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Cesana D, Cicalese MP, Calabria A, Merli P, Caruso R, Volpin M, Rudilosso L, Migliavacca M, Barzaghi F, Fossati C, Gazzo F, Pizzi S, Ciolfi A, Bruselles A, Tucci F, Spinozzi G, Pais G, Benedicenti F, Barcella M, Merelli I, Gallina P, Giannelli S, Dionisio F, Scala S, Casiraghi M, Strocchio L, Vinti L, Pacillo L, Draghi E, Cesana M, Riccardo S, Colantuono C, Six E, Cavazzana M, Carlucci F, Schmidt M, Cancrini C, Ciceri F, Vago L, Cacchiarelli D, Gentner B, Naldini L, Tartaglia M, Montini E, Locatelli F, Aiuti A. A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID. Nat Commun 2024; 15:3662. [PMID: 38688902 PMCID: PMC11061298 DOI: 10.1038/s41467-024-47866-5] [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: 10/13/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter. The insertion is detected years before T-ALL in multiple lineages, suggesting that further hits occurred in a thymic progenitor. Blast cells contain known and novel somatic mutations as well as germline mutations which may have contributed to transformation. Before T-ALL onset, the insertion profile is similar to those of other ADA-deficient patients. The limited incidence of vector-related adverse events in ADA-deficiency compared to other γ-RV GT trials could be explained by differences in transgenes, background disease and patient's specific factors.
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Affiliation(s)
- Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Monica Volpin
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Rudilosso
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maddalena Migliavacca
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Fossati
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Gazzo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Tucci
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Pais
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Pierangela Gallina
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Giannelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Dionisio
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miriam Casiraghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Lucia Pacillo
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Eleonora Draghi
- Immunogenetics, Leukemia Genomics and Immunobiology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Naples, Italy
| | - Sara Riccardo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA S.r.l., Pozzuoli, Italy
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- NEGEDIA S.r.l., Pozzuoli, Italy
| | - Emmanuelle Six
- Laboratory of Human Lympho-hematopoiesis, INSERM, Paris, France
| | | | - Filippo Carlucci
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Caterina Cancrini
- Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
- Department of Systems Medicine University of Rome Tor Vergata, Rome, Italy
| | - Fabio Ciceri
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Vago
- Università Vita-Salute San Raffaele, Milan, Italy
- Immunogenetics, Leukemia Genomics and Immunobiology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples "Federico II", Naples, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Haematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Paediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Università Vita-Salute San Raffaele, Milan, Italy.
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Kim J, Park M, Baek G, Kim JI, Kwon E, Kang BC, Kim JI, Kang HJ. Tagmentation-based analysis reveals the clonal behavior of CAR-T cells in association with lentivector integration sites. Mol Ther Oncolytics 2023; 30:1-13. [PMID: 37360944 PMCID: PMC10285042 DOI: 10.1016/j.omto.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Integration site (IS) analysis is essential in ensuring safety and efficacy of gene therapies when integrating vectors are used. Although clinical trials of gene therapy are rapidly increasing, current methods have limited use in clinical settings because of their lengthy protocols. Here, we describe a novel genome-wide IS analysis method, "detection of the integration sites in a time-efficient manner, quantifying clonal size using tagmentation sequencing" (DIStinct-seq). In DIStinct-seq, a bead-linked Tn5 transposome is used, allowing the sequencing library to be prepared within a single day. We validated the quantification performance of DIStinct-seq for measuring clonal size with clones of known IS. Using ex vivo chimeric antigen receptor (CAR)-T cells, we revealed the characteristics of lentiviral IS. We then applied it to CAR-T cells collected at various times from tumor-engrafted mice, detecting 1,034-6,233 IS. Notably, we observed that the highly expanded clones had a higher integration frequency in the transcription units and vice versa in genomic safe harbors (GSH). Also, in GSH, persistent clones had more frequent IS. Together with these findings, the new IS analysis method will help to improve the safety and efficacy of gene therapies.
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Affiliation(s)
- Jaeryuk Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Miyoung Park
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Gyungwon Baek
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Joo-Il Kim
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Euna Kwon
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byeong-Cheol Kang
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Biomedical Center for Animal Resource and Development; Seoul National University College of Medicine, Seoul, Republic of Korea
- Designed Animal Resource Center, Institute of GreenBio Science Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Hyoung Jin Kang
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
- Wide River Institute of Immunology, Hongcheon, Republic of Korea
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [PMID: 37403182 DOI: 10.1186/s40364-023-00509-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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Affiliation(s)
- Hamed Dabiri
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mohadeseh Mirzaee Godarzee
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Mohsen Basiri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Vahab Ziaei
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ensiyeh Hajizadeh Saffar
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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4
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Dabiri H, Safarzadeh Kozani P, Habibi Anbouhi M, Mirzaee Godarzee M, Haddadi MH, Basiri M, Ziaei V, Sadeghizadeh M, Hajizadeh Saffar E. Site-specific transgene integration in chimeric antigen receptor (CAR) T cell therapies. Biomark Res 2023; 11:67. [DOI: https:/doi.org/10.1186/s40364-023-00509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/09/2023] [Indexed: 09/15/2023] Open
Abstract
AbstractChimeric antigen receptor (CAR) T cells and natural killer (NK) cells are genetically engineered immune cells that can detect target antigens on the surface of target cells and eliminate them following adoptive transfer. Recent progress in CAR-based therapies has led to outstanding clinical success in certain patients with leukemias and lymphomas and offered therapeutic benefits to those resistant to conventional therapies. The universal approach to stable CAR transgene delivery into the T/NK cells is the use of viral particles. Such approaches mediate semi-random transgene insertions spanning the entire genome with a high preference for integration into sites surrounding highly-expressed genes and active loci. Regardless of the variable CAR expression level based on the integration site of the CAR transgene, foreign integrated DNA fragments may affect the neighboring endogenous genes and chromatin structure and potentially change a transduced T/NK cell behavior and function or even favor cellular transformation. In contrast, site-specific integration of CAR constructs using recent genome-editing technologies could overcome the limitations and disadvantages of universal random gene integration. Herein, we explain random and site-specific integration of CAR transgenes in CAR-T/NK cell therapies. Also, we tend to summarize the methods for site-specific integration as well as the clinical outcomes of certain gene disruptions or enhancements due to CAR transgene integration. Also, the advantages and limitations of using site-specific integration methods are discussed in this review. Ultimately, we will introduce the genomic safe harbor (GSH) standards and suggest some appropriate safety prospects for CAR integration in CAR-T/NK cell therapies.
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Mudde A, Booth C. Gene therapy for inborn error of immunity - current status and future perspectives. Curr Opin Allergy Clin Immunol 2023; 23:51-62. [PMID: 36539381 DOI: 10.1097/aci.0000000000000876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Development of hematopoietic stem cell (HSC) gene therapy (GT) for inborn errors of immunity (IEIs) continues to progress rapidly. Although more patients are being treated with HSC GT based on viral vector mediated gene addition, gene editing techniques provide a promising new approach, in which transgene expression remains under the control of endogenous regulatory elements. RECENT FINDINGS Many gene therapy clinical trials are being conducted and evidence showing that HSC GT through viral vector mediated gene addition is a successful and safe curative treatment option for various IEIs is accumulating. Gene editing techniques for gene correction are, on the other hand, not in clinical use yet, despite rapid developments during the past decade. Current studies are focussing on improving rates of targeted integration, while preserving the primitive HSC population, which is essential for future clinical translation. SUMMARY As HSC GT is becoming available for more diseases, novel developments should focus on improving availability while reducing costs of the treatment. Continued follow up of treated patients is essential for providing information about long-term safety and efficacy. Editing techniques have great potential but need to be improved further before the translation to clinical studies can happen.
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Affiliation(s)
- Anne Mudde
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health
| | - Claire Booth
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health
- Department of Immunology and Gene Therapy, Great Ormond Street Hospital, London, UK
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Fischer A. Gene therapy for inborn errors of immunity: past, present and future. Nat Rev Immunol 2022:10.1038/s41577-022-00800-6. [DOI: 10.1038/s41577-022-00800-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/27/2022]
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Wolff JH, Mikkelsen JG. Delivering genes with human immunodeficiency virus-derived vehicles: still state-of-the-art after 25 years. J Biomed Sci 2022; 29:79. [PMID: 36209077 PMCID: PMC9548131 DOI: 10.1186/s12929-022-00865-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses are naturally endowed with the capacity to transfer genetic material between cells. Following early skepticism, engineered viruses have been used to transfer genetic information into thousands of patients, and genetic therapies are currently attracting large investments. Despite challenges and severe adverse effects along the way, optimized technologies and improved manufacturing processes are driving gene therapy toward clinical translation. Fueled by the outbreak of AIDS in the 1980s and the accompanying focus on human immunodeficiency virus (HIV), lentiviral vectors derived from HIV have grown to become one of the most successful and widely used vector technologies. In 2022, this vector technology has been around for more than 25 years. Here, we celebrate the anniversary by portraying the vector system and its intriguing properties. We dive into the technology itself and recapitulate the use of lentiviral vectors for ex vivo gene transfer to hematopoietic stem cells and for production of CAR T-cells. Furthermore, we describe the adaptation of lentiviral vectors for in vivo gene delivery and cover the important contribution of lentiviral vectors to basic molecular research including their role as carriers of CRISPR genome editing technologies. Last, we dwell on the emerging capacity of lentiviral particles to package and transfer foreign proteins.
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Affiliation(s)
- Jonas Holst Wolff
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark
| | - Jacob Giehm Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark.
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Jiang Z, Fu M, Zhu D, Wang X, Li N, Ren L, He J, Yang G. Genetically modified immunomodulatory cell-based biomaterials in tissue regeneration and engineering. Cytokine Growth Factor Rev 2022; 66:53-73. [PMID: 35690567 DOI: 10.1016/j.cytogfr.2022.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022]
Abstract
To date, the wide application of cell-based biomaterials in tissue engineering and regeneration is remarkably hampered by immune rejection. Reducing the immunogenicity of cell-based biomaterials has become the latest direction in biomaterial research. Recently, genetically modified cell-based biomaterials with immunomodulatory genes have become a feasible solution to the immunogenicity problem. In this review, recent advances and future challenges of genetically modified immunomodulatory cell-based biomaterials are elaborated, including fabrication approaches, mechanisms of common immunomodulatory genes, application and, more importantly, current preclinical and clinical advances. The fabrication approaches can be categorized into commonly used (e.g., virus transfection) and newly developed approaches. The immunomodulatory mechanisms of representative genes involve complicated cell signaling pathways and metabolic activities. Wide application in curing multiple end-term diseases and replacing lifelong immunosuppressive therapy in multiple cell and organ transplantation models is demonstrated. Most significantly, practices of genetically modified organ transplantation have been conducted on brain-dead human decedent and even on living patients after a series of experiments on nonhuman primates. Nevertheless, uncertain biosecurity, nonspecific effects and overlooked personalization of current genetically modified immunomodulatory cell-based biomaterials are shortcomings that remain to be overcome.
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Affiliation(s)
- Zhiwei Jiang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Mengdie Fu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Danji Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Xueting Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Na Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Lingfei Ren
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Jin He
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Guoli Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China.
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Nonconditioned ADA-SCID gene therapy reveals ADA requirement in the hematopoietic system and clonal dominance of vector-marked clones. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:424-433. [PMID: 34786435 PMCID: PMC8566957 DOI: 10.1016/j.omtm.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 11/22/2022]
Abstract
Two patients with adenosine deaminase (ADA)-deficient severe combined immunodeficiency (ADA-SCID) received stem cell-based gene therapy (SCGT) using GCsapM-ADA retroviral vectors without preconditioning in 2003 and 2004. The first patient (Pt1) was treated at 4.7 years old, and the second patient (Pt2), who had previously received T cell gene therapy (TCGT), was treated at 13 years old. More than 10 years after SCGT, T cells showed a higher vector copy number (VCN) than other lineages. Moreover, the VCN increased with differentiation toward memory T and B cells. The distribution of vector-marked cells reflected variable levels of ADA requirements in hematopoietic subpopulations. Although neither patient developed leukemia, clonal expansion of SCGT-derived clones was observed in both patients. The use of retroviral vectors yielded clonal dominance of vector-marked clones, irrespective of the lack of leukemic changes. Vector integration sites common to all hematopoietic lineages suggested the engraftment of gene-marked progenitors in Pt1, who showed severe osteoblast (OB) insufficiency compared to Pt2, which might cause a reduction in the stem/progenitor cells in the bone marrow (BM). The impaired BM microenvironment due to metabolic abnormalities may create space for the engraftment of vector-marked cells in ADA-SCID, despite the lack of preconditioning.
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Reinhardt B, Habib O, Shaw KL, Garabedian E, Carbonaro-Sarracino DA, Terrazas D, Fernandez BC, De Oliveira S, Moore TB, Ikeda AK, Engel BC, Podsakoff GM, Hollis RP, Fernandes A, Jackson C, Shupien S, Mishra S, Davila A, Mottahedeh J, Vitomirov A, Meng W, Rosenfeld AM, Roche AM, Hokama P, Reddy S, Everett J, Wang X, Luning Prak ET, Cornetta K, Hershfield MS, Sokolic R, De Ravin SS, Malech HL, Bushman FD, Candotti F, Kohn DB. Long-term outcomes after gene therapy for adenosine deaminase severe combined immune deficiency. Blood 2021; 138:1304-1316. [PMID: 33974038 PMCID: PMC8525336 DOI: 10.1182/blood.2020010260] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Patients lacking functional adenosine deaminase activity have severe combined immunodeficiency (ADA SCID), which can be treated with ADA enzyme replacement therapy (ERT), allogeneic hematopoietic stem cell transplantation (HSCT), or autologous HSCT with gene-corrected cells (gene therapy [GT]). A cohort of 10 ADA SCID patients, aged 3 months to 15 years, underwent GT in a phase 2 clinical trial between 2009 and 2012. Autologous bone marrow CD34+ cells were transduced ex vivo with the MND (myeloproliferative sarcoma virus, negative control region deleted, dl587rev primer binding site)-ADA gammaretroviral vector (gRV) and infused following busulfan reduced-intensity conditioning. These patients were monitored in a long-term follow-up protocol over 8 to 11 years. Nine of 10 patients have sufficient immune reconstitution to protect against serious infections and have not needed to resume ERT or proceed to secondary allogeneic HSCT. ERT was restarted 6 months after GT in the oldest patient who had no evidence of benefit from GT. Four of 9 evaluable patients with the highest gene marking and B-cell numbers remain off immunoglobulin replacement therapy and responded to vaccines. There were broad ranges of responses in normalization of ADA enzyme activity and adenine metabolites in blood cells and levels of cellular and humoral immune reconstitution. Outcomes were generally better in younger patients and those receiving higher doses of gene-marked CD34+ cells. No patient experienced a leukoproliferative event after GT, despite persisting prominent clones with vector integrations adjacent to proto-oncogenes. These long-term findings demonstrate enduring efficacy of GT for ADA SCID but also highlight risks of genotoxicity with gRVs. This trial was registered at www.clinicaltrials.gov as #NCT00794508.
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Affiliation(s)
- Bryanna Reinhardt
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Omar Habib
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Kit L Shaw
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Elizabeth Garabedian
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Denise A Carbonaro-Sarracino
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Dayna Terrazas
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Beatriz Campo Fernandez
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Satiro De Oliveira
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Theodore B Moore
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Alan K Ikeda
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Barbara C Engel
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Roger P Hollis
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Augustine Fernandes
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Connie Jackson
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Sally Shupien
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Suparna Mishra
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Alejandra Davila
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Jack Mottahedeh
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Andrej Vitomirov
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine and
| | | | - Aoife M Roche
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Pascha Hokama
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - John Everett
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | | | - Kenneth Cornetta
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Michael S Hershfield
- Departments of Medicine and Biochemistry, Duke University School of Medicine, Durham, NC
| | - Robert Sokolic
- Department of Medicine, Alpert Medical School, Brown University, Providence, RI
| | - Suk See De Ravin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD; and
| | - Harry L Malech
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD; and
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Donald B Kohn
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA
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11
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Izotova N, Rivat C, Baricordi C, Blanco E, Pellin D, Watt E, Gkazi AS, Adams S, Gilmour K, Bayford J, Booth C, Gaspar HB, Thrasher AJ, Biasco L. Long-term lymphoid progenitors independently sustain naïve T and NK cell production in humans. Nat Commun 2021; 12:1622. [PMID: 33712608 PMCID: PMC7954865 DOI: 10.1038/s41467-021-21834-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/06/2021] [Indexed: 12/01/2022] Open
Abstract
Our mathematical model of integration site data in clinical gene therapy supported the existence of long-term lymphoid progenitors capable of surviving independently from hematopoietic stem cells. To date, no experimental setting has been available to validate this prediction. We here report evidence of a population of lymphoid progenitors capable of independently maintaining T and NK cell production for 15 years in humans. The gene therapy patients of this study lack vector-positive myeloid/B cells indicating absence of engineered stem cells but retain gene marking in both T and NK. Decades after treatment, we can still detect and analyse transduced naïve T cells whose production is likely maintained by a population of long-term lymphoid progenitors. By tracking insertional clonal markers overtime, we suggest that these progenitors can support both T and NK cell production. Identification of these long-term lymphoid progenitors could be utilised for the development of next generation gene- and cancer-immunotherapies.
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Affiliation(s)
- Natalia Izotova
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
| | - Christine Rivat
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
- Orchard Therapeutics, University College of London (UCL), London, UK
| | - Cristina Baricordi
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Elena Blanco
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | | | - Athina S Gkazi
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
| | | | | | | | - Claire Booth
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
- Great Ormond Street Hospital, London, UK
| | - H Bobby Gaspar
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK
- Orchard Therapeutics, University College of London (UCL), London, UK
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK.
- Great Ormond Street Hospital, London, UK.
| | - Luca Biasco
- Great Ormond Street Institute of Child Health Faculty of Population Health Sciences, London, UK.
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA.
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12
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Houghton BC, Booth C. Gene Therapy for Primary Immunodeficiency. Hemasphere 2021; 5:e509. [PMID: 33403354 PMCID: PMC7773329 DOI: 10.1097/hs9.0000000000000509] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
Over the past 3 decades, there has been significant progress in refining gene therapy technologies and procedures. Transduction of hematopoietic stem cells ex vivo using lentiviral vectors can now create a highly effective therapeutic product, capable of reconstituting many different immune system dysfunctions when reinfused into patients. Here, we review the key developments in the gene therapy landscape for primary immune deficiency, from an experimental therapy where clinical efficacy was marred by adverse events, to a commercialized product with enhanced safety and efficacy. We also discuss progress being made in preclinical studies for challenging disease targets and emerging gene editing technologies that are showing promising results, particularly for conditions where gene regulation is important for efficacy.
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Affiliation(s)
- Benjamin C. Houghton
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claire Booth
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Paediatric Immunology, Great Ormond Street NHS Foundation Trust, London, United Kingdom
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13
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Abstract
Haematopoietic stem and progenitor cell (HSPC) gene therapy has emerged as an effective treatment modality for monogenic disorders of the blood system such as primary immunodeficiencies and β-thalassaemia. Medicinal products based on autologous HSPCs corrected using lentiviral and gammaretroviral vectors have now been approved for clinical use, and the site-specific genome modification of HSPCs using gene editing techniques such as CRISPR-Cas9 has shown great clinical promise. Preclinical studies have shown engineered HSPCs could also be used to cross-correct non-haematopoietic cells in neurodegenerative metabolic diseases. Here, we review the most recent advances in HSPC gene therapy and discuss emerging strategies for using HSPC gene therapy for a range of diseases.
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14
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Abstract
INTRODUCTION Primary immunodeficiencies (PIDs) are monogenic disorders of the immune system associated with increased susceptibility to life-threatening infection. Curative treatment has been limited to hematopoietic stem cell transplant (HSCT), however toxic immunosuppression, graft failure, and graft versus host disease greatly reduce overall survival rates. Gene therapy is a targeted curative therapy that reduces these risks by utilizing autologous hematopoietic stem cells. The treatment has found significant success and is anticipated to become the standard of care in a number of PIDs. AREAS COVERED This review is a summary of the developments in gene therapy, gene editing, and current gene therapy approaches in specific PIDs. EXPERT OPINION The field of gene therapy has rapidly developed over the last three decades, with the first licensed pharmaceutical gene therapy product now available. After initial clinical trials discovered serious adverse events in the form of insertional oncogenesis, significant improvements in vector design have made the treatment a viable curative therapy. Cryopreservation has expanded the scope of gene therapy by increasing accessibility of the product to wider geographic locations. Targeted gene editing using engineered nucleases, while still in early stages of development, will further add to the repertoire of potential treatments available for PIDs.
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Affiliation(s)
- Kritika Chetty
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom.,Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Claire Booth
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom.,Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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15
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Straetemans T, Janssen A, Jansen K, Doorn R, Aarts T, van Muyden ADD, Simonis M, Bergboer J, de Witte M, Sebestyen Z, Kuball J. TEG001 Insert Integrity from Vector Producer Cells until Medicinal Product. Mol Ther 2019; 28:561-571. [PMID: 31882320 DOI: 10.1016/j.ymthe.2019.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
Despite extensive usage of gene therapy medicinal products (GTMPs) in clinical studies and recent approval of chimeric antigen receptor (CAR) T cell therapy, little information has been made available on the precise molecular characterization and possible variations in terms of insert integrity and vector copy numbers of different GTMPs during the complete production chain. Within this context, we characterize αβT cells engineered to express a defined γδT cell engineered to express a defined γδT receptor (TEG) currently used in a first-in-human clinical study (NTR6541). Utilizing targeted locus amplification in combination with next generation sequencing for the vector producer clone and TEG001 products, we report on five single-nucleotide variants and nine intact vector copies integrated in the producer clone. The vector copy number in TEG001 cells was on average a factor 0.72 (SD 0.11) below that of the producer cell clone. All nucleotide variants were transferred to TEG001 without having an effect on cellular proliferation during extensive in vitro culture. Based on an environmental risk assessment of the five nucleotide variants present in the non-coding viral region of the TEG001 insert, there was no altered environmental impact of TEG001 cells. We conclude that TEG001 cells do not have an increased risk for malignant transformation in vivo.
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Affiliation(s)
- Trudy Straetemans
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Anke Janssen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Koen Jansen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ruud Doorn
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Tineke Aarts
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anna D D van Muyden
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | | | - Moniek de Witte
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jurgen Kuball
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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16
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Hao L, Li T, Chang LJ, Chen X. Adoptive Immunotherapy for B-cell Malignancies Using CD19- Targeted Chimeric Antigen Receptor T-Cells: A Systematic Review of Efficacy and Safety. Curr Med Chem 2019; 26:3068-3079. [PMID: 28762313 DOI: 10.2174/0929867324666170801101842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 06/15/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Adoptive infusion of chimeric antigen receptor transduced T- cells (CAR-T) is a powerful tool of immunotherapy for hematological malignancies, as evidenced by recently published and unpublished clinical results. OBJECTIVE In this report, we performed a meta-analysis to evaluate the efficacy and side effects of CAR-T on refractory and/or relapsed B-cell malignancies, including leukemia and lymphoma. METHODS Clinical studies investigating efficacy and safety of CAR-T in acute and chronic lymphocytic leukemia and lymphoma were identified by searching PubMed and EMBASE. Outcomes of efficacy subjected to analysis were the rates of complete remission (CR) and partial remission (PR). The safety parameters were the prevalence of adverse effects including fever, hypotension, and acute renal failure. Meta analyses were performed using R software. Weighted hazard ratio (HR) with 95% confidence intervals was calculated for each outcome. Fixed or random-effects models were employed depending on the heterogeneity across the included studies. RESULTS Nineteen published clinical studies with a total of 391 patients were included for the meta-analysis. The pooled rate of complete remission was 55% (95% CI 41%-69%); the pooled rate of partial remission was 25% (95% CI: 19%-33%). The prevalence of fever was 62% (95% CI: 41%-79%), the hypotension was 22% (95% CI: 15%-31%), and the acute renal failure was 24% (95% CI: 16%-34%). All adverse effects were manageable and no death was reported due to toxicity. CONCLUSION CD19-targeted CAR-T is an effective modality in treating refractory B-cell malignancies including leukemia and lymphoma. However, there is still a need to develop strategies to improve the safety in its clinical use.
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Affiliation(s)
- Lu Hao
- Shenzhen Geno-Immune Medical Institute, Shenzhen 518057, China.,Institute of Cancer Stem Cells, Dalian Medical University, Dalian 116044, China
| | - Tongtong Li
- Clinical Medicine Program, Nanchang University Medical College, Nanchang 330006, China.,Department of Obstetrics and Gynecology, Anfu People's Hospital, Jiangxi Province 343200, China
| | - Lung-Ji Chang
- Shenzhen Geno-Immune Medical Institute, Shenzhen 518057, China.,Gene Therapy Center, University of Florida College of Medicine, Gainesville, FL 32610, United States
| | - Xiaochuan Chen
- Shenzhen Geno-Immune Medical Institute, Shenzhen 518057, China.,Department of Oriental Medicine, New York College of Health Professions, New York, NY 10016, United States
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17
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Poletti V, Urbinati F, Charrier S, Corre G, Hollis RP, Campo Fernandez B, Martin S, Rothe M, Schambach A, Kohn DB, Mavilio F. Pre-clinical Development of a Lentiviral Vector Expressing the Anti-sickling βAS3 Globin for Gene Therapy for Sickle Cell Disease. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 11:167-179. [PMID: 30533448 PMCID: PMC6276308 DOI: 10.1016/j.omtm.2018.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 01/10/2023]
Abstract
Sickle cell disease (SCD) is caused by a mutation (E6V) in the hemoglobin (Hb) β-chain that induces polymerization of Hb tetramers, red blood cell deformation, ischemia, anemia, and multiple organ damage. Gene therapy is a potential alternative to human leukocyte antigen (HLA)-matched allogeneic hematopoietic stem cell transplantation, available to a minority of patients. We developed a lentiviral vector expressing a β-globin carrying three anti-sickling mutations (T87Q, G16D, and E22A) inhibiting axial and lateral contacts in the HbS polymer, under the control of the β-globin promoter and a reduced version of the β-globin locus-control region. The vector (GLOBE-AS3) transduced 60%–80% of mobilized CD34+ hematopoietic stem-progenitor cells (HSPCs) and drove βAS3-globin expression at potentially therapeutic levels in erythrocytes differentiated from transduced HSPCs from SCD patients. Transduced HSPCs were transplanted in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG)-immunodeficient mice to analyze biodistribution, chimerism, and transduction efficiency in bone marrow (BM), spleen, thymus, and peripheral blood 12–14 weeks after transplantation. Vector integration site analysis, performed in pre-transplant HSPCs and post-transplant BM cells from individual mice, showed a normal lentiviral integration pattern and no evidence of clonal dominance. An in vitro immortalization (IVIM) assay showed the low genotoxic potential of GLOBE-AS3. This study enables a phase I/II clinical trial aimed at correcting the SCD phenotype in juvenile patients by transplantation of autologous hematopoietic stem cells (HSC) transduced by GLOBE-AS3.
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Affiliation(s)
| | - Fabrizia Urbinati
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | | | | | - Roger P. Hollis
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | | | | | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Donald B. Kohn
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Paris Descartes University, Imagine Institute, Paris, France
- Corresponding author: Fulvio Mavilio, PhD, Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy.
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18
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Biasco L. Integration Site Analysis in Gene Therapy Patients: Expectations and Reality. Hum Gene Ther 2018; 28:1122-1129. [PMID: 29160103 DOI: 10.1089/hum.2017.183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Integration site (IS) analysis is one of the major tools for addressing the safety of gene therapy clinical protocols based on the use of integrating vectors. Over the past years, the study of viral insertions in gene therapy-treated patients has allowed identifying insertional mutagenesis events, evaluating the safety of new viral vector platforms and tracking the in vivo clonal dynamics of genetically engineered cell products. While gene therapy is progressively expanding its impact on a broader area of clinical applications, increasingly more accessible, faster, and more reliable safety readouts are required from IS analysis. Several actors, from researchers to clinicians, from regulatory agencies to private companies, have to interface to different degrees with the results of IS analysis while developing and evaluating gene therapy products based on retroviral vectors. This review is aimed at providing a brief overview of what the current state and the future is of these studies with a particular focus on what are the main analytical constraints that should be considered upon conducting IS analysis in clinical gene therapy.
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Affiliation(s)
- Luca Biasco
- 1 Harvard Medical School, Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts.,2 University College London , Great Ormond Street Institute of Child Health, Faculty of Population Health Sciences, London, United Kingdom
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19
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Ferrua F, Aiuti A. Twenty-Five Years of Gene Therapy for ADA-SCID: From Bubble Babies to an Approved Drug. Hum Gene Ther 2018; 28:972-981. [PMID: 28847159 DOI: 10.1089/hum.2017.175] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Twenty-five years have passed since first attempts of gene therapy (GT) in children affected by severe combined immunodeficiency (SCID) due to adenosine deaminase (ADA) defect, also known by the general public as bubble babies. ADA-SCID is fatal early in life if untreated. Unconditioned hematopoietic stem cell (HSC) transplant from matched sibling donor represents a curative treatment but is available for few patients. Enzyme replacement therapy can be life-saving, but its chronic use has many drawbacks. This review summarizes the history of ADA-SCID GT over the last 25 years, starting from first pioneering studies in the early 1990s using gamma-retroviral vectors, based on multiple infusions of genetically corrected autologous peripheral blood lymphocytes. HSC represented the ideal target for gene correction to guarantee production of engineered multi-lineage progeny, but it required a decade to achieve therapeutic benefit with this approach. Introduction of low-intensity conditioning represented a crucial step in achieving stable gene-corrected HSC engraftment and therapeutic levels of ADA-expressing cells. Recent clinical trials demonstrated that gamma-retroviral GT for ADA-SCID has a favorable safety profile and is effective in restoring normal purine metabolism and immune functions in patients >13 years after treatment. No abnormal clonal proliferation or leukemia development have been observed in >40 patients treated experimentally in five different centers worldwide. In 2016, the medicinal product Strimvelis™ received marketing approval in Europe for patients affected by ADA-SCID without a suitable human leukocyte antigen-matched related donor. Positive safety and efficacy results have been obtained in GT clinical trials using lentiviral vectors encoding ADA. The results obtained in last 25 years in ADA-SCID GT development fundamentally contributed to improve patients' prognosis, together with earlier diagnosis thanks to newborn screening. These advances open the way to further clinical development of GT as treatment for broader applications, from inherited diseases to cancer.
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Affiliation(s)
- Francesca Ferrua
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute , Milan, Italy.,2 Vita-Salute San Raffaele University , Milan, Italy
| | - Alessandro Aiuti
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute , Milan, Italy.,2 Vita-Salute San Raffaele University , Milan, Italy
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20
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21
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Abstract
Replication-defective retroviral vectors have been used for more than 25 years as a tool for efficient and stable insertion of therapeutic transgenes in human cells. Patients suffering from severe genetic diseases have been successfully treated by transplantation of autologous hematopoietic stem-progenitor cells (HSPCs) transduced with retroviral vectors, and the first of this class of therapies, Strimvelis, has recently received market authorization in Europe. Some clinical trials, however, resulted in severe adverse events caused by vector-induced proto-oncogene activation, which showed that retroviral vectors may retain a genotoxic potential associated to proviral integration in the human genome. The adverse events sparked a renewed interest in the biology of retroviruses, which led in a few years to a remarkable understanding of the molecular mechanisms underlying retroviral integration site selection within mammalian genomes. This review summarizes the current knowledge on retrovirus-host interactions at the genomic level, and the peculiar mechanisms by which different retroviruses, and their related gene transfer vectors, integrate in, and interact with, the human genome. This knowledge provides the basis for the development of safer and more efficacious retroviral vectors for human gene therapy.
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Affiliation(s)
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
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22
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Cicalese MP, Ferrua F, Castagnaro L, Rolfe K, De Boever E, Reinhardt RR, Appleby J, Roncarolo MG, Aiuti A. Gene Therapy for Adenosine Deaminase Deficiency: A Comprehensive Evaluation of Short- and Medium-Term Safety. Mol Ther 2018; 26:917-931. [PMID: 29433935 PMCID: PMC5910668 DOI: 10.1016/j.ymthe.2017.12.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 12/20/2017] [Accepted: 12/24/2017] [Indexed: 12/22/2022] Open
Abstract
Loss of adenosine deaminase activity leads to severe combined immunodeficiency (ADA-SCID); production and function of T, B, and natural killer (NK) cells are impaired. Gene therapy (GT) with an autologous CD34+-enriched cell fraction that contains CD34+ cells transduced with a retroviral vector encoding the human ADA cDNA sequence leads to immune reconstitution in most patients. Here, we report short- and medium-term safety analyses from 18 patients enrolled as part of single-arm, open-label studies or compassionate use programs. Survival was 100% with a median of 6.9 years follow-up (range, 2.3 to 13.4 years). Adverse events were mostly grade 1 or grade 2 and were reported by all 18 patients following GT. Thirty-nine serious adverse events (SAEs) were reported by 15 of 18 patients; no SAEs were considered related to GT. The most common adverse events reported post-GT include upper respiratory tract infection, gastroenteritis, rhinitis, bronchitis, oral candidiasis, cough, neutropenia, diarrhea, and pyrexia. Incidence rates for all of these events were highest during pre-treatment, treatment, and/or 3-month follow-up and then declined over medium-term follow-up. GT did not impact the incidence of neurologic/hearing impairments. No event indicative of leukemic transformation was reported.
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Affiliation(s)
- Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Vita-Salute San Raffaele University, Milan, Italy, 20132
| | - Laura Castagnaro
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132
| | - Katie Rolfe
- GSK Research and Development, GlaxoSmithKline, UB11 1BT and SG1 2NY, UK
| | - Erika De Boever
- GSK Research and Development, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Rickey R Reinhardt
- GSK Research and Development, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Jonathan Appleby
- GSK Research and Development, GlaxoSmithKline, UB11 1BT and SG1 2NY, UK
| | - Maria Grazia Roncarolo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Vita-Salute San Raffaele University, Milan, Italy, 20132; Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy, 20132; Vita-Salute San Raffaele University, Milan, Italy, 20132.
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23
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Hirsch T, Rothoeft T, Teig N, Bauer JW, Pellegrini G, De Rosa L, Scaglione D, Reichelt J, Klausegger A, Kneisz D, Romano O, Secone Seconetti A, Contin R, Enzo E, Jurman I, Carulli S, Jacobsen F, Luecke T, Lehnhardt M, Fischer M, Kueckelhaus M, Quaglino D, Morgante M, Bicciato S, Bondanza S, De Luca M. Regeneration of the entire human epidermis using transgenic stem cells. Nature 2017; 551:327-332. [PMID: 29144448 PMCID: PMC6283270 DOI: 10.1038/nature24487] [Citation(s) in RCA: 448] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/10/2017] [Indexed: 12/24/2022]
Abstract
Junctional epidermolysis bullosa (JEB) is a severe and often lethal genetic disease caused by mutations in genes encoding the basement membrane component laminin-332. Surviving patients with JEB develop chronic wounds to the skin and mucosa, which impair their quality of life and lead to skin cancer. Here we show that autologous transgenic keratinocyte cultures regenerated an entire, fully functional epidermis on a seven-year-old child suffering from a devastating, life-threatening form of JEB. The proviral integration pattern was maintained in vivo and epidermal renewal did not cause any clonal selection. Clonal tracing showed that the human epidermis is sustained not by equipotent progenitors, but by a limited number of long-lived stem cells, detected as holoclones, that can extensively self-renew in vitro and in vivo and produce progenitors that replenish terminally differentiated keratinocytes. This study provides a blueprint that can be applied to other stem cell-mediated combined ex vivo cell and gene therapies.
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Affiliation(s)
- Tobias Hirsch
- Department of Plastic Surgery, Burn Centre, BG University Hospital Bergmannsheil - Ruhr-University Bochum, Germany
| | - Tobias Rothoeft
- Department of Neonatology and Pediatric Intensive Care, University Children’s Hospital, Ruhr University Bochum, Germany
| | - Norbert Teig
- Department of Neonatology and Pediatric Intensive Care, University Children’s Hospital, Ruhr University Bochum, Germany
| | - Johann W. Bauer
- EB House Austria and Department of Dermatology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Graziella Pellegrini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura De Rosa
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Julia Reichelt
- EB House Austria and Department of Dermatology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Alfred Klausegger
- EB House Austria and Department of Dermatology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Daniela Kneisz
- EB House Austria and Department of Dermatology, University Hospital of the Paracelsus Medical University, Salzburg, Austria
| | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessia Secone Seconetti
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Contin
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Enzo
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata and Dipartimento di Scienze agroalimentari, ambientali e animali, University of Udine, Italy
| | | | - Frank Jacobsen
- Department of Plastic Surgery, Burn Centre, BG University Hospital Bergmannsheil - Ruhr-University Bochum, Germany
| | - Thomas Luecke
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr University Bochum, Germany
| | - Marcus Lehnhardt
- Department of Plastic Surgery, Burn Centre, BG University Hospital Bergmannsheil - Ruhr-University Bochum, Germany
| | - Meike Fischer
- Department of Neonatology and Pediatric Intensive Care, University Children’s Hospital, Ruhr University Bochum, Germany
| | - Maximilian Kueckelhaus
- Department of Plastic Surgery, Burn Centre, BG University Hospital Bergmannsheil - Ruhr-University Bochum, Germany
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata and Dipartimento di Scienze agroalimentari, ambientali e animali, University of Udine, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Michele De Luca
- Center for Regenerative Medicine “Stefano Ferrari”, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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24
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Analyzing the Genotoxicity of Retroviral Vectors in Hematopoietic Cell Gene Therapy. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 8:21-30. [PMID: 29159200 PMCID: PMC5684499 DOI: 10.1016/j.omtm.2017.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Retroviral vectors, including those derived from gammaretroviruses and lentiviruses, have found their way into the clinical arena and demonstrated remarkable efficacy for the treatment of immunodeficiencies, leukodystrophies, and globinopathies. Despite these successes, gene therapy unfortunately also has had to face severe adverse events in the form of leukemias and myelodysplastic syndromes, related to the semi-random vector integration into the host cell genome that caused deregulation of neighboring proto-oncogenes. Although improvements in vector design clearly lowered the risk of this insertional mutagenesis, analysis of potential genotoxicity and the consequences of vector integration remain important parameters for basic and translational research and most importantly for the clinic. Here, we review current assays to analyze biodistribution and genotoxicity in the pre-clinical setting and describe tools to monitor vector integration sites in vector-treated patients as a biosafety readout.
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25
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Biasco L, Rothe M, Schott JW, Schambach A. Integrating Vectors for Gene Therapy and Clonal Tracking of Engineered Hematopoiesis. Hematol Oncol Clin North Am 2017; 31:737-752. [DOI: 10.1016/j.hoc.2017.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Scholz SJ, Fronza R, Bartholomä CC, Cesana D, Montini E, von Kalle C, Gil-Farina I, Schmidt M. Lentiviral Vector Promoter is Decisive for Aberrant Transcript Formation. Hum Gene Ther 2017; 28:875-885. [PMID: 28825370 DOI: 10.1089/hum.2017.162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Lentiviral vectors hold great promise for the genetic correction of various inherited diseases. However, lentiviral vector biology is still not completely understood and warrants the precise decoding of molecular mechanisms underlying integration and post-translational modification. This study investigated a series of self-inactivating (SIN) and full long terminal repeat (LTR) lentiviral vectors that contained different types of promoters with or without a transgene to gain deeper insights in lentiviral target site selection and potential perturbation of cellular gene expression. Using an optimized nonrestrictive linear amplification-mediated polymerase chain reaction (nrLAM-PCR) protocol, vector structure-dependent integration site profiles were observed upon transduction of mouse lin- hematopoietic progenitors in vitro. Initial target site selection mainly depended on the presence of the promoter while being independent of its nature. Despite the increased propensity for read-through transcription of SIN lentiviral vectors, the incidence of viral-cellular fusion transcript formation involving the canonical viral splice donor or cryptic splice sites was reduced in both unselected primary lin- cells and transformed 32D cells. Moreover, the strength of the internal promoter in vectors with SIN LTRs is decisive for in vitro selection and for the abundance of chimeric transcripts, which are decreased by moderately active promoters. These results will help to better understand vector biology and to optimize therapeutic vectors for future gene therapy applications.
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Affiliation(s)
- Simone J Scholz
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany
| | - Raffaele Fronza
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany .,2 GeneWerk GmbH, Heidelberg, Germany
| | - Cynthia C Bartholomä
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany
| | - Daniela Cesana
- 3 San Raffaele Telethon Institute for Gene Therapy , Milan, Italy
| | - Eugenio Montini
- 3 San Raffaele Telethon Institute for Gene Therapy , Milan, Italy
| | - Christof von Kalle
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany
| | - Irene Gil-Farina
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany
| | - Manfred Schmidt
- 1 Department of Translational Oncology, German Cancer Research Center and National Center for Tumor Diseases , Heidelberg, Germany .,2 GeneWerk GmbH, Heidelberg, Germany
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27
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Romano O, Cifola I, Poletti V, Severgnini M, Peano C, De Bellis G, Mavilio F, Miccio A. Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions. J Vis Exp 2017. [PMID: 28605390 DOI: 10.3791/55919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Moloney murine leukemia (MLV) virus-based retroviral vectors integrate predominantly in acetylated enhancers and promoters. For this reason, mLV integration sites can be used as functional markers of active regulatory elements. Here, we present a retroviral scanning tool, which allows the genome-wide identification of cell-specific enhancers and promoters. Briefly, the target cell population is transduced with an mLV-derived vector and genomic DNA is digested with a frequently cutting restriction enzyme. After ligation of genomic fragments with a compatible DNA linker, linker-mediated polymerase chain reaction (LM-PCR) allows the amplification of the virus-host genome junctions. Massive sequencing of the amplicons is used to define the mLV integration profile genome-wide. Finally, clusters of recurrent integrations are defined to identify cell-specific regulatory regions, responsible for the activation of cell-type specific transcriptional programs. The retroviral scanning tool allows the genome-wide identification of cell-specific promoters and enhancers in prospectively isolated target cell populations. Notably, retroviral scanning represents an instrumental technique for the retrospective identification of rare populations (e.g. somatic stem cells) that lack robust markers for prospective isolation.
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Affiliation(s)
- Oriana Romano
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia; Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute
| | | | | | | | | | | | - Fulvio Mavilio
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia; Généthon
| | - Annarita Miccio
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia; Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute; Généthon; Sorbonne Paris Cité - Université Paris Descartes;
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28
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Thrasher AJ, Williams DA. Evolving Gene Therapy in Primary Immunodeficiency. Mol Ther 2017; 25:1132-1141. [PMID: 28366768 DOI: 10.1016/j.ymthe.2017.03.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 12/29/2022] Open
Abstract
Prior to the first successful bone marrow transplant in 1968, patients born with severe combined immunodeficiency (SCID) invariably died. Today, with a widening availability of newborn screening, major improvements in the application of allogeneic procedures, and the emergence of successful hematopoietic stem and progenitor cell (HSC/P) gene therapy, the majority of these children can be identified and cured. Here, we trace key steps in the development of clinical gene therapy for SCID and other primary immunodeficiencies (PIDs), and review the prospects for adoption of new targets and technologies.
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Affiliation(s)
- Adrian J Thrasher
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK; University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK.
| | - David A Williams
- Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School and Harvard Stem Cell Institute, 300 Longwood Avenue, Boston, MA 02115, USA.
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29
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Shaw KL, Garabedian E, Mishra S, Barman P, Davila A, Carbonaro D, Shupien S, Silvin C, Geiger S, Nowicki B, Smogorzewska EM, Brown B, Wang X, de Oliveira S, Choi Y, Ikeda A, Terrazas D, Fu PY, Yu A, Fernandez BC, Cooper AR, Engel B, Podsakoff G, Balamurugan A, Anderson S, Muul L, Jagadeesh GJ, Kapoor N, Tse J, Moore TB, Purdy K, Rishi R, Mohan K, Skoda-Smith S, Buchbinder D, Abraham RS, Scharenberg A, Yang OO, Cornetta K, Gjertson D, Hershfield M, Sokolic R, Candotti F, Kohn DB. Clinical efficacy of gene-modified stem cells in adenosine deaminase-deficient immunodeficiency. J Clin Invest 2017; 127:1689-1699. [PMID: 28346229 DOI: 10.1172/jci90367] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/24/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Autologous hematopoietic stem cell transplantation (HSCT) of gene-modified cells is an alternative to enzyme replacement therapy (ERT) and allogeneic HSCT that has shown clinical benefit for adenosine deaminase-deficient (ADA-deficient) SCID when combined with reduced intensity conditioning (RIC) and ERT cessation. Clinical safety and therapeutic efficacy were evaluated in a phase II study. METHODS Ten subjects with confirmed ADA-deficient SCID and no available matched sibling or family donor were enrolled between 2009 and 2012 and received transplantation with autologous hematopoietic CD34+ cells that were modified with the human ADA cDNA (MND-ADA) γ-retroviral vector after conditioning with busulfan (90 mg/m2) and ERT cessation. Subjects were followed from 33 to 84 months at the time of data analysis. Safety of the procedure was assessed by recording the number of adverse events. Efficacy was assessed by measuring engraftment of gene-modified hematopoietic stem/progenitor cells, ADA gene expression, and immune reconstitution. RESULTS With the exception of the oldest subject (15 years old at enrollment), all subjects remained off ERT with normalized peripheral blood mononuclear cell (PBMC) ADA activity, improved lymphocyte numbers, and normal proliferative responses to mitogens. Three of nine subjects were able to discontinue intravenous immunoglobulin replacement therapy. The MND-ADA vector was persistently detected in PBMCs (vector copy number [VCN] = 0.1-2.6) and granulocytes (VCN = 0.01-0.3) through the most recent visits at the time of this writing. No patient has developed a leukoproliferative disorder or other vector-related clinical complication since transplant. CONCLUSION These results demonstrate clinical therapeutic efficacy from gene therapy for ADA-deficient SCID, with an excellent clinical safety profile. TRIAL REGISTRATION ClinicalTrials.gov NCT00794508. FUNDING Food and Drug Administration Office of Orphan Product Development award, RO1 FD003005; NHLBI awards, PO1 HL73104 and Z01 HG000122; UCLA Clinical and Translational Science Institute awards, UL1RR033176 and UL1TR000124.
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30
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Tordini F, Aldinucci M, Milanesi L, Liò P, Merelli I. The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer. Front Genet 2016; 7:194. [PMID: 27895661 PMCID: PMC5108817 DOI: 10.3389/fgene.2016.00194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level. Using this representation, we can describe how driver and passenger mutations accumulate during the development of diseases providing, for example, a tool able to characterize the evolution of cancer. Indeed, our test case concerns the MCF-7 breast cancer cell line, before and after the stimulation with estrogen, since many datasets are available for this case study. In particular, the integration of data about cancer mutations, gene functional annotations, genome conformation, epigenetic patterns, gene expression, and metabolic pathways in our multi-layer representation will allow a better interpretation of the mechanisms behind a complex disease such as cancer. Thanks to this multi-layer approach, we focus on the interplay of chromatin conformation and cancer mutations in different pathways, such as metabolic processes, that are very important for tumor development. Working on this model, a variance analysis can be implemented to identify normal variations within each omics and to characterize, by contrast, variations that can be accounted to pathological samples compared to normal ones. This integrative model can be used to identify novel biomarkers and to provide innovative omic-based guidelines for treating many diseases, improving the efficacy of decision trees currently used in clinic.
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Affiliation(s)
- Fabio Tordini
- Computer Science Department, University of Torino Torino, Italy
| | - Marco Aldinucci
- Computer Science Department, University of Torino Torino, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge Cambridge, UK
| | - Ivan Merelli
- Institute of Biomedical Technologies, Italian National Research Council Milan, Italy
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31
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Abstract
Viral vector use in gene therapy has highlighted several safety concerns, including genotoxic events. Generally, vector-mediated genotoxicity results from upregulation of cellular proto-oncogenes via promoter insertion, promoter activation, or gene transcript truncation, with enhancer-mediated activation of nearby genes the primary mechanism reported in gene therapy trials. Vector-mediated genotoxicity can be influenced by virus type, integration target site, and target cell type; different vectors have distinct integration profiles which are cell-specific. Non-viral factors, including patient age, disease, and dose can also influence genotoxic potential, thus the choice of test models and clinical trial populations is important to ensure they are indicative of efficacy and safety. Efforts have been made to develop viral vectors with less risk of insertional mutagenesis, including self-inactivating (SIN) vectors, enhancer-blocking insulators, and microRNA targeting of vectors, although insertional mutagenesis is not completely abrogated. Here we provide an overview of the current understanding of viral vector-mediated genotoxicity risk from factors contributing to viral vector-mediated genotoxicity to efforts made to reduce genotoxicity, and testing strategies required to adequately assess the risk of insertional mutagenesis. It is clear that there is not a 'one size fits all' approach to vector modification for reducing genotoxicity, and addressing these challenges will be a key step in the development of therapies such as CRISPR-Cas9 and delivery of future gene-editing technologies.
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Affiliation(s)
- Rhiannon M David
- Genetic Toxicology, Discovery Safety, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Ann T Doherty
- Genetic Toxicology, Discovery Safety, AstraZeneca, Cambridge, CB4 0WG, UK
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32
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Bernardo ME, Aiuti A. The Role of Conditioning in Hematopoietic Stem-Cell Gene Therapy. Hum Gene Ther 2016; 27:741-748. [DOI: 10.1089/hum.2016.103] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Maria Ester Bernardo
- San Raffaele Telethon Institute for Gene Therapy, SR-TIGET; Pediatric Immunohematology, San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, SR-TIGET; Pediatric Immunohematology, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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33
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Update on the safety and efficacy of retroviral gene therapy for immunodeficiency due to adenosine deaminase deficiency. Blood 2016; 128:45-54. [PMID: 27129325 DOI: 10.1182/blood-2016-01-688226] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/14/2016] [Indexed: 12/16/2022] Open
Abstract
Adenosine deaminase (ADA) deficiency is a rare, autosomal-recessive systemic metabolic disease characterized by severe combined immunodeficiency (SCID). The treatment of choice for ADA-deficient SCID (ADA-SCID) is hematopoietic stem cell transplant from an HLA-matched sibling donor, although <25% of patients have such a donor available. Enzyme replacement therapy (ERT) partially and temporarily relieves immunodeficiency. We investigated the medium-term outcome of gene therapy (GT) in 18 patients with ADA-SCID for whom an HLA-identical family donor was not available; most were not responding well to ERT. Patients were treated with an autologous CD34(+)-enriched cell fraction that contained CD34(+) cells transduced with a retroviral vector encoding the human ADA complementary DNA sequence (GSK2696273) as part of single-arm, open-label studies or compassionate use programs. Overall survival was 100% over 2.3 to 13.4 years (median, 6.9 years). Gene-modified cells were stably present in multiple lineages throughout follow up. GT resulted in a sustained reduction in the severe infection rate from 1.17 events per person-year to 0.17 events per person-year (n = 17, patient 1 data not available). Immune reconstitution was demonstrated by normalization of T-cell subsets (CD3(+), CD4(+), and CD8(+)), evidence of thymopoiesis, and sustained T-cell proliferative capacity. B-cell function was evidenced by immunoglobulin production, decreased intravenous immunoglobulin use, and antibody response after vaccination. All 18 patients reported infections as adverse events; infections of respiratory and gastrointestinal tracts were reported most frequently. No events indicative of leukemic transformation were reported. Trial details were registered at www.clinicaltrials.gov as #NCT00598481.
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34
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Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A. Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment. Sci Rep 2016; 6:24724. [PMID: 27095295 PMCID: PMC4837375 DOI: 10.1038/srep24724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France
| | - Clelia Peano
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | - Luca Petiti
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | | | - Ermanno Rizzi
- Institute of Biomedical Technologies, CNR, Milan, Italy.,Telethon Foundation, Milan, Italy
| | | | - Alessia Cavazza
- Dana Farber Cancer Institute, Harvard Medical School, Boston, US
| | - Claudia Rossi
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy
| | - Pasqualepaolo Pagliaro
- Az. Osp. Policlinico Universitario di Bologna, Policlinico S. Orsola-Malpighi, Unità Operativa di Immunoematologia e Trasfusionale, Bologna, Italy
| | | | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Silvio Bicciato
- Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Genethon, Evry, France
| | - Annarita Miccio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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35
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Cavazza A, Miccio A, Romano O, Petiti L, Malagoli Tagliazucchi G, Peano C, Severgnini M, Rizzi E, De Bellis G, Bicciato S, Mavilio F. Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation. Stem Cell Reports 2016; 6:618-632. [PMID: 27050947 PMCID: PMC4834057 DOI: 10.1016/j.stemcr.2016.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 12/20/2022] Open
Abstract
Human skin is maintained by the differentiation and maturation of interfollicular stem and progenitors cells. We used DeepCAGE, genome-wide profiling of histone modifications and retroviral integration analysis, to map transcripts, promoters, enhancers, and super-enhancers (SEs) in prospectively isolated keratinocytes and transit-amplifying progenitors, and retrospectively defined keratinocyte stem cells. We show that >95% of the active promoters are in common and differentially regulated in progenitors and differentiated keratinocytes, while approximately half of the enhancers and SEs are stage specific and account for most of the epigenetic changes occurring during differentiation. Transcription factor (TF) motif identification and correlation with TF binding site maps allowed the identification of TF circuitries acting on enhancers and SEs during differentiation. Overall, our study provides a broad, genome-wide description of chromatin dynamics and differential enhancer and promoter usage during epithelial differentiation, and describes a novel approach to identify active regulatory elements in rare stem cell populations. Differentiation of epidermal progenitors is accompanied by enhancer remodeling A TF circuitry operating on super-enhancers regulates epidermal differentiation TP63 is a key master regulator of stage-specific super-enhancers MLV integration marks enhancers in retrospectively defined epidermal stem cells
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Affiliation(s)
- Alessia Cavazza
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Luca Petiti
- Institute for Biomedical Technologies, National Research Council, 20132 Milan, Italy
| | | | - Clelia Peano
- Institute for Biomedical Technologies, National Research Council, 20132 Milan, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council, 20132 Milan, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, 20132 Milan, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, 20132 Milan, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; Genethon, 1bis rue de l'Internationale, 91002 Evry, France.
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36
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Cicalese MP, Aiuti A. Clinical applications of gene therapy for primary immunodeficiencies. Hum Gene Ther 2016; 26:210-9. [PMID: 25860576 DOI: 10.1089/hum.2015.047] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Primary immunodeficiencies (PIDs) have represented a paradigmatic model for successes and pitfalls of hematopoietic stem cells gene therapy. First clinical trials performed with gamma retroviral vectors (γ-RV) for adenosine deaminase severe combined immunodeficiency (ADA-SCID), X-linked SCID (SCID-X1), and Wiskott-Aldrich syndrome (WAS) showed that gene therapy is a valid therapeutic option in patients lacking an HLA-identical donor. No insertional mutagenesis events have been observed in more than 40 ADA-SCID patients treated so far in the context of different clinical trials worldwide, suggesting a favorable risk-benefit ratio for this disease. On the other hand, the occurrence of insertional oncogenesis in SCID-X1, WAS, and chronic granulomatous disease (CGD) RV clinical trials prompted the development of safer vector construct based on self-inactivating (SIN) retroviral or lentiviral vectors (LVs). Here we present the recent results of LV-mediated gene therapy for WAS showing stable multilineage engraftment leading to hematological and immunological improvement, and discuss the differences with respect to the WAS RV trial. We also describe recent clinical results of SCID-X1 gene therapy with SIN γ-RV and the perspectives of targeted genome editing techniques, following early preclinical studies showing promising results in terms of specificity of gene correction. Finally, we provide an overview of the gene therapy approaches for other PIDs and discuss its prospects in relation to the evolving arena of allogeneic transplant.
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Affiliation(s)
- Maria Pia Cicalese
- 1 San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute , 20132 Milan, Italy
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37
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Biasco L, Scala S, Basso Ricci L, Dionisio F, Baricordi C, Calabria A, Giannelli S, Cieri N, Barzaghi F, Pajno R, Al-Mousa H, Scarselli A, Cancrini C, Bordignon C, Roncarolo MG, Montini E, Bonini C, Aiuti A. In vivo tracking of T cells in humans unveils decade-long survival and activity of genetically modified T memory stem cells. Sci Transl Med 2015; 7:273ra13. [PMID: 25653219 DOI: 10.1126/scitranslmed.3010314] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A definitive understanding of survival and differentiation potential in humans of T cell subpopulations is of paramount importance for the development of effective T cell therapies. In particular, uncovering the dynamics in vivo in humans of the recently described T memory stem cells (TSCM) would be crucial for therapeutic approaches that aim at taking advantage of a stable cellular vehicle with precursor potential. We exploited data derived from two gene therapy clinical trials for an inherited immunodeficiency, using either retrovirally engineered hematopoietic stem cells or mature lymphocytes to trace individual T cell clones directly in vivo in humans. We compared healthy donors and bone marrow-transplanted patients, studied long-term in vivo T cell composition under different clinical conditions, and specifically examined TSCM contribution according to age, conditioning regimen, disease background, cell source, long-term reconstitution, and ex vivo gene correction processing. High-throughput sequencing of retroviral vector integration sites (ISs) allowed tracing the fate of more than 1700 individual T cell clones in gene therapy patients after infusion of gene-corrected hematopoietic stem cells or mature lymphocytes. We shed light on long-term in vivo clonal relationships among different T cell subtypes, and we unveiled that TSCM are able to persist and to preserve their precursor potential in humans for up to 12 years after infusion of gene-corrected lymphocytes. Overall, this work provides high-resolution tracking of T cell fate and activity and validates, in humans, the safe and functional decade-long survival of engineered TSCM, paving the way for their future application in clinical settings.
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Affiliation(s)
- Luca Biasco
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy.
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy. Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luca Basso Ricci
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | - Francesca Dionisio
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | - Cristina Baricordi
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | - Stefania Giannelli
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Federica Barzaghi
- Pediatric Immunohematology and Stem Cell Programme, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Roberta Pajno
- Pediatric Immunohematology and Stem Cell Programme, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Hamoud Al-Mousa
- King Faisal Specialist Hospital & Research Centre, Riyadh 11211, Saudi Arabia
| | - Alessia Scarselli
- Department of Pediatrics, Ospedale Pediatrico Bambino Gesù and University of Rome "Tor Vergata," Rome 00165, Italy
| | - Caterina Cancrini
- Department of Pediatrics, Ospedale Pediatrico Bambino Gesù and University of Rome "Tor Vergata," Rome 00165, Italy
| | | | - Maria Grazia Roncarolo
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy. Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (TIGET), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan 20132, Italy
| | - Chiara Bonini
- IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessandro Aiuti
- Department of Pediatrics, Ospedale Pediatrico Bambino Gesù and University of Rome "Tor Vergata," Rome 00165, Italy. TIGET, Pediatric Immunohematology and Stem Cell Programme, San Raffaele Scientific Institute, Milan 20132, Italy.
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38
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Shavit Y, Merelli I, Milanesi L, Lio’ P. How computer science can help in understanding the 3D genome architecture. Brief Bioinform 2015; 17:733-44. [DOI: 10.1093/bib/bbv085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 01/20/2023] Open
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Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2015; 2:15015. [PMID: 26029726 PMCID: PMC4445430 DOI: 10.1038/mtm.2015.15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 12/28/2022]
Abstract
Unequivocal demonstration of the therapeutic utility of γ-retroviral vectors for gene therapy applications targeting the hematopoietic system was accompanied by instances of insertional mutagenesis. These events stimulated the ongoing development of putatively safer integrating vector systems and analysis methods to characterize and compare integration site (IS) biosafety profiles. Continuing advances in next-generation sequencing technologies are driving the generation of ever-more complex IS datasets. Available bioinformatic tools to compare such datasets focus on the association of integration sites (ISs) with selected genomic and epigenetic features, and the choice of these features determines the ability to discriminate between datasets. We describe the scalable application of point-process coherence analysis (CA) to compare patterns produced by vector ISs across genomic intervals, uncoupled from association with genomic features. To explore the utility of CA in the context of an unresolved question, we asked whether the differing transduction conditions used in the initial Paris and London SCID-X1 gene therapy trials result in divergent genome-wide integration profiles. We tested a transduction carried out under each condition, and showed that CA could indeed resolve differences in IS distributions. Existence of these differences was confirmed by the application of established methods to compare integration datasets.
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40
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Calero-Garcia M, Gaspar HB. Gene Therapy for SCID. CURRENT PEDIATRICS REPORTS 2015. [DOI: 10.1007/s40124-014-0069-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Doi K, Takeuchi Y. [Gene therapy using retrovirus vectors: vector development and biosafety at clinical trials]. Uirusu 2015; 65:27-36. [PMID: 26923955 DOI: 10.2222/jsv.65.27] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Retrovirus vectors (gammaretroviral and lentiviral vectors) have been considered as promising tools to transfer therapeutic genes into patient cells because they can permanently integrate into host cellular genome. To treat monogenic, inherited diseases, retroviral vectors have been used to add correct genes into patient cells. Conventional gammaretroviral vectors achieved successful results in clinical trials: treated patients had therapeutic gene expression in target cells and had improved symptoms of diseases. However, serious side-effects of leukemia occurred, caused by retroviral insertional mutagenesis (IM). These incidences stressed the importance of monitoring vector integration sites in patient cells as well as of re-consideration on safer vectors. More recently lentiviral vectors which can deliver genes into non-dividing cells started to be used in clinical trials including neurological disorders, showing their efficacy. Vector integration site analysis revealed that lentiviruses integrate less likely to near promoter regions of oncogenes than gammaretroviruses and no adverse events have been reported in lentiviral vector-mediated gene therapy clinical trials. Therefore lentiviral vectors have promises to be applied to a wide range of common diseases in near future. For example, T cells from cancer patients were transduced to express chimeric T cell receptors recognizing their tumour cells enhancing patients' anti-cancer immunity.
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Affiliation(s)
- Knayo Doi
- MRC/UCL Centre for Medical Molecular Virology and Wohl Virion Centre, Division of infection and Immunity, University College London
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42
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Ramachandra DL, Shaw SSW, Shangaris P, Loukogeorgakis S, Guillot PV, Coppi PD, David AL. In utero therapy for congenital disorders using amniotic fluid stem cells. Front Pharmacol 2014; 5:270. [PMID: 25566071 PMCID: PMC4271591 DOI: 10.3389/fphar.2014.00270] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
Congenital diseases are responsible for over a third of all pediatric hospital admissions. Advances in prenatal screening and molecular diagnosis have allowed the detection of many life-threatening genetic diseases early in gestation. In utero transplantation (IUT) with stem cells could cure affected fetuses but so far in humans, successful IUT using allogeneic hematopoietic stem cells (HSCs), has been limited to fetuses with severe immunologic defects and more recently IUT with allogeneic mesenchymal stem cell transplantation, has improved phenotype in osteogenesis imperfecta. The options of preemptive treatment of congenital diseases in utero by stem cell or gene therapy changes the perspective of congenital diseases since it may avoid the need for postnatal treatment and reduce future costs. Amniotic fluid stem (AFS) cells have been isolated and characterized in human, mice, rodents, rabbit, and sheep and are a potential source of cells for therapeutic applications in disorders for treatment prenatally or postnatally. Gene transfer to the cells with long-term transgenic protein expression is feasible. Recently, pre-clinical autologous transplantation of transduced cells has been achieved in fetal sheep using minimally invasive ultrasound guided injection techniques. Clinically relevant levels of transgenic protein were expressed in the blood of transplanted lambs for at least 6 months. The cells have also demonstrated the potential of repair in a range of pre-clinical disease models such as neurological disorders, tracheal repair, bladder injury, and diaphragmatic hernia repair in neonates or adults. These results have been encouraging, and bring personalized tissue engineering for prenatal treatment of genetic disorders closer to the clinic.
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Affiliation(s)
- Durrgah L. Ramachandra
- Stem Cells and Regenerative Medicine, Institute of Child Health, University College London, London, UK
| | - Steven S. W. Shaw
- Department of Obstetrics and Gynaecology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- Department of Obstetrics and Gynaecology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Prenatal Therapy, Institute for Women’s Health, University College London, London, UK
| | - Panicos Shangaris
- Prenatal Therapy, Institute for Women’s Health, University College London, London, UK
| | - Stavros Loukogeorgakis
- Stem Cells and Regenerative Medicine, Institute of Child Health, University College London, London, UK
| | - Pascale V. Guillot
- Stem Cells and Regenerative Medicine, Institute of Child Health, University College London, London, UK
- Cellular Reprogramming and Perinatal Therapy, Institute for Women’s Health, University College London, London, UK
| | - Paolo De Coppi
- Stem Cells and Regenerative Medicine, Institute of Child Health, University College London, London, UK
| | - Anna L. David
- Prenatal Therapy, Institute for Women’s Health, University College London, London, UK
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Kohn DB. Eliminating SCID row: new approaches to SCID. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2014; 2014:475-480. [PMID: 25696897 DOI: 10.1182/asheducation-2014.1.475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Treatments for patients with SCID by hematopoietic stem cell transplantation (HSCT) have changed this otherwise lethal primary immune deficiency disorder into one with an increasingly good prognosis. SCID has been the paradigm disorder supporting many key advances in the field of HSCT, with first-in-human successes with matched sibling, haploidentical, and matched unrelated donor allogeneic transplantations. Nevertheless, the optimal approaches for HSCT are still being defined, including determining the optimal stem cell sources, the use and types of pretransplantation conditioning, and applications for SCID subtypes associated with radiosensitivity, for patients with active viral infections and for neonates. Alternatively, autologous transplantation after ex vivo gene correction (gene therapy) has been applied successfully to the treatment of adenosine deaminase-deficient SCID and X-linked SCID by vector-mediated gene addition. Gene therapy holds the prospect of avoiding risks of GVHD and would allow each patient to be their own donor. New approaches to gene therapy by gene correction in autologous HSCs using site-specific endonuclease-mediated homology-driven gene repair are under development. With newborn screening becoming more widely adopted to detect SCID patients before they develop complications, the prognosis for SCID is expected to improve further. This chapter reviews recent advances and ongoing controversies in allogeneic and autologous HSCT for SCID.
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Affiliation(s)
- Donald B Kohn
- Departments of Microbiology, Immunology, and Molecular Genetics and Pediatrics; David Geffen School of Medicine, Mattel Children's Hospital; and Eli & Edythe Broad Center for Regenerative Medicine and Stem Cells, University of California, Los Angeles, CA
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Niederer HA, Bangham CRM. Integration site and clonal expansion in human chronic retroviral infection and gene therapy. Viruses 2014; 6:4140-64. [PMID: 25365582 PMCID: PMC4246213 DOI: 10.3390/v6114140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/09/2014] [Accepted: 10/21/2014] [Indexed: 12/20/2022] Open
Abstract
Retroviral vectors have been successfully used therapeutically to restore expression of genes in a range of single-gene diseases, including several primary immunodeficiency disorders. Although clinical trials have shown remarkable results, there have also been a number of severe adverse events involving malignant outgrowth of a transformed clonal population. This clonal expansion is influenced by the integration site profile of the viral integrase, the transgene expressed, and the effect of the viral promoters on the neighbouring host genome. Infection with the pathogenic human retrovirus HTLV-1 also causes clonal expansion of cells containing an integrated HTLV-1 provirus. Although the majority of HTLV-1-infected people remain asymptomatic, up to 5% develop an aggressive T cell malignancy. In this review we discuss recent findings on the role of the genomic integration site in determining the clonality and the potential for malignant transformation of cells carrying integrated HTLV-1 or gene therapy vectors, and how these results have contributed to the understanding of HTLV-1 pathogenesis and to improvements in gene therapy vector safety.
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Affiliation(s)
- Heather A Niederer
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London W2 1PG, UK.
| | - Charles R M Bangham
- Department of Immunology, Wright-Fleming Institute, Imperial College London, London W2 1PG, UK.
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45
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Wagemaker G. Lentiviral hematopoietic stem cell gene therapy in inherited metabolic disorders. Hum Gene Ther 2014; 25:862-5. [PMID: 25184354 DOI: 10.1089/hum.2014.102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
After more than 20 years of development, lentiviral hematopoietic stem cell gene therapy has entered the stage of initial clinical implementation for immune deficiencies and storage disorders. This brief review summarizes the development and applications, focusing on the lysosomal enzyme deficiencies, especially Pompe disease.
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Affiliation(s)
- Gerard Wagemaker
- Erasmus University Rotterdam, 3005 LA Rotterdam, The Netherlands
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46
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Farinelli G, Capo V, Scaramuzza S, Aiuti A. Lentiviral vectors for the treatment of primary immunodeficiencies. J Inherit Metab Dis 2014; 37:525-33. [PMID: 24619149 DOI: 10.1007/s10545-014-9690-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/06/2014] [Accepted: 02/07/2014] [Indexed: 01/22/2023]
Abstract
In the last years important progress has been made in the treatment of several primary immunodeficiency disorders (PIDs) with gene therapy. Hematopoietic stem cell (HSC) gene therapy indeed represents a valid alternative to conventional transplantation when a compatible donor is not available and recent success confirmed the great potential of this approach. First clinical trials performed with gamma retroviral vectors were promising and guaranteed clinical benefits to the patients. On the other hand, the outcome of severe adverse events as the development of hematological abnormalities highlighted the necessity to develop a safer platform to deliver the therapeutic gene. Self-inactivating (SIN) lentiviral vectors (LVVs) were studied to overcome this hurdle through their preferable integration pattern into the host genome. In this review, we describe the recent advancements achieved both in vitro and at preclinical level with LVVs for the treatment of Wiskott-Aldrich syndrome (WAS), chronic granulomatous disease (CGD), ADA deficiency (ADA-SCID), Artemis deficiency, RAG1/2 deficiency, X-linked severe combined immunodeficiency (γchain deficiency, SCIDX1), X-linked lymphoproliferative disease (XLP) and immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome.
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Affiliation(s)
- Giada Farinelli
- Department of Pediatrics, Children's Hospital Bambino Gesù and University of Rome Tor Vergata School of Medicine, Rome, Italy
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47
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Sokol M, Wabl M, Ruiz IR, Pedersen FS. Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors. Retrovirology 2014; 11:36. [PMID: 24886479 PMCID: PMC4098794 DOI: 10.1186/1742-4690-11-36] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 04/28/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Insertional mutagenesis screens of retrovirus-induced mouse tumors have proven valuable in human cancer research and for understanding adverse effects of retroviral-based gene therapies. In previous studies, the assignment of mouse genes to individual retroviral integration sites has been based on close proximity and expression patterns of annotated genes at target positions in the genome. We here employed next-generation RNA sequencing to map retroviral-mouse chimeric junctions genome-wide, and to identify local patterns of transcription activation in T-lymphomas induced by the murine leukemia gamma-retrovirus SL3-3. Moreover, to determine epigenetic integration preferences underlying long-range gene activation by retroviruses, the colocalization propensity with common epigenetic enhancer markers (H3K4Me1 and H3K27Ac) of 6,117 integrations derived from end-stage tumors of more than 2,000 mice was examined. RESULTS We detected several novel mechanisms of retroviral insertional mutagenesis: bidirectional activation of mouse transcripts on opposite sides of a provirus including transcription of unannotated mouse sequence; sense/antisense-type activation of genes located on opposite DNA strands; tandem-type activation of distal genes that are positioned adjacently on the same DNA strand; activation of genes that are not the direct integration targets; combination-type insertional mutagenesis, in which enhancer activation, alternative chimeric splicing and retroviral promoter insertion are induced by a single retrovirus. We also show that irrespective of the distance to transcription start sites, the far majority of retroviruses in end-stage tumors colocalize with H3K4Me1 and H3K27Ac-enriched regions in murine lymphoid tissues. CONCLUSIONS We expose novel retrovirus-induced host transcription activation patterns that reach beyond a single and nearest annotated gene target. Awareness of this previously undescribed layer of complexity may prove important for elucidation of adverse effects in retroviral-based gene therapies. We also show that wild-type gamma-retroviruses are frequently positioned at enhancers, suggesting that integration into regulatory regions is specific and also subject to positive selection for sustaining long-range gene activation in end-stage tumors. Altogether, this study should prove useful for extrapolating adverse outcomes of retroviral vector therapies, and for understanding fundamental cellular regulatory principles and retroviral biology.
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Affiliation(s)
- Martin Sokol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Matthias Wabl
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Irene Rius Ruiz
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Finn Skou Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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48
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Moiani A, Suerth JD, Gandolfi F, Rizzi E, Severgnini M, De Bellis G, Schambach A, Mavilio F. Genome-wide analysis of alpharetroviral integration in human hematopoietic stem/progenitor cells. Genes (Basel) 2014; 5:415-29. [PMID: 24840152 PMCID: PMC4094940 DOI: 10.3390/genes5020415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/30/2014] [Accepted: 05/06/2014] [Indexed: 01/12/2023] Open
Abstract
Gene transfer vectors derived from gamma-retroviruses or lentiviruses are currently used for the gene therapy of genetic or acquired diseases. Retroviral vectors display a non-random integration pattern in the human genome, targeting either regulatory regions (gamma-retroviruses) or the transcribed portion of expressed genes (lentiviruses), and have the potential to deregulate gene expression at the transcriptional or post-transcriptional level. A recently developed alternative vector system derives from the avian sarcoma-leukosis alpha-retrovirus (ASLV) and shows favorable safety features compared to both gamma-retroviral and lentiviral vectors in preclinical models. We performed a high-throughput analysis of the integration pattern of self-inactivating (SIN) alpha-retroviral vectors in human CD34+ hematopoietic stem/progenitor cells (HSPCs) and compared it to previously reported gamma-retroviral and lentiviral vectors integration profiles obtained in the same experimental setting. Compared to gamma-retroviral and lentiviral vectors, the SIN-ASLV vector maintains a preference for open chromatin regions, but shows no bias for transcriptional regulatory elements or transcription units, as defined by genomic annotations and epigenetic markers (H3K4me1 and H3K4me3 histone modifications). Importantly, SIN-ASLV integrations do not cluster in hot spots and target potentially dangerous genomic loci, such as the EVI2A/B, RUNX1 and LMO2 proto-oncogenes at a virtually random frequency. These characteristics predict a safer profile for ASLV-derived vectors for clinical applications.
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Affiliation(s)
- Arianna Moiani
- Genethon, 1bis Rue de l'Internationale, 91020 Evry, France.
| | - Julia Debora Suerth
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, D-30625 Hannover, Germany.
| | | | - Ermanno Rizzi
- Institute for Biomedical Technologies, Consiglio Nazionale delle Ricerche, Milan 20132, Italy.
| | - Marco Severgnini
- Institute for Biomedical Technologies, Consiglio Nazionale delle Ricerche, Milan 20132, Italy.
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, Consiglio Nazionale delle Ricerche, Milan 20132, Italy.
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, D-30625 Hannover, Germany.
| | - Fulvio Mavilio
- Genethon, 1bis Rue de l'Internationale, 91020 Evry, France.
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De Ravin SS, Su L, Theobald N, Choi U, Macpherson JL, Poidinger M, Symonds G, Pond SM, Ferris AL, Hughes SH, Malech HL, Wu X. Enhancers are major targets for murine leukemia virus vector integration. J Virol 2014; 88:4504-13. [PMID: 24501411 PMCID: PMC3993722 DOI: 10.1128/jvi.00011-14] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 01/30/2014] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Retroviral vectors have been used in successful gene therapies. However, in some patients, insertional mutagenesis led to leukemia or myelodysplasia. Both the strong promoter/enhancer elements in the long terminal repeats (LTRs) of murine leukemia virus (MLV)-based vectors and the vector-specific integration site preferences played an important role in these adverse clinical events. MLV integration is known to prefer regions in or near transcription start sites (TSS). Recently, BET family proteins were shown to be the major cellular proteins responsible for targeting MLV integration. Although MLV integration sites are significantly enriched at TSS, only a small fraction of the MLV integration sites (<15%) occur in this region. To resolve this apparent discrepancy, we created a high-resolution genome-wide integration map of more than one million integration sites from CD34(+) hematopoietic stem cells transduced with a clinically relevant MLV-based vector. The integration sites form ∼60,000 tight clusters. These clusters comprise ∼1.9% of the genome. The vast majority (87%) of the integration sites are located within histone H3K4me1 islands, a hallmark of enhancers. The majority of these clusters also have H3K27ac histone modifications, which mark active enhancers. The enhancers of some oncogenes, including LMO2, are highly preferred targets for integration without in vivo selection. IMPORTANCE We show that active enhancer regions are the major targets for MLV integration; this means that MLV preferentially integrates in regions that are favorable for viral gene expression in a variety of cell types. The results provide insights for MLV integration target site selection and also explain the high risk of insertional mutagenesis that is associated with gene therapy trials using MLV vectors.
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Affiliation(s)
- Suk See De Ravin
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ling Su
- Laboratory of Molecular Technology, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Narda Theobald
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Uimook Choi
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Geoff Symonds
- Johnson and Johnson Research Pty. Ltd., Sydney, Australia
| | - Susan M. Pond
- Johnson and Johnson Research Pty. Ltd., Sydney, Australia
| | - Andrea L. Ferris
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, USA
| | - Harry L. Malech
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaolin Wu
- Laboratory of Molecular Technology, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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50
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Advances in siRNA delivery to T-cells: potential clinical applications for inflammatory disease, cancer and infection. Biochem J 2013; 455:133-47. [DOI: 10.1042/bj20130950] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The specificity of RNAi and its ability to silence ‘undruggable’ targets has made inhibition of gene expression in T-cells with siRNAs an attractive potential therapeutic strategy for the treatment of inflammatory disease, cancer and infection. However, delivery of siRNAs into primary T-cells represents a major hurdle to their use as potential therapeutic agents. Recent advances in siRNA delivery through the use of electroporation/nucleofection, viral vectors, peptides/proteins, nanoparticles, aptamers and other agents have now enabled efficient gene silencing in primary T-cells both in vitro and in vivo. Overcoming such barriers in siRNA delivery offers exciting new prospects for directly targeting T-cells systemically with siRNAs, or adoptively transferring T-cells back into patients following ex vivo manipulation with siRNAs. In the present review, we outline the challenges in delivering siRNAs into primary T-cells and discuss the mechanism and therapeutic opportunities of each delivery method. We emphasize studies that have exploited RNAi-mediated gene silencing in T-cells for the treatment of inflammatory disease, cancer and infection using mouse models. We also discuss the potential therapeutic benefits of manipulating T-cells using siRNAs for the treatment of human diseases.
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