe the most commonly used upstream methods to produce rAAVs, paying particular attention to the starting materials (input) used in each platform and which related impurities can be expected in final products (output). The most commonly found impurities in rAAV stocks include defective particles (i.e., AAV capsids that do contain the therapeutic gene or are not infectious), residual proteins from host cells and helper viruses (adenovirus, herpes simplex virus, or baculoviruses), and illegitimate DNA from plasmids, cells, or helper viruses that may be encapsidated into rAAV particles. Given the role that impurities may play in immunotoxicity, this article reviews the impurities inherently associated with each manufacturing platform.
Collapse
Affiliation(s)
- Magalie Penaud-Budloo
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Achille François
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Nathalie Clément
- Powell Gene Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Eduard Ayuso
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| |
Collapse
|
14
|
Aponte-Ubillus JJ, Barajas D, Peltier J, Bardliving C, Shamlou P, Gold D. Molecular design for recombinant adeno-associated virus (rAAV) vector production. Appl Microbiol Biotechnol 2017; 102:1045-1054. [PMID: 29204900 PMCID: PMC5778157 DOI: 10.1007/s00253-017-8670-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
Abstract
Recombinant adeno-associated virus (rAAV) vectors are increasingly popular tools for gene therapy applications. Their non-pathogenic status, low inflammatory potential, availability of viral serotypes with different tissue tropisms, and prospective long-lasting gene expression are important attributes that make rAAVs safe and efficient therapeutic options. Over the last three decades, several groups have engineered recombinant AAV-producing platforms, yielding high titers of transducing vector particles. Current specific productivity yields from different platforms range from 103 to 105 vector genomes (vg) per cell, and there is an ongoing effort to improve vector yields in order to satisfy high product demands required for clinical trials and future commercialization. Crucial aspects of vector production include the molecular design of the rAAV-producing host cell line along with the design of AAV genes, promoters, and regulatory elements. Appropriately, configuring and balancing the expression of these elements not only contributes toward high productivity, it also improves process robustness and product quality. In this mini-review, the rational design of rAAV-producing expression systems is discussed, with special attention to molecular strategies that contribute to high-yielding, biomanufacturing-amenable rAAV production processes. Details on molecular optimization from four rAAV expression systems are covered: adenovirus, herpesvirus, and baculovirus complementation systems, as well as a recently explored yeast expression system.
Collapse
Affiliation(s)
- Juan Jose Aponte-Ubillus
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA.
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA.
| | - Daniel Barajas
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
| | - Joseph Peltier
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
| | - Cameron Bardliving
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA
| | - Parviz Shamlou
- Keck Graduate Institute of Applied Life Sciences, 535 Watson drive, Claremont, CA, 91711, USA
| | - Daniel Gold
- Biomarin Pharmaceutical Inc., 105 Digital drive, Novato, CA, 94949, USA
| |
Collapse
|
15
|
Satkunanathan S, Thorpe R, Zhao Y. The function of DNA binding protein nucleophosmin in AAV replication. Virology 2017; 510:46-54. [PMID: 28704696 PMCID: PMC5572047 DOI: 10.1016/j.virol.2017.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 01/11/2023]
Abstract
Adeno-associated viruses (AAV) contain minimal viral proteins necessary for their replication. During virus assembly, AAV acquire, inherently and submissively, various cellular proteins. Our previous studies identified the association of AAV vectors with the DNA binding protein nucleophosmin (NPM1). Nucleophosmin has been reported to enhance AAV infection by mobilizing AAV capsids into and out of the nucleolus, indicating the importance of NPM1 in the AAV life cycle; however the role of NPM1 in AAV production remains unknown. In this study, we systematically investigated NPM1 function on AAV production using NPM1 knockdown cells and revealing for the first time the presence of G-quadruplex DNA sequences (GQRS) in the AAV genome, the synergistic NPM1-GQRS function in AAV production and the significant enhancement of NPM1 gene knockdown on AAV vector production. Understanding the role of cellular proteins in the AAV life cycle will greatly facilitate high titre production of AAV vectors for clinical use.
Collapse
Affiliation(s)
- Stifani Satkunanathan
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Robin Thorpe
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Yuan Zhao
- Division of Advanced Therapies, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| |
Collapse
|
16
|
Abstract
AAV has been studied for 55 years and has been developed as a vector for about 35 years. By now, there is a fairly good idea of the dimensions of what would be useful to know to employ AAV optimally as a vector, but there are still many unanswered questions within the system. As with all biological systems, each good experiment raises further questions to answer. This article provides an overview of those areas in which unknown information can be identified and of those questions that have not yet been recognized. Some of these are touched on in the six review articles in this issue of Human Gene Therapy.
Collapse
Affiliation(s)
- Kenneth I Berns
- Guest Co-Editors, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine , Gainesville, Florida
| | - Nicholas Muzyczka
- Guest Co-Editors, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine , Gainesville, Florida
| |
Collapse
|
17
|
Burnham B, Nass S, Kong E, Mattingly M, Woodcock D, Song A, Wadsworth S, Cheng SH, Scaria A, O'Riordan CR. Analytical Ultracentrifugation as an Approach to Characterize Recombinant Adeno-Associated Viral Vectors. Hum Gene Ther Methods 2015; 26:228-42. [PMID: 26414997 DOI: 10.1089/hgtb.2015.048] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recombinant adeno-associated viral (rAAV) vectors represent a novel class of biopharmaceutical drugs. The production of clinical-grade rAAV vectors for gene therapy would benefit from analytical methods that are able to monitor drug product quality with regard to homogeneity, purity, and manufacturing consistency. Here, we demonstrate the novel application of analytical ultracentrifugation (AUC) to characterize the homogeneity of preparations of rAAV vectors. We show that a single sedimentation velocity run of rAAV vectors detected and quantified a number of different viral species, such as vectors harboring an intact genome, lacking a vector genome (empty particles), and containing fragmented or incomplete vector genomes. This information is obtained by direct boundary modeling of the AUC data generated from refractometric or UV detection systems using the computer program SEDFIT. Using AUC, we show that multiple parameters contributed to vector quality, including the AAV genome form (i.e., self-complementary vs. single-stranded), vector genome size, and the production and purification methods. Hence, AUC is a critical tool for identifying optimal production and purification processes and for monitoring the physical attributes of rAAV vectors to ensure their quality.
Collapse
Affiliation(s)
- Brenda Burnham
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Shelley Nass
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Elton Kong
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | | | - Denise Woodcock
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Antonius Song
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Samuel Wadsworth
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Seng H Cheng
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | - Abraham Scaria
- Gene Therapy, Genzyme, a Sanofi Company , Framingham, Massachusetts
| | | |
Collapse
|