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Liu H, Zhang Y, Yip M, Ren L, Liang J, Chen X, Liu N, Du A, Wang J, Chang H, Oh H, Zhou C, Xing R, Xu M, Guo P, Gessler D, Xie J, Tai PW, Gao G, Wang D. Producing high-quantity and high-quality recombinant adeno-associated virus by low-cis triple transfection. Mol Ther Methods Clin Dev 2024; 32:101230. [PMID: 38558570 PMCID: PMC10979107 DOI: 10.1016/j.omtm.2024.101230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Recombinant adeno-associated virus (rAAV)-based gene therapy is entering clinical and commercial stages at an unprecedented pace. Triple transfection of HEK293 cells is currently the most widely used platform for rAAV manufacturing. Here, we develop low-cis triple transfection that decreases transgene plasmid use by 10- to 100-fold and overcomes several major limitations associated with standard triple transfection. This new method improves packaging of yield-inhibiting transgenes by up to 10-fold, and generates rAAV batches with reduced plasmid backbone contamination that otherwise cannot be eliminated in downstream processing. When tested in mice and compared with rAAV produced by standard triple transfection, low-cis rAAV shows comparable or superior potency and results in diminished plasmid backbone DNA and RNA persistence in tissue. Mechanistically, low-cis triple transfection relies on the extensive replication of transgene cassette (i.e., inverted terminal repeat-flanked vector DNA) in HEK293 cells during production phase. This cost-effective method can be easily implemented and is widely applicable to producing rAAV of high quantity, purity, and potency.
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Affiliation(s)
- Hao Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yue Zhang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Mitchell Yip
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lingzhi Ren
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jialing Liang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xiupeng Chen
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nan Liu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ailing Du
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jiaming Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hao Chang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hyejin Oh
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Chen Zhou
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ruxiao Xing
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Mengyao Xu
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Peiyi Guo
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dominic Gessler
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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2
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Namkung S, Tran NT, Manokaran S, He R, Su Q, Xie J, Gao G, Tai PW. Direct ITR-to-ITR Nanopore Sequencing of AAV Vector Genomes. Hum Gene Ther 2022; 33:1187-1196. [PMID: 36178359 PMCID: PMC9700346 DOI: 10.1089/hum.2022.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/30/2022] [Indexed: 01/06/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) are currently the most prominently investigated vector platform for human gene therapy. The rAAV capsid serves as a potent and efficient vehicle for delivering genetic payloads into the host cell, while the vector genome determines the function and effectiveness of these biotherapies. However, current production schemes yield vectors that may consist of heterogeneous populations, compromising their potencies. The development of next-generation sequencing methods within the past few years have helped investigators profile the diversity and relative abundances of heterogenous species in vector preparations. Specifically, long-read sequencing methods, like single molecule real-time (SMRT) sequencing, have been used to uncover truncations, chimeric genomes, and inverted terminal repeat (ITR) mutations in vectors. Unfortunately, these sequencing platforms may be inaccessible to investigators with limited resources, require large amounts of input material, or may require long wait times for sequencing and analyses. Recent advances with nanopore sequencing have helped to bridge the gap for quick and relatively inexpensive long-read sequencing needs. However, their limitations and sample biases are not well-defined for sequencing rAAV. In this study, we explored the capacity for nanopore sequencing to directly interrogate rAAV content to obtain full-length resolution of encapsidated genomes. We found that the nanopore platform can cover the entirety of rAAV genomes from ITR to ITR without the need for pre-fragmentation. However, the accuracy for base calling was low, resulting in a high degree of miscalled bases and false indels. These false indels led to read-length compression; thus, assessing heterogeneity based on read length is not advisable with current nanopore technologies. Nonetheless, nanopore sequencing was able to correctly identify truncation hotspots in single-strand and self-complementary vectors similar to SMRT sequencing. In summary, nanopore sequencing can serve as a rapid and low-cost alternative for proofing AAV vectors.
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Affiliation(s)
- Suk Namkung
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Ngoc Tam Tran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA; and
| | - Sangeetha Manokaran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Ran He
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Qin Su
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Jun Xie
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA; and
| | - Guangping Gao
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA; and
- Li Weibo Institute of Rare Diseases Research, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA; and
- Li Weibo Institute of Rare Diseases Research, UMass Chan Medical School, Worcester, Massachusetts, USA
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3
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Tran NT, Lecomte E, Saleun S, Namkung S, Robin C, Weber K, Devine E, Blouin V, Adjali O, Ayuso E, Gao G, Penaud-Budloo M, Tai PW. Human and Insect Cell-Produced Recombinant Adeno-Associated Viruses Show Differences in Genome Heterogeneity. Hum Gene Ther 2022; 33:371-388. [PMID: 35293222 PMCID: PMC9063199 DOI: 10.1089/hum.2022.050] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
In the past two decades, adeno-associated virus (AAV) vector manufacturing has made remarkable advancements to meet large-scale production demands for preclinical and clinical trials. In addition, AAV vectors have been extensively studied for their safety and efficacy. In particular, the presence of empty AAV capsids and particles containing "inaccurate" vector genomes in preparations has been a subject of concern. Several methods exist to separate empty capsids from full particles; but thus far, no single technique can produce vectors that are free of empty or partial (non-unit length) capsids. Unfortunately, the exact genome compositions of full, intermediate, and empty capsids remain largely unknown. In this work, we used AAV-genome population sequencing to explore the compositions of DNase-resistant, encapsidated vector genomes produced by two common production pipelines: plasmid transfection in human embryonic kidney cells (pTx/HEK293) and baculovirus expression vectors in Spodoptera frugiperda insect cells (rBV/Sf9). Intriguingly, our results show that vectors originating from the same construct design that were manufactured by the rBV/Sf9 system produced a higher degree of truncated and unresolved species than those generated by pTx/HEK293 production. We also demonstrate that empty particles purified by cesium chloride gradient ultracentrifugation are not truly empty but are instead packaged with genomes composed of a single truncated and/or unresolved inverted terminal repeat (ITR). Our data suggest that the frequency of these "mutated" ITRs correlates with the abundance of inaccurate genomes in all fractions. These surprising findings shed new light on vector efficacy, safety, and how clinical vectors should be quantified and evaluated.
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Affiliation(s)
- Ngoc Tam Tran
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Emilie Lecomte
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Sylvie Saleun
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Suk Namkung
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
| | - Cécile Robin
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | | | - Eric Devine
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Veronique Blouin
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Oumeya Adjali
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Eduard Ayuso
- INSERM UMR 1089, University of Nantes, CHU of Nantes, Nantes, France
| | - Guangping Gao
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute of Rare Diseases Research; UMass Chan Medical School, Worcester, Massachusetts, USA
| | | | - Phillip W.L. Tai
- Horae Gene Therapy Center, UMass Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, USA
- Li Weibo Institute of Rare Diseases Research; UMass Chan Medical School, Worcester, Massachusetts, USA
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Tran NT, Heiner C, Weber K, Weiand M, Wilmot D, Xie J, Wang D, Brown A, Manokaran S, Su Q, Zapp ML, Gao G, Tai PW. AAV-Genome Population Sequencing of Vectors Packaging CRISPR Components Reveals Design-Influenced Heterogeneity. Mol Ther Methods Clin Dev 2020; 18:639-651. [PMID: 32775498 PMCID: PMC7397707 DOI: 10.1016/j.omtm.2020.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
The gene therapy field has been galvanized by two technologies that have revolutionized treating genetic diseases: vectors based on adeno-associated viruses (AAVs), and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene-editing tools. When combined into one platform, these safe and broadly tropic biotherapies can be engineered to target any region in the human genome to correct genetic flaws. Unfortunately, few investigations into the design compatibility of CRISPR components in AAV vectors exist. Using AAV-genome population sequencing (AAV-GPseq), we previously found that self-complementary AAV vector designs with strong DNA secondary structures can cause a high degree of truncation events, impacting production and vector efficacy. We hypothesized that the single-guide RNA (sgRNA) scaffold, which contains several loop regions, may also compromise vector integrity. We have therefore advanced the AAV-GPseq method to also interrogate single-strand AAV vectors to investigate whether vector genomes carrying Cas9-sgRNA cassettes can cause truncation events. We found that on their own, sgRNA sequences do not produce a high degree of truncation events. However, we demonstrate that vector genome designs that carry dual sgRNA expression cassettes in tail-to-tail configurations lead to truncations. In addition, we revealed that heterogeneity in inverted terminal repeat sequences in the form of regional deletions inherent to certain AAV vector plasmids can be interrogated.
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Affiliation(s)
- Ngoc Tam Tran
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Cheryl Heiner
- Pacific Biosciences, Inc., Menlo Park, CA 94025, USA
| | | | | | - Daniella Wilmot
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Alexander Brown
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sangeetha Manokaran
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Maria L. Zapp
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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5
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Yang YS, Xie J, Chaugule S, Wang D, Kim JM, Kim J, Tai PW, Seo SK, Gravallese E, Gao G, Shim JH. Bone-Targeting AAV-Mediated Gene Silencing in Osteoclasts for Osteoporosis Therapy. Mol Ther Methods Clin Dev 2020; 17:922-935. [PMID: 32405514 PMCID: PMC7210389 DOI: 10.1016/j.omtm.2020.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022]
Abstract
Improper activity of bone-resorbing osteoclasts results in low bone density and deterioration of bone structure, which increase the risk of fractures. Anti-resorptive therapies targeting osteoclasts have proven effective in preserving bone mass, but these therapeutic agents lead to defective new bone formation and numerous potential side effects. In this study, we demonstrate that recombinant adeno-associated virus, serotype 9 (rAAV9) can deliver to osteoclasts an artificial microRNA (amiR) that silences expression of key osteoclast regulators, RANK (receptor activator for nuclear factor κB) and cathepsin K (rAAV9.amiR-rank, rAAV9.amiR-ctsk), to prevent bone loss in osteoporosis. As rAAV9 is highly effective for the transduction of osteoclasts, systemic administration of rAAV9 carrying amiR-rank or amiR-ctsk results in a significant increase of bone mass in mice. Furthermore, the bone-targeting peptide motif (Asp)14 or (AspSerSer)6 was grafted onto the AAV9-VP2 capsid protein, resulting in significant reduction of transgene expression in non-bone peripheral organs. Finally, systemic delivery of bone-targeting rAAV9.amiR-ctsk counteracts bone loss and improves bone mechanical properties in mouse models of postmenopausal and senile osteoporosis. Collectively, inhibition of osteoclast-mediated bone resorption via bone-targeting rAAV9-mediated silencing of ctsk is a promising gene therapy that can preserve bone formation and mitigate osteoporosis, while limiting adverse off-target effects.
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Affiliation(s)
- Yeon-Suk Yang
- Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sachin Chaugule
- Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jung-Min Kim
- Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, USA
| | - JiHea Kim
- Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Seok-kyo Seo
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Ellen Gravallese
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jae-Hyuck Shim
- Division of Rheumatology, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
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6
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Affiliation(s)
- Phillip W.L. Tai
- Horae Gene Therapy Center and the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
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7
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Xu M, Li J, Xie J, He R, Su Q, Gao G, Tai PW. High-Throughput Quantification of In Vivo Adeno-Associated Virus Transduction with Barcoded Non-Coding RNAs. Hum Gene Ther 2019; 30:946-956. [PMID: 31072208 PMCID: PMC6703241 DOI: 10.1089/hum.2018.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) have become favorable gene delivery vehicles for expressing therapeutic transgenes. Capsid engineering efforts to produce novel AAVs with improved transduction efficiencies, unique tissue specificities, and reduced host immunities are a direct response to the high demand for treatment needs that preexisting rAAVs cannot currently fulfill. New AAV capsids discovered by directed evolution methods, in silico design, or from natural proviral sequences ultimately require extensive characterization in relevant in vivo models. Consequently, quantitative screening of candidate capsid libraries now requires reliable high-throughput sequencing approaches. In this study, we have developed a vector/transgene tracking system that employs the indexing of a non-coding RNA. Specifically, a barcoded Tough Decoy (bcTuD) that express highly stable RNA transcripts that can be used as readouts for transduction efficiency. The pseudo-hairpin structure of the bcTuD contains a variable region that is amenable to barcode insertion, which can be detected by target amplicon sequencing. The described approach, named AAV-bcTuD screening, offers a new alternative for in vivo assessment of rAAV that can accurately quantify vector genomes and transcript abundances in tissues, as exampled by the demonstration in liver and brain infections. Proof-of-concept is provided to show that vector genome and transcript detection in tissues with this method is accurate and consistent for a vector dose range of upwards to four logs in a mixed vector injection, showing that this technique is robust, sensitive, and applicable for multiplexed screening of capsid performance in vivo.
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Affiliation(s)
- Meiyu Xu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ran He
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
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8
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Tai PW, Xie J, Fong K, Seetin M, Heiner C, Su Q, Weiand M, Wilmot D, Zapp ML, Gao G. Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras. Mol Ther Methods Clin Dev 2018; 9:130-141. [PMID: 29766023 PMCID: PMC5948225 DOI: 10.1016/j.omtm.2018.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/05/2018] [Indexed: 02/05/2023]
Abstract
Recombinant adeno-associated virus (rAAV)-based gene therapy has entered a phase of clinical translation and commercialization. Despite this progress, vector integrity following production is often overlooked. Compromised vectors may negatively impact therapeutic efficacy and safety. Using single molecule, real-time (SMRT) sequencing, we can comprehensively profile packaged genomes as a single intact molecule and directly assess vector integrity without extensive preparation. We have exploited this methodology to profile all heterogeneic populations of self-complementary AAV genomes via bioinformatics pipelines and have coined this approach AAV-genome population sequencing (AAV-GPseq). The approach can reveal the relative distribution of truncated genomes versus full-length genomes in vector preparations. Preparations that seemingly show high genome homogeneity by gel electrophoresis are revealed to consist of less than 50% full-length species. With AAV-GPseq, we can also detect many reverse-packaged genomes that encompass sequences originating from plasmid backbone, as well as sequences from packaging and helper plasmids. Finally, we detect host-cell genomic sequences that are chimeric with inverted terminal repeat (ITR)-containing vector sequences. We show that vector populations can contain between 1.3% and 2.3% of this type of undesirable genome. These discoveries redefine quality control standards for viral vector preparations and highlight the degree of foreign products in rAAV-based therapeutic vectors.
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Affiliation(s)
- Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kaiyuen Fong
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Daniella Wilmot
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Maria L. Zapp
- Program in Molecular Medicine and Center for AIDS Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Cancer Center and National Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Corresponding author: Guangping Gao, Horae Gene Therapy Center, University of Massachusetts Medical School, 386 Plantation Street, Worcester, MA 01605, USA.
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9
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Ai J, Tai PW, Lu Y, Li J, Ma H, Su Q, Wei Q, Li H, Gao G. Characterization of adenoviral transduction profile in prostate cancer cells and normal prostate tissue. Prostate 2017; 77:1265-1270. [PMID: 28726259 PMCID: PMC5576497 DOI: 10.1002/pros.23386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/22/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Prostate diseases are common in males worldwide with high morbidity. Gene therapy is an attractive therapeutic strategy for prostate diseases, however, it is currently underdeveloped. As well known, adeno virus (Ad) is the most widely used gene therapy vector. The aims of this study are to explore transduction efficiency of Ad in prostate cancer cells and normal prostate tissue, thus further providing guidance for future prostate pathophysiological studies and therapeutic development of prostate diseases. METHODS We produced Ad expressing enhanced green fluorescence protein (EGFP), and characterized the transduction efficiency of Ad in both human and mouse prostate cancer cell lines in vitro, as well as prostate tumor xenograft, and wild-type mouse prostate tissue in vivo. Ad transduction efficiency was determined by EGFP fluorescence using microscopy and flow cytometry. Cell type-specific transduction was examined by immunofluorescence staining of cell markers. RESULTS Our data showed that Ad efficiently transduced human and mouse prostate cancer cells in vitro in a dose dependent manner. Following intratumoral and intraprostate injection, Ad could efficiently transduce prostate tumor xenograft and the major prostatic cell types in vivo, respectively. CONCLUSIONS Our findings suggest that Ad can efficiently transduce prostate tumor cells in vitro as well as xenograft and normal prostate tissue in vivo, and further indicate that Ad could be a potentially powerful toolbox for future gene therapy of prostate diseases.
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Affiliation(s)
- Jianzhong Ai
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiology Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yi Lu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Hong Ma
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Qiang Wei
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hong Li
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiology Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P.R. China
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Ai J, Ibraheim R, Tai PW, Gao G. A Scalable and Accurate Method for Quantifying Vector Genomes of Recombinant Adeno-Associated Viruses in Crude Lysate. Hum Gene Ther Methods 2017; 28:139-147. [PMID: 28488944 PMCID: PMC5488319 DOI: 10.1089/hgtb.2016.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/12/2017] [Indexed: 02/05/2023] Open
Abstract
Increasing interest and application of recombinant adeno-associated viruses (rAAVs) in basic and clinical research have urged efforts to improve rAAV production quality and yield. Standard vector production workflows call for genome titration of purified vectors at the endpoint of production to assess yield. Unfortunately, quality control measures for preparations during mid-production steps and economical means to assess the fidelity of multiple batches of rAAV preparations are lacking. Here we describe a scalable and accurate method for the direct quantitative polymerase chain reaction (qPCR) titration of rAAV genomes in crude lysate. Lysate samples are pretreated with DNase I to remove vector and packaging plasmid DNAs, followed by proteinase K to release endonuclease-resistant packaged viral genomes and to proteolyze factors inherent to crude lysates that can impinge upon quantitative PCR efficiencies. We show that this method is precise, scalable, and applicable for vector genome titrations of both single-stranded and self-complementary AAV genomes irrespective of serotype differences-a major limitation for standard lysate transduction methods that indirectly screen for vector packaging efficiency. Our described method therefore represents a significant improvement to rAAV vector production in terms of alleviating time and cost burdens, in-process quality control assessment, batch/lot monitoring in large-scale preparations, and good manufacturing practices.
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Affiliation(s)
- Jianzhong Ai
- Institute of Urology, Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Raed Ibraheim
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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11
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Xie J, He R, Su Q, Tai PW, Ma H, Li J, Gao G. 9. rAAV Designs Harboring DNA Secondary Structures with High Thermal Stabilities Produce Heterogenic Viral Genome Populations. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)32818-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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12
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Xu G, Luo L, Tai PW, Qin W, Xiao Y, Wang C, Su Q, Ma H, He R, Wei Y, Gao G. 7. High-Throughput Sequencing of AAV Proviral Libraries from the Human Population Reveals Novel Variants with Unprecedented Intra-and Inter-Tissue Diversity. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)32816-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Sung FC, Chen KP, Chen CY, Tai PW, Yang CF. Studies of the effect of salt iodization on endemic goiter in Taiwan. IV. A survey of drinking-water in relation to endemic goiter. Taiwan Yi Xue Hui Za Zhi 1973; 72:96-103. [PMID: 4512135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Sung FC, Chen CY, Fitzgerald EL, Lin YC, Tai PW. A comprehensive study of the Kaohsiung harbor and the Jen Ai river pollution. (Water pollution survey in 1971). Taiwan Yi Xue Hui Za Zhi 1972; 71:580-92. [PMID: 4510390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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