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Berkowitz SA, Larson N, Bou-Assaf G, Laue T. Rapid high-resolution size distribution protocol for adeno-associated virus using high speed SV-AUC. Anal Biochem 2024; 689:115482. [PMID: 38342199 DOI: 10.1016/j.ab.2024.115482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Simulated SV-AUC data for an adeno-associated virus (AAV) sample consisting of four components having closely spaced sedimentation coefficients were used to develop a high-speed protocol that optimized the size distribution analysis resolution. The resulting high speed (45K rpm) SV-AUC (hs-SV-AUC) protocol poses several experimental challenges: 1) the need for rapid data acquisition, 2) increased potential for optical artifacts from steep and fast moving boundaries and 3) the increased potential for convection. To overcome these challenges the protocol uses interference detection at low temperatures and data that are confined to a limited radial-time window. In addition to providing higher resolution AAV SV-AUC data and very short run times (<20 min after temperature equilibration), the need to match the sample and reference solvent composition and meniscus positions is relaxed making interference detection as simple to employ as absorbance detection. Finally, experimental data comparing hs-SV-AUC (at 45K rpm) with standard low-speed (15K rpm) SV-AUC on the same AAV sample demonstrate the size distribution resolution improvement. These experiments also validate the use of a radial-time window and show how quickly data can be acquired using the hs-SV-AUC protocol.
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Affiliation(s)
| | - Nicholas Larson
- Analytical Development, Biogen, 225 Binney St, Cambridge, MA, 02142, USA
| | - George Bou-Assaf
- Analytical Development, Biogen, 225 Binney St, Cambridge, MA, 02142, USA
| | - Thomas Laue
- University of New Hampshire, 10 Kelsey Road, Lee, NH, 03861, USA
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput Biol 2023; 19:e1011454. [PMID: 37669309 PMCID: PMC10503714 DOI: 10.1371/journal.pcbi.1011454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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Henrickson A, Ding X, Seal AG, Qu Z, Tomlinson L, Forsey J, Gradinaru V, Oka K, Demeler B. Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan. Nanomedicine (Lond) 2023; 18:1519-1534. [PMID: 37877696 PMCID: PMC10652292 DOI: 10.2217/nnm-2023-0156] [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: 05/30/2023] [Accepted: 09/04/2023] [Indexed: 10/26/2023] Open
Abstract
Aim: We present multi-wavelength (MW) analytical ultracentrifugation (AUC) methods offering superior accuracy for adeno-associated virus characterization and quantification. Methods: Experimental design guidelines are presented for MW sedimentation velocity and analytical buoyant density equilibrium AUC. Results: Our results were compared with dual-wavelength AUC, transmission electron microscopy and mass photometry. In contrast to dual-wavelength AUC, MW-AUC correctly quantifies adeno-associated virus capsid ratios and identifies contaminants. In contrast to transmission electron microscopy, partially filled capsids can also be detected and quantified. In contrast to mass photometry, first-principle results are obtained. Conclusion: Our study demonstrates the improved information provided by MW-AUC, highlighting the utility of several recently integrated UltraScan programs, and reinforces AUC as the gold-standard analysis for viral vectors.
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Affiliation(s)
- Amy Henrickson
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Xiaozhe Ding
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Austin G Seal
- Gene Vector Core, Advanced Technology Cores, Baylor College of Medicine Houston, TX 77030, USA
| | - Zhe Qu
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - John Forsey
- Pharmaron Biologics Ltd, Speke, Liverpool, L24 8RB, UK
| | - Viviana Gradinaru
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kazuhiro Oka
- Gene Vector Core, Advanced Technology Cores, Baylor College of Medicine Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, TX 77030, USA
| | - Borries Demeler
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, USA
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540690. [PMID: 37425873 PMCID: PMC10327192 DOI: 10.1101/2023.05.14.540690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Bou-Assaf GM, Budyak IL, Brenowitz M, Day ES, Hayes D, Hill J, Majumdar R, Ringhieri P, Schuck P, Lin JC. Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci 2022; 111:2121-2133. [PMID: 34986360 DOI: 10.1016/j.xphs.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.
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Affiliation(s)
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Eric S Day
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080
| | - David Hayes
- IntlSoSci, 23 Washington St., Gorham, NH 03581
| | - John Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98105
| | - Ranajoy Majumdar
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paola Ringhieri
- Analytical Development Biotech Department, Merck Serono S.p.a, Guidonia, RM, Italy; an affiliate of Merck KGaA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Jasper C Lin
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080.
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