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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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2
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Oziolor EM, Kumpf SW, Qian J, Gosink M, Sheehan M, Rubitski DM, Newman L, Whiteley LO, Lanz TA. Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs. Mol Ther Methods Clin Dev 2023; 29:395-405. [PMID: 37251978 PMCID: PMC10209688 DOI: 10.1016/j.omtm.2023.04.009] [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: 06/28/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Many current gene therapy targets use recombinant adeno-associated virus (AAV). The majority of delivered AAV therapeutics persist as episomes, separate from host DNA, yet some viral DNA can integrate into host DNA in different proportions and at genomic locations. The potential for viral integration leading to oncogenic transformation has led regulatory agencies to require investigation into AAV integration events following gene therapy in preclinical species. In the present study, tissues were collected from cynomolgus monkeys and mice 6 and 8 weeks, respectively, following administration of an AAV vector delivering transgene cargo. We compared three different next-generation sequencing approaches (shearing extension primer tag selection ligation-mediated PCR, targeted enrichment sequencing [TES], and whole-genome sequencing) to contrast the specificity, scope, and frequency of integration detected by each method. All three methods detected dose-dependent insertions with a limited number of hotspots and expanded clones. While the functional outcome was similar for all three methods, TES was the most cost-effective and comprehensive method of detecting viral integration. Our findings aim to inform the direction of molecular efforts to ensure a thorough hazard assessment of AAV viral integration in our preclinical gene therapy studies.
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Affiliation(s)
- Elias M. Oziolor
- Global Computational Safety Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Steven W. Kumpf
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Jessie Qian
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Mark Gosink
- Global Computational Safety Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Mark Sheehan
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - David M. Rubitski
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | - Leah Newman
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
| | | | - Thomas A. Lanz
- Global Discovery, Investigative and Translational Sciences, Pfizer Inc., Groton, CT 06340, USA
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3
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Characterizing piggyBat-a transposase for genetic modification of T cells. Mol Ther Methods Clin Dev 2022; 25:250-263. [PMID: 35474955 PMCID: PMC9018555 DOI: 10.1016/j.omtm.2022.03.012] [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: 10/31/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Chimeric antigen receptor (CAR) T cells targeting CD19 have demonstrated remarkable efficacy in the treatment of B cell malignancies. Current CAR T cell manufacturing protocols are complex and costly due to their reliance on viral vectors. Non-viral systems of genetic modification, such as with transposase and transposon systems, offer a potential streamlined alternative for CAR T cell manufacture and are currently being evaluated in clinical trials. In this study, we utilized the previously described transposase from the little brown bat, designated piggyBat, for production of CD19-specific CAR T cells. PiggyBat demonstrates efficient CAR transgene delivery, with a relatively low variability in integration copy number across a range of manufacturing conditions as well as a similar integration site profile to super-piggyBac transposon and viral vectors. PiggyBat-generated CAR T cells demonstrate CD19-specific cytotoxic efficacy in vitro and in vivo. These data demonstrate that alternative, naturally occurring DNA transposons can be efficiently re-tooled to be exploited in real-world applications.
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4
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PSMA-targeting TGFβ-insensitive armored CAR T cells in metastatic castration-resistant prostate cancer: a phase 1 trial. Nat Med 2022; 28:724-734. [PMID: 35314843 DOI: 10.1038/s41591-022-01726-1] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/31/2022] [Indexed: 02/07/2023]
Abstract
Chimeric antigen receptor (CAR) T cells have demonstrated promising efficacy, particularly in hematologic malignancies. One challenge regarding CAR T cells in solid tumors is the immunosuppressive tumor microenvironment (TME), characterized by high levels of multiple inhibitory factors, including transforming growth factor (TGF)-β. We report results from an in-human phase 1 trial of castration-resistant, prostate cancer-directed CAR T cells armored with a dominant-negative TGF-β receptor (NCT03089203). Primary endpoints were safety and feasibility, while secondary objectives included assessment of CAR T cell distribution, bioactivity and disease response. All prespecified endpoints were met. Eighteen patients enrolled, and 13 subjects received therapy across four dose levels. Five of the 13 patients developed grade ≥2 cytokine release syndrome (CRS), including one patient who experienced a marked clonal CAR T cell expansion, >98% reduction in prostate-specific antigen (PSA) and death following grade 4 CRS with concurrent sepsis. Acute increases in inflammatory cytokines correlated with manageable high-grade CRS events. Three additional patients achieved a PSA reduction of ≥30%, with CAR T cell failure accompanied by upregulation of multiple TME-localized inhibitory molecules following adoptive cell transfer. CAR T cell kinetics revealed expansion in blood and tumor trafficking. Thus, clinical application of TGF-β-resistant CAR T cells is feasible and generally safe. Future studies should use superior multipronged approaches against the TME to improve outcomes.
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5
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Micklethwaite KP, Gowrishankar K, Gloss BS, Li Z, Street JA, Moezzi L, Mach MA, Sutrave G, Clancy LE, Bishop DC, Louie RHY, Cai C, Foox J, MacKay M, Sedlazeck FJ, Blombery P, Mason CE, Luciani F, Gottlieb DJ, Blyth E. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells. Blood 2021; 138:1391-1405. [PMID: 33974080 PMCID: PMC8532197 DOI: 10.1182/blood.2021010858] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/24/2021] [Indexed: 11/20/2022] Open
Abstract
We performed a phase 1 clinical trial to evaluate outcomes in patients receiving donor-derived CD19-specific chimeric antigen receptor (CAR) T cells for B-cell malignancy that relapsed or persisted after matched related allogeneic hemopoietic stem cell transplant. To overcome the cost and transgene-capacity limitations of traditional viral vectors, CAR T cells were produced using the piggyBac transposon system of genetic modification. Following CAR T-cell infusion, 1 patient developed a gradually enlarging retroperitoneal tumor due to a CAR-expressing CD4+ T-cell lymphoma. Screening of other patients led to the detection, in an asymptomatic patient, of a second CAR T-cell tumor in thoracic para-aortic lymph nodes. Analysis of the first lymphoma showed a high transgene copy number, but no insertion into typical oncogenes. There were also structural changes such as altered genomic copy number and point mutations unrelated to the insertion sites. Transcriptome analysis showed transgene promoter-driven upregulation of transcription of surrounding regions despite insulator sequences surrounding the transgene. However, marked global changes in transcription predominantly correlated with gene copy number rather than insertion sites. In both patients, the CAR T-cell-derived lymphoma progressed and 1 patient died. We describe the first 2 cases of malignant lymphoma derived from CAR gene-modified T cells. Although CAR T cells have an enviable record of safety to date, our results emphasize the need for caution and regular follow-up of CAR T recipients, especially when novel methods of gene transfer are used to create genetically modified immune therapies. This trial was registered at www.anzctr.org.au as ACTRN12617001579381.
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MESH Headings
- Aged
- DNA Transposable Elements
- Gene Expression Regulation, Neoplastic
- Gene Transfer Techniques
- Humans
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/therapy
- Lymphoma/etiology
- Lymphoma/genetics
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/therapy
- Male
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/therapeutic use
- T-Lymphocytes/metabolism
- Transcriptome
- Transgenes
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Affiliation(s)
- Kenneth P Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Kavitha Gowrishankar
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ziduo Li
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Janine A Street
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Leili Moezzi
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Melanie A Mach
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Gaurav Sutrave
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Leighton E Clancy
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - David C Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Raymond H Y Louie
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - Curtis Cai
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - Jonathan Foox
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
| | - Matthew MacKay
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, College of Medicine, Baylor University, Houston, TX
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Clinical Haematology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Christopher E Mason
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
- The Feil Family Brain and Mind Research Institute, New York, NY; and
- The WorldQuant Initiative for Quantitative Prediction, New York, NY
| | - Fabio Luciani
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - David J Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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6
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A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:467-473. [PMID: 33313334 PMCID: PMC7701009 DOI: 10.1016/j.omtm.2020.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/17/2020] [Indexed: 11/23/2022]
Abstract
While clonal heterogeneity has been demonstrated in most cancers, quantitative assessment of individual tumor clones has not been translated to inform clinical practice. A few methods have been developed to investigate the tumor clonality of adult T cell leukemia/lymphoma (ATLL), but currently there is no clinically translatable method available for quantifying individual tumor clones in ATLL patients. Here, we present a methodology to assess the tumor clonality of ATLL and quantify patient-specific tumor clones in a clinical setting. The methodology consists of three steps: (1) selective amplification of restriction fragments containing a human T cell leukemia virus type 1 (HTLV-1) integration site, (2) amplicon deep sequencing to estimate the clonal structure and identify HTLV-1 integration sites of dominant clones, and (3) digital PCR targeting the HTLV-1 integration sites of the dominant clones to quantify specific tumor clones. We successfully tracked individual tumor clones using this approach and demonstrated that each clone had a distinct response to therapies. The procedure is straightforward and clinically feasible, which should facilitate the proper assessment and management of ATLL.
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7
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Abstract
Chimeric antigen receptor-T (CAR-T) cell therapy is a promising frontier of immunoengineering and cancer immunotherapy. Methods that detect, quantify, track, and visualize the CAR, have catalyzed the rapid advancement of CAR-T cell therapy from preclinical models to clinical adoption. For instance, CAR-staining/labeling agents have enabled flow cytometry analysis, imaging applications, cell sorting, and high-dimensional clinical profiling. Molecular assays, such as quantitative polymerase chain reaction, integration site analysis, and RNA-sequencing, have characterized CAR transduction, expression, and in vivo CAR-T cell expansion kinetics. In vitro visualization methods, including confocal and total internal reflection fluorescence microscopy, have captured the molecular details underlying CAR immunological synapse formation, signaling, and cytotoxicity. In vivo tracking methods, including two-photon microscopy, bioluminescence imaging, and positron emission tomography scanning, have monitored CAR-T cell biodistribution across blood, tissue, and tumor. Here, we review the plethora of CAR detection methods, which can operate at the genomic, transcriptomic, proteomic, and organismal levels. For each method, we discuss: (1) what it measures; (2) how it works; (3) its scientific and clinical importance; (4) relevant examples of its use; (5) specific protocols for CAR detection; and (6) its strengths and weaknesses. Finally, we consider current scientific and clinical needs in order to provide future perspectives for improved CAR detection.
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Affiliation(s)
- Yifei Hu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
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8
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Schenkwein D, Afzal S, Nousiainen A, Schmidt M, Ylä-Herttuala S. Efficient Nuclease-Directed Integration of Lentivirus Vectors into the Human Ribosomal DNA Locus. Mol Ther 2020; 28:1858-1875. [PMID: 32504545 PMCID: PMC7403359 DOI: 10.1016/j.ymthe.2020.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/03/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
Lentivirus vectors (LVs) are efficient tools for gene transfer, but the non-specific nature of transgene integration by the viral integration machinery carries an inherent risk for genotoxicity. We modified the integration machinery of LVs and harnessed the cellular DNA double-strand break repair machinery to integrate transgenes into ribosomal DNA, a promising genomic safe-harbor site for transgenes. LVs carrying modified I-PpoI-derived homing endonuclease proteins were characterized in detail, and we found that at least 21% of all integration sites localized to ribosomal DNA when LV transduction was coupled to target DNA cleavage. In addition to the primary sequence recognized by the endonuclease, integration was also enriched in chromatin domains topologically associated with nucleoli, which contain the targeted ribosome RNA genes. Targeting of this highly repetitive region for integration was not associated with detectable DNA deletions or negative impacts on cell health in transduced primary human T cells. The modified LVs characterized here have an overall lower risk for insertional mutagenesis than regular LVs and can thus improve the safety of gene and cellular therapy.
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Affiliation(s)
- Diana Schenkwein
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Saira Afzal
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Alisa Nousiainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 69120 Heidelberg, Germany
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Heart Center and Gene Therapy Unit, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland.
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9
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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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10
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Yabe IM, Truitt LL, Espinoza DA, Wu C, Koelle S, Panch S, Corat MA, Winkler T, Yu KR, Hong SG, Bonifacino A, Krouse A, Metzger M, Donahue RE, Dunbar CE. Barcoding of Macaque Hematopoietic Stem and Progenitor Cells: A Robust Platform to Assess Vector Genotoxicity. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 11:143-154. [PMID: 30547048 PMCID: PMC6258888 DOI: 10.1016/j.omtm.2018.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/19/2018] [Indexed: 12/19/2022]
Abstract
Gene therapies using integrating retrovirus vectors to modify hematopoietic stem and progenitor cells have shown great promise for the treatment of immune system and hematologic diseases. However, activation of proto-oncogenes via insertional mutagenesis has resulted in the development of leukemia. We have utilized cellular bar coding to investigate the impact of different vector designs on the clonal behavior of hematopoietic stem and progenitor cells (HSPCs) during in vivo expansion, as a quantitative surrogate assay for genotoxicity in a non-human primate model with high relevance for human biology. We transplanted two rhesus macaques with autologous CD34+ HSPCs transduced with three lentiviral vectors containing different promoters and/or enhancers of a predicted range of genotoxicities, each containing a high-diversity barcode library that uniquely tags each individual transduced HSPC. Analysis of clonal output from thousands of individual HSPCs transduced with these barcoded vectors revealed sustained clonal diversity, with no progressive dominance of clones containing any of the three vectors for up to almost 3 years post-transplantation. Our data support a low genotoxic risk for lentivirus vectors in HSPCs, even those containing strong promoters and/or enhancers. Additionally, this flexible system can be used for the testing of future vector designs.
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Affiliation(s)
- Idalia M. Yabe
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Lauren L. Truitt
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Diego A. Espinoza
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Chuanfeng Wu
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Samson Koelle
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Sandhya Panch
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marcus A.F. Corat
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Multidisciplinary Center for Biological Research, University of Campinas, Campinas, SP 13083-877, Brazil
| | - Thomas Winkler
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kyung-Rok Yu
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - So Gun Hong
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Aylin Bonifacino
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Allen Krouse
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Mark Metzger
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Robert E. Donahue
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Cynthia E. Dunbar
- Hematology Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
- Corresponding author: Cynthia E. Dunbar, National Heart, Lung and Blood Institute, NIH, Building 10 CRC Room 4E-5132, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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11
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Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME. Medical Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1069:1-33. [PMID: 30076565 DOI: 10.1007/978-3-319-89354-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The aim of this volume is to encourage the use of systems-level methodologies to contribute to the improvement of human-health . We intend to motivate biomedical researchers to complement their current theoretical and empirical practice with up-to-date systems biology conceptual approaches. Our perspective is based on the deep understanding of the key biomolecular regulatory mechanisms that underlie health, as well as the emergence and progression of human-disease . We strongly believe that the contemporary systems biology perspective opens the door to the effective development of novel methodologies to the improvement of prevention . This requires a deeper and integrative understanding of the involved underlying systems-level mechanisms. In order to explain our proposal in a simple way, in this chapter we privilege the conceptual exposition of our chosen framework over formal considerations. The formal exposition of our proposal will be expanded and discussed later in the next chapters.
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12
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Fraietta JA, Nobles CL, Sammons MA, Lundh S, Carty SA, Reich TJ, Cogdill AP, Morrissette JJD, DeNizio JE, Reddy S, Hwang Y, Gohil M, Kulikovskaya I, Nazimuddin F, Gupta M, Chen F, Everett JK, Alexander KA, Lin-Shiao E, Gee MH, Liu X, Young RM, Ambrose D, Wang Y, Xu J, Jordan MS, Marcucci KT, Levine BL, Garcia KC, Zhao Y, Kalos M, Porter DL, Kohli RM, Lacey SF, Berger SL, Bushman FD, June CH, Melenhorst JJ. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature 2018; 558:307-312. [PMID: 29849141 DOI: 10.1038/s41586-018-0178-z] [Citation(s) in RCA: 519] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/27/2018] [Indexed: 12/18/2022]
Abstract
Cancer immunotherapy based on genetically redirecting T cells has been used successfully to treat B cell malignancies1-3. In this strategy, the T cell genome is modified by integration of viral vectors or transposons encoding chimaeric antigen receptors (CARs) that direct tumour cell killing. However, this approach is often limited by the extent of expansion and persistence of CAR T cells4,5. Here we report mechanistic insights from studies of a patient with chronic lymphocytic leukaemia treated with CAR T cells targeting the CD19 protein. Following infusion of CAR T cells, anti-tumour activity was evident in the peripheral blood, lymph nodes and bone marrow; this activity was accompanied by complete remission. Unexpectedly, at the peak of the response, 94% of CAR T cells originated from a single clone in which lentiviral vector-mediated insertion of the CAR transgene disrupted the methylcytosine dioxygenase TET2 gene. Further analysis revealed a hypomorphic mutation in this patient's second TET2 allele. TET2-disrupted CAR T cells exhibited an epigenetic profile consistent with altered T cell differentiation and, at the peak of expansion, displayed a central memory phenotype. Experimental knockdown of TET2 recapitulated the potency-enhancing effect of TET2 dysfunction in this patient's CAR T cells. These findings suggest that the progeny of a single CAR T cell induced leukaemia remission and that TET2 modification may be useful for improving immunotherapies.
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Affiliation(s)
- Joseph A Fraietta
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher L Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Morgan A Sammons
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biology, University at Albany, State University of New York, Albany, NY, USA
| | - Stefan Lundh
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shannon A Carty
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Internal Medicine and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Tyler J Reich
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandria P Cogdill
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E DeNizio
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mercy Gohil
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Irina Kulikovskaya
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Farzana Nazimuddin
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minnal Gupta
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Chen
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John K Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine A Alexander
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enrique Lin-Shiao
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marvin H Gee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaojun Liu
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Regina M Young
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Ambrose
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yan Wang
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Xu
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martha S Jordan
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine T Marcucci
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce L Levine
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yangbing Zhao
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Kalos
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David L Porter
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simon F Lacey
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA.
| | - J Joseph Melenhorst
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA.
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13
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Kamboj A, Hallwirth CV, Alexander IE, McCowage GB, Kramer B. Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data. BMC Bioinformatics 2017. [PMID: 28623888 PMCID: PMC5474025 DOI: 10.1186/s12859-017-1719-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. RESULTS We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. CONCLUSION Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .
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Affiliation(s)
- Atul Kamboj
- Children's Cancer Research Unit, Kids' Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia.
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, NSW, Australia.,The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, NSW, Australia
| | - Geoffrey B McCowage
- Cancer Centre for Children, The Children's Hospital, Westmead, NSW, Australia
| | - Belinda Kramer
- Children's Cancer Research Unit, Kids' Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia
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14
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Suryawanshi GW, Xu S, Xie Y, Chou T, Kim N, Chen ISY, Kim S. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow. J Vis Exp 2017. [PMID: 28654067 DOI: 10.3791/55812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.
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Affiliation(s)
- Gajendra W Suryawanshi
- UCLA AIDS Institute, University of California at Los Angeles (UCLA); Department of Microbiology, Immunology, & Molecular Genetics, University of California at Los Angeles (UCLA)
| | - Song Xu
- Departments of Biomathematics and Mathematics, University of California at Los Angeles (UCLA)
| | - Yiming Xie
- UCLA AIDS Institute, University of California at Los Angeles (UCLA)
| | - Tom Chou
- Departments of Biomathematics and Mathematics, University of California at Los Angeles (UCLA)
| | - Namshin Kim
- Personalized Genomic Medicine Research Center, Division of Strategic Research Groups, Korea Research Institute of Bioscience and Biotechnology
| | - Irvin S Y Chen
- UCLA AIDS Institute, University of California at Los Angeles (UCLA); Department of Medicine, University of California at Los Angeles (UCLA);
| | - Sanggu Kim
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University (OSU);
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15
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Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. MICROBIOME 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
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Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
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16
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Mansilla-Soto J, Riviere I, Boulad F, Sadelain M. Cell and Gene Therapy for the Beta-Thalassemias: Advances and Prospects. Hum Gene Ther 2016; 27:295-304. [PMID: 27021486 DOI: 10.1089/hum.2016.037] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The beta-thalassemias are inherited anemias caused by mutations that severely reduce or abolish expression of the beta-globin gene. Like sickle cell disease, a related beta-globin gene disorder, they are ideal candidates for performing a genetic correction in patient hematopoietic stem cells (HSCs). The most advanced approach utilizes complex lentiviral vectors encoding the human β-globin gene, as first reported by May et al. in 2000. Considerable progress toward the clinical implementation of this approach has been made in the past five years, based on effective CD34+ cell mobilization and improved lentiviral vector manufacturing. Four trials have been initiated in the United States and Europe. Of 16 evaluable subjects, 6 have achieved transfusion independence. One of them developed a durable clonal expansion, which regressed after several years without transformation. Although globin lentiviral vectors have so far proven to be safe, this occurrence suggests that powerful insulators with robust enhancer-blocking activity will further enhance this approach. The combined discovery of Bcl11a-mediated γ-globin gene silencing and advances in gene editing are the foundations for another gene therapy approach, which aims to reactivate fetal hemoglobin (HbF) production. Its clinical translation will hinge on the safety and efficiency of gene targeting in true HSCs and the induction of sufficient levels of HbF to achieve transfusion independence. Altogether, the progress achieved over the past 15 years bodes well for finding a genetic cure for severe globin disorders in the next decade.
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Affiliation(s)
- Jorge Mansilla-Soto
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Isabelle Riviere
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Farid Boulad
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York.,2 Department of Pediatrics, Memorial Sloan Kettering Cancer Center , New York, New York
| | - Michel Sadelain
- 1 Center for Cell Engineering, Memorial Sloan Kettering Cancer Center , New York, New York
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17
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Sherman E, Nobles C, Berry CC, Six E, Wu Y, Dryga A, Malani N, Male F, Reddy S, Bailey A, Bittinger K, Everett JK, Caccavelli L, Drake MJ, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 4:39-49. [PMID: 28344990 PMCID: PMC5363316 DOI: 10.1016/j.omtm.2016.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/15/2016] [Indexed: 01/24/2023]
Abstract
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences. During library preparation, DNAs are broken by sonication, so that after ligation-mediated PCR the number of ligation junction sites can be used to infer abundance of gene-modified cells. We generated integration sites of known positions in silico, and we describe optimization of sample processing parameters refined by comparison to truth. We also present a novel graph-theory-based method for quantifying integration sites in repeated sequences, and we characterize the consequences using synthetic and experimental data. In an accompanying paper, we describe an additional set of statistical tools for data analysis and visualization. Software is available at https://github.com/BushmanLab/INSPIIRED.
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Affiliation(s)
- Eric Sherman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Christopher Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Charles C Berry
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emmanuelle Six
- Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, 75014 Paris, France; Laboratory of Human Lymphohematopoiesis, INSERM 24, 75014 Paris, France
| | - Yinghua Wu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Anatoly Dryga
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Nirav Malani
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Frances Male
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Aubrey Bailey
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Kyle Bittinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Laure Caccavelli
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Mary J Drake
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Salima Hacein-Bey-Abina
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
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18
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Berry CC, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 4:17-26. [PMID: 28344988 PMCID: PMC5363318 DOI: 10.1016/j.omtm.2016.11.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/15/2016] [Indexed: 01/08/2023]
Abstract
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50 (unique cell progenitors contributing the most expanded 50% of progeny cell clones), which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1 (SCID-X1), showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED.
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Affiliation(s)
- Charles C Berry
- Department of Family Medicine and Public Health, UC San Diego, La Jolla, CA 92093, USA
| | - Christopher Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Emmanuelle Six
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; INSERM 24, Laboratory of Human Lymphohematopoiesis, 75015 Paris, France
| | - Yinghua Wu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Nirav Malani
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Eric Sherman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Anatoly Dryga
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Frances Male
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Aubrey Bailey
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Kyle Bittinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Mary J Drake
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Laure Caccavelli
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Salima Hacein-Bey-Abina
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
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Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 2016; 17:151. [PMID: 27038897 PMCID: PMC4818877 DOI: 10.1186/s12859-016-0999-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Results Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Conclusions Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0999-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost B Beltman
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC, Leiden, The Netherlands.
| | - Jos Urbanus
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Shalin H Naik
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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20
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Serrao E, Cherepanov P, Engelman AN. Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites. J Vis Exp 2016. [PMID: 27023428 DOI: 10.3791/53840] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients.
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Affiliation(s)
- Erik Serrao
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute
| | | | - Alan N Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute;
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21
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Recombinant AAV Integration Is Not Associated With Hepatic Genotoxicity in Nonhuman Primates and Patients. Mol Ther 2016; 24:1100-1105. [PMID: 26948440 DOI: 10.1038/mt.2016.52] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/28/2016] [Indexed: 12/14/2022] Open
Abstract
Recombinant adeno-associated viral vectors (rAAV) currently constitute a real therapeutic strategy for the sustained correction of diverse genetic conditions. Though a wealth of preclinical and clinical studies have been conducted with rAAV, the oncogenic potential of these vectors is still controversial, particularly when considering liver-directed gene therapy. Few preclinical studies and the recent discovery of incomplete wild-type AAV2 genomes integrated in human hepatocellular carcinoma biopsies have raised concerns on rAAV safety. In the present study, we have characterized the integration of both complete and partial rAAV2/5 genomes in nonhuman primate tissues and clinical liver biopsies from a trial aimed to treat acute intermittent porphyria. We applied a new multiplex linear amplification-mediated polymerase chain reaction (PCR) assay capable of detecting integration events that are originated throughout the rAAV genome. The integration rate was low both in nonhuman primates and patient's samples. Importantly, no integration clusters or events were found in genes previously reported to link rAAV integration with hepatocellular carcinoma development, thus showing the absence of genotoxicity of a systemically administered rAAV2/5 in a large animal model and in the clinical context.
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22
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Abstract
Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.
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23
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Hou R, Niu X, Cui F. A label-free biosensor for selective detection of DNA and Pb2+ based on a G-quadruplex. RSC Adv 2016. [DOI: 10.1039/c5ra21939f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Schematic representation of the DNA and Pb2+ detection method.
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Affiliation(s)
- Ruipeng Hou
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
| | - Xiaoqing Niu
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
| | - Fengling Cui
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Henan Normal University
- Xinxiang
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24
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High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2015; 2:14061. [PMID: 26052530 PMCID: PMC4449016 DOI: 10.1038/mtm.2014.61] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/02/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022]
Abstract
Gene transfer to hematopoietic stem cells with integrating vectors not only allows sustained correction of monogenic diseases but also tracking of individual clones in vivo. Quantitative real-time PCR (qPCR) has been shown to be an accurate method to quantify individual stem cell clones, yet due to frequently limited amounts of target material (especially in clinical studies), it is not useful for large-scale analyses. To explore whether vector integration site (IS) recovery techniques may be suitable to describe clonal contributions if combined with next-generation sequencing techniques, we designed artificial ISs of different sizes which were mixed to simulate defined clonal situations in clinical settings. We subjected all mixes to either linear amplification–mediated PCR (LAM-PCR) or nonrestrictive LAM-PCR (nrLAM-PCR), both combined with 454 sequencing. We showed that nrLAM-PCR/454-detected clonality allows estimating qPCR-detected clonality in vitro. We then followed the kinetics of two clones detected in a patient enrolled in a clinical gene therapy trial using both, nrLAM-PCR/454 and qPCR and also saw nrLAM-PCR/454 to correlate to qPCR-measured clonal contributions. The method presented here displays a feasible high-throughput strategy to monitor clonality in clinical gene therapy trials is at hand.
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25
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Zhou S, Bonner MA, Wang YD, Rapp S, De Ravin SS, Malech HL, Sorrentino BP. Quantitative shearing linear amplification polymerase chain reaction: an improved method for quantifying lentiviral vector insertion sites in transplanted hematopoietic cell systems. Hum Gene Ther Methods 2015; 26:4-12. [PMID: 25545666 DOI: 10.1089/hgtb.2014.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In gene therapy trials targeting blood disorders, it is important to detect dominance of transduced hematopoietic stem cell (HSC) clones arising from vector insertion site (VIS) effects. Current methods for VIS analysis often do not have defined levels of quantitative accuracy and therefore can fail to detect early clonal dominance. We have developed a rapid and inexpensive method for measuring clone size based on random shearing of genomic DNA, minimal exponential PCR amplification, and shear site counts as a quantitative endpoint. This quantitative shearing linear amplification PCR (qsLAM PCR) assay utilizes an internal control sample containing 19 lentiviral insertion sites per cell that is mixed with polyclonal samples derived from transduced human CD34+ cells. Samples were analyzed from transplanted pigtail macaques and from a participant in our X-linked severe combined immunodeficiency (XSCID) lentiviral vector trial and yielded controlled and quantitative results in all cases. One case of early clonal dominance was detected in a monkey transplanted with limiting numbers of transduced HSCs, while the clinical samples from the XSCID trial participant showed highly diverse clonal representation. These studies demonstrate that qsLAM PCR is a facile and quantitative assay for measuring clonal repertoires in subjects enrolled in human gene therapy trials using lentiviral-transduced HSCs.
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Affiliation(s)
- Sheng Zhou
- 1 Division of Experimental Hematology, Department of Hematology, St. Jude Children's Research Hospital , Memphis, TN 38120
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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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27
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Hacein-Bey-Abina S, Pai SY, Gaspar HB, Armant M, Berry CC, Blanche S, Bleesing J, Blondeau J, de Boer H, Buckland KF, Caccavelli L, Cros G, De Oliveira S, Fernández KS, Guo D, Harris CE, Hopkins G, Lehmann LE, Lim A, London WB, van der Loo JCM, Malani N, Male F, Malik P, Marinovic MA, McNicol AM, Moshous D, Neven B, Oleastro M, Picard C, Ritz J, Rivat C, Schambach A, Shaw KL, Sherman EA, Silberstein LE, Six E, Touzot F, Tsytsykova A, Xu-Bayford J, Baum C, Bushman FD, Fischer A, Kohn DB, Filipovich AH, Notarangelo LD, Cavazzana M, Williams DA, Thrasher AJ. A modified γ-retrovirus vector for X-linked severe combined immunodeficiency. N Engl J Med 2014; 371:1407-17. [PMID: 25295500 PMCID: PMC4274995 DOI: 10.1056/nejmoa1404588] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND In previous clinical trials involving children with X-linked severe combined immunodeficiency (SCID-X1), a Moloney murine leukemia virus-based γ-retrovirus vector expressing interleukin-2 receptor γ-chain (γc) complementary DNA successfully restored immunity in most patients but resulted in vector-induced leukemia through enhancer-mediated mutagenesis in 25% of patients. We assessed the efficacy and safety of a self-inactivating retrovirus for the treatment of SCID-X1. METHODS We enrolled nine boys with SCID-X1 in parallel trials in Europe and the United States to evaluate treatment with a self-inactivating (SIN) γ-retrovirus vector containing deletions in viral enhancer sequences expressing γc (SIN-γc). RESULTS All patients received bone marrow-derived CD34+ cells transduced with the SIN-γc vector, without preparative conditioning. After 12.1 to 38.7 months of follow-up, eight of the nine children were still alive. One patient died from an overwhelming adenoviral infection before reconstitution with genetically modified T cells. Of the remaining eight patients, seven had recovery of peripheral-blood T cells that were functional and led to resolution of infections. The patients remained healthy thereafter. The kinetics of CD3+ T-cell recovery was not significantly different from that observed in previous trials. Assessment of insertion sites in peripheral blood from patients in the current trial as compared with those in previous trials revealed significantly less clustering of insertion sites within LMO2, MECOM, and other lymphoid proto-oncogenes in our patients. CONCLUSIONS This modified γ-retrovirus vector was found to retain efficacy in the treatment of SCID-X1. The long-term effect of this therapy on leukemogenesis remains unknown. (Funded by the National Institutes of Health and others; ClinicalTrials.gov numbers, NCT01410019, NCT01175239, and NCT01129544.).
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Affiliation(s)
- Salima Hacein-Bey-Abina
- From the Departments of Biotherapy (S.H.-B.-A., J. Blondeau, L.C., F.T., M.C.) and Immunology and Pediatric Hematology (S.B., G.C., D.M., B.N., C.P., F.T., A.F.) and the Centre d'Étude des Déficits Immunitaires (C.P.), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), the Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, AP-HP, INSERM (S.H.-B.-A., J. Blondeau, L.C., F.T., M.C.), Unité de Technologies Chimiques et Biologiques pour la Santé, Centre National de la Recherche Scientifique, 8258-INSERM Unité 1022, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes (S.H.-B.-A.), Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, AP-HP, Le Kremlin-Bicêtre (S.H.-B.-A.), Imagine Institute, Paris Descartes-Sorbonne Paris Cité University (S.B., J. Blondeau, L.C., D.M., B.N., C.P., E.S., A.F., M.C.), INSERM Unités Mixtes de Recherche 1163, Laboratory of Human Lymphohematopoiesis (J. Blondeau, L.C., E.S., F.T., A.F., M.C.), Groupe Immunoscope, Immunology Department, Institut Pasteur (A.L.), and Collège de France (A.F.) - all in Paris; Division of Hematology-Oncology (S.-Y.P., H.B., D.G., C.E.H., G.H., L.E.L., W.B.L., D.A.W.) and Division of Immunology (L.D.N.), Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute (S.-Y.P., D.G., L.E.L., W.B.L., D.A.W.), Harvard Medical School (S.-Y.P., M.A., L.E.L., W.B.L., J.R., L.E.S., A.T., L.D.N., D.A.W.), Center for Human Cell Therapy, Program in Cellular and Molecular Medicine, Boston Children's Hospital (M.A., J.R., L.E.S., A.T.), Division of Hematologic Malignancies, Dana-Farber Cancer Institute (J.R.), and the Manton Center for Orphan Disease Research (L.D.N.) - all in Boston; Great Ormond Street Hospital for Children NHS Foundation Trust (H.B.G., J.X.-B., A.J.T.) and Section of Molecular and Cellular Immunology, University College London Institute of Child Health (H.B.G., K.F.B., A
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Clonal Dominance With Retroviral Vector Insertions Near the ANGPT1 and ANGPT2 Genes in a Human Xenotransplant Mouse Model. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e200. [PMID: 25291142 PMCID: PMC4217076 DOI: 10.1038/mtna.2014.51] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/10/2014] [Indexed: 12/22/2022]
Abstract
Insertional leukemogenesis represents the major risk factor of hematopoietic stem cell (HSC) based gene therapy utilizing integrating viral vectors. To develop a pre-clinical model for the evaluation of vector-related genotoxicity directly in the relevant human target cells, cord blood CD34+ HSCs were transplanted into immunodeficient NOD.SCID.IL2rg−/− (NSG) mice after transduction with an LTR-driven gammaretroviral vector (GV). Furthermore, we specifically investigated the effect of prolonged in vitro culture in the presence of cytokines recently described to promote HSC expansion or maintenance. Clonality of human hematopoiesis in NSG mice was assessed by high throughput insertion site analyses and validated by insertion site-specific PCR depicting a GV typical integration profile with insertion sites resembling to 25% those of clinical studies. No overrepresentation of integrations in the vicinity of cancer-related genes was observed, however, several dominant clones were identified including two clones harboring integrations in the ANGPT1 and near the ANGPT2 genes associated with deregulated ANGPT1- and ANGPT2-mRNA levels. While these data underscore the potential value of the NSG model, our studies also identified short-comings such as overall low numbers of engrafted HSCs, limited in vivo observation time, and the challenges of in-depth insertion site analyses by low contribution of gene modified hematopoiesis.
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Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, Alexander IE, Hallwirth CV. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res 2014; 42:e129. [PMID: 25013183 PMCID: PMC4176369 DOI: 10.1093/nar/gku607] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
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Affiliation(s)
- Claire T Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Jeffrey J Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Paul Young
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - David Humphreys
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Catherine M Suter
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead Clinical School, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
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30
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Bushman FD. Engineering the human genome: reflections on the beginning. Hum Gene Ther 2014; 25:395-400. [PMID: 24848314 DOI: 10.1089/hum.2014.2524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine , Philadelphia, PA 19104-6076
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31
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LaFave MC, Varshney GK, Gildea DE, Wolfsberg TG, Baxevanis AD, Burgess SM. MLV integration site selection is driven by strong enhancers and active promoters. Nucleic Acids Res 2014; 42:4257-69. [PMID: 24464997 PMCID: PMC3985626 DOI: 10.1093/nar/gkt1399] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Retroviruses integrate into the host genome in patterns specific to each virus. Understanding the causes of these patterns can provide insight into viral integration mechanisms, pathology and genome evolution, and is critical to the development of safe gene therapy vectors. We generated murine leukemia virus integrations in human HepG2 and K562 cells and subjected them to second-generation sequencing, using a DNA barcoding technique that allowed us to quantify independent integration events. We characterized >3,700,000 unique integration events in two ENCODE-characterized cell lines. We find that integrations were most highly enriched in a subset of strong enhancers and active promoters. In both cell types, approximately half the integrations were found in <2% of the genome, demonstrating genomic influences even narrower than previously believed. The integration pattern of murine leukemia virus appears to be largely driven by regions that have high enrichment for multiple marks of active chromatin; the combination of histone marks present was sufficient to explain why some strong enhancers were more prone to integration than others. The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors.
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Affiliation(s)
| | | | - Derek E. Gildea
- Division of Intramural Research, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
| | - Tyra G. Wolfsberg
- Division of Intramural Research, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
| | - Andreas D. Baxevanis
- Division of Intramural Research, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
| | - Shawn M. Burgess
- Division of Intramural Research, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
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Serrao E, Krishnan L, Shun MC, Li X, Cherepanov P, Engelman A, Maertens GN. Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding. Nucleic Acids Res 2014; 42:5164-76. [PMID: 24520116 PMCID: PMC4005685 DOI: 10.1093/nar/gku136] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retroviruses favor target-DNA (tDNA) distortion and particular bases at sites of integration, but the mechanism underlying HIV-1 selectivity is unknown. Crystal structures revealed a network of prototype foamy virus (PFV) integrase residues that distort tDNA: Ala188 and Arg329 interact with tDNA bases, while Arg362 contacts the phosphodiester backbone. HIV-1 integrase residues Ser119, Arg231, and Lys258 were identified here as analogs of PFV integrase residues Ala188, Arg329 and Arg362, respectively. Thirteen integrase mutations were analyzed for effects on integrase activity in vitro and during virus infection, yielding a total of 1610 unique HIV-1 integration sites. Purine (R)/pyrimidine (Y) dinucleotide sequence analysis revealed HIV-1 prefers the tDNA signature (0)RYXRY(4), which accordingly favors overlapping flexible dinucleotides at the center of the integration site. Consistent with roles for Arg231 and Lys258 in sequence specific and non-specific binding, respectively, the R231E mutation altered integration site nucleotide preferences while K258E had no effect. S119A and S119T integrase mutations significantly altered base preferences at positions −3 and 7 from the site of viral DNA joining. The S119A preference moreover mimicked wild-type PFV selectivity at these positions. We conclude that HIV-1 IN residue Ser119 and PFV IN residue Ala188 contact analogous tDNA bases to effect virus integration.
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Affiliation(s)
- Erik Serrao
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA, Division of Infectious Diseases, Imperial College London, St-Mary's Campus, Norfolk Place, London W2 1PG, UK and Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire EN6 3LD, UK
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The development of APE-PCR for the cloning of genomic insertion sites of DNA elements. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0214-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Brugman MH, Suerth JD, Rothe M, Suerbaum S, Schambach A, Modlich U, Kustikova O, Baum C. Evaluating a ligation-mediated PCR and pyrosequencing method for the detection of clonal contribution in polyclonal retrovirally transduced samples. Hum Gene Ther Methods 2013; 24:68-79. [PMID: 23384086 DOI: 10.1089/hgtb.2012.175] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Retroviral gene transfer has proven therapeutic potential in clinical gene therapy trials but may also cause abnormal cell growth via perturbation of gene expression in the locus surrounding the insertion site. By establishing clonal marks, retroviral insertions are also used to describe the regenerative potential of individual cells. Deep sequencing approaches have become the method of choice to study insertion profiles in preclinical models and clinical trials. We used a protocol combining ligation-mediated polymerase chain reaction (LM-PCR) and pyrosequencing for insertion profiling and quantification in cells of various tissues transduced with various retroviral vectors. The presented method allows simultaneous analysis of a multitude of DNA-barcoded samples per pyrosequencing run, thereby allowing cost-effective insertion screening in studies with multiple samples. In addition, we investigated whether the number of pyrosequencing reads can be used to quantify clonal abundance. By comparing pyrosequencing reads against site-specific quantitative PCR and by performing spike-in experiments, we show that considerable variation exists in the quantification of insertion sites even when present in the same clone. Our results suggest that the protocol used here and similar approaches might misinterpret abundance clones defined by insertion sites, unless careful calibration measures are taken. The crucial variables causing this variation need to be defined and methodological improvements are required to establish pyrosequencing reads as a quantification measure in polyclonal situations.
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Affiliation(s)
- Martijn H Brugman
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
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35
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Colovos C, Villena-Vargas J, Adusumilli PS. Safety and stability of retrovirally transduced chimeric antigen receptor T cells. Immunotherapy 2013; 4:899-902. [PMID: 23046233 DOI: 10.2217/imt.12.91] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Evaluation of: Scholler J, Brady TL, Binder-Scholl G et al. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci. Transl Med. 4(132), 132-153 (2012). Adoptive cellular therapy with genetically engineered T cells is predicated on generating effective and persisting T-cell-mediated immunity. Gammaretroviral vector-mediated gene transfer in T cells is the technological basis for promising therapy in both HIV and cancer. Because of concerns over delayed adverse events caused by persisting retroviral vector-engineered cells, the US FDA mandates long-term follow-up of clinical trials. Scholler et al. report FDA-mandated safety data and demonstrate that retrovirally transduced T cells persist in the blood of patients for more than a decade after treatment. These persisting T cells proliferated ex vivo in the presence of antigens and showed no evidence of either insertional oncogenesis or clonal expansion in 11 subjects followed for up to 11 years, supporting the long-term safety and persistence of retrovirally transduced T cells.
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Affiliation(s)
- Christos Colovos
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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36
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Glauche I, Bystrykh L, Eaves C, Roeder I. Stem cell clonality -- theoretical concepts, experimental techniques, and clinical challenges. Blood Cells Mol Dis 2013; 50:232-40. [PMID: 23433531 DOI: 10.1016/j.bcmd.2013.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 01/29/2023]
Abstract
Here we report highlights of discussions and results presented at an International Workshop on Concepts and Models of Stem Cell Organization held on July 16th and 17th, 2012 in Dresden, Germany. The goal of the workshop was to undertake a systematic survey of state-of-the-art methods and results of clonality studies of tissue regeneration and maintenance with a particular emphasis on the hematopoietic system. The meeting was the 6th in a series of similar conceptual workshops, termed StemCellMathLab,(2) all of which have had the general objective of using an interdisciplinary approach to discuss specific aspects of stem cell biology. The StemCellMathLab 2012, which was jointly organized by the Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Dresden University of Technology and the Institute for Medical Informatics, Statistics and Epidemiology, Medical Faculty, University of Leipzig, brought together 32 scientists from 8 countries, with scientific backgrounds in medicine, cell biology, virology, physics, computer sciences, bioinformatics and mathematics. The workshop focused on the following questions: (1) How heterogeneous are stem cells and their progeny? and (2) What are the characteristic differences in the clonal dynamics between physiological and pathophysiological situations? In discussing these questions, particular emphasis was placed on (a) the methods for quantifying clones and their dynamics in experimental and clinical settings and (b) general concepts and models for their description. In this workshop summary we start with an introduction to the current state of clonality research and a proposal for clearly defined terminology. Major topics of discussion include clonal heterogeneity in unperturbed tissues, clonal dynamics due to physiological and pathophysiological pressures and conceptual and technical issues of clone quantification. We conclude that an interactive cross-disciplinary approach to research in this field will continue to promote a conceptual understanding of tissue organization.
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Affiliation(s)
- Ingmar Glauche
- Institute for Medical Informatics and Biometry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, D-01307 Dresden, Germany
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Cornils K, Bartholomae CC, Thielecke L, Lange C, Arens A, Glauche I, Mock U, Riecken K, Gerdes S, von Kalle C, Schmidt M, Roeder I, Fehse B. Comparative clonal analysis of reconstitution kinetics after transplantation of hematopoietic stem cells gene marked with a lentiviral SIN or a γ-retroviral LTR vector. Exp Hematol 2013; 41:28-38.e3. [DOI: 10.1016/j.exphem.2012.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 08/28/2012] [Accepted: 09/10/2012] [Indexed: 12/13/2022]
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Ding D, Lou X, Hua D, Yu W, Li L, Wang J, Gao F, Zhao N, Ren G, Li L, Lin B. Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach. PLoS Genet 2012; 8:e1003065. [PMID: 23236287 PMCID: PMC3516541 DOI: 10.1371/journal.pgen.1003065] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 09/20/2012] [Indexed: 02/07/2023] Open
Abstract
Integration of the viral DNA into host chromosomes was found in most of the hepatitis B virus (HBV)–related hepatocellular carcinomas (HCCs). Here we devised a massive anchored parallel sequencing (MAPS) method using next-generation sequencing to isolate and sequence HBV integrants. Applying MAPS to 40 pairs of HBV–related HCC tissues (cancer and adjacent tissues), we identified 296 HBV integration events corresponding to 286 unique integration sites (UISs) with precise HBV–Human DNA junctions. HBV integration favored chromosome 17 and preferentially integrated into human transcript units. HBV targeted genes were enriched in GO terms: cAMP metabolic processes, T cell differentiation and activation, TGF beta receptor pathway, ncRNA catabolic process, and dsRNA fragmentation and cellular response to dsRNA. The HBV targeted genes include 7 genes (PTPRJ, CNTN6, IL12B, MYOM1, FNDC3B, LRFN2, FN1) containing IPR003961 (Fibronectin, type III domain), 7 genes (NRG3, MASP2, NELL1, LRP1B, ADAM21, NRXN1, FN1) containing IPR013032 (EGF-like region, conserved site), and three genes (PDE7A, PDE4B, PDE11A) containing IPR002073 (3′, 5′-cyclic-nucleotide phosphodiesterase). Enriched pathways include hsa04512 (ECM-receptor interaction), hsa04510 (Focal adhesion), and hsa04012 (ErbB signaling pathway). Fewer integration events were found in cancers compared to cancer-adjacent tissues, suggesting a clonal expansion model in HCC development. Finally, we identified 8 genes that were recurrent target genes by HBV integration including fibronectin 1 (FN1) and telomerase reverse transcriptase (TERT1), two known recurrent target genes, and additional novel target genes such as SMAD family member 5 (SMAD5), phosphatase and actin regulator 4 (PHACTR4), and RNA binding protein fox-1 homolog (C. elegans) 1 (RBFOX1). Integrating analysis with recently published whole-genome sequencing analysis, we identified 14 additional recurrent HBV target genes, greatly expanding the HBV recurrent target list. This global survey of HBV integration events, together with recently published whole-genome sequencing analyses, furthered our understanding of the HBV–related HCC. Integration of the hepatitis B virus (HBV) into the human liver cells was found in most of the related hepatocellular carcinomas (HCCs). Here, taking the recent advances in high-throughput sequencing, we devised an efficient and cost-effective method that we named massive anchored parallel sequencing (MAPS) method, to conduct a global survey of HBV integration events in 40 pairs of HBV–related HCC tissues (cancer and adjacent tissues). We identified 286 unique integration sites (UISs) with precise HBV–Human DNA junctions. We identified a higher number of HBV integration events in cancer adjacent tissues than in HCC tissues, suggesting a clonal expansion process during HCC development. We also found that fibronectin and its related genes (fibronectin type III-like fold domain containing genes) were frequently targeted by HBV. Fibronectin is a protein produced abundantly by the liver cells and also serves as a linker in the extracellular matrix. Our findings might suggest a role for the disruption of fibronectin and associated cellular matrix in HBV related liver cancers. We also identified 14 additional recurrent HBV target genes, greatly expanding the HBV recurrent target list. This study would add significantly to our understanding of HCC development.
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Affiliation(s)
- Dong Ding
- Hangzhou Proprium Biotech, Hangzhou, China
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Xiaoyan Lou
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Dasong Hua
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Wei Yu
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Lisha Li
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Jun Wang
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Feng Gao
- Department of General Surgery, The Second Affiliated Hospital, Shanxi Medical University, Taiyuan, China
| | - Na Zhao
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
| | - Guoping Ren
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- The First Affiliated Hospital, Zhejiang University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, Zhejiang University, Hangzhou, China
- * E-mail: (Lanjuan Li); (Biaoyang Lin)
| | - Biaoyang Lin
- Systems Biology Division and Proprium Research Center, Zhejiang–California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, China
- Department of Urology, University of Washington, Seattle, Washington, United States of America
- Swedish Medical Center, Seattle, Washington, United States of America
- * E-mail: (Lanjuan Li); (Biaoyang Lin)
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39
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Current world literature. Curr Opin Pediatr 2012; 24:770-9. [PMID: 23146873 DOI: 10.1097/mop.0b013e32835af8de] [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: 11/26/2022]
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40
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Wu C, Jares A, Winkler T, Xie J, Metais JY, Dunbar CE. High efficiency restriction enzyme-free linear amplification-mediated polymerase chain reaction approach for tracking lentiviral integration sites does not abrogate retrieval bias. Hum Gene Ther 2012; 24:38-47. [PMID: 22992116 DOI: 10.1089/hum.2012.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retroviral vectors are an efficient and widely employed means of introducing an exogenous expression cassette into target cells. These vectors have been shown to integrate semi-randomly into the cellular genome, and can be associated with genotoxicity due to impact on expression of proximate genes. Therefore, efficient and accurate integration site analysis, while quantifying contributions of individual vector-containing clones, is desirable. Linear amplification-mediated polymerase chain reaction (LAM-PCR) is a widely used technique for identifying integrated proviral and host genomic DNA junctions. However, LAM-PCR is subject to selection bias inherent in the reliance of the assay on the presence of a restriction enzyme-cutting site adjacent to a retrievable integration site, and it is further limited by an inability to discriminate prior to sequencing between the flanking genomic DNA of interest and uninformative internal vector DNA. We report a modified restriction enzyme-free LAM-PCR (Re-free LAM-PCR) approach that is less time and labor intensive compared to conventional LAM-PCR, but in contrast to some other nonrestrictive methods, compares in efficiency and sensitivity, excludes retrieval of uninformative internal vector sequences, and allows retrieval of integration sites unbiased by the presence of nearby restriction sites. However, we report that Re-free LAM-PCR remains inaccurate for quantitation of the relative contributions of individual integration site-containing clones in a polyclonal setting, suggesting that bias in LAM-PCR retrieval of integration sites is not wholly explained by restriction enzyme-related factors.
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Affiliation(s)
- Chuanfeng Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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41
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Scholler J, Brady TL, Binder-Scholl G, Hwang WT, Plesa G, Hege KM, Vogel AN, Kalos M, Riley JL, Deeks SG, Mitsuyasu RT, Bernstein WB, Aronson NE, Levine BL, Bushman FD, June CH. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med 2012; 4:132ra53. [PMID: 22553251 DOI: 10.1126/scitranslmed.3003761] [Citation(s) in RCA: 481] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The success of adoptive T cell gene transfer for treatment of cancer and HIV is predicated on generating a response that is both durable and safe. We report long-term results from three clinical trials to evaluate gammaretroviral vector-engineered T cells for HIV. The vector encoded a chimeric antigen receptor (CAR) composed of CD4 linked to the CD3ζ signaling chain (CD4ζ). CAR T cells were detected in 98% of samples tested for at least 11 years after infusion at frequencies that exceeded average T cell levels after most vaccine approaches. The CD4ζ transgene retained expression and function. There was no evidence of vector-induced immortalization of cells; integration site distributions showed no evidence of persistent clonal expansion or enrichment for integration sites near genes implicated in growth control or transformation. The CD4ζ T cells had stable levels of engraftment, with decay half-lives that exceeded 16 years, in marked contrast to previous trials testing engineered T cells. These findings indicate that host immunosuppression before T cell transfer is not required to achieve long-term persistence of gene-modified T cells. Further, our results emphasize the safety of T cells modified by retroviral gene transfer in clinical application, as measured in >500 patient-years of follow-up. Thus, previous safety issues with integrating viral vectors are hematopoietic stem cell or transgene intrinsic, and not a general feature of retroviral vectors. Engineered T cells are a promising form of synthetic biology for long-term delivery of protein-based therapeutics. These results provide a framework to guide the therapy of a wide spectrum of human diseases.
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Affiliation(s)
- John Scholler
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
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42
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Gabriel R, Schmidt M, von Kalle C. Integration of retroviral vectors. Curr Opin Immunol 2012; 24:592-7. [DOI: 10.1016/j.coi.2012.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/23/2012] [Indexed: 11/26/2022]
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43
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Kohn DB, Pai SY, Sadelain M. Gene therapy through autologous transplantation of gene-modified hematopoietic stem cells. Biol Blood Marrow Transplant 2012; 19:S64-9. [PMID: 23032601 DOI: 10.1016/j.bbmt.2012.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Donald B Kohn
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA.
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44
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Lu CH, Wang F, Willner I. Zn2+-Ligation DNAzyme-Driven Enzymatic and Nonenzymatic Cascades for the Amplified Detection of DNA. J Am Chem Soc 2012; 134:10651-8. [DOI: 10.1021/ja3037838] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fuan Wang
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Rasila TS, Vihinen M, Paulin L, Haapa-Paananen S, Savilahti H. Flexibility in MuA transposase family protein structures: functional mapping with scanning mutagenesis and sequence alignment of protein homologues. PLoS One 2012; 7:e37922. [PMID: 22666413 PMCID: PMC3362531 DOI: 10.1371/journal.pone.0037922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/26/2012] [Indexed: 12/13/2022] Open
Abstract
MuA transposase protein is a member of the retroviral integrase superfamily (RISF). It catalyzes DNA cleavage and joining reactions via an initial assembly and subsequent structural transitions of a protein-DNA complex, known as the Mu transpososome, ultimately attaching transposon DNA to non-specific target DNA. The transpososome functions as a molecular DNA-modifying machine and has been used in a wide variety of molecular biology and genetics/genomics applications. To analyze structure-function relationships in MuA action, a comprehensive pentapeptide insertion mutagenesis was carried out for the protein. A total of 233 unique insertion variants were generated, and their activity was analyzed using a quantitative in vivo DNA transposition assay. The results were then correlated with the known MuA structures, and the data were evaluated with regard to the protein domain function and transpososome development. To complement the analysis with an evolutionary component, a protein sequence alignment was produced for 44 members of MuA family transposases. Altogether, the results pinpointed those regions, in which insertions can be tolerated, and those where insertions are harmful. Most insertions within the subdomains Iγ, IIα, IIβ, and IIIα completely destroyed the transposase function, yet insertions into certain loop/linker regions of these subdomains increased the protein activity. Subdomains Iα and IIIβ were largely insertion-tolerant. The comprehensive structure-function data set will be useful for designing MuA transposase variants with improved properties for biotechnology/genomics applications, and is informative with regard to the function of RISF proteins in general.
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Affiliation(s)
- Tiina S. Rasila
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- BioMediTech, Tampere, Finland
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Saija Haapa-Paananen
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
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46
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Baum C, Modlich U, Göhring G, Schlegelberger B. Concise review: managing genotoxicity in the therapeutic modification of stem cells. Stem Cells 2012; 29:1479-84. [PMID: 21898683 DOI: 10.1002/stem.716] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The therapeutic use of procedures for genetic stem cell modification is limited by potential adverse events related to uncontrolled mutagenesis. Prominent findings have been made in hematopoietic gene therapy, demonstrating the risk of clonal, potentially malignant outgrowth on the basis of mutations acquired during or after therapeutic genome modification. The incidence and the growth rate of insertional mutants have been linked to the "stemness" of the target cells and vector-related features such as the integration pattern, the architecture, and the exact content of transgene cassettes. Milieu factors supporting the survival and expansion of mutants may eventually allow oncogenic progression. Similar concerns apply for medicinal products based on pluripotent stem cells. Focusing on the genetic stress induced by insertional mutagenesis and culture adaptation, we propose four conclusions. (a) Mutations occurring in the production of stem cell-based medicines may be unavoidable and need to be classified according to their risk to trigger the formation of clones that are sufficiently long-lived and mitotically active to acquire secondary transforming mutations. (b) The development of rational prevention strategies depends upon the identification of the specific mutations forming such "dominant clones" (which can also be addressed as cancer stem cell precursors) and a better knowledge of the mechanisms underlying their creation, expansion, and homeostatic control. (c) Quantitative assay systems are required to assess the practical value of preventive actions. (d) Improved approaches for the genetic modification of stem cells can address all critical steps in the origin and growth control of mutants.
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Affiliation(s)
- Christopher Baum
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.
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47
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Kebriaei P, Huls H, Jena B, Munsell M, Jackson R, Lee DA, Hackett PB, Rondon G, Shpall E, Champlin RE, Cooper LJN. Infusing CD19-directed T cells to augment disease control in patients undergoing autologous hematopoietic stem-cell transplantation for advanced B-lymphoid malignancies. Hum Gene Ther 2012; 23:444-50. [PMID: 22107246 DOI: 10.1089/hum.2011.167] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Limited curative treatment options exist for patients with advanced B-lymphoid malignancies, and new therapeutic approaches are needed to augment the efficacy of hematopoietic stem-cell transplantation (HSCT). Cellular therapies, such as adoptive transfer of T cells that are being evaluated to target malignant disease, use mechanisms independent of chemo- and radiotherapy with nonoverlapping toxicities. Gene therapy is employed to generate tumor-specific T cells, as specificity can be redirected through enforced expression of a chimeric antigen receptor (CAR) to achieve antigen recognition based on the specificity of a monoclonal antibody. By combining cell and gene therapies, we have opened a new Phase I protocol at the MD Anderson Cancer Center (Houston, TX) to examine the safety and feasibility of administering autologous genetically modified T cells expressing a CD19-specific CAR (capable of signaling through chimeric CD28 and CD3-ζ) into patients with high-risk B-lymphoid malignancies undergoing autologous HSCT. The T cells are genetically modified by nonviral gene transfer of the Sleeping Beauty system and CAR(+) T cells selectively propagated in a CAR-dependent manner on designer artificial antigen-presenting cells. The results of this study will lay the foundation for future protocols including CAR(+) T-cell infusions derived from allogeneic sources.
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Affiliation(s)
- Partow Kebriaei
- Division of Cancer Medicine, M.D. Anderson Cancer Center, Houston, TX 77005, USA
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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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Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CRM, Bushman FD. Estimating abundances of retroviral insertion sites from DNA fragment length data. ACTA ACUST UNITED AC 2012; 28:755-62. [PMID: 22238265 DOI: 10.1093/bioinformatics/bts004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION The relative abundance of retroviral insertions in a host genome is important in understanding the persistence and pathogenesis of both natural retroviral infections and retroviral gene therapy vectors. It could be estimated from a sample of cells if only the host genomic sites of retroviral insertions could be directly counted. When host genomic DNA is randomly broken via sonication and then amplified, amplicons of varying lengths are produced. The number of unique lengths of amplicons of an insertion site tends to increase according to its abundance, providing a basis for estimating relative abundance. However, as abundance increases amplicons of the same length arise by chance leading to a non-linear relation between the number of unique lengths and relative abundance. The difficulty in calibrating this relation is compounded by sample-specific variations in the relative frequencies of clones of each length. RESULTS A likelihood function is proposed for the discrete lengths observed in each of a collection of insertion sites and is maximized with a hybrid expectation-maximization algorithm. Patient data illustrate the method and simulations show that relative abundance can be estimated with little bias, but that variation in highly abundant sites can be large. In replicated patient samples, variation exceeds what the model implies-requiring adjustment as in Efron (2004) or using jackknife standard errors. Consequently, it is advantageous to collect replicate samples to strengthen inferences about relative abundance.
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Affiliation(s)
- Charles C Berry
- Department of Family and Preventive Medicine, University of California, La Jolla, CA, USA.
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Abstract
Upon cell infection, some viruses integrate their genome into the host chromosome, either as part of their life cycle (such as retroviruses), or incidentally. While possibly promoting long-term persistence of the virus into the cell, viral genome integration may also lead to drastic consequences for the host cell, including gene disruption, insertional mutagenesis and cell death, as well as contributing to species evolution. This review summarizes the current knowledge on viruses integrating their genome into the host genome and the consequences for the host cell.
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Affiliation(s)
- Günther Witzany
- Telos - Philosophische Praxis, Vogelsangstr. 18c, Bürmoos, 5111 Austria
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