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Wang G, Ma Q, Wei C, Yu L, Bi H, Jin J, Qin X, Zhou Y, Wang J. Assessment of Key Factors Impacting Variability in AAV Vector Genome Titration by Digital PCR. Int J Mol Sci 2024; 25:5149. [PMID: 38791184 PMCID: PMC11121146 DOI: 10.3390/ijms25105149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Recombinant adeno-associated virus (rAAV) has emerged as a prominent vector for in vivo gene therapy, owing to its distinct advantages. Accurate determination of the rAAV genome titer is crucial for ensuring the safe and effective administration of clinical doses. The evolution of the rAAV genome titer assay from quantitative PCR (qPCR) to digital PCR (dPCR) has enhanced accuracy and precision, yet practical challenges persist. This study systematically investigated the impact of various operational factors on genome titration in a single-factor manner, aiming to address potential sources of variability in the quantitative determination process. Our findings revealed that a pretreatment procedure without genome extraction exhibits superior precision compared with titration with genome extraction. Additionally, notable variations in titration results across different brands of dPCR instruments were documented, with relative standard deviation (RSD) reaching 23.47% for AAV5 and 11.57% for AAV8. Notably, optimal operations about DNase I digestion were identified; we thought treatment time exceeding 30 min was necessary, and there was no need for thermal inactivation after digestion. And we highlighted that thermal capsid disruption before serial dilution substantially affected AAV genome titers, causing a greater than ten-fold decrease. Conversely, this study found that additive components of dilution buffer are not significant contributors to titration variations. Furthermore, we found that repeated freeze-thaw cycles significantly compromised AAV genome titers. In conclusion, a comprehensive dPCR titration protocol, incorporating insights from these impact factors, was proposed and successfully tested across multiple serotypes of AAV. The results demonstrate acceptable variations, with the RSD consistently below 5.00% for all tested AAV samples. This study provides valuable insights to reduce variability and improve the reproducibility of AAV genome titration using dPCR.
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Affiliation(s)
- Guangyu Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Qiang Ma
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Changlong Wei
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Lei Yu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Hua Bi
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Jing Jin
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Xi Qin
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yong Zhou
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Junzhi Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
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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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3
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Tereshko L, Zhao X, Gagnon J, Lin T, Ewald T, Wang Y, Feschenko M, Mason C. A novel method for quantitation of AAV genome integrity using duplex digital PCR. PLoS One 2023; 18:e0293277. [PMID: 38096204 PMCID: PMC10721069 DOI: 10.1371/journal.pone.0293277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/10/2023] [Indexed: 12/17/2023] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have become a reliable strategy for delivering gene therapies. As rAAV capsid content is known to be heterogeneous, methods for rAAV characterization are critical for assessing the efficacy and safety of drug products. Multiplex digital PCR (dPCR) has emerged as a popular molecular approach for characterizing capsid content due to its high level of throughput, accuracy, and replicability. Despite growing popularity, tools to accurately analyze multiplexed data are scarce. Here, we introduce a novel statistical model to estimate genome integrity from duplex dPCR assays. This work demonstrates that use of a Poisson-multinomial mixture distribution significantly improves the accuracy and quantifiable range of duplex dPCR assays over currently available models.
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Affiliation(s)
- Lauren Tereshko
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
| | - Xiaohui Zhao
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
| | - Jake Gagnon
- Biostatistics, Biogen, Cambridge, Massachusetts, United States of America
| | - Tinchi Lin
- Analytics and Data Sciences, Biogen, Cambridge, Massachusetts, United States of America
| | - Trevor Ewald
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
| | - Yu Wang
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
| | - Marina Feschenko
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
| | - Cullen Mason
- Analytical Development, Biogen, Cambridge, Massachusetts, United States of America
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Zanker J, Hüser D, Savy A, Lázaro-Petri S, Hammer EM, Schwarzer C, Heilbronn R. Evaluation of the SH-SY5Y cell line as an in vitro model for potency testing of a neuropeptide-expressing AAV vector. Front Mol Neurosci 2023; 16:1280556. [PMID: 38098942 PMCID: PMC10720649 DOI: 10.3389/fnmol.2023.1280556] [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: 08/20/2023] [Accepted: 10/23/2023] [Indexed: 12/17/2023] Open
Abstract
Viral vectors have become important tools for basic research and clinical gene therapy over the past years. However, in vitro testing of vector-derived transgene function can be challenging when specific post-translational modifications are needed for biological activity. Similarly, neuropeptide precursors need to be processed to yield mature neuropeptides. SH-SY5Y is a human neuroblastoma cell line commonly used due to its ability to differentiate into specific neuronal subtypes. In this study, we evaluate the suitability of SH-SY5Y cells in a potency assay for neuropeptide-expressing adeno-associated virus (AAV) vectors. We looked at the impact of neuronal differentiation and compared single-stranded (ss) AAV and self-complementary (sc) AAV transduction at increasing MOIs, RNA transcription kinetics, as well as protein expression and mature neuropeptide production. SH-SY5Y cells proved highly transducible with AAV1 already at low MOIs in the undifferentiated state and even better after neuronal differentiation. Readouts were GFP or neuropeptide mRNA expression. Production of mature neuropeptides was poor in undifferentiated cells. By contrast, differentiated cells produced and sequestered mature neuropeptides into the medium in a MOI-dependent manner.
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Affiliation(s)
- Jeanette Zanker
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniela Hüser
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Adrien Savy
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sara Lázaro-Petri
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eva-Maria Hammer
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christoph Schwarzer
- Institute of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Regine Heilbronn
- Department of Neurology, AG Gene Therapy, Berlin Institute of Health, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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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: 4] [Impact Index Per Article: 4.0] [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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Doan TNK, Le MD, Bajrovic I, Celentano L, Krause C, Balyan HG, Svancarek A, Mote A, Tretiakova A, Jude Samulski R, Croyle MA. Thermostability and in vivo performance of AAV9 in a film matrix. COMMUNICATIONS MEDICINE 2022; 2:148. [DOI: 10.1038/s43856-022-00212-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Abstract
Background
Adeno-associated virus (AAV) vectors are stored and shipped frozen which poses logistic and economic barriers for global access to these therapeutics. To address this issue, we developed a method to stabilize AAV serotype 9 (AAV9) in a film matrix that can be stored at ambient temperature and administered by systemic injection.
Methods
AAV9 expressing the luciferase transgene was mixed with formulations, poured into molds and films dried under aseptic conditions. Films were packaged in individual particle-free bags with foil overlays and stored at various temperatures under controlled humidity. Recovery of AAV9 from films was determined by serial dilution of rehydrated film in media and infection of HeLa RC32 cells. Luciferase expression was compared to that of films rehydrated immediately after drying. Biodistribution of vector was determined by in vivo imaging and quantitative real-time PCR. Residual moisture in films was determined by Karl Fischer titration.
Results
AAV9 embedded within a film matrix and stored at 4 °C for 5 months retained 100% of initial titer. High and low viscosity formulations maintained 90 and 85% of initial titer after 6 months at 25 °C respectively. AAV was not detected after 4 months in a Standard Control Formulation under the same conditions. Biodistribution and transgene expression of AAV stored in film at 25 or 4 °C were as robust as vector stored at −80 °C in a Standard Control Formulation.
Conclusions
These results suggest that storage of AAV in a film matrix facilitates easy transport of vector to remote sites without compromising in vivo performance.
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