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Wu J, Chen Y, Shen W, Zhang J, Zeng F. Reducing the transcriptional read-through rate of a lentiviral vector for β-thalassemia gene therapy. J Gene Med 2024; 26:e3640. [PMID: 37989259 DOI: 10.1002/jgm.3640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/27/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND LentiGlobin BB305 is a self-inactivating lentiviral vector carrying a human β-globin expressing cassette for treating β-thalassemia. Initially, a 2 × 250 bp chicken Locus Control Region fragment of cHS4, functioning as an insulator, was placed at its ΔU3, which was removed after the first clinical trial led by a French team to avoid abnormal splicing, etc. This action could potentially lead to an increasing risk of the transcriptional read-through rate driven by the β-globin promoter to a significant level, posing a biosafety risk in clinical trials. METHODS In the present study, a read-through reducing agent (C-U+ or WPRE) was designed to be placed at the 3' UTR of the β-globin gene. The Enhancer Activities and/or Transcriptional Read-Through (EATRT) rate at the mRNA level and the protein expression level regarding lentiviral preparation titer were examined. RESULTS We found that the insertion of the element (C-U+ or WPRE) reduced the EATRT effectively by 53% or 41%, respectively. C-U+ has less impact on virus package efficiency. Furthermore, there was no significant difference in the protein expression level after the C-U+ or WPRE insertion. CONCLUSIONS The results of the present study show that inserting C-U+ or WPRE before the polyA sequence of the BB305 would reduce the EATRT rate at no cost of its expressing efficacy and viral preparation titers. Thus, we present an alternative improvement for a safer lentiviral vector for β-thalassemia clinical trials.
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Affiliation(s)
- Jiahui Wu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yuan Chen
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Wenchen Shen
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jingzhi Zhang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Pharmacy, Macau University of Science and Technology, Macau, China
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HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency. Sci Rep 2021; 11:12067. [PMID: 34103612 PMCID: PMC8187449 DOI: 10.1038/s41598-021-91309-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/17/2021] [Indexed: 11/12/2022] Open
Abstract
Many lentiviral vectors used for gene therapy are derived from HIV-1. An optimal vector genome would include only the viral sequences required for transduction efficiency and gene expression to minimize the amount of foreign sequence inserted into a patient’s genome. However, it remains unclear whether all of the HIV-1 sequence in vector genomes is essential. To determine which viral sequences are required, we performed a systematic deletion analysis, which showed that most of the gag region and over 50% of the env region could be deleted. Because the splicing profile for lentiviral vectors is poorly characterized, we used long-read sequencing to determine canonical and cryptic splice site usage. Deleting specific regions of env sequence reduced the number of splicing events per transcript and increased the proportion of unspliced genomes. Finally, combining a large deletion in gag with repositioning the Rev-response element downstream of the 3’ R to prevent its reverse transcription showed that 1201 nucleotides of HIV-1 sequence can be removed from the integrated vector genome without substantially compromising transduction efficiency. Overall, this allows the creation of lentiviral vector genomes that contain minimal HIV-1 sequence, which could improve safety and transfer less viral sequence into a patient’s DNA.
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Song L, He J, Gao Y, Fang Y, Zhang L, Wang J, Sun F, Zhang F, Zeng Y, Zeng F, Zhang J. Improved biosafety of a lentiviral vector by reducing cellular gene activation. J Gene Med 2019; 21:e3087. [PMID: 30901108 DOI: 10.1002/jgm.3087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Lentiviral vectors (LVs) have enhancer activity and/or transcriptional read-through (EATRT) properties that can lead to the activation of adjacent genes. Consequently, patients may be at increased risk for adverse effects if such vectors are used clinically. METHODS In the present study, we assessed the abilities of different "pro-LV"-like constructs with respect to decreasing its EATRT, including the "pro-LV" vector bearing a chimeric ΔLTR of the human foamy virus R-U5 region replaced by that of an LV (HF). RESULTS By analyzing the EATRT of "pro-LV" constructs transfected in 293T cells, we observed that the inclusion of the first 400 bp of the chicken β-globin locus HS4 insulator core sequence oriented in the reverse direction (C-) combined with two copies of the simian virus 40 upstream-sequence element (U) at the ΔU3 of ΔLTR region of "pro-LV" tended to shield the adjacent genomic sequences, such that the EATRT rate was lower than when either of the C- or U was included in the "pro-LV". Moreover, upon transduction, the pro-HF appears to reduce the EATRT rate in the chromosomes of 293T (by 80%) and human peripheral blood mononuclear cells (PBMCs) (by 75%) compared to when pro-LV C-U was included (with a 60% and 89% reduction in 293T and PBMCs, respectively). The HF construct had a significant reduction of viral biological titer compared tiowhen the pro-LV C-U was used in 293T cells. CONCLUSIONS The results of the present study provide an important basis for the clinical applicability of LVs in gene and cell therapy.
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Affiliation(s)
- Li Song
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jiaping He
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yue Gao
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yudan Fang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Liping Zhang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Juan Wang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fengqiang Sun
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fan Zhang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yitao Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Jingzhi Zhang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology, Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
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Berkhout B. A Fourth Generation Lentiviral Vector: Simplifying Genomic Gymnastics. Mol Ther 2018; 25:1741-1743. [PMID: 28772133 DOI: 10.1016/j.ymthe.2017.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center (AMC), University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands.
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Biswas M, Kumar SRP, Terhorst C, Herzog RW. Gene Therapy With Regulatory T Cells: A Beneficial Alliance. Front Immunol 2018; 9:554. [PMID: 29616042 PMCID: PMC5868074 DOI: 10.3389/fimmu.2018.00554] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 03/05/2018] [Indexed: 12/12/2022] Open
Abstract
Gene therapy aims to replace a defective or a deficient protein at therapeutic or curative levels. Improved vector designs have enhanced safety, efficacy, and delivery, with potential for lasting treatment. However, innate and adaptive immune responses to the viral vector and transgene product remain obstacles to the establishment of therapeutic efficacy. It is widely accepted that endogenous regulatory T cells (Tregs) are critical for tolerance induction to the transgene product and in some cases the viral vector. There are two basic strategies to harness the suppressive ability of Tregs: in vivo induction of adaptive Tregs specific to the introduced gene product and concurrent administration of autologous, ex vivo expanded Tregs. The latter may be polyclonal or engineered to direct specificity to the therapeutic antigen. Recent clinical trials have advanced adoptive immunotherapy with Tregs for the treatment of autoimmune disease and in patients receiving cell transplants. Here, we highlight the potential benefit of combining gene therapy with Treg adoptive transfer to achieve a sustained transgene expression. Furthermore, techniques to engineer antigen-specific Treg cell populations, either through reprogramming conventional CD4+ T cells or transferring T cell receptors with known specificity into polyclonal Tregs, are promising in preclinical studies. Thus, based upon these observations and the successful use of chimeric (IgG-based) antigen receptors (CARs) in antigen-specific effector T cells, different types of CAR-Tregs could be added to the repertoire of inhibitory modalities to suppress immune responses to therapeutic cargos of gene therapy vectors. The diverse approaches to harness the ability of Tregs to suppress unwanted immune responses to gene therapy and their perspectives are reviewed in this article.
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Affiliation(s)
- Moanaro Biswas
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, United States
| | - Sandeep R P Kumar
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, United States
| | - Cox Terhorst
- Division of Immunology, Beth Israel Deaconess Medical Center (BIDMC), Harvard Medical School, Boston, MA, United States
| | - Roland W Herzog
- Division of Cellular and Molecular Therapy, Department of Pediatrics, University of Florida, Gainesville, FL, United States
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6
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Vink CA, Counsell JR, Perocheau DP, Karda R, Buckley SMK, Brugman MH, Galla M, Schambach A, McKay TR, Waddington SN, Howe SJ. Eliminating HIV-1 Packaging Sequences from Lentiviral Vector Proviruses Enhances Safety and Expedites Gene Transfer for Gene Therapy. Mol Ther 2017; 25:1790-1804. [PMID: 28550974 PMCID: PMC5542766 DOI: 10.1016/j.ymthe.2017.04.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 12/30/2022] Open
Abstract
Lentiviral vector genomic RNA requires sequences that partially overlap wild-type HIV-1 gag and env genes for packaging into vector particles. These HIV-1 packaging sequences constitute 19.6% of the wild-type HIV-1 genome and contain functional cis elements that potentially compromise clinical safety. Here, we describe the development of a novel lentiviral vector (LTR1) with a unique genomic structure designed to prevent transfer of HIV-1 packaging sequences to patient cells, thus reducing the total HIV-1 content to just 4.8% of the wild-type genome. This has been achieved by reconfiguring the vector to mediate reverse-transcription with a single strand transfer, instead of the usual two, and in which HIV-1 packaging sequences are not copied. We show that LTR1 vectors offer improved safety in their resistance to remobilization in HIV-1 particles and reduced frequency of splicing into human genes. Following intravenous luciferase vector administration to neonatal mice, LTR1 sustained a higher level of liver transgene expression than an equivalent dose of a standard lentivirus. LTR1 vectors produce reverse-transcription products earlier and start to express transgenes significantly quicker than standard lentiviruses after transduction. Finally, we show that LTR1 is an effective lentiviral gene therapy vector as demonstrated by correction of a mouse hemophilia B model.
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Affiliation(s)
- Conrad A Vink
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - John R Counsell
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK.
| | - Dany P Perocheau
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - Rajvinder Karda
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - Suzanne M K Buckley
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Tristan R McKay
- School of Healthcare Science, John Dalton Building, Manchester Metropolitan University, Chester Street, Manchester M15 6BH, UK
| | - Simon N Waddington
- Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK; MRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg 2000, South Africa
| | - Steven J Howe
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; Gene Transfer Technology Group, Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
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