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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: 136] [Impact Index Per Article: 15.1] [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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Williams DA, Thrasher AJ. Concise review: lessons learned from clinical trials of gene therapy in monogenic immunodeficiency diseases. Stem Cells Transl Med 2014; 3:636-42. [PMID: 24682287 DOI: 10.5966/sctm.2013-0206] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Thirty years ago, retroviral transfer of genetic material into hematopoietic stem and progenitor cells (HSC/Ps) led to predictions that this technology would transform modern medicine [Nature 1983;305:556-558; Nature 1984;310:476-480]. Studies in several immunodeficiency diseases in the past 15 years have demonstrated clear proof of principle that gene therapy can have long-lasting, potentially curative effects without the need to search for allogeneic donors and without risk of graft-versus-host disease. Improvement in gene transfer efficiency for target HSC/Ps brought to light issues of insertional mutagenesis caused by transfer vectors, resulting in oncogene transactivation and leukemias. Lessons from these adverse events have now led to a new generation of vectors, refinements in conditioning regimens, and manufacturing, which are paving the way for expanded applications of the current technology and recent emphasis on gene targeting/genome editing as the next advancements in the field.
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Affiliation(s)
- David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, and Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts, USA; Centre for Immunodeficiency, Molecular Immunology Unit, Institute of Child Health, London, United Kingdom
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Mouse transplant models for evaluating the oncogenic risk of a self-inactivating XSCID lentiviral vector. PLoS One 2013; 8:e62333. [PMID: 23626802 PMCID: PMC3633865 DOI: 10.1371/journal.pone.0062333] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/20/2013] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem cell gene therapy requires the use of integrating retroviral vectors in order to stably transmit a therapeutic gene to mature blood cells. Human clinical trials have shown that some vector integration events lead to disrupted regulation of proto-oncogenes resulting in disordered hematopoiesis including T-cell leukemia. Newer vectors have been designed to decrease the incidence of these adverse events but require appropriate pre-clinical assays to demonstrate safety. We have used two distinct mouse serial transplant assays to evaluate the safety of a self-inactivating lentiviral vector intended for use in X-linked severe combined immunodeficiency (XSCID) gene therapy trials. These experiments entailed 28 months of total follow-up and included 386 mice. There were no cases in which the XSCID lentiviral vector clearly caused hematopoietic malignancies, although a single case of B cell malignancy was observed that contained the lentiviral vector as a likely passenger event. In contrast, a SFFV-DsRed γ-retroviral vector resulted in clonal transformation events in multiple secondary recipients. Non-specific pathology not related to vector insertions was noted including T cell leukemias arising from irradiated recipient cells. Overall, this comprehensive study of mouse transplant safety assays demonstrate the relative safety of the XSCID lentiviral vector but also highlight the limitations of these assays.
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Hackett PB, Largaespada DA, Switzer KC, Cooper LJN. Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy. Transl Res 2013; 161:265-83. [PMID: 23313630 PMCID: PMC3602164 DOI: 10.1016/j.trsl.2012.12.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/30/2022]
Abstract
Investigational therapy can be successfully undertaken using viral- and nonviral-mediated ex vivo gene transfer. Indeed, recent clinical trials have established the potential for genetically modified T cells to improve and restore health. Recently, the Sleeping Beauty (SB) transposon/transposase system has been applied in clinical trials to stably insert a chimeric antigen receptor (CAR) to redirect T-cell specificity. We discuss the context in which the SB system can be harnessed for gene therapy and describe the human application of SB-modified CAR(+) T cells. We have focused on theoretical issues relating to insertional mutagenesis in the context of human genomes that are naturally subjected to remobilization of transposons and the experimental evidence over the last decade of employing SB transposons for defining genes that induce cancer. These findings are put into the context of the use of SB transposons in the treatment of human disease.
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Affiliation(s)
- Perry B Hackett
- Department of Genetics Cell Biology and Development, Center for Genome Engineering and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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Abstract
BACKGROUND Wiskott-Aldrich syndrome (WAS) is a rare X-linked primary immunodeficiency (PID) characterized by micro-thrombocytopenia, recurrent infections, eczema, which is associated with a high incidence of auto-immunity and lymphoreticular malignancy. One of the first diseases to be successfully treated by allogeneic hematopoietic stem cell transplantation, WAS is currently the subject of several phase I/II gene therapy trials for patients without HLA-compatible donors. PURPOSE OF REVIEW This article reviews the preclinical and clinical data leading to the development of gene therapy of WAS with lentiviral vectors. RECENT FINDINGS A recent clinical trial using a conventional gammaretroviral vector has demonstrated the proof of principle of gene therapy in WAS, but has also highlighted a common limitation of the technology. Encouraging preclinical efficacy and safety results using refined lentiviral vectors, and the development of robust clinical-grade manufacturing processes have supported the initiation of several phase I/II new studies. SUMMARY WAS is amenable to hematopoietic stem cell gene therapy. New trials using lentiviral vectors are expected to improve efficacy and safety profiles. Beyond proof of principle, ongoing international efforts to coordinate trials of gene therapy for the WAS may also provide a model for the expedited development of new treatments for other rare diseases.
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Abstract
γ-Retroviral and lentiviral vectors allow the permanent integration of a therapeutic transgene in target cells and have provided in the last decade a delivery platform for several successful gene therapy (GT) clinical approaches. However, the occurrence of adverse events due to insertional mutagenesis in GT treated patients poses a strong challenge to the scientific community to identify the mechanisms at the basis of vector-driven genotoxicity. Along the last decade, the study of retroviral integration sites became a fundamental tool to monitor vector–host interaction in patients overtime. This review is aimed at critically revising the data derived from insertional profiling, with a particular focus on the evidences collected from GT clinical trials. We discuss the controversies and open issues associated to the interpretation of integration site analysis during patient's follow up, with an update on the latest results derived from the use of high-throughput technologies. Finally, we provide a perspective on the future technical development and on the application of these studies to address broader biological questions, from basic virology to human hematopoiesis.
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Affiliation(s)
- Luca Biasco
- San Raffaele Telethon Institute for Gene Therapy, Milan, Italy
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Nowrouzi A, Glimm H, von Kalle C, Schmidt M. Retroviral vectors: post entry events and genomic alterations. Viruses 2011; 3:429-55. [PMID: 21994741 PMCID: PMC3185758 DOI: 10.3390/v3050429] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/24/2011] [Accepted: 04/05/2011] [Indexed: 12/16/2022] Open
Abstract
The curative potential of retroviral vectors for somatic gene therapy has been demonstrated impressively in several clinical trials leading to sustained long-term correction of the underlying genetic defect. Preclinical studies and clinical monitoring of gene modified hematopoietic stem and progenitor cells in patients have shown that biologically relevant vector induced side effects, ranging from in vitro immortalization to clonal dominance and oncogenesis in vivo, accompany therapeutic efficiency of integrating retroviral gene transfer systems. Most importantly, it has been demonstrated that the genotoxic potential is not identical among all retroviral vector systems designed for clinical application. Large scale viral integration site determination has uncovered significant differences in the target site selection of retrovirus subfamilies influencing the propensity for inducing genetic alterations in the host genome. In this review we will summarize recent insights gained on the mechanisms of insertional mutagenesis based on intrinsic target site selection of different retrovirus families. We will also discuss examples of side effects occurring in ongoing human gene therapy trials and future prospectives in the field.
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Affiliation(s)
- Ali Nowrouzi
- Department of Translational Oncology, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; E-Mail: (A.N.)
- National Center for Tumor Diseases, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Oncology, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; E-Mail: (A.N.)
- National Center for Tumor Diseases, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; E-Mail: (A.N.)
- National Center for Tumor Diseases, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
- Authors to whom correspondence should be addressed; E-Mails: (C.v.K.); (M.S.); Tel.: +49-6221-56-6991; +49-6221-42-1600; Fax: +49-6221-56-6930; +49-6221-42-1611
| | - Manfred Schmidt
- Department of Translational Oncology, German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; E-Mail: (A.N.)
- National Center for Tumor Diseases, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
- Authors to whom correspondence should be addressed; E-Mails: (C.v.K.); (M.S.); Tel.: +49-6221-56-6991; +49-6221-42-1600; Fax: +49-6221-56-6930; +49-6221-42-1611
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