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Penaud-Budloo M, Broucque F, Harrouet K, Bouzelha M, Saleun S, Douthe S, D’Costa S, Ogram S, Adjali O, Blouin V, Lock M, Snyder RO, Ayuso E. Stability of the adeno-associated virus 8 reference standard material. Gene Ther 2019; 26:211-215. [DOI: 10.1038/s41434-019-0072-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 12/27/2022]
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Abstract
The adeno-associated viral vector (AAV) platform has developed into a primary modality for efficient in vivo, and in more limited settings, in vitro or ex vivo gene transfer. Its applications range from a tool for experimental purposes to preclinical and clinical gene therapy. The ability to accurately and reproducibly quantify vector concentration is critical for any of these applications. While several quantification assays are available, here we outline a detailed protocol for the quantification of DNase-I protected vector genomes reliant on the polymerase chain reaction (PCR) as a measure of the active component of the vector, namely its transgene cargo. With the emergence of droplet digital PCR (ddPCR), we provide side-by-side protocols for traditional TaqMan™ real-time, quantitative PCR (qPCR) and ddPCR, as well as comparative data generated with both methods. Lastly, we discuss the importance of the use of surfactant (here, Pluronic® F-68) in the execution of the assay to limit DNA and AAV adherence to various carriers during the titration, particularly at low concentrations. We believe these protocols can lead to reduced variability and increased comparability between AAV studies.
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Pacouret S, Bouzelha M, Shelke R, Andres-Mateos E, Xiao R, Maurer A, Mevel M, Turunen H, Barungi T, Penaud-Budloo M, Broucque F, Blouin V, Moullier P, Ayuso E, Vandenberghe LH. AAV-ID: A Rapid and Robust Assay for Batch-to-Batch Consistency Evaluation of AAV Preparations. Mol Ther 2017; 25:1375-1386. [PMID: 28427840 DOI: 10.1016/j.ymthe.2017.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are promising clinical candidates for therapeutic gene transfer, and a number of AAV-based drugs may emerge on the market over the coming years. To insure the consistency in efficacy and safety of any drug vial that reaches the patient, regulatory agencies require extensive characterization of the final product. Identity is a key characteristic of a therapeutic product, as it ensures its proper labeling and batch-to-batch consistency. Currently, there is no facile, fast, and robust characterization assay enabling to probe the identity of AAV products at the protein level. Here, we investigated whether the thermostability of AAV particles could inform us on the composition of vector preparations. AAV-ID, an assay based on differential scanning fluorimetry (DSF), was evaluated in two AAV research laboratories for specificity, sensitivity, and reproducibility, for six different serotypes (AAV1, 2, 5, 6.2, 8, and 9), using 67 randomly selected AAV preparations. In addition to enabling discrimination of AAV serotypes based on their melting temperatures, the obtained fluorescent fingerprints also provided information on sample homogeneity, particle concentration, and buffer composition. Our data support the use of AAV-ID as a reproducible, fast, and low-cost method to ensure batch-to-batch consistency in manufacturing facilities and academic laboratories.
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Affiliation(s)
- Simon Pacouret
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Mohammed Bouzelha
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Rajani Shelke
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Eva Andres-Mateos
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Ru Xiao
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Anna Maurer
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Biological and Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Mathieu Mevel
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Heikki Turunen
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Trisha Barungi
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA
| | - Magalie Penaud-Budloo
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Frédéric Broucque
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Véronique Blouin
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Philippe Moullier
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Eduard Ayuso
- Atlantic Gene Therapies, INSERM UMR 1089, University of Nantes, Nantes University Hospital, 22 Boulevard Benoni Goullin, 44200 Nantes, France
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, 20 Staniford Street, Boston, MA 02114, USA; Department of Ophthalmology, Ocular Genomics Institute, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA; Schepens Eye Research Institute, 20 Staniford Street, Boston MA 02114, USA; Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e260. [PMID: 26506038 PMCID: PMC4881760 DOI: 10.1038/mtna.2015.32] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022]
Abstract
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.
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