1
|
Ginn SL, Hallwirth CV, Liao SHY, Teber ET, Arthur JW, Wu J, Lee HC, Tay SS, Hu M, Reddel RR, McCormack MP, Thrasher AJ, Cavazzana M, Alexander SI, Alexander IE. Limiting Thymic Precursor Supply Increases the Risk of Lymphoid Malignancy in Murine X-Linked Severe Combined Immunodeficiency. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 6:1-14. [PMID: 28325276 PMCID: PMC5363493 DOI: 10.1016/j.omtn.2016.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 11/25/2022]
Abstract
In early gene therapy trials for SCID-X1, using γ-retroviral vectors, T cell leukemias developed in a subset of patients secondary to insertional proto-oncogene activation. In contrast, we have reported development of T cell leukemias in SCID-X1 mice following lentivirus-mediated gene therapy independent of insertional mutagenesis. A distinguishing feature in our study was that only a proportion of transplanted γc-deficient progenitors were transduced and therefore competent for reconstitution. We hypothesized that reconstitution of SCID-X1 mice with limiting numbers of hematopoietic progenitors might be a risk factor for lymphoid malignancy. To test this hypothesis, in the absence of transduction, SCID-X1 mice were reconstituted with serially fewer wild-type hematopoietic progenitors. A robust inverse correlation between hematopoietic progenitor cell dose and T-lymphoid malignancy was observed, with earlier disease onset at lower cell doses. Malignancies were of donor origin and carried activating Notch1 mutations. These findings align with emerging evidence that thymocyte self-renewal induced by progenitor deprivation carries an oncogenic risk that is modulated by intra-thymic competition from differentiation-committed cells. Although insertional proto-oncogene activation is required for the development of malignancy in humans, failure of γc-deficient thymocytes to effectively compete with this at-risk cell population may have also contributed to oncogenesis observed in early SCID-X1 trials.
Collapse
Affiliation(s)
- Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney and The Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney and The Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney and The Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Erdahl T Teber
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jianmin Wu
- Kinghorn Cancer Centre & Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Hong Ching Lee
- Kinghorn Cancer Centre & Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Szun S Tay
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney and The Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Min Hu
- Centre for Kidney Research of The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthew P McCormack
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3800, Australia
| | - Adrian J Thrasher
- Infection, Immunity, Inflammation, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Marina Cavazzana
- Department of Biotherapy, Hôpital Necker-Enfants Malades, Paris 75015, France
| | - Stephen I Alexander
- Centre for Kidney Research of The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, The University of Sydney and The Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Westmead, NSW 2145, Australia.
| |
Collapse
|
5
|
Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD. DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer. Nucleic Acids Res 2008; 36:e49. [PMID: 18411205 PMCID: PMC2396413 DOI: 10.1093/nar/gkn125] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 03/04/2008] [Accepted: 03/05/2008] [Indexed: 11/15/2022] Open
Abstract
Gene transfer has been used to correct inherited immunodeficiencies, but in several patients integration of therapeutic retroviral vectors activated proto-oncogenes and caused leukemia. Here, we describe improved methods for characterizing integration site populations from gene transfer studies using DNA bar coding and pyrosequencing. We characterized 160,232 integration site sequences in 28 tissue samples from eight mice, where Rag1 or Artemis deficiencies were corrected by introducing the missing gene with gamma-retroviral or lentiviral vectors. The integration sites were characterized for their genomic distributions, including proximity to proto-oncogenes. Several mice harbored abnormal lymphoproliferations following therapy--in these cases, comparison of the location and frequency of isolation of integration sites across multiple tissues helped clarify the contribution of specific proviruses to the adverse events. We also took advantage of the large number of pyrosequencing reads to show that recovery of integration sites can be highly biased by the use of restriction enzyme cleavage of genomic DNA, which is a limitation in all widely used methods, but describe improved approaches that take advantage of the power of pyrosequencing to overcome this problem. The methods described here should allow integration site populations from human gene therapy to be deeply characterized with spatial and temporal resolution.
Collapse
Affiliation(s)
- Gary P. Wang
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Alexandrine Garrigue
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Angela Ciuffi
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Keshet Ronen
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Jeremy Leipzig
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Charles Berry
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Chantal Lagresle-Peyrou
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Fatine Benjelloun
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Salima Hacein-Bey-Abina
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Alain Fischer
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Marina Cavazzana-Calvo
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| | - Frederic D. Bushman
- University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA, INSERM Unit 768Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France, Department of Family/Preventive Medicine, University of California, San Diego School of Medicine, San Diego, CA 92093, USA, Faculté de Médecine René Descartes, Université Paris-Descartes, Assistance Publique, Département de Biotherapie and Assistance Publique, Hôpitaux de Paris (AP/HP), Service d’Immunologie et d’Hématologie Pédiatriques, Hôpital Necker Enfants Malades, Hôpital Necker Enfants Malades 149 rue de Sèvres, 75015 Paris, France
| |
Collapse
|