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Eisenhut P, Andorfer P, Haid A, Jokl B, Mannhartsberger R, Fuchsberger F, Innthaler B, Lengler J, Kraus B, Pletzenauer R, Hernandez Bort JA, Unterthurner S. Orthogonal characterization of rAAV9 reveals unexpected transgene heterogeneity. J Biotechnol 2024; 393:S0168-1656(24)00207-4. [PMID: 39106910 DOI: 10.1016/j.jbiotec.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is the most widely used viral vector for in vivo human gene therapy. To ensure safety and efficacy of gene therapy products, a comprehensive analytical profile of the rAAVs is needed, which provides crucial information for therapeutic development and manufacturing. Besides information on rAAV quantities and possible contaminating DNA and protein species, assessing rAAV quality is of utmost importance. In vitro biopotency and methods to determine the full/empty ratio of rAAV capsids are commonly applied, but methods to assess the integrity of the viral genome are still rarely used. Here we describe an orthogonal approach to characterize rAAV quality. Two biologically different rAAV9s from different stages of the bioprocess, generated each with two different transfection reagents, were investigated. In vitro biopotency tests in all cases demonstrated that rAAV9s generated with transfection reagent FectoVIR® possessed a higher biological activity. Mass-based analytical methods, such as sedimentation velocity analytical ultracentrifugation (AUC) and mass photometry, showed a high share of full capsids (>80%) at late process stages but did not detect any differences in the rAAV9s from the different transfection reagents. Multiplex dPCR and Nanopore long-read sequencing both demonstrated that, also in late-stage process samples, sample heterogeneity was relatively high with a rather small share of full-length transgenes of ~10 to 40%. Intriguingly, both methods detected a higher share of complete transgenes in rAAV9 generated with transfection reagent FectoVIR® instead of Polyethylenimine (PEI), and thereby explain the differences already observed in the biopotency assays. This study therefore emphasizes the necessity to utilize multiple, orthogonal methods to gain a better understanding of recombinantly manufactured AAVs.
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Affiliation(s)
- Peter Eisenhut
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Peter Andorfer
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Andrea Haid
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Beatrice Jokl
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Raffaela Mannhartsberger
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Felix Fuchsberger
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Bernd Innthaler
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Johannes Lengler
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Barbara Kraus
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Robert Pletzenauer
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria
| | - Juan A Hernandez Bort
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria; Department of Analytical Chemistry, University of Vienna, Vienna, 1090, Austria.
| | - Sabine Unterthurner
- Gene Therapy Process Development, Baxalta Innovations GmbH, part of Takeda companies, Orth an der Donau, 2304 Orth an der Donau, Austria.
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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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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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Korotkaja K, Zajakina A. Recombinant Virus Quantification Using Single-Cell Droplet Digital PCR: A Method for Infectious Titer Quantification. Viruses 2023; 15:v15051060. [PMID: 37243145 DOI: 10.3390/v15051060] [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: 03/25/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The quantification of viruses is necessary for both research and clinical applications. The methods available for RNA virus quantification possess several drawbacks, including sensitivity to inhibitors and the necessity of a standard curve generation. The main purpose of this study was to develop and validate a method for the quantification of recombinant, replication-deficient Semliki Forest virus (SFV) vectors using droplet digital PCR (ddPCR). This technique demonstrated stability and reproducibility using various sets of primers that targeted inserted transgenes, as well as the nsP1 and nsP4 genes of the SFV genome. Furthermore, the genome titers in the mixture of two types of replication-deficient recombinant virus particles were successfully measured after optimizing the annealing/extension temperature and virus:virus ratios. To measure the infectious units, we developed a single-cell ddPCR, adding the whole infected cells to the droplet PCR mixture. Cell distribution in the droplets was investigated, and β-actin primers were used to normalize the quantification. As a result, the number of infected cells and the virus infectious units were quantified. Potentially, the proposed single-cell ddPCR approach could be used to quantify infected cells for clinical applications.
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Affiliation(s)
- Ksenija Korotkaja
- Cancer Gene Therapy Group, Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k.1, LV-1067 Riga, Latvia
| | - Anna Zajakina
- Cancer Gene Therapy Group, Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, k.1, LV-1067 Riga, Latvia
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