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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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2
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Rajawat YS, Humbert O, Cook SM, Radtke S, Pande D, Enstrom M, Wohlfahrt ME, Kiem HP. In Vivo Gene Therapy for Canine SCID-X1 Using Cocal-Pseudotyped Lentiviral Vector. Hum Gene Ther 2020; 32:113-127. [PMID: 32741228 DOI: 10.1089/hum.2020.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC)-based ex vivo gene therapy has demonstrated clinical success for X-linked severe combined immunodeficiency (SCID-X1) patients who lack a suitable donor for HSPC transplantation. Nevertheless, this form of treatment is associated with an increased risk of infectious disease complications and genotoxicity mainly due to the conditioning regimen. In addition, ex vivo gene therapy approaches require sophisticated facilities to manufacture gene-modified cells and to care for the patients after chemotherapy. Considering these impediments, we have developed an in vivo gene therapy approach to treat canine SCID-X1 after HSPC mobilization and systemic delivery of the therapeutic vector. Here, we investigated the use of the cocal envelope to pseudotype a lentiviral (LV) vector expressing a functional gammaC gene. The cocal envelope is resistant to serum inactivation compared with the commonly used vesicular stomatitis virus envelope glycoprotein (VSV-G) envelope and thus well suited for systemic delivery. Two SCID-X1 neonatal canines treated with this approach achieved long-term therapeutic immune reconstitution with no prior conditioning. Therapeutic levels of gene-corrected CD3+ T cells were demonstrated for at least 16 months, and all other correlates of T cell functionality were within normal range. Retroviral integration-site analysis demonstrated polyclonal T cell reconstitution. Comparative analysis of integration profiles of foamy viral (FV) vector and cocal LV vector after in vivo gene therapy found distinct integration-site patterns. These data demonstrate that clinically relevant and durable correction of canine SCID-X1 can be achieved with in vivo delivery of cocal LV. Since manufacturing of cocal LV is similar to VSV-G LV, this approach is easily translatable to a clinical setting, thus providing for a highly portable and accessible gene therapy platform for SCID-X1.
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Affiliation(s)
- Yogendra S Rajawat
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Savannah M Cook
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stefan Radtke
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Dnyanada Pande
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark Enstrom
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Martin E Wohlfahrt
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.,Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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3
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Rajawat YS, Humbert O, Kiem HP. In-Vivo Gene Therapy with Foamy Virus Vectors. Viruses 2019; 11:v11121091. [PMID: 31771194 PMCID: PMC6950547 DOI: 10.3390/v11121091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022] Open
Abstract
Foamy viruses (FVs) are nonpathogenic retroviruses that infect various animals including bovines, felines, nonhuman primates (NHPs), and can be transmitted to humans through zoonotic infection. Due to their non-pathogenic nature, broad tissue tropism and relatively safe integration profile, FVs have been engineered as novel vectors (foamy virus vector, FVV) for stable gene transfer into different cells and tissues. FVVs have emerged as an alternative platform to contemporary viral vectors (e.g., adeno associated and lentiviral vectors) for experimental and therapeutic gene therapy of a variety of monogenetic diseases. Some of the important features of FVVs include the ability to efficiently transduce hematopoietic stem and progenitor cells (HSPCs) from humans, NHPs, canines and rodents. We have successfully used FVV for proof of concept studies to demonstrate safety and efficacy following in-vivo delivery in large animal models. In this review, we will comprehensively discuss FVV based in-vivo gene therapy approaches established in the X-linked severe combined immunodeficiency (SCID-X1) canine model.
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Affiliation(s)
- Yogendra Singh Rajawat
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (O.H.); (Y.S.R.)
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (O.H.); (Y.S.R.)
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (O.H.); (Y.S.R.)
- Departments of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Departments of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Correspondence: ; Tel.: +1-206-667-4425
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4
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Everson EM, Hocum JD, Trobridge GD. Efficacy and safety of a clinically relevant foamy vector design in human hematopoietic repopulating cells. J Gene Med 2018; 20:e3028. [PMID: 29935087 DOI: 10.1002/jgm.3028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Previous studies have shown that foamy viral (FV) vectors are a promising alternative to gammaretroviral and lentiviral vectors and also that insulators can improve FV vector safety. However, in a previous analysis of insulator effects on FV vector safety, strong viral promoters were used to elicit genotoxic events. In the present study, we developed and analyzed the efficacy and safety of a high-titer, clinically relevant FV vector driven by the housekeeping promoter elongation factor-1α and insulated with an enhancer blocking A1 insulator (FV-EGW-A1). METHODS Human CD34+ cord blood cells were exposed to an enhanced green fluorescent protein expressing vector, FV-EGW-A1, at a multiplicity of infection of 10 and then maintained in vitro or transplanted into immunodeficient mice. Flow cytometry was used to measure engraftment and marking in vivo. FV vector integration sites were analyzed to assess safety. RESULTS FV-EGW-A1 resulted in high-marking, multilineage engraftment of human repopulating cells with no evidence of silencing. Engraftment was highly polyclonal with no clonal dominance and a promising safety profile based on integration site analysis. CONCLUSIONS An FV vector with an elongation factor-1α promoter and an A1 insulator is a promising vector design for use in the clinic.
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Affiliation(s)
- Elizabeth M Everson
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA
| | - Jonah D Hocum
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA
| | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, WSU Spokane, Spokane, WA, USA.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
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5
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Humbert O, Chan F, Rajawat YS, Torgerson TR, Burtner CR, Hubbard NW, Humphrys D, Norgaard ZK, O'Donnell P, Adair JE, Trobridge GD, Scharenberg AM, Felsburg PJ, Rawlings DJ, Kiem HP. Rapid immune reconstitution of SCID-X1 canines after G-CSF/AMD3100 mobilization and in vivo gene therapy. Blood Adv 2018; 2:987-999. [PMID: 29720491 PMCID: PMC5942001 DOI: 10.1182/bloodadvances.2018016451] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/25/2018] [Indexed: 11/20/2022] Open
Abstract
Hematopoietic stem-cell gene therapy is a promising treatment of X-linked severe combined immunodeficiency disease (SCID-X1), but currently, it requires recipient conditioning, extensive cell manipulation, and sophisticated facilities. With these limitations in mind, we explored a simpler therapeutic approach to SCID-X1 treatment by direct IV administration of foamy virus (FV) vectors in the canine model. FV vectors were used because they have a favorable integration site profile and are resistant to serum inactivation. Here, we show improved efficacy of our in vivo gene therapy platform by mobilization with granulocyte colony-stimulating factor (G-CSF) and AMD3100 before injection of an optimized FV vector incorporating the human phosphoglycerate kinase enhancerless promoter. G-CSF/AMD3100 mobilization before FV vector delivery accelerated kinetics of CD3+ lymphocyte recovery, promoted thymopoiesis, and increased immune clonal diversity. Gene-corrected T lymphocytes exhibited a normal CD4:CD8 ratio and a broad T-cell receptor repertoire and showed restored γC-dependent signaling function. Treated animals showed normal primary and secondary antibody responses to bacteriophage immunization and evidence for immunoglobulin class switching. These results demonstrate safety and efficacy of an accessible, portable, and translatable platform with no conditioning regimen for the treatment of SCID-X1 and other genetic diseases.
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Affiliation(s)
- Olivier Humbert
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Frieda Chan
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Yogendra S Rajawat
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Troy R Torgerson
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
- Department of Pediatrics and
| | - Christopher R Burtner
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Nicholas W Hubbard
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
| | - Daniel Humphrys
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Zachary K Norgaard
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Patricia O'Donnell
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jennifer E Adair
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Pullman, WA; and
| | - Andrew M Scharenberg
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
- Department of Pediatrics and
- Department of Immunology, University of Washington, Seattle, WA
| | - Peter J Felsburg
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA
- Department of Pediatrics and
- Department of Immunology, University of Washington, Seattle, WA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Department of Pathology, University of Washington School of Medicine, Seattle, WA
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6
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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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7
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Richter M, Stone D, Miao C, Humbert O, Kiem HP, Papayannopoulou T, Lieber A. In Vivo Hematopoietic Stem Cell Transduction. Hematol Oncol Clin North Am 2017; 31:771-785. [PMID: 28895846 DOI: 10.1016/j.hoc.2017.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Current protocols for hematopoietic stem cell (HSC) gene therapy, involving the transplantation of ex vivo lentivirus vector-transduced HSCs into myeloablated recipients, are complex and not without risk for the patient. In vivo HSC gene therapy can be achieved by the direct modification of HSCs in the bone marrow after intraosseous injection of gene delivery vectors. A recently developed approach involves the mobilization of HSCs from the bone marrow into peripheral the blood circulation, intravenous vector injection, and re-engraftment of genetically modified HSCs in the bone marrow. We provide examples for in vivo HSC gene therapy and discuss advantages and disadvantages.
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Affiliation(s)
- Maximilian Richter
- Division of Medical Genetics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
| | - Carol Miao
- Department of Pediatrics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA; Center for Immunity and Immunotherapy, Research Institute, Seattle Children's Hospital, 1900 9th Avenue, Seattle, WA 98101, USA
| | - Olivier Humbert
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Aveune N, Seattle, WA 98109, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Aveune N, Seattle, WA 98109, USA; Department of Medicine, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Thalia Papayannopoulou
- Division of Hematology, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - André Lieber
- Division of Medical Genetics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA; Department of Pathology, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA.
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8
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Browning DL, Everson EM, Leap DJ, Hocum JD, Wang H, Stamatoyannopoulos G, Trobridge GD. Evidence for the in vivo safety of insulated foamy viral vectors. Gene Ther 2016; 24:187-198. [PMID: 28024082 PMCID: PMC5374020 DOI: 10.1038/gt.2016.88] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
Retroviral vector mediated stem cell gene therapy is a promising approach for the treatment of hematopoietic disorders. However, genotoxic side effects from integrated vector proviruses are a significant concern for the use of retroviral vectors in the clinic. Insulated foamy viral (FV) vectors are potentially safer retroviral vectors for hematopoietic stem cell gene therapy. We evaluated two newly identified human insulators, A1 and A2 for use in FV vectors. These insulators had moderate insulating capacity and higher titers than previously developed insulated FV vectors. The A1 insulated FV vector was chosen for comparison with the previously described 650cHS4 insulated FV vector in human cord blood CD34+ repopulating cells in an immunodeficient mouse model. To maximize the effects of the insulators on the safety of FV vectors, FV vectors containing a highly genotoxic spleen focus forming virus (SFFV) promoter was used to elicit differences in genotoxicity. In vivo, the A1 insulated FV vector showed an approximate 50% reduction in clonal dominance compared to either the 650cHS4 insulated or control FV vectors, although the transduction efficiency of the A1 insulated vector was higher. This data suggests that the A1 insulated FV vector is promising for future pre-clinical and clinical studies.
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Affiliation(s)
- D L Browning
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - E M Everson
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - D J Leap
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - J D Hocum
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - H Wang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - G Stamatoyannopoulos
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - G D Trobridge
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
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9
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Retroviral vector interactions with hematopoietic cells. Curr Opin Virol 2016; 21:41-46. [PMID: 27521874 DOI: 10.1016/j.coviro.2016.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 01/01/2023]
Abstract
Hematopoietic stem cell (HSC) gene therapy using retroviral vectors is a powerful and promising approach to permanently correct many hematopoietic disorders. Increasing the transduction of quiescent HSCs and reducing genotoxicity are major challenges in the field. Retroviral vectors, including lentiviral and foamy vectors, have been extensively modified resulting in improved safety and efficacy. This review will focus on recent advances to improve vector entry, transduction efficiency, control of transgene expression and approaches to improve safety by modifying the retroviral integration profile.
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