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Tang Q, Keeler AM, Zhang S, Su Q, Lyu Z, Cheng Y, Gao G, Flotte TR. Two-Plasmid Packaging System for Recombinant Adeno-Associated Virus. Biores Open Access 2020; 9:219-228. [PMID: 33117614 PMCID: PMC7590824 DOI: 10.1089/biores.2020.0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
A number of packaging systems are available for production of recombinant adeno-associated virus vectors (rAAVs). Among these, the use of a two-plasmid cotransfection system, in which Rep and Cap genes and Ad helper genes are on the same plasmid, has not been frequently employed for good manufacturing practices (GMP) production, even though it presents some practical advantages over the common three-plasmid (triple) transfection method. To confirm and expand the utility of the two-plasmid system, we generated GMP-compatible versions of this system and used those package reporter genes in multiple capsid variants in direct comparison with triple transfection. Vector yields, purity, and empty-to-full ratios were comparable between double and triple transfection methods for all capsid variants tested. We performed an in vivo side-by-side comparison of double and triple transfection vectors following both intravenous injection and intramuscular injection in mice. Expression and transduction were evaluated in muscle and liver 4 weeks after injection. Additional studies of bioactivity were conducted in vivo using packaged vectors carrying a variety of cargos, including the therapeutic transgene, microRNA, and single- or double-stranded vector. Results showed that cargos packaged using double transfection were equivalently bioactive to those packaged using a triple transfection system. In conclusion, these data suggest the utility of midrange (1E12-1E16) GMP-compatible packaging of adeno-associated virus (AAV) vectors for several AAV capsids.
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Affiliation(s)
- Qiushi Tang
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Allison M. Keeler
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Songbo Zhang
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- 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
- Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Zhuoyao Lyu
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yangfan Cheng
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiology Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Terence R. Flotte
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- 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
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Adair JE, Enstrom MR, Haworth KG, Schefter LE, Shahbazi R, Humphrys DR, Porter S, Tam K, Porteus MH, Kiem HP. DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:796-809. [PMID: 32355868 PMCID: PMC7184234 DOI: 10.1016/j.omtm.2020.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022]
Abstract
In vivo tracking of retrovirus-tagged blood stem and progenitor cells is used to study hematopoiesis. Two techniques are used most frequently: sequencing the locus of retrovirus insertion, termed integration site analysis, or retrovirus DNA barcode sequencing. Of these, integration site analysis is currently the only available technique for monitoring clonal pools in patients treated with retrovirus-modified blood cells. A key question is how these two techniques compare in their ability to detect and quantify clonal contributions. In this study, we assessed both methods simultaneously in a clinically relevant nonhuman primate model of autologous, myeloablative transplantation. Our data demonstrate that both methods track abundant clones; however, DNA barcode sequencing is at least 5-fold more efficient than integration site analysis. Using computational simulation to identify the sources of low efficiency, we identify sampling depth as the major factor. We show that the sampling required for integration site analysis to achieve minimal coverage of the true clonal pool is likely prohibitive, especially in cases of low gene-modified cell engraftment. We also show that early subsampling of different blood cell lineages adds value to clone tracking information in terms of safety and hematopoietic biology. Our analysis demonstrates DNA barcode sequencing as a useful guide to maximize integration site analysis interpretation in gene therapy patients.
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Affiliation(s)
- Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mark R Enstrom
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kevin G Haworth
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lauren E Schefter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Reza Shahbazi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel R Humphrys
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shaina Porter
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Kenric Tam
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,School of Medicine, University of Washington, Seattle, WA 98195, USA
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Hurdles Associated with the Translational Use of Genetically Modified Cells. CURRENT STEM CELL REPORTS 2018; 4:39-45. [PMID: 33381387 DOI: 10.1007/s40778-018-0115-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of Review Recent advancements in the use of genetically modified hematopoietic stem cells (HSCs) and the emergent use of chimeric antigen receptor (CAR) T-cell immunotherapy has highlighted issues associated with the use of genetically engineered cellular products. This review explores some of the challenges linked with translating the use of genetically modified cells. Recent Findings The use of genetically modified HSCs for ADA-SCID now has European approval and the U.S. Food and Drug Administration recently approved the use of CAR-T cells for relapsed/refractory B-cell acute lymphoblastic leukemia. Current good manufacturing processes have now been developed for the collection, expansion, storage, modification, and administration of genetically modified cells. Summary Genetically engineered cells can be used for several therapeutic purposes. However, significant challenges remain in making these cellular therapeutics readily available. A better understanding of this technology along with improvements in the manufacturing process is allowing the translation process to become more standardized.
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Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential. J Virol 2017; 92:JVI.01639-17. [PMID: 29046446 DOI: 10.1128/jvi.01639-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in "enhancerless" self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the LMO2 gene and then measuring LMO2 expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, LMO2 expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required.IMPORTANCE Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene therapy. Self-inactivating vectors devoid of viral long-terminal-repeat enhancers have proven safe; however, transgene expression from cellular promoters is often insufficient for full phenotypic correction. Foamy virus is an attractive vector for gene therapy. We found foamy virus vectors to be remarkably less genotoxic, well below what was expected from their integration site preferences. We demonstrate that the foamy virus long terminal repeats contain an insulator element that binds CCCTC-binding factor and reduces its insertional genotoxicity. Our study elucidates a mechanism behind the low genotoxic potential of foamy virus, identifies a unique insulator, and supports the use of foamy virus as a vector for gene therapy.
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Singh S, Khan I, Khim S, Seymour B, Sommer K, Wielgosz M, Norgaard Z, Kiem HP, Adair J, Liggitt D, Nienhuis A, Rawlings DJ. Safe and Effective Gene Therapy for Murine Wiskott-Aldrich Syndrome Using an Insulated Lentiviral Vector. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 4:1-16. [PMID: 28344987 PMCID: PMC5363182 DOI: 10.1016/j.omtm.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/15/2016] [Indexed: 12/18/2022]
Abstract
Wiskott-Aldrich syndrome (WAS) is a life-threatening immunodeficiency caused by mutations within the WAS gene. Viral gene therapy to restore WAS protein (WASp) expression in hematopoietic cells of patients with WAS has the potential to improve outcomes relative to the current standard of care, allogeneic bone marrow transplantation. However, the development of viral vectors that are both safe and effective has been problematic. While use of viral transcriptional promoters may increase the risk of insertional mutagenesis, cellular promoters may not achieve WASp expression levels necessary for optimal therapeutic effect. Here we evaluate a self-inactivating (SIN) lentiviral vector combining a chromatin insulator upstream of a viral MND (MPSV LTR, NCR deleted, dl587 PBS) promoter driving WASp expression. Used as a gene therapeutic in Was−/− mice, this vector resulted in stable WASp+ cells in all hematopoietic lineages and rescue of T and B cell defects with a low number of viral integrations per cell, without evidence of insertional mutagenesis in serial bone marrow transplants. In a gene transfer experiment in non-human primates, the insulated MND promoter (driving GFP expression) demonstrated long-term polyclonal engraftment of GFP+ cells. These observations demonstrate that the insulated MND promoter safely and efficiently reconstitutes clinically effective WASp expression and should be considered for future WAS therapy.
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Affiliation(s)
- Swati Singh
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Iram Khan
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Socheath Khim
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Brenda Seymour
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karen Sommer
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Matthew Wielgosz
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zachary Norgaard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA 98105, USA
| | - Jennifer Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medical Oncology, University of Washington, Seattle, WA 98105, USA
| | - Denny Liggitt
- Department of Comparative Medicine, University of Washington, Seattle, WA 98105, USA
| | - Arthur Nienhuis
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Department of Immunology, University of Washington, Seattle, WA 98105, USA
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Jenkins CL, Bagarazzi ML, Kiem HP, Levine AJ, Ando D, June CH, Reid T, Emery DW. Rethinking the Regulatory Infrastructure for Human Gene Transfer Clinical Trials. Mol Ther 2016; 24:1173-7. [PMID: 27506378 PMCID: PMC5088757 DOI: 10.1038/mt.2016.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | | | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Arnold J Levine
- Institute for Advanced Study, The Simons Center for Systems Biology, Princeton, New Jersey, USA
| | - Dale Ando
- Therapeutic Development, Sangamo BioSciences, Inc., Richmond, California, USA
| | - Carl H June
- Department of Pathology and Laboratory Medicine and Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tony Reid
- Department of Medicine, University of California San Diego Health, La Jolla, California, USA
| | - David W Emery
- WCG Biosafety, WIRB-Copernicus Group, Puyallup, Washington, USA
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Derisking Drug-Induced Carcinogenicity for Novel Therapeutics. Trends Cancer 2016; 2:398-408. [DOI: 10.1016/j.trecan.2016.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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Evaluating the Safety of Retroviral Vectors Based on Insertional Oncogene Activation and Blocked Differentiation in Cultured Thymocytes. Mol Ther 2016; 24:1090-1099. [PMID: 26957223 PMCID: PMC4923324 DOI: 10.1038/mt.2016.55] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/24/2016] [Indexed: 12/20/2022] Open
Abstract
Insertional oncogenesis due to retroviral (RV) vector integration has caused recurrent leukemia in multiple gene therapy trials, predominantly due to vector integration effects at the LMO2 locus. While currently available preclinical safety models have been used for evaluating vector safety, none have predicted or reproduced the recurrent LMO2 integrations seen in previous X-linked severe combined immunodeficiency (X-SCID) and Wiskott–Aldrich clinical gene therapy trials. We now describe a new assay for assessing vector safety that recapitulates naturally occurring insertions into Lmo2 and other T-cell proto-oncogenes leading to a preleukemic developmental arrest in primary murine thymocytes cultured in vitro. This assay was used to compare the relative oncogenic potential of a variety of gamma-RV and lentiviral vectors and to assess the risk conferred by various transcriptional elements contained in these genomes. Gamma-RV vectors that contained full viral long-terminal repeats were most prone to causing double negative 2 (DN2) arrest and led to repeated cases of Lmo2 pathway activation, while lentiviral vectors containing these same elements were significantly less prone to activate proto-oncogenes or cause DN2 arrest. This work provides a new preclinical assay that is especially relevant for assessing safety in SCID disorders and provides a new tool for designing safer RV vectors.
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Huang Y, Havert M, Gavin D, Serabian M, Ong LL, McIntyre MC, Ferry N, Kume A, Petrin D, Fu YH, Marti A, Oliveira F, Pavittranon S, Shin W. Biodistribution studies: understanding international expectations. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016. [PMCID: PMC4837973 DOI: 10.1038/mtm.2016.22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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