1
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Middelkamp S, Manders F, Peci F, van Roosmalen MJ, González DM, Bertrums EJ, van der Werf I, Derks LL, Groenen NM, Verheul M, Trabut L, Pleguezuelos-Manzano C, Brandsma AM, Antoniou E, Reinhardt D, Bierings M, Belderbos ME, van Boxtel R. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox. CELL GENOMICS 2023; 3:100389. [PMID: 37719152 PMCID: PMC10504672 DOI: 10.1016/j.xgen.2023.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023]
Abstract
Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole-genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole-genome sequencing (WGS) but still generate hundreds of artifacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolbox (PTATO), to accurately detect single base substitutions, insertions-deletions (indels), and structural variants in PTA-based WGS data. PTATO includes a machine learning approach and filtering based on recurrence to distinguish PTA artifacts from true mutations with high sensitivity (up to 90%), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that hematopoietic stem cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS, have normal somatic single base substitution burdens but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.
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Affiliation(s)
- Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Flavia Peci
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Diego Montiel González
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Eline J.M. Bertrums
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Department of Pediatric Oncology, Erasmus Medical Center – Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Inge van der Werf
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lucca L.M. Derks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Laurianne Trabut
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, the Netherlands
| | - Arianne M. Brandsma
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Evangelia Antoniou
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Marc Bierings
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
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2
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Bueren JA, Auricchio A. Advances and Challenges in the Development of Gene Therapy Medicinal Products for Rare Diseases. Hum Gene Ther 2023; 34:763-775. [PMID: 37694572 DOI: 10.1089/hum.2023.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
The development of viral vectors and recombinant DNA technology since the 1960s has enabled gene therapy to become a real therapeutic option for several inherited and acquired diseases. After several ups and downs in the gene therapy field, we are currently living a new era in the history of medicine in which several ex vivo and in vivo gene therapies have reached maturity. This is testified by the recent marketing authorization of several gene therapy medicinal products. In addition, many others are currently under evaluation after exhaustive investigation in human clinical trials. In this review, we summarize some of the most significant milestones in the development of gene therapy medicinal products that have already facilitated the treatment of a significant number of rare diseases. Despite progresses in the gene therapy field, the transfer of these innovative therapies to clinical practice is also finding important restrictions. Advances and also challenges in the progress of gene therapy for rare diseases are discussed in this opening review of a Human Gene Therapy issue dedicated to the 30th annual Congress of the European Society for Gene and Cell Therapy.
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Affiliation(s)
- Juan A Bueren
- Biomedical Innovation Unit, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Auricchio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
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3
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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4
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Inducible Sbds Deletion Impairs Bone Marrow Niche Capacity to Engraft Donor Bone Marrow After Transplantation. Blood Adv 2021; 6:108-120. [PMID: 34625796 PMCID: PMC8753223 DOI: 10.1182/bloodadvances.2021004640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022] Open
Abstract
Bone marrow (BM) niche-derived signals are critical for facilitating engraftment after hematopoietic stem cell (HSC) transplantation (HSCT). HSCT is required for restoration of hematopoiesis in patients with inherited bone marrow failure syndromes (iBMFS). Shwachman-Diamond syndrome (SDS) is a rare iBMFS associated with mutations in SBDS. Previous studies have demonstrated that SBDS deficiency in osteolineage niche cells causes bone marrow dysfunction that promotes leukemia development. However, it is unknown whether BM niche defects caused by SBDS deficiency also impair efficient engraftment of healthy donor HSC following HSCT, a hypothesis that could explain morbidity seen after clinical HSCT for patients with SDS. Here, we report a mouse model with inducible Sbds deletion in hematopoietic and osteolineage cells. Primary and secondary BM transplantation (BMT) studies demonstrated that SBDS deficiency within BM niches caused poor donor hematopoietic recovery and specifically poor HSC engraftment after myeloablative BMT. We have additionally identified multiple molecular and cellular defects within niche populations that are driven by SBDS deficiency and that are accentuated or develop specifically following myeloablative conditioning. These abnormalities include altered frequencies of multiple niche cell subsets including mesenchymal lineage cells, macrophages and endothelial cells; disruption of growth factor signaling, chemokine pathway activation, and adhesion molecule expression; and p53 pathway activation, and signals involved in cell cycle arrest. Taken together, this study demonstrates that SBDS deficiency profoundly impacts recipient hematopoietic niche function in the setting of HSCT, suggesting that novel therapeutic strategies targeting host niches could improve clinical HSCT outcomes for patients with SDS.
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5
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Sevilla J, Navarro S, Rio P, Sánchez-Domínguez R, Zubicaray J, Gálvez E, Merino E, Sebastián E, Azqueta C, Casado JA, Segovia JC, Alberquilla O, Bogliolo M, Román-Rodríguez FJ, Giménez Y, Larcher L, Salgado R, Pujol RM, Hladun R, Castillo A, Soulier J, Querol S, Fernández J, Schwartz J, García de Andoín N, López R, Catalá A, Surralles J, Díaz-de-Heredia C, Bueren JA. Improved collection of hematopoietic stem cells and progenitors from Fanconi anemia patients for gene therapy purposes. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 22:66-75. [PMID: 34485595 PMCID: PMC8390450 DOI: 10.1016/j.omtm.2021.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
Difficulties in the collection of hematopoietic stem and progenitor cells (HSPCs) from Fanconi anemia (FA) patients have limited the gene therapy in this disease. We have investigated (ClinicalTrials.gov, NCT02931071) the safety and efficacy of filgrastim and plerixafor for mobilization of HSPCs and collection by leukapheresis in FA patients. Nine of eleven enrolled patients mobilized beyond the threshold level of 5 CD34+ cells/μL required to initiate apheresis. A median of 21.8 CD34+ cells/μL was reached at the peak of mobilization. Significantly, the oldest patients (15 and 16 years old) were the only ones who did not reach that threshold. A median of 4.27 million CD34+ cells/kg was collected in 2 or 3 aphereses. These numbers were markedly decreased to 1.1 million CD34+ cells/kg after immunoselection, probably because of weak expression of the CD34 antigen. However, these numbers were sufficient to facilitate the engraftment of corrected HSPCs in non-conditioned patients. No procedure-associated serious adverse events were observed. Mobilization of CD34+ cells correlated with younger age, higher leukocyte counts and hemoglobin values, lower mean corpuscular volume, and higher proportion of CD34+ cells in bone marrow (BM). All these values offer crucial information for the enrollment of FA patients for gene therapy protocols.
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Affiliation(s)
- Julián Sevilla
- Servicio Hematología y Oncología Pediátrica, Fundación Investigación Biomédica, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain
| | - Susana Navarro
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Paula Rio
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Rebeca Sánchez-Domínguez
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Josune Zubicaray
- Servicio Hematología y Oncología Pediátrica, Fundación Investigación Biomédica, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain
| | - Eva Gálvez
- Servicio Hematología y Oncología Pediátrica, Fundación Investigación Biomédica, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain
| | - Eva Merino
- Servicio Hematología y Oncología Pediátrica, Fundación Investigación Biomédica, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain
| | - Elena Sebastián
- Servicio Hematología y Oncología Pediátrica, Fundación Investigación Biomédica, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain
| | - Carmen Azqueta
- Banc de Sang i Teixits de Catalunya, 08005 Barcelona, Spain
| | - José A Casado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - José C Segovia
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Omaira Alberquilla
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Massimo Bogliolo
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Servicio de Genética e Institut de Reserca, IIB-Sant Pau, Hospital Sant Pau, 08041 Barcelona, Spain.,Departmento de Genética y Microbiología, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Francisco J Román-Rodríguez
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Yari Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Lise Larcher
- Université de Paris, Institut de Recherche Saint-Louis, 75010 Paris, France
| | - Rocío Salgado
- Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Roser M Pujol
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Servicio de Genética e Institut de Reserca, IIB-Sant Pau, Hospital Sant Pau, 08041 Barcelona, Spain.,Departmento de Genética y Microbiología, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Raquel Hladun
- Servicio de Oncología y Hematología Pediátrica, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Ana Castillo
- Análisis Clínicos Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain
| | - Jean Soulier
- Université de Paris, Institut de Recherche Saint-Louis, 75010 Paris, France
| | - Sergi Querol
- Banc de Sang i Teixits de Catalunya, 08005 Barcelona, Spain
| | | | | | | | | | - Albert Catalá
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Department of Hematology/Oncology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain.,Institut de Recerca Pediàtrica Sant Joan de Déu, Barcelona, Spain
| | - Jordi Surralles
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Servicio de Genética e Institut de Reserca, IIB-Sant Pau, Hospital Sant Pau, 08041 Barcelona, Spain.,Departmento de Genética y Microbiología, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
| | - Cristina Díaz-de-Heredia
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Servicio de Oncología y Hematología Pediátrica, Vall d'Hebron Institut de Recerca, Hospital Universitari Vall d'Hebron, 08035 Barcelona, Spain
| | - Juan A Bueren
- Centro de Investigación Biomédica en Red de Enfermedades Raras, 28029 Madrid, Spain.,Hematopoietic Innovative Therapies Division, Centro de investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avenida Complutense 40, 28040 Madrid, Spain.,Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
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6
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Rust BJ, Becker PS, Chandrasekaran D, Kubek SP, Peterson CW, Adair JE, Kiem HP. Envelope-Specific Adaptive Immunity following Transplantation of Hematopoietic Stem Cells Modified with VSV-G Lentivirus. Mol Ther Methods Clin Dev 2020; 19:438-446. [PMID: 33294492 PMCID: PMC7683283 DOI: 10.1016/j.omtm.2020.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023]
Abstract
Current approaches for hematopoietic stem cell gene therapy typically involve lentiviral gene transfer in tandem with a conditioning regimen to aid stem cell engraftment. Although many pseudotyped envelopes have the capacity to be immunogenic due to their viral origins, thus far immune responses against the most common envelope, vesicular stomatitis virus glycoprotein G (VSV-G), have not been reported in hematopoietic stem cell gene therapy trials. Herein, we report on two Fanconi anemia patients who underwent autologous transplantation of a lineage-depleted, gene-modified hematopoietic stem cell product without conditioning. We observed the induction of robust VSV-G-specific immunity, consistent with low/undetectable gene marking in both patients. Upon further interrogation, adaptive immune mechanisms directed against VSV-G were detected following transplantation in both patients, including increased VSV-G-specific T cell responses, anti-VSV-G immunoglobulin G (IgG), and cytotoxic responses that can specifically kill VSV-G-expressing target cell lines. A proportion of healthy controls also displayed preexisting VSV-G-specific CD4+ and CD8+ T cell responses, as well as VSV-G-specific IgG. Taken together, these data show that VSV-G-pseudotyped lentiviral vectors have the ability to elicit interfering adaptive immune responses in the context of certain hematopoietic stem cell transplantation settings.
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Affiliation(s)
- Blake J. Rust
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
| | - Pamela S. Becker
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Devikha Chandrasekaran
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
| | - Sara P. Kubek
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
| | - Christopher W. Peterson
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer E. Adair
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 91911, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
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7
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Radtke S, Pande D, Cui M, Perez AM, Chan YY, Enstrom M, Schmuck S, Berger A, Eunson T, Adair JE, Kiem HP. Purification of Human CD34 +CD90 + HSCs Reduces Target Cell Population and Improves Lentiviral Transduction for Gene Therapy. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:679-691. [PMID: 32802914 PMCID: PMC7424231 DOI: 10.1016/j.omtm.2020.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/09/2020] [Indexed: 01/09/2023]
Abstract
Hematopoietic stem cell (HSC) gene therapy has the potential to cure many genetic, malignant, and infectious diseases. We have shown in a nonhuman primate gene therapy and transplantation model that the CD34+CD90+ cell fraction was exclusively responsible for multilineage engraftment and hematopoietic reconstitution. In this study, we show the translational potential of this HSC-enriched CD34 subset for lentivirus-mediated gene therapy. Alternative HSC enrichment strategies include the purification of CD133+ cells or CD38low/– subsets of CD34+ cells from human blood products. We directly compared these strategies to the isolation of CD90+ cells using a good manufacturing practice (GMP) grade flow-sorting protocol with clinical applicability. We show that CD90+ cell selection results in about 30-fold fewer target cells in comparison to CD133+ or CD38low/– CD34+ hematopoietic stem and progenitor cell (HSPC) subsets without compromising the engraftment potential in vivo. Single-cell RNA sequencing confirmed nearly complete depletion of lineage-committed progenitor cells in CD90+ fractions compared to alternative selections. Importantly, lentiviral transduction efficiency in purified CD90+ cells resulted in up to 3-fold higher levels of engrafted gene-modified blood cells. These studies should have important implications for the manufacturing of patient-specific HSC gene therapy and gene-engineered cell products.
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Affiliation(s)
- Stefan Radtke
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Dnyanada Pande
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Margaret Cui
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anai M Perez
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yan-Yi Chan
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark Enstrom
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Stefanie Schmuck
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew Berger
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Tom Eunson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jennifer E Adair
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Medical Oncology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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8
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Srikanthan MA, Humbert O, Haworth KG, Ironside C, Rajawat YS, Blazar BR, Palchaudhuri R, Boitano AE, Cooke MP, Scadden DT, Kiem HP. Effective Multi-lineage Engraftment in a Mouse Model of Fanconi Anemia Using Non-genotoxic Antibody-Based Conditioning. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:455-464. [PMID: 32226796 PMCID: PMC7096734 DOI: 10.1016/j.omtm.2020.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/03/2020] [Indexed: 02/08/2023]
Abstract
Conditioning chemotherapy is used to deplete hematopoietic stem cells in the recipient’s marrow, facilitating donor cell engraftment. Although effective, a major issue with chemotherapy is the systemic genotoxicity that increases the risk for secondary malignancies. Antibody conjugates targeting hematopoietic cells are an emerging non-genotoxic method of opening the marrow niche and promoting engraftment of transplanted cells while maintaining intact marrow cellularity. Specifically, this platform would be useful in diseases associated with DNA damage or cancer predisposition, such as dyskeratosis congenita, Schwachman-Diamond syndrome, and Fanconi anemia (FA). Our approach utilizes antibody-drug conjugates (ADC) as an alternative conditioning regimen in an FA mouse model of autologous transplantation. Antibodies targeting either CD45 or CD117 were conjugated to saporin (SAP), a ribosomal toxin. FANCA knockout mice were conditioned with either CD45-SAP or CD117-SAP prior to receiving whole marrow from a heterozygous healthy donor. Bone marrow and peripheral blood analysis revealed equivalent levels of donor engraftment, with minimal toxicity in ADC-treated groups as compared with cyclophosphamide-treated controls. Our findings suggest ADCs may be an effective conditioning strategy in stem cell transplantation not only for diseases where traditional chemotherapy is not tolerated, but also more broadly for the field of blood and marrow transplantation.
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Affiliation(s)
- Meera A Srikanthan
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Seattle Children's Hospital, Seattle, WA, USA
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kevin G Haworth
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christina Ironside
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yogendra S Rajawat
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
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Abstract
Fanconi anemia (FA) is a rare inherited disease that is associated with bone marrow failure and a predisposition to cancer. Previous clinical trials emphasized the difficulties that accompany the use of gene therapy to treat bone marrow failure in patients with FA. Nevertheless, the discovery of new drugs that can efficiently mobilize hematopoietic stem cells (HSCs) and the development of optimized procedures for transducing HSCs, using safe, integrative vectors, markedly improved the efficiency by which the phenotype of hematopoietic repopulating cells from patients with FA can be corrected. In addition, these achievements allowed the demonstration of the in vivo proliferation advantage of gene-corrected FA repopulating cells in immunodeficient mice. Significantly, new gene therapy trials are currently ongoing to investigate the progressive restoration of hematopoiesis in patients with FA by gene-corrected autologous HSCs. Further experimental studies are focused on the ex vivo transduction of unpurified FA HSCs, using new pseudotyped vectors that have HSC tropism. Because of the resistance of some of these vectors to serum complement, new strategies for in vivo gene therapy for FA HSCs are in development. Finally, because of the rapid advancements in gene-editing techniques, correction of CD34+ cells isolated from patients with FA is now feasible, using gene-targeting strategies. Taken together, these advances indicate that gene therapy can soon be used as an efficient and safe alternative for the hematopoietic treatment of patients with FA.
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Affiliation(s)
- Paula Río
- 1 Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Madrid, Spain .,2 Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; and Madrid, Spain .,3 Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD) , Madrid, Spain
| | - Susana Navarro
- 1 Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Madrid, Spain .,2 Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; and Madrid, Spain .,3 Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD) , Madrid, Spain
| | - Juan A Bueren
- 1 Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Madrid, Spain .,2 Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain; and Madrid, Spain .,3 Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-FJD) , Madrid, Spain
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10
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Haworth KG, Ironside C, Ramirez MA, Weitz S, Beard BC, Schwartz JD, Adair JE, Kiem HP. Minimal conditioning in Fanconi anemia promotes multi-lineage marrow engraftment at 10-fold lower cell doses. J Gene Med 2018; 20:e3050. [PMID: 30129972 DOI: 10.1002/jgm.3050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Gene therapy approaches for the treatment of Fanconi anemia (FA) hold promise for patients without a suitably matched donor for an allogeneic bone marrow transplant. However, significant limitations include the collection of sufficient stem cell numbers from patients, the fragility of these cells during ex vivo manipulation, and clinically meaningful engraftment following transplantation. With these challenges in mind, we were interested in determining (i) whether gene-corrected cells at progressively lower numbers can successfully engraft in FA; (ii) whether low-dose conditioning facilitates this engraftment; and (iii) whether these cells can be selected for post-transplant. METHODS Utilizing a well characterized mouse model of FA, we infused donor bone marrow from healthy heterozygote littermates that are unaffected carriers of the FANCA mutation to mimic a gene-corrected product, after administering low-dose conditioning. Once baseline engraftment was observed, we administered a second, very-low selective dose to determine whether gene-corrected cells could be selected for in vivo. RESULTS We demonstrate that upfront low-dose conditioning greatly increases successful engraftment of hematopoietic corrected cells in a pre-clinical animal model of FA. Additionally, without conditioning, cells can still engraft and demonstrate a selective advantage in vivo over time following transplantation, and these corrected cells can be directly selected for in vivo after engraftment. CONCLUSIONS Minimal conditioning prior to bone marrow transplant in Fanconi anemia promotes the multi-lineage engraftment of 10-fold fewer cells compared to nonconditioned controls. These data provide important insights into the potential of minimally toxic conditioning protocols for FA gene therapy applications.
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Affiliation(s)
- Kevin G Haworth
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christina Ironside
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Megan A Ramirez
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sarah Weitz
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Pathology, University of Washington, Seattle, WA, USA
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