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Cotham VC, Wang S, Li N. An Online Native Mass Spectrometry Approach for Fast, Sensitive, and Quantitative Assessment of Adeno-Associated Virus Capsid Content Ratios. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1567-1575. [PMID: 38888112 DOI: 10.1021/jasms.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Adeno-associated viruses (AAVs) have emerged as a leading platform for in vivo therapeutic gene delivery and offer tremendous potential in the treatment and prevention of human disease. The fast-paced development of this growing class of therapeutics, coupled with their intrinsic structural complexity, places a high demand on analytical methods capable of efficiently monitoring product quality to ensure safety and efficacy, as well as to support manufacturing and process optimization. Importantly, the presence and relative abundance of both empty and partially filled AAV capsid subpopulations are of principal concern, as these represent the most common product-related impurities in AAV manufacturing and have a direct impact on therapeutic potential. For this reason, the capsid content, or ratio of empty and partial capsids to those packaged with the full-length therapeutic genome, has been identified by regulatory agencies as a critical quality attribute (CQA) that must be carefully controlled to meet clinical specifications. Established analytical methods for the quantitation of capsid content ratios often suffer from long turnaround times, low throughput, and high sample demands that are not well-suited to the narrow timelines and limited sample availability typical of process development. In this study, we present an integrated online native mass spectrometry platform that aims to minimize sample handling and maximize throughput and robustness for rapid and sensitive quantitation of AAV capsid content ratios. The primary advantages of this platform for AAV analysis include the ability to perform online buffer exchange under low flow conditions to maintain sample stability with minimal sample dilution, as well as the ability to achieve online charge reduction via dopant-modified desolvation gas. By exploiting the latter, enhanced spectral resolution of signals arising from empty, partial, and full AAV capsids was accomplished in the m/z domain to facilitate improved spectral interpretation and quantitation that correlated well with the industry standard analytical ultracentrifugation (AUC) method for capsid content ratio determination. The utility of this approach was further demonstrated in several applications, including the rapid and universal screening of different AAV serotypes, evaluation of capsid content for in-process samples, and the monitoring of capsid stability when subjected to thermal stress conditions.
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Affiliation(s)
- Victoria C Cotham
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., Tarrytown, New York 10591, United States
| | - Shunhai Wang
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., Tarrytown, New York 10591, United States
| | - Ning Li
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., Tarrytown, New York 10591, United States
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2
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Sripada SA, Hosseini M, Ramesh S, Wang J, Ritola K, Menegatti S, Daniele MA. Advances and opportunities in process analytical technologies for viral vector manufacturing. Biotechnol Adv 2024; 74:108391. [PMID: 38848795 DOI: 10.1016/j.biotechadv.2024.108391] [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: 11/14/2023] [Revised: 03/14/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Viral vectors are an emerging, exciting class of biologics whose application in vaccines, oncology, and gene therapy has grown exponentially in recent years. Following first regulatory approval, this class of therapeutics has been vigorously pursued to treat monogenic disorders including orphan diseases, entering hundreds of new products into pipelines. Viral vector manufacturing supporting clinical efforts has spurred the introduction of a broad swath of analytical techniques dedicated to assessing the diverse and evolving panel of Critical Quality Attributes (CQAs) of these products. Herein, we provide an overview of the current state of analytics enabling measurement of CQAs such as capsid and vector identities, product titer, transduction efficiency, impurity clearance etc. We highlight orthogonal methods and discuss the advantages and limitations of these techniques while evaluating their adaptation as process analytical technologies. Finally, we identify gaps and propose opportunities in enabling existing technologies for real-time monitoring from hardware, software, and data analysis viewpoints for technology development within viral vector biomanufacturing.
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Affiliation(s)
- Sobhana A Sripada
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Mahshid Hosseini
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA
| | - Srivatsan Ramesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA
| | - Junhyeong Wang
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA
| | - Kimberly Ritola
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Neuroscience Center, Brain Initiative Neurotools Vector Core, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Biomanufacturing Training and Education Center, North Carolina State University, 890 Main Campus Dr, Raleigh, NC 27695, USA.
| | - Michael A Daniele
- Joint Department of Biomedical Engineering, North Carolina State University, and University of North Carolina, Chapel Hill, 911 Oval Dr., Raleigh, NC 27695, USA; North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC 27695, USA.
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3
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Guapo F, Donohue N, Strasser L, Boi S, Füssl F, Rainbow-Fletcher A, Getty P, Anderson I, Barron N, Bones J. A Direct Comparison of rAAV5 Variants Derived from the Baculovirus Expression System Using LC-MS Workflows Demonstrates Key Differences in Overall Production Yield, Product Quality and Vector Efficiency. Int J Mol Sci 2024; 25:2785. [PMID: 38474031 PMCID: PMC10932283 DOI: 10.3390/ijms25052785] [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: 12/21/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Gene therapy holds great promise for the treatment of severe diseases, and adeno-associated virus (AAV) vectors have emerged as valuable tools in this field. However, challenges such as immunogenicity and high production costs complicate the commercial viability of AAV-based therapies. To overcome these barriers, improvements in production yield, driven through the availability of robust and sensitive characterization techniques that allow for the monitoring of critical quality attributes to deepen product and process understanding are crucial. Among the main attributes affecting viral production and performance, the ratio between empty and full capsids along with capsid protein stoichiometry are emerging as potential parameters affecting product quality and safety. This study focused on the production of AAV vectors using the baculovirus expression vector system (BEVS) in Sf9 cells and the complete characterization of AAV5 variants using novel liquid chromatography and mass spectrometry techniques (LC-MS) that, up to this point, had only been applied to reference commercially produced virions. When comparing virions produced using ATG, CTG or ACG start codons of the cap gene, we determined that although ACG was the most productive in terms of virus yield, it was also the least effective in transducing mammalian cells. This correlated with a low VP1/VP2 ratio and a higher percentage of empty capsids. Overall, this study provides insights into the impact of translational start codon modifications during rAAV5 production using the BEVS, the associated relationship with capsid packaging, capsid protein stoichiometry and potency. The developed characterization workflow using LC-MS offers a comprehensive and transferable analysis of AAV-based gene therapies, with the potential to aid in process optimization and facilitate the large-scale commercial manufacturing of these promising treatments.
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Affiliation(s)
- Felipe Guapo
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Nicholas Donohue
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Lisa Strasser
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Stefano Boi
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | - Florian Füssl
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
| | | | - Paul Getty
- Pharmaron, 12 Estuary Banks, Speke, Liverpool L24 8RB, UK
| | - Ian Anderson
- Pharmaron, 12 Estuary Banks, Speke, Liverpool L24 8RB, UK
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, A94 X099 Dublin, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
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4
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Guapo F, Füssl F, Strasser L, Bones J. Mass spectrometry friendly pH-gradient anion exchange chromatography for the separation of full and empty adeno-associated virus (AAV) capsids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5788-5792. [PMID: 37870407 DOI: 10.1039/d3ay01560b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The proportion of full and empty capsids represents a critical quality attribute of adeno-associated virus (AAV)-based therapeutics. In this study, pH-gradient anion exchange chromatography was utilized for the separation of full and empty capsid species. The developed method allowed for applicability to multiple AAV serotypes and facilitated subsequent mass spectrometric detection of intact AAVs. This is the first study demonstrating generic applicability as well as mass spectrometric compatibility, allowing for a more sophisticated analysis of AAV-based gene therapy and paving the way for future developments in the field.
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Affiliation(s)
- Felipe Guapo
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland.
| | - Florian Füssl
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland.
| | - Lisa Strasser
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland.
- School of Chemical Engineering and Bioprocessing, University College of Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
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5
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Yin V, Devine PWA, Saunders JC, Barendregt A, Cusdin F, Ristani A, Hines A, Shepherd S, Dembek M, Dobson CL, Snijder J, Bond NJ, Heck AJR. Stochastic assembly of biomacromolecular complexes: impact and implications on charge interpretation in native mass spectrometry. Chem Sci 2023; 14:9316-9327. [PMID: 37712025 PMCID: PMC10498669 DOI: 10.1039/d3sc03228k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Abstract
Native mass spectrometry is a potent method for characterizing biomacromolecular assemblies. A critical aspect to extracting accurate mass information is the correct inference of the ion ensemble charge states. While a variety of experimental strategies and algorithms have been developed to facilitate this, virtually all approaches rely on the implicit assumption that any peaks in a native mass spectrum can be directly attributed to an underlying charge state distribution. Here, we demonstrate that this paradigm breaks down for several types of macromolecular protein complexes due to the intrinsic heterogeneity induced by the stochastic nature of their assembly. Utilizing several protein assemblies of adeno-associated virus capsids and ferritin, we demonstrate that these particles can produce a variety of unexpected spectral appearances, some of which appear superficially similar to a resolved charge state distribution. When interpreted using conventional charge inference strategies, these distorted spectra can lead to substantial errors in the calculated mass (up to ∼5%). We provide a novel analytical framework to interpret and extract mass information from these spectra by combining high-resolution native mass spectrometry, single particle Orbitrap-based charge detection mass spectrometry, and sophisticated spectral simulations based on a stochastic assembly model. We uncover that these mass spectra are extremely sensitive to not only mass heterogeneity within the subunits, but also to the magnitude and width of their charge state distributions. As we postulate that many protein complexes assemble stochastically, this framework provides a generalizable solution, further extending the usability of native mass spectrometry in the characterization of biomacromolecular assemblies.
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Affiliation(s)
- Victor Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Paul W A Devine
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Janet C Saunders
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Fiona Cusdin
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Alexandra Ristani
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Alistair Hines
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Sam Shepherd
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Marcin Dembek
- Purification Process Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Claire L Dobson
- In Vivo Expressed Biologics, Discovery Sciences, R & D, AstraZeneca Granta Park Cambridge UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, R & D, AstraZeneca Granta Park Cambridge UK
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Center Padualaan 8, 3584 CH Utrecht The Netherlands
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6
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Soni H, Lako I, Placidi M, Cramer SM. Implications of AAV affinity column reuse and vector stability on product quality attributes. Biotechnol Bioeng 2023. [PMID: 37485847 DOI: 10.1002/bit.28500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
In this work, the implications of AAV9 capsid design and column reuse on AAV9 vector product quality were assessed with POROS CaptureSelect (PCS) AAVX and AAV9 resins using sf9 insect cell-derived model AAV9 vectors with varying viral protein (VP) ratios. Chromatographic experiments with purified drug substance AAV9 model feeds indicated consistent vector elution profiles, independent of adeno-associated virus (AAV) VP ratio, or cycle number. In contrast, the presence of process impurities in the clarified lysate feeds resulted in clear changes in the elution patterns. This included increased aggregate content in the vector eluates over multiple cycles as well as clear differences in the performance of these affinity resin systems. The AAV9-serotype specific PCS AAV9 column, with lower vector elution pH, resulted in higher aggregate content over multiple cycles as compared to the serotype-independent PCS AAVX column. Further, the results with vectors of varying VP ratio indicated that while one vector type eluate displayed higher aggregation in both affinity columns over column reuse, the eluate with the other vector type did not exhibit changes in the aggregation profile. Interestingly, vector aggregates in the affinity eluates also contained double-stranded DNA impurities and histone proteins, with similar trends to the aggregate levels. This behavior upon column reuse indicates that these host cell impurities are likely carried over to subsequent runs due to incomplete clean-in-place (CIP). These results indicate that feed impurities, affinity resin characteristics, elution pH, column CIP, and vector stability can impact the reusability of AAV affinity columns and product quality.
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Affiliation(s)
- Harshal Soni
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Ira Lako
- Voyager Therapeutics, Cambridge, Massachusetts, USA
| | | | - Steven M Cramer
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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7
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Mietzsch M, Liu W, Ma K, Bennett A, Nelson AR, Gliwa K, Chipman P, Fu X, Bechler S, McKenna R, Viner R. Production and characterization of an AAV1-VP3-only capsid: An analytical benchmark standard. Mol Ther Methods Clin Dev 2023; 29:460-472. [PMID: 37273903 PMCID: PMC10238842 DOI: 10.1016/j.omtm.2023.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023]
Abstract
Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six approved biologics on the market. As such new analytical methods are continually being developed to characterize and monitor the quality and purity of manufactured AAV vectors, these include ion-exchange chromatography and Direct Mass Technology. However, these methods require homogeneous analytical standards with a high molecular weight standard comparable to the mass of an AAV capsid. Described here is the design, production, purification, characterization, and the cryo-electron microscopy structure of an AAV1-VP3-only capsid that fulfills this need as a calibrant to determine capsid mass, charge, homogeneity, and transgene packaging characteristics.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Weijing Liu
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA
| | - Ke Ma
- Thermo Fisher Scientific, 490 Lakeside Dr., Sunnyvale, CA 94085, USA
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Austin R. Nelson
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Keely Gliwa
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Shane Bechler
- Thermo Fisher Scientific, 490 Lakeside Dr., Sunnyvale, CA 94085, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA
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8
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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.
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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
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9
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Kostelic MM, Hsieh CC, Sanders HM, Zak CK, Ryan JP, Baker ES, Aspinwall CA, Marty MT. Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1031-1037. [PMID: 35588532 DOI: 10.1021/jasms.2c00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Native mass spectrometry (MS) and charge detection-mass spectrometry (CD-MS) have become versatile tools for characterizing a wide range of proteins and macromolecular complexes. Both commonly use nanoelectrospray ionization (nESI) from pulled borosilicate needles, but some analytes are known to nonspecifically adsorb to the glass, which may lower sensitivity and limit the quality of the data. To improve the sensitivity of native MS and CD-MS, we modified the surface of nESI needles with inert surface modifiers, including polyethylene-glycol. We found that the surface modification improved the signal intensity for native MS of proteins and for CD-MS of adeno-associated viral capsids. Based on mechanistic comparisons, we hypothesize that the improvement is more likely due to an increased flow rate with coated ESI needles rather than less nonspecific adsorption. In any case, these surface-modified needles provide a simple and inexpensive method for improving the sensitivity of challenging analytes.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack P Ryan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27659, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27659, United States
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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10
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Deng JZ, Rustandi R, Barbacci D, Swartz A, Gulasarian A, Loughney JW. RP-UPLC method for Oncolytic Coxsackievirus Viral Protein Separation and Empty to Full Capsid Quantification. Hum Gene Ther 2022; 33:765-775. [PMID: 35387488 PMCID: PMC9347376 DOI: 10.1089/hum.2022.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oncolytic virus immunotherapy is emerging as a novel therapeutic approach for cancer treatment. Immunotherapy clinical drug candidate V937 is currently in phase I/II clinical trials and consists of a proprietary formulation of Coxsackievirus A21 (CVA21), which specifically infects and lyses cells with overexpressed ICAM-1 receptors in a range of tumors. Mature Coxsackievirus virions, consisting of four structural virion proteins, (VPs) VP1, VP2, VP3, and VP4, and the RNA genome, are the only viral particles capable of being infectious. In addition to mature virions, empty procapsids with VPs, VP0, VP1, and VP3, and other virus particles are produced in V937 production cell culture. Viral protein VP0 is cleaved into VP2 and VP4 after RNA genome encapsidation to form mature virions. Clearance of viral particles containing VP0, and quantification of viral protein distribution are important in V937 downstream processing. Existing analytical methods for the characterization of viral proteins and particles may lack sensitivity or are low throughput. We developed a sensitive and robust reverse-phase ultra-performance chromatography method to separate, identify, and quantify all five CVA21 VPs. Quantification of virus capsid concentration and empty/full capsid ratio was achieved with good linearity, accuracy, and precision. ClinicalTrials.gov ID: NCT04521621 and NCT04152863.
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Affiliation(s)
- James Z Deng
- Merck & Co Inc, 2793, Vaccine Analytical Development, 770 Sumneytown Pike, WP46-3, PO Box 4, West Point, Pennsylvania, United States, 19486;
| | - Richard Rustandi
- Merck & Co Inc, 2793, Vaccine Analytical Development, West Point, Pennsylvania, United States;
| | - Damon Barbacci
- Spark Therapeutics Inc, 538392, Philadelphia, Pennsylvania, United States;
| | - Andrew Swartz
- Merck & Co Inc, 2793, Vaccine Process Development, West Point, Pennsylvania, United States;
| | - Amanda Gulasarian
- Merck & Co Inc, 2793, Vaccine Process Development, West Point, Pennsylvania, United States;
| | - John W Loughney
- Merck & Co Inc, 2793, Vaccine Analytical Development, West Point, Pennsylvania, United States;
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11
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PCR-Based Analytical Methods for Quantification and Quality Control of Recombinant Adeno-Associated Viral Vector Preparations. Pharmaceuticals (Basel) 2021; 15:ph15010023. [PMID: 35056080 PMCID: PMC8779925 DOI: 10.3390/ph15010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
Recombinant adeno-associated viral vectors (rAAV) represent a gene therapy tool of ever-increasing importance. Their utilization as a delivery vehicle for gene replacement, silencing and editing, among other purposes, demonstrate considerable versatility. Emerging vector utilization in various experimental, preclinical and clinical applications establishes the necessity of producing and characterizing a wide variety of rAAV preparations. Critically important characteristics concerning quality control are rAAV titer quantification and the detection of impurities. Differences in rAAV constructs necessitate the development of highly standardized quantification assays to make direct comparisons of different preparations in terms of assembly or purification efficiency, as well as experimental or therapeutic dosages. The development of universal methods for impurities quantification is rather complicated, since variable production platforms are utilized for rAAV assembly. However, general agreements also should be achieved to address this issue. The majority of methods for rAAV quantification and quality control are based on PCR techniques. Despite the progress made, increasing evidence concerning high variability in titration assays indicates poor standardization of the methods undertaken to date. This review summarizes successes in the field of rAAV quality control and emphasizes ongoing challenges in PCR applications for rAAV characterization. General considerations regarding possible solutions are also provided.
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Zanker J, Lázaro-Petri S, Hüser D, Heilbronn R, Savy A. Insight & Development of Advanced rAAV Analysis Tools Exploiting Single Particle Quantification by Multidimensional ddPCR. Hum Gene Ther 2021; 33:977-989. [PMID: 34937401 PMCID: PMC10112877 DOI: 10.1089/hum.2021.182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombinant Adeno-Associated Virus (rAAV) has become the most widely used vector in the gene therapy field with hundreds of clinical trials ongoing and already several products on the market. AAV's physico-chemical stability, and the various natural and engineered serotypes allow for targeting a broad range of cell types and tissue by diverse routes of administration. Progressing from early clinical studies to eventual market approval, many critical quality attributes (CQAs) have to be defined and reproducibly quantified, such as AAV stability, purity, aggregates, empty/full particles ratio and rAAV genome titration. Droplet digital PCR (ddPCR) is becoming the tool of choice to perform absolute quantification of rAAV genomes. In the present study, we have identified critical parameters that could impact AAV titration and characterization accuracy, such as Poisson distribution confidence interval, primers/probe position and potential aggregates. Our work presents how ddPCR can help to better characterize AAV vectors on the single particle level and highlights challenges that we are facing today in term of AAV titration.
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Affiliation(s)
- Jeanette Zanker
- Charité Universitätsmedizin Berlin Campus Benjamin Franklin, 9164, Institute of Health, Department of Neurology, AG Gene Therapy, Berlin, Berlin, Germany;
| | - Sara Lázaro-Petri
- Charité Universitätsmedizin Berlin Campus Benjamin Franklin, 9164, Institute of Health, Department of Neurology, AG Gene Therapy, Berlin, Berlin, Germany;
| | - Daniela Hüser
- Charité Universitätsmedizin Berlin Campus Benjamin Franklin, 9164, Institute of Health, Department of Neurology, AG Gene Therapy, Berlin, Berlin, Germany;
| | - Regine Heilbronn
- Charité Universitätsmedizin Berlin Campus Benjamin Franklin, 9164, Institute of Health, Department of Neurology, AG Gene Therapy, Berlin, Berlin, Germany;
| | - Adrien Savy
- Charité Universitätsmedizin Berlin Campus Benjamin Franklin, 9164, Institute of Health, Department of Neurology, AG Gene Therapy, Berlin, Berlin, Germany.,Kolibri, BioProcess, Paris, France;
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Li Z, Kitov PI, Kitova EN, Bui DT, Moremen KW, Wakarchuk WW, Mahal LK, Macauley MS, Klassen JS. Quantifying Carbohydrate-Active Enzyme Activity with Glycoprotein Substrates Using Electrospray Ionization Mass Spectrometry and Center-of-Mass Monitoring. Anal Chem 2021; 93:15262-15270. [PMID: 34752696 DOI: 10.1021/acs.analchem.1c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbohydrate-active enzymes (CAZymes) play critical roles in diverse physiological and pathophysiological processes and are important for a wide range of biotechnology applications. Kinetic measurements offer insight into the activity and substrate specificity of CAZymes, information that is of fundamental interest and supports diverse applications. However, robust and versatile kinetic assays for monitoring the kinetics of intact glycoprotein and glycolipid substrates are lacking. Here, we introduce a simple but quantitative electrospray ionization mass spectrometry (ESI-MS) method for measuring the kinetics of CAZyme reactions involving glycoprotein substrates. The assay, referred to as center-of-mass (CoM) monitoring (CoMMon), relies on continuous (real-time) monitoring of the CoM of an ensemble of glycoprotein substrates and their corresponding CAZyme products. Notably, there is no requirement for calibration curves, internal standards, labeling, or mass spectrum deconvolution. To demonstrate the reliability of CoMMon, we applied the method to the neuraminidase-catalyzed cleavage of N-acetylneuraminic acid (Neu5Ac) residues from a series of glycoproteins of varying molecular weights and degrees of glycosylation. Reaction progress curves and initial rates determined with CoMMon are in good agreement (initial rates within ≤5%) with results obtained, simultaneously, using an isotopically labeled Neu5Ac internal standard, which enabled the time-dependent concentration of released Neu5Ac to be precisely measured. To illustrate the applicability of CoMMon to glycosyltransferase reactions, the assay was used to measure the kinetics of sialylation of a series of asialo-glycoproteins by a human sialyltransferase. Finally, we show how combining CoMMon and the competitive universal proxy receptor assay enables the relative reactivity of glycoprotein substrates to be quantitatively established.
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Affiliation(s)
- Zhixiong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I Kitov
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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