1
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Nishiumi H, Hirohata K, Fukuhara M, Matsushita A, Tsunaka Y, Rocafort MAV, Maruno T, Torisu T, Uchiyama S. Combined 100 keV Cryo-Electron Microscopy and Image Analysis Methods to Characterize the Wider Adeno-Associated Viral Products. J Pharm Sci 2024; 113:1804-1815. [PMID: 38570072 DOI: 10.1016/j.xphs.2024.03.026] [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: 12/13/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Adeno-associated viruses (AAVs) are effective vectors for gene therapy. However, AAV drug products are inevitably contaminated with empty particles (EP), which lack a genome, owing to limitations of the purification steps. EP contamination can reduce the transduction efficiency and induce immunogenicity. Therefore, it is important to remove EPs and to determine the ratio of full genome-containing AAV particles to empty particles (F/E ratio). However, most of the existing methods fail to reliably evaluate F/E ratios that are greater than 90 %. In this study, we developed two approaches based on the image analysis of cryo-electron micrographs to determine the F/E ratios of various AAV products. Using our developed convolutional neural network (CNN) and morphological analysis, we successfully calculated the F/E ratios of various AAV products and determined the slight differences in the F/E ratios of highly purified AAV products (purity > 95 %). In addition, the F/E ratios calculated by analyzing more than 1000 AAV particles had good correlations with theoretical F/E ratios. Furthermore, the CNN reliably determined the F/E ratio with a smaller number of AAV particles than morphological analysis. Therefore, combining 100 keV cryo-EM with the developed image analysis methods enables the assessment of a wide range of AAV products.
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Affiliation(s)
- Haruka Nishiumi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kiichi Hirohata
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsuko Fukuhara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; U-medico Inc., 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Aoba Matsushita
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuo Tsunaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mark Allen Vergara Rocafort
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; U-medico Inc., 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; U-medico Inc., 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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2
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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. [PMID: 38888112 DOI: 10.1021/jasms.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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3
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Tsutsui M, Wada M, Arima A, Tsunekawa Y, Sasaki T, Sakamoto K, Yokota K, Baba Y, Kawai T, Okada T. Identifying Viral Vector Characteristics by Nanopore Sensing. ACS NANO 2024; 18:15695-15704. [PMID: 38836590 DOI: 10.1021/acsnano.4c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Using viral vectors as gene delivery vehicles for gene therapy necessitates their quality control. Here, we report on nanopore sensing for nondestructively inspecting genomes inside the nanoscale cargoes at the single-molecule level. Using ionic current measurements, we motion-tracked the adeno-associated virus (AAV) vectors as they translocated through a solid-state nanopore. Considering the varying contributions of the electrophoretic forces from the negatively charged internal polynucleotides of different lengths, the nanocargoes carrying longer DNA moved more slowly in the nanochannel. Moreover, ion blockage characteristics revealed their larger volume by up to approximately 3600 nm3 in proportion to the length of single-stranded DNA packaged inside, thereby allowing electrical discriminations of AAV vectors by the gene-derived physical features. The present findings can be a promising tool for the enhanced quality control of AAV products by enabling the screening of empty and intermediate vectors at the single-particle level.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Mikako Wada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
| | - Yuji Tsunekawa
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takako Sasaki
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kenji Sakamoto
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Kagawa 761-0395, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society, Nagoya University, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Takashi Okada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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4
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D'Atri V, Imiołek M, Quinn C, Finny A, Lauber M, Fekete S, Guillarme D. Size exclusion chromatography of biopharmaceutical products: From current practices for proteins to emerging trends for viral vectors, nucleic acids and lipid nanoparticles. J Chromatogr A 2024; 1722:464862. [PMID: 38581978 DOI: 10.1016/j.chroma.2024.464862] [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: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
The 21st century has been particularly productive for the biopharmaceutical industry, with the introduction of several classes of innovative therapeutics, such as monoclonal antibodies and related compounds, gene therapy products, and RNA-based modalities. All these new molecules are susceptible to aggregation and fragmentation, which necessitates a size variant analysis for their comprehensive characterization. Size exclusion chromatography (SEC) is one of the reference techniques that can be applied. The analytical techniques for mAbs are now well established and some of them are now emerging for the newer modalities. In this context, the objective of this review article is: i) to provide a short historical background on SEC, ii) to suggest some clear guidelines on the selection of packing material and mobile phase for successful method development in modern SEC; and iii) to highlight recent advances in SEC, such as the use of narrow-bore and micro-bore columns, ultra-wide pore columns, and low-adsorption column hardware. Some important innovations, such as recycling SEC, the coupling of SEC with mass spectrometry, and the use of alternative detectors such as charge detection mass spectrometry and mass photometry are also described. In addition, this review discusses the use of SEC in multidimensional setups and shows some of the most recent advances at the preparative scale. In the third part of the article, the possibility of SEC for the characterization of new modalities is also reviewed. The final objective of this review is to provide a clear summary of opportunities and limitations of SEC for the analysis of different biopharmaceutical products.
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Affiliation(s)
- Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland
| | | | | | - Abraham Finny
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | - Matthew Lauber
- Waters Corporation, Wyatt Technology, Santa Barbara, CA, USA
| | | | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU - Rue Michel Servet 1,4, 1211 Geneva, Switzerland.
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5
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Gizardin-Fredon H, Santo PE, Chagot ME, Charpentier B, Bandeiras TM, Manival X, Hernandez-Alba O, Cianférani S. Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions. Nat Commun 2024; 15:3516. [PMID: 38664367 PMCID: PMC11045720 DOI: 10.1038/s41467-024-47732-4] [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: 01/22/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Chemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95% of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa-5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20-100×) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
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Affiliation(s)
- Hugo Gizardin-Fredon
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France.
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France.
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6
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Yuan Y, Higashiyama K, Hashiba N, Masumi-Koizumi K, Yusa K, Uchida K. Concise Analysis of Single-Stranded DNA of Recombinant Adeno-Associated Virus By Automated Electrophoresis System. Hum Gene Ther 2024; 35:104-113. [PMID: 38062752 PMCID: PMC10890949 DOI: 10.1089/hum.2023.148] [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: 08/22/2023] [Accepted: 11/29/2023] [Indexed: 02/01/2024] Open
Abstract
Recombinant adeno-associated virus (rAAV) is a prominent viral vector currently available for human gene therapy. The diameter of the rAAV capsid is ∼25 nm, and a positive or negative single-stranded DNA is packaged within the vector capsid. In this report, we describe a concise method to examine the extracted rAAV genome using an automated electrophoresis system. The rAAV genome, prepared from vector particles through either heat treatment at 95°C for 10 min or the phenol-chloroform extraction method, was analyzed using an automated electrophoresis system under denaturation conditions. The heat treatment protocol demonstrated a comparable yield with the phenol-chloroform extraction protocol, and the quantified amounts of the rAAV genome obtained using the automated electrophoresis system were consistent with those quantitated by quantitative PCR. Additionally, crude rAAV extractions could also be analyzed by the automated electrophoresis system after DNase I treatment. These results indicated that this simple and quick analysis using automated electrophoresis is highly useful for confirming the purity and integrity of the rAAV genome.
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Affiliation(s)
- Yuzhe Yuan
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
| | - Kiyoko Higashiyama
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
| | - Noriko Hashiba
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
| | - Kyoko Masumi-Koizumi
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
| | - Keisuke Yusa
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
| | - Kazuhisa Uchida
- Graduate School of Science, Technology and Innovation, Kobe University, Chuo-ku, Kobe, Japan
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7
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Coll De Peña A, White JD, Mehta DR, Ben Frej M, Tripathi A. Microfluidic AAV Purity Characterization: New Insights into Serotype and Sample Treatment Variability. ACS OMEGA 2024; 9:4027-4036. [PMID: 38284067 PMCID: PMC10809679 DOI: 10.1021/acsomega.3c09006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
Despite recent advances in nucleic acid delivery systems with the success of LNP vehicles, adeno-associated virus (AAV) remains the leading platform for targeted gene delivery due to its low immunogenicity to humans, high transduction efficiency, and range of serotypes with varying tropisms. Depending on the therapeutic goals and serotype used, different production conditions may be more amenable, generating an ever-growing need for rapid yet robust analytical techniques to support the high-quality manufacturing of AAV. A critical bottleneck exists for assessing full capsids where rapid, high-throughput techniques capable of analyzing a range of serotypes are needed. Here, we present a rapid, high-throughput analytical technique, microfluidic electrophoresis, for the assessment of full capsids compatible with AAV1, AAV2, AAV6, AAV8, and AAV9 without the need for assay modifications or optimizations, and AAV5 with some constraints. The method presented in this study uses a mathematical formulation we developed previously with a reference standard to combine the independently obtained capsid protein and single-stranded DNA (ssDNA) profiles to estimate the percentage of full capsids in a sample of unknown concentration. We assessed the ability to use a single serotype (AAV8) as the reference standard regardless of the serotype of the sample being analyzed so long as the melting temperature (Tm) of the capsids is within 12 °C from the Tm of AAV8. Using this method, we are able to characterize samples ±6.1% with an average analytical turnaround time of <5 min/sample, using only 10 μL/sample at a concentration of 2.5 × 1012 VG/mL.
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Affiliation(s)
- Adriana Coll De Peña
- Center
for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - James D. White
- Applied
Genomics, Revvity, Hopkinton, Massachusetts 01748, United States
| | - Dipti R. Mehta
- Applied
Genomics, Revvity, Hopkinton, Massachusetts 01748, United States
| | - Menel Ben Frej
- Applied
Genomics, Revvity, Hopkinton, Massachusetts 01748, United States
| | - Anubhav Tripathi
- Center
for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
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8
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Hirohata K, Yamaguchi Y, Maruno T, Shibuya R, Torisu T, Onishi T, Chono H, Mineno J, Yuzhe Y, Higashiyama K, Masumi-Koizumi K, Uchida K, Yamamoto T, Uchida E, Okada T, Uchiyama S. Applications and Limitations of Equilibrium Density Gradient Analytical Ultracentrifugation for the Quantitative Characterization of Adeno-Associated Virus Vectors. Anal Chem 2024; 96:642-651. [PMID: 38165078 PMCID: PMC10794998 DOI: 10.1021/acs.analchem.3c01955] [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: 05/06/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Adeno-associated virus (AAV) vectors are produced as a mixture of the desired particle (full particle, FP), which is filled with the designed DNA, product-related impurities such as particle without DNA (empty particle, EP), and aggregates. Cesium chloride or iodixanol equilibrium density gradient ultracentrifugation (DGE-UC) has been used for the purification of AAV vectors. DGE-UC can separate FP from impurities based on the difference in their buoyant densities. Here, we report the applications and limitations of equilibrium density gradient analytical ultracentrifugation (DGE-AUC) using a modern AUC instrument that employs DGE-UC principles for the characterization and quantitation of AAV vectors. We evaluated the quantitative ability of DGE-AUC in comparison with sedimentation velocity AUC (SV-AUC) or band sedimentation AUC (BS-AUC) using AAVs with different DNA lengths and different serotypes. DGE-AUC enabled the accurate quantification of the ratio of FP to EP when the AAV vector primarily contains these particles. Furthermore, we developed a new workflow to identify the components of separated peaks in addition to FP and EP. Ultraviolet absorption spectra obtained by multiwavelength detection can also support peak assignment following component identification. DGE-AUC experiments for AAV vectors have limitations with regard to minor components with low absorption at the detected wavelength or those with a density similar to that of major components of AAV vectors. DGE-AUC is the only analytical method that can evaluate particle density heterogeneity; therefore, SV-AUC or BS-AUC and DGE-AUC are complementary methods for reliable assessment of the purity of AAV vectors.
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Affiliation(s)
- Kiichi Hirohata
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Yamaguchi
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahiro Maruno
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Risa Shibuya
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Torisu
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takayuki Onishi
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hideto Chono
- Takara
Bio Inc., 7-4-38 Nojihigashi, Kusatsu, Shiga 525-0058, Japan
| | - Junichi Mineno
- Takara
Bio Inc., 7-4-38 Nojihigashi, Kusatsu, Shiga 525-0058, Japan
| | - Yuan Yuzhe
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kiyoko Higashiyama
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kyoko Masumi-Koizumi
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kazuhisa Uchida
- Graduate
School of Science, Technology and Innovation, Kobe University, 1-7-49 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takenori Yamamoto
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-city, Kanagawa 210-9501, Japan
| | - Eriko Uchida
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-city, Kanagawa 210-9501, Japan
| | - Takashi Okada
- Institute
of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Susumu Uchiyama
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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9
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Fu Q, Lee YS, Green EA, Wang Y, Park SY, Polanco A, Lee KH, Betenbaugh M, McNally D, Yoon S. Design space determination to optimize DNA complexation and full capsid formation in transient rAAV manufacturing. Biotechnol Bioeng 2023; 120:3148-3162. [PMID: 37475681 DOI: 10.1002/bit.28508] [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: 12/26/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Recombinant adeno-associated virus (rAAV) vectors are a promising platform for in vivo gene therapies. However, cost-effective, well-characterized processes necessary to manufacture rAAV therapeutics are challenging to develop without an understanding of how process parameters (PPs) affect rAAV product quality attributes (PQAs). In this work, a central composite orthogonal experimental design was employed to examine the influence of four PPs for transient transfection complex formation (polyethylenimine:DNA [PEI:DNA] ratio, total DNA/cell, cocktail volume, and incubation time) on three rAAV PQAs related to capsid content (vector genome titer, vector genome:capsid particle ratio, and two-dimensional vector genome titer ratio). A regression model was established for each PQA using partial least squares, and a design space (DS) was defined in which Monte Carlo simulations predicted < 1% probability of failure (POF) to meet predetermined PQA specifications. Of the three PQAs, viral genome titer was most strongly correlated with changes in complexation PPs. The DS and acceptable PP ranges were largest when incubation time and cocktail volume were kept at mid-high setpoints, and PEI:DNA ratio and total DNA/cell were at low-mid setpoints. Verification experiments confirmed model predictive capability, and this work establishes a framework for studying other rAAV PPs and their relationship to PQAs.
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Affiliation(s)
- Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Erica A Green
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Ashli Polanco
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - David McNally
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
- MassBiologics, University of Massachusetts Chan Medical School, Mattapan, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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10
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Brimble MA, Winston SM, Davidoff AM. Stowaways in the cargo: Contaminating nucleic acids in rAAV preparations for gene therapy. Mol Ther 2023; 31:2826-2838. [PMID: 37533254 PMCID: PMC10556190 DOI: 10.1016/j.ymthe.2023.07.025] [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: 04/29/2023] [Revised: 07/11/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023] Open
Abstract
Recombinant AAV (rAAV) is the most used delivery vector for clinical gene therapy. However, many issues must be addressed before safer and more widespread implementation can be achieved. At present, efficacies are highly variable across trials and patients, and immune responses after treatment are widely reported. Although rAAV is capable of directly delivering gene-encoded therapeutic sequences, increased scrutiny of viral preparations for translational use have revealed contaminating nucleic acid species packaged within rAAV preparations. The introduction of non-therapeutic nucleic acids into a recipient patient adds to the risk burden, immunogenic or otherwise, of rAAV therapies. DNA from incomplete expression cassettes, portions of plasmids or vectors used to facilitate viral replication, and production cell line genomes all have the potential to be packaged within rAAV. Here, we review what is currently known about the profile, abundance, and post-treatment consequences of nucleic acid impurities within rAAV and cover strategies that have been developed to improve rAAV purity. Furthering our understanding of these aberrantly packaged DNA species will help to ensure the continued safe implementation of rAAV therapies as the number of patients treated with this modality increases.
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Affiliation(s)
- Mark A Brimble
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Stephen M Winston
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; St. Jude Children's Research Hospital Graduate School of Biomedical Sciences, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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11
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Kumar P, Wang M, Kumru OS, Hickey JM, Sanmiguel J, Zabaleta N, Vandenberghe LH, Joshi SB, Volkin DB. Correlating physicochemical and biological properties to define critical quality attributes of a rAAV vaccine candidate. Mol Ther Methods Clin Dev 2023; 30:103-121. [PMID: 37746246 PMCID: PMC10512015 DOI: 10.1016/j.omtm.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/08/2023] [Indexed: 09/26/2023]
Abstract
Recombinant adeno-associated viruses (rAAVs) are a preferred vector system in clinical gene transfer. A fundamental challenge to formulate and deliver rAAVs as stable and efficacious vaccines is to elucidate interrelationships between the vector's physicochemical properties and biological potency. To this end, we evaluated an rAAV-based coronavirus disease 2019 (COVID-19) vaccine candidate that encodes the Spike antigen (AC3) and is produced by a commercially viable process. First, state-of-the-art analytical techniques were employed to determine key structural attributes of AC3, including primary and higher-order structures, particle size, empty/full capsid ratios, aggregates, and multi-step thermal degradation pathway analysis. Next, several quantitative potency measures for AC3 were implemented, and data were correlated with the physicochemical analyses on thermally stressed and control samples. Results demonstrate links between decreasing AC3 physical stability profiles, in vitro transduction efficiency in a cell-based assay, and, importantly, in vivo immunogenicity in a mouse model. These findings are discussed in the general context of future development of rAAV-based vaccine candidates as well as specifically for the rAAV vaccine application under study.
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Affiliation(s)
- Prashant Kumar
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Michael Wang
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - John M. Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Julio Sanmiguel
- Grousbeck Gene Therapy Center, Mass Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Mass Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Luk H. Vandenberghe
- Grousbeck Gene Therapy Center, Mass Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
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12
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Wu D, Zhao X, Jimenez DA, Piszczek G. Size Exclusion Chromatography-Mass Photometry: A New Method for Adeno-Associated Virus Product Characterization. Cells 2023; 12:2264. [PMID: 37759487 PMCID: PMC10528216 DOI: 10.3390/cells12182264] [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: 08/10/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Over the past decade, adeno-associated viruses (AAVs) have attained significant prominence in gene therapy and genome editing applications, necessitating the development of robust and precise methodologies to ensure the quality and purity of AAV products. Existing AAV characterization techniques have proven effective for the analysis of pure and homogeneous AAV samples. However, there is still a demand for a rapid and low-sample-consumption method suitable for the characterization of lower purity or heterogeneous AAV samples commonly encountered in AAV products. Addressing this challenge, we propose the SEC-MP method, which combines size exclusion chromatography (SEC) with mass photometry (MP). In this novel approach, SEC effectively separates monomeric AAV particles from impurities, while the UV detector determines the virus particle concentration. MP complements this process by estimating the fraction of fully packaged AAVs in the total population of AAV particles. This combined methodology enables accurate determination of the titer of effective, fully packaged AAVs in samples containing aggregates, incorrectly packaged AAVs with incomplete genomes, protein or DNA fragments, and other impurities. Our experimental results demonstrate that SEC-MP provides valuable guidance for sample quality control and subsequent applications in the field of AAV research.
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Affiliation(s)
- Di Wu
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Xiaonan Zhao
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (D.A.J.)
| | - Diego Antonio Jimenez
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (X.Z.); (D.A.J.)
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
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13
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Grossen P, Skaripa Koukelli I, van Haasteren J, H E Machado A, Dürr C. The ice age - A review on formulation of Adeno-associated virus therapeutics. Eur J Pharm Biopharm 2023; 190:1-23. [PMID: 37423416 DOI: 10.1016/j.ejpb.2023.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Gene therapies offer promising therapeutic alternatives for many disorders that currently lack efficient treatment options. Due to their chemical nature and physico-chemical properties, delivery of polynucleic acids into target cells and subcellular compartments remains a significant challenge. Adeno-associated viruses (AAV) have gained a lot of interest for the efficient delivery of therapeutic single-stranded DNA (ssDNA) genomes over the past decades. More than a hundred products have been tested in clinical settings and three products have received market authorization by the US FDA in recent years. A lot of effort is being made to generate potent recombinant AAV (rAAV) vectors that show favorable safety and immunogenicity profiles for either local or systemic administration. Manufacturing processes are gradually being optimized to deliver a consistently high product quality and to serve potential market needs beyond rare indications. In contrast to protein therapeutics, most rAAV products are still supplied as frozen liquids within rather simple formulation buffers to enable sufficient product shelf life, significantly hampering global distribution and access. In this review, we aim to outline the hurdles of rAAV drug product development and discuss critical formulation and composition aspects of rAAV products under clinical evaluation. Further, we highlight recent development efforts in order to achieve stable liquid or lyophilized products. This review therefore provides a comprehensive overview on current state-of-the-art rAAV formulations and can further serve as a map for rational formulation development activities in the future.
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Affiliation(s)
- Philip Grossen
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland.
| | - Irini Skaripa Koukelli
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Joost van Haasteren
- F.Hoffmann-La Roche AG, Cell and Gene Therapy Unit, Gene Therapy Development Clinical Manufacturing, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexandra H E Machado
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christoph Dürr
- F.Hoffmann-La Roche AG, Pharma Technical Development, Pharmaceutical Development and Supplies EU, Grenzacherstrasse 124, 4070 Basel, Switzerland
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14
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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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15
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Richter K, Wurm C, Strasser K, Bauer J, Bakou M, VerHeul R, Sternisha S, Hawe A, Salomon M, Menzen T, Bhattacharya A. Purity and DNA content of AAV capsids assessed by analytical ultracentrifugation and orthogonal biophysical techniques. Eur J Pharm Biopharm 2023; 189:68-83. [PMID: 37196871 DOI: 10.1016/j.ejpb.2023.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Development and manufacturing adeno-associated virus (AAV)-based vectors for gene therapy requires suitable analytical methods to assess the quality of the formulations during development, as well as the quality of different batches and the consistency of the processes. Here, we compare biophysical methods to characterize purity and DNA content of viral capsids from five different serotypes (AAV2, AAV5, AAV6, AAV8, and AAV9). For this purpose, we apply multiwavelength sedimentation velocity analytical ultracentrifugation (SV-AUC) to obtain the species' contents and to derive the wavelength-specific correction factors for the respective insert-size. In an orthogonal manner we perform anion exchange chromatography (AEX) and UV-spectroscopy and the three methods yield comparable results on empty/filled capsid contents with these correction factors. Whereas AEX and UV-spectroscopy can quantify empty and filled AAVs, only SV-AUC could identify the low amounts of partially filled capsids present in the samples used in this study. Finally, we employ negative-staining transmission electron microscopy and mass photometry to support the empty/filled ratios with methods that classify individual capsids. The obtained ratios are consistent throughout the orthogonal approaches as long as no other impurities and aggregates are present. Our results show that the combination of selected orthogonal methods can deliver consistent empty/filled contents on non-standard genome sizes, as well as information on other relevant critical quality attributes, such as AAV capsid concentration, genome concentration, insert size length and sample purity to characterize and compare AAV preparations.
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Affiliation(s)
- Klaus Richter
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany.
| | - Christine Wurm
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Kim Strasser
- Sirion Biotech GmbH, am Haag 6, 82166 Gräfelfing, Germany
| | - Jana Bauer
- Sirion Biotech GmbH, am Haag 6, 82166 Gräfelfing, Germany
| | - Maria Bakou
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Ross VerHeul
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA
| | - Shawn Sternisha
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA
| | - Andrea Hawe
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | | | - Tim Menzen
- Coriolis Pharma Research GmbH, Fraunhoferstr. 18 b, 82152 Martinsried, Germany
| | - Akash Bhattacharya
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Dr, Indianapolis, IN 46268, USA.
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16
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Hiemenz C, Pacios-Michelena A, Helbig C, Vezočnik V, Strebl M, Nikels F, Hawe A, Garidel P, Menzen T. Characterization of Virus Particles and Submicron-Sized Particulate Impurities in Recombinant Adeno-Associated Virus Drug Product. J Pharm Sci 2023; 112:2190-2202. [PMID: 37211315 DOI: 10.1016/j.xphs.2023.05.009] [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: 03/20/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/23/2023]
Abstract
Characterization of particulate impurities such as aggregates is necessary to develop safe and efficacious adeno-associated virus (AAV) drug products. Although aggregation of AAVs can reduce the bioavailability of the virus, only a limited number of studies focus on the analysis of aggregates. We explored three technologies for their capability to characterize AAV monomers and aggregates in the submicron (<1 µm) size range: (i) mass photometry (MP), (ii) asymmetric flow field flow fractionation coupled to a UV-detector (AF4-UV/Vis) and (iii) microfluidic resistive pulse sensing (MRPS). Although low counts for aggregates impeded a quantitative analysis, MP was affirmed as an accurate and rapid method for quantifying the genome content of empty/filled/double-filled capsids, consistent with sedimentation velocity analytical ultracentrifugation results. MRPS and AF4-UV/Vis enabled the detection and quantification of aggregate content. The developed AF4-UV/Vis method separated AAV monomers from smaller aggregates, thereby enabling a quantification of aggregates <200 nm. MRPS was experienced as a straightforward method to determine the particle concentration and size distribution between 250-2000 nm, provided that the samples do not block the microfluidic cartridge. Overall, within this study we explored the benefits and limitations of the complementary technologies for assessing aggregate content in AAV samples.
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Affiliation(s)
| | | | | | | | - Michael Strebl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Felix Nikels
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany.
| | - Andrea Hawe
- Coriolis Pharma Research GmbH, Martinsried, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Innovation Unit, Germany
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, Germany.
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17
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Wu D, Xu P, Kelly M, Ryan ET, Kováč P, Piszczek G. Mass photometry: A powerful tool for carbohydrates-proteins conjugation monitoring and glycoconjugates molecular mass determination. Glycoconj J 2023; 40:401-412. [PMID: 37392327 PMCID: PMC10374364 DOI: 10.1007/s10719-023-10126-7] [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: 05/04/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 07/03/2023]
Abstract
Glycoconjugate vaccines are important additions to the existing means for prevention of diseases caused by bacterial and viral pathogens. Conjugating carbohydrates to proteins is a crucial step in the development of these vaccines. Traditional mass spectrometry techniques, such as MALDI-TOF and SELDI-TOF, have difficulties in detecting glycoconjugates with high molecular masses. Mass photometry (MP) is a single-molecule technique that has been recently developed, which allows mass measurements of individual molecules and generates mass distributions based on hundreds to thousands of these measurements. In this study, we evaluated the performance of MP in monitoring carbohydrate-protein conjugation reactions and characterization of conjugates. Three different glycoconjugates were prepared from carrier protein BSA, and one from a large protein complex, a virus capsid with 3.74 MDa molecular mass. The masses measured by MP were consistent with those obtained by SELDI-TOF-MS and SEC-MALS. The conjugation of BSA dimer to carbohydrate antigen was also successfully characterized. This study shows that the MP technique is a promising alternative to methods developed earlier for monitoring glycoconjugation reactions and characterization of glycoconjugates. It measures intact molecules in solution and it is highly accurate over a wide mass range. MP requires only a very small amount of sample and has no specific buffer constraints. Other MP advantages include minimal cost of consumables and rapid data collection and analysis. Its advantages over other methods make it a valuable tool for researchers in the glycoconjugation field.
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Affiliation(s)
- Di Wu
- Biophysics Core Facility, NHLBI, NIH, Bethesda, MD, 20892, USA.
| | - Peng Xu
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, 20892, USA
| | - Meagan Kelly
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pavol Kováč
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, 20892, USA
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18
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Bepperling A, Best J. Comparison of three AUC techniques for the determination of the loading status and capsid titer of AAVs. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:401-413. [PMID: 37245172 DOI: 10.1007/s00249-023-01661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
Due to the rise of adeno-associated viruses (AAVs) as gene therapy delivery vectors, boundary sedimentation velocity analytical ultracentrifugation (boundary SV-AUC) has been developed into a widely used quality control assay even for release analytics. It can be considered as the "gold standard" for the determination of the loading status of empty, partially filled, and full capsids especially when conducted in multiwavelength (MWL) mode. It can be considered to provide the most accurate determination of the loading status, and it also provides information on the capsid titer, aggregates, and potential contaminants such as free DNA. MWL boundary SV-AUC can be regarded as a multi-attribute (MAM) method for the characterization of AAVs. One major drawback of the method is the high sample consumption both in terms of concentration and volume. Here, we compare two alternative AUC techniques, band SV-AUC and analytical CsCl density gradient sedimentation equilibrium AUC (CsCl SE-AUC) with the boundary SV-AUC and the MWL-SV-AUC experiment. Our data show a high consistency of the determined full/empty ratios between these techniques if the appropriate wavelengths and extinction coefficients are used.
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Affiliation(s)
| | - Janine Best
- Novartis TRD, Keltenring 1+3, 82041, Oberhaching, Germany
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19
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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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20
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Abstract
Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.
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Affiliation(s)
- Jesse A Jones
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Robert Benisch
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
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21
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [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: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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22
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Troxell B, Tsai IW, Shah K, Knuckles CI, Shelton ST, Lindsey KA, Barbosa Cardenas SM, Roberts TB. Application of Size Exclusion Chromatography with Multi-Angle Light Scattering in the Analytical Development of a Preclinical Stage Gene Therapy Program. Hum Gene Ther 2023; 34:325-338. [PMID: 36927085 PMCID: PMC10125404 DOI: 10.1089/hum.2022.218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
To provide safe recombinant adeno-associated viruses (rAAV) to patients, scalable manufacturing processes are required. However, these processes may introduce impurities that impact the performance and quality of the final drug product. Empty rAAV capsids are product-related impurities. Regulatory guidance requires that accurate analytical methods be implemented early in product development to measure the level of empty capsids. A process confirmation vector, produced from 200L production, was used to develop and optimize a size exclusion chromatography with UV and multi-angle light scattering (SEC-MALS) method. Vector produced from a 500L production was used to assess the full-to-empty ratio using the following analytical methods: sedimentation velocity analytical ultracentrifugation (SV-AUC), ddPCR with capsid ELISA, bulk absorbance at 260nm/280nm, cryogenic electron microscopy (cryo-EM), and SEC-MALS. This test article was used for a 30-day, non-Good Laboratory Practices (GLP) animal study that assessed biodistribution of the product (STRX-330). SEC-MALS outperformed the other methods and correlated well with SV-AUC values of full-to-empty particles. In addition, SEC-MALS agreed with ddPCR and ELISA measurements for Vector Genomes (VG)/mL and Capsid Particles (CP)/mL, respectively. SEC-MALS was linear, accurate, and precise while achieving chromatography quality control (QC) recommendations. Compared to other stability-indicating assays, SEC-MALS performed similarly to ddPCR, capsid ELISA, and infectivity assays in accelerated stress studies. In response to alkaline, but not acidic stress, SEC-MALS indicated distinct changes in the DNA content of the monomer AAV peak for STRX-330, which was supported by ddPCR data. Conversely, acidic treatment resulted in more aggregated vector, but didn't impact the DNA content. This work indicates that SEC-MALS is a valuable analytical tool in the analytical development and quality control testing of AAV. In addition, this work suggests SEC-MALS can provide fundamental understanding of AAV in response to environmental stress. This may impact steps of the manufacturing process to minimize conditions that reduce performance.
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Affiliation(s)
- Bryan Troxell
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States.,AjaxBio, LLC, Holly Springs, North Carolina, United States;
| | - I-Wei Tsai
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Kinjal Shah
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Christopher I Knuckles
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Sarah T Shelton
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Kate A Lindsey
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Selene M Barbosa Cardenas
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
| | - Taylor B Roberts
- StrideBio, Analytical Development and Quality Control, Research Triangle Park, North Carolina, United States;
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23
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Coll De Peña A, Masto L, Atwood J, Tripathi A. Electrophoresis-Mediated Characterization of Full and Empty Adeno-Associated Virus Capsids. ACS OMEGA 2022; 7:23457-23466. [PMID: 35847322 PMCID: PMC9280930 DOI: 10.1021/acsomega.2c01813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Adeno-associated virus (AAV) has shown great potential in gene therapy due to its low immunogenicity, lack of pathogenicity to humans, and ability to provide long-term gene expression in vivo. However, there is currently a need for fast, high-throughput characterization systems that require low volumes for the determination of its sample composition in terms of full and empty capsids since empty capsids are a natural byproduct of AAV synthesis. To address this need, the following study proposes a high-throughput electrophoresis-mediated microfluidics approach that is independent of sample input concentration to estimate the composition of a given sample by combining its protein and ssDNA information relative to a standard. Using this novel approach, we were able to estimate the percentage of full capsids of six AAV8 samples with an average deviation from the actual percentage of 4%. The experiments used for these estimations were conducted with samples of varying percentages of full capsids (21-75%) and varying concentrations (5 × 1011-1 × 1012 VP/mL) with a total volume requirement of 3-10 μL for triplicate analysis of the sample. This method offers a rapid way to evaluate the quality and purity of AAV products. We believe that our method addresses the critical need as recognized by the gene and molecular therapy community.
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Affiliation(s)
- Adriana Coll De Peña
- Center
for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Lucy Masto
- Division
of Biology and Medicine, Brown University, Providence, Rhode Island 02912, United States
| | - James Atwood
- Applied
Genomics, PerkinElmer, Hopkinton, Massachusetts 01748, United States
| | - Anubhav Tripathi
- Center
for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, United States
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24
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Katsikis G, Hwang IE, Wang W, Bhat VS, McIntosh NL, Karim OA, Blus BJ, Sha S, Agache V, Wolfrum JM, Springs SL, Sinskey AJ, Barone PW, Braatz RD, Manalis SR. Weighing the DNA Content of Adeno-Associated Virus Vectors with Zeptogram Precision Using Nanomechanical Resonators. NANO LETTERS 2022; 22:1511-1517. [PMID: 35148107 DOI: 10.1021/acs.nanolett.1c04092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-associated virus (AAV) vectors, which are the most widely used viral vectors for in vivo gene therapy, are typically characterized using PCR, ELISA, and analytical ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as charge-detection mass spectroscopy, static light scattering, and mass photometry offer turnaround times of minutes for measuring AAV mass using optical or charge properties of AAV. Here, we demonstrate an orthogonal method where suspended nanomechanical resonators (SNR) are used to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a precision near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.
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Affiliation(s)
- Georgios Katsikis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Iris E Hwang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wade Wang
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Vikas S Bhat
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Nicole L McIntosh
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Omair A Karim
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Bartlomiej J Blus
- BioMarin Pharmaceutical, Inc., San Rafael, California 94901, United States
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent Agache
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard D Braatz
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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