1
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Aalam SMM, Nguyen LV, Ritting ML, Kannan N. Clonal tracking in cancer and metastasis. Cancer Metastasis Rev 2024; 43:639-656. [PMID: 37910295 DOI: 10.1007/s10555-023-10149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
The eradication of many cancers has proven challenging due to the presence of functionally and genetically heterogeneous clones maintained by rare cancer stem cells (CSCs), which contribute to disease progression, treatment refractoriness, and late relapse. The characterization of functional CSC activity has necessitated the development of modern clonal tracking strategies. This review describes viral-based and CRISPR-Cas9-based cellular barcoding, lineage tracing, and imaging-based approaches. DNA-based cellular barcoding technology is emerging as a powerful and robust strategy that has been widely applied to in vitro and in vivo model systems, including patient-derived xenograft models. This review also highlights the potential of these methods for use in the clinical and drug discovery contexts and discusses the important insights gained from such approaches.
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Affiliation(s)
| | - Long Viet Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Megan L Ritting
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA.
- Center for Regenerative Biotherapeutics, Mayo Clinic, Rochester, MN, USA.
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2
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Michaels V, Chalabi S, Legrand A, Renard J, Tejerina E, Daouya M, Fabrega S, Megret J, Olaso R, Boland A, Deleuze JF, Battail C, Tronik-Le Roux D, Ezine S. Co-Transplantation of Barcoded Lymphoid-Primed Multipotent (LMPP) and Common Lymphocyte (CLP) Progenitors Reveals a Major Contribution of LMPP to the Lymphoid Lineage. Int J Mol Sci 2023; 24:ijms24054368. [PMID: 36901798 PMCID: PMC10002536 DOI: 10.3390/ijms24054368] [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] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
T cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays.
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Affiliation(s)
- Victoria Michaels
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades-INEM, 75015 Paris, France
| | - Smahane Chalabi
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Agnes Legrand
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades-INEM, 75015 Paris, France
| | - Julie Renard
- Atomic Energy and Alternative Energies Agency (CEA), Department of Research in Hemato-Immunology (SRHI), Saint-Louis Hospital, 75010 Paris, France
| | - Emmanuel Tejerina
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades-INEM, 75015 Paris, France
| | - Marina Daouya
- Atomic Energy and Alternative Energies Agency (CEA), Department of Research in Hemato-Immunology (SRHI), Saint-Louis Hospital, 75010 Paris, France
- Université Paris Cité, IRSL, HIPI-UMRS 976, 75010 Paris, France
| | - Sylvie Fabrega
- SFR Necker—US24/UAR 3633/—Structure Fédérative de Recherche Necker Plateformes Vecteurs Viraux et Transfert de Gènes et Cytométrie, Faculté de Médecine de Necker, 75015 Paris, France
| | - Jérôme Megret
- SFR Necker—US24/UAR 3633/—Structure Fédérative de Recherche Necker Plateformes Vecteurs Viraux et Transfert de Gènes et Cytométrie, Faculté de Médecine de Necker, 75015 Paris, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France
| | - Christophe Battail
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057 Evry, France
- Université Grenoble Alpes, IRIG, Laboratoire Biosciences et Bioingénierie pour la Santé, UA 13 INSERM-CEA-UGA, 38000 Grenoble, France
- Correspondence:
| | - Diana Tronik-Le Roux
- Atomic Energy and Alternative Energies Agency (CEA), Department of Research in Hemato-Immunology (SRHI), Saint-Louis Hospital, 75010 Paris, France
- Université Paris Cité, IRSL, HIPI-UMRS 976, 75010 Paris, France
| | - Sophie Ezine
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades-INEM, 75015 Paris, France
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3
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Rodriguez Y Baena A, Manso BA, Forsberg EC. CFU-S assay: a historical single-cell assay that offers modern insight into clonal hematopoiesis. Exp Hematol 2021; 104:1-8. [PMID: 34688837 DOI: 10.1016/j.exphem.2021.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Hematopoietic stem cells (HSCs) have been studied extensively since their initial functional description in 1961 when Dr. James Till and Dr. Ernest McCulloch developed the first in vivo clonal strategy, termed the spleen colony-forming unit (CFU-S) assay, to assess the functional capacity of bone marrow-derived hematopoietic progenitors at the single-cell level. Through transplantation of bone marrow cells and analysis of the resulting cellular nodules in the spleen, the CFU-S assay revealed both the self-renewal and clonal differentiation capacity of hematopoietic progenitors. Further development and use of this assay have identified highly proliferative, self-renewing, and differentiating HSCs that possess clonal, multilineage differentiation. The CFU-S strategy has also been adapted to interrogating single purified hematopoietic stem and progenitor cell populations, advancing our knowledge of the hematopoietic hierarchy. In this review, we explore the major discoveries made with the CFU-S assay, consider its modern use and recent improvements, and compare it with commonly used long-term transplantation assays to determine the continued value of the CFU-S assay for understanding HSC biology and hematopoiesis.
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Affiliation(s)
- Alessandra Rodriguez Y Baena
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA
| | - Bryce A Manso
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, University of California-Santa Cruz, Santa Cruz, CA; Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA.
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4
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Clonal tracking in gene therapy patients reveals a diversity of human hematopoietic differentiation programs. Blood 2020; 135:1219-1231. [PMID: 32040546 DOI: 10.1182/blood.2019002350] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
In gene therapy with human hematopoietic stem and progenitor cells (HSPCs), each gene-corrected cell and its progeny are marked in a unique way by the integrating vector. This feature enables lineages to be tracked by sampling blood cells and using DNA sequencing to identify the vector integration sites. Here, we studied 5 cell lineages (granulocytes, monocytes, T cells, B cells, and natural killer cells) in patients having undergone HSPC gene therapy for Wiskott-Aldrich syndrome or β hemoglobinopathies. We found that the estimated minimum number of active, repopulating HSPCs (which ranged from 2000 to 50 000) was correlated with the number of HSPCs per kilogram infused. We sought to quantify the lineage output and dynamics of gene-modified clones; this is usually challenging because of sparse sampling of the various cell types during the analytical procedure, contamination during cell isolation, and different levels of vector marking in the various lineages. We therefore measured the residual contamination and corrected our statistical models accordingly to provide a rigorous analysis of the HSPC lineage output. A cluster analysis of the HSPC lineage output highlighted the existence of several stable, distinct differentiation programs, including myeloid-dominant, lymphoid-dominant, and balanced cell subsets. Our study evidenced the heterogeneous nature of the cell lineage output from HSPCs and provided methods for analyzing these complex data.
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Sii-Felice K, Castillo Padilla J, Relouzat F, Cheuzeville J, Tantawet S, Maouche L, Le Grand R, Leboulch P, Payen E. Enhanced Transduction of Macaca fascicularis Hematopoietic Cells with Chimeric Lentiviral Vectors. Hum Gene Ther 2019; 30:1306-1323. [DOI: 10.1089/hum.2018.179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Karine Sii-Felice
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Javier Castillo Padilla
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Francis Relouzat
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Joëlle Cheuzeville
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- bluebird bio France, Fontenay aux Roses, France
| | - Siriporn Tantawet
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Leïla Maouche
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- INSERM, Paris, France
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases, UMR 1184, IDMIT Department, Institute of Biology François Jacob, INSERM, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Philippe Leboulch
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- Ramathibodi Hospital and Mahidol University, Bangkok, Thailand
- Harvard Medical School and Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston Massachusetts
| | - Emmanuel Payen
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- INSERM, Paris, France
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6
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Chapellier M, Peña-Martínez P, Ramakrishnan R, Eriksson M, Talkhoncheh MS, Orsmark-Pietras C, Lilljebjörn H, Högberg C, Hagström-Andersson A, Fioretos T, Larsson J, Järås M. Arrayed molecular barcoding identifies TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells. Haematologica 2019; 104:2006-2016. [PMID: 30819903 PMCID: PMC6886409 DOI: 10.3324/haematol.2018.192062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of cytokines in the bone marrow (BM) microenvironment promotes acute myeloid leukemia (AML) cell growth. Due to the complexity and low throughput of in vivo stem-cell based assays, studying the role of cytokines in the BM niche in a screening setting is challenging. Here, we developed an ex vivo cytokine screen using 11 arrayed molecular barcodes, allowing for a competitive in vivo readout of leukemia-initiating capacity. With this approach, we assessed the effect of 114 murine cytokines on MLL-AF9 AML mouse cells and identified the tumor necrosis factor ligand superfamily member 13 (TNFSF13) as a positive regulator of leukemia-initiating cells. By using Tnfsf13−/− recipient mice, we confirmed that TNFSF13 supports leukemia initiation also under physiological conditions. TNFSF13 was secreted by normal myeloid cells but not by leukemia mouse cells, suggesting that mature myeloid BM cells support leukemia cells by secreting TNFSF13. TNFSF13 supported leukemia cell proliferation in an NF-κB-dependent manner by binding TNFRSF17 and suppressed apoptosis. Moreover, TNFSF13 supported the growth and survival of several human myeloid leukemia cell lines, demonstrating that our findings translate to human disease. Taken together, using arrayed molecular barcoding, we identified a previously unrecognized role of TNFSF13 as a positive regulator of AML-initiating cells. The arrayed barcoded screening methodology is not limited to cytokines and leukemia, but can be extended to other types of ex vivo screens, where a multiplexed in vivo read-out of stem cell functionality is needed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jonas Larsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
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7
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Cohen EM, Kobiler O. Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells. PLoS Pathog 2016; 12:e1006082. [PMID: 27923068 PMCID: PMC5161387 DOI: 10.1371/journal.ppat.1006082] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 11/21/2016] [Indexed: 12/11/2022] Open
Abstract
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells. Single cell variation is of major interest in understanding key biological processes, like cancer, development and host pathogen interaction. During viral infection, these cell to cell variations can change the outcome of the whole organism infection. We suggested that differences in the number of parental viral genomes that initiate the replication process alter the outcome of infection among single cells. In this work we present a method based on genetically barcoded herpesvirus recombinants to identify the number of viral genomes initiating replication in individual cells. Our results indicate that viral gene expression is tightly linked to the number of viral genomes replicating per cell. Remarkably, we found that high cellular gene expression was an indicator for a lower viral gene expression in a given cell. We suggest that variations among single cells result from preexisting differences among cells, as well as from random viral host interactions.
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Affiliation(s)
- Efrat M. Cohen
- Department of Clinical Microbiology and Immunology,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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8
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Cavazzana M, Six E, Lagresle-Peyrou C, André-Schmutz I, Hacein-Bey-Abina S. Gene Therapy for X-Linked Severe Combined Immunodeficiency: Where Do We Stand? Hum Gene Ther 2016; 27:108-16. [PMID: 26790362 DOI: 10.1089/hum.2015.137] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
More than 20 years ago, X-linked severe combined immunodeficiency (SCID-X1) appeared to be the best condition to test the feasibility of hematopoietic stem cell gene therapy. The seminal SCID-X1 clinical studies, based on first-generation gammaretroviral vectors, demonstrated good long-term immune reconstitution in most treated patients despite the occurrence of vector-related leukemia in a few of them. This gene therapy has successfully enabled correction of the T cell defect. Natural killer and B cell defects were only partially restored, most likely due to the absence of a conditioning regimen. The success of these pioneering trials paved the way for the extension of gene-based treatment to many other diseases of the hematopoietic system, but the unfortunate serious adverse events led to extensive investigations to define the retrovirus integration profiles. This review puts into perspective the clinical experience of gene therapy for SCID-X1, with the development and implementation of new generations of safer vectors such as self-inactivating gammaretroviral or lentiviral vectors as well as major advances in integrome knowledge.
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Affiliation(s)
- Marina Cavazzana
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris.,2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Emmanuelle Six
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Chantal Lagresle-Peyrou
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Isabelle André-Schmutz
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Salima Hacein-Bey-Abina
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris.,2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,5 UTCBS CNRS 8258-INSERM U1022, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , Paris.,6 Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud , AP-HP, Le-Kremlin-Bicêtre, France
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9
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Weber TS, Dukes M, Miles DC, Glaser SP, Naik SH, Duffy KR. Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system. BMC SYSTEMS BIOLOGY 2016; 10:43. [PMID: 27363727 PMCID: PMC4929723 DOI: 10.1186/s12918-016-0290-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/14/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND Cellular barcoding is a recently developed biotechnology tool that enables the familial identification of progeny of individual cells in vivo. In immunology, it has been used to track the burst-sizes of multiple distinct responding T cells over several adaptive immune responses. In the study of hematopoiesis, it revealed fate heterogeneity amongst phenotypically identical multipotent cells. Most existing approaches rely on ex vivo viral transduction of cells with barcodes followed by adoptive transfer into an animal, which works well for some systems, but precludes barcoding cells in their native environment such as those inside solid tissues. RESULTS With a view to overcoming this limitation, we propose a new design for a genetic barcoding construct based on the Cre Lox system that induces randomly created stable barcodes in cells in situ by exploiting inherent sequence distance constraints during site-specific recombination. We identify the cassette whose provably maximal code diversity is several orders of magnitude higher than what is attainable with previously considered Cre Lox barcoding approaches, exceeding the number of lymphocytes or hematopoietic progenitor cells in mice. CONCLUSIONS Its high diversity and in situ applicability, make the proposed Cre Lox based tagging system suitable for whole tissue or even whole animal barcoding. Moreover, it can be built using established technology.
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Affiliation(s)
- Tom S Weber
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | | | - Denise C Miles
- The Walter and Eliza Hall Institute of Medical Research & The University of Melbourne, Parkville, Melbourne, Australia
| | - Stefan P Glaser
- The Walter and Eliza Hall Institute of Medical Research & The University of Melbourne, Parkville, Melbourne, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research & The University of Melbourne, Parkville, Melbourne, Australia
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland.
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10
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Kobayashi H, Suda T, Takubo K. How hematopoietic stem/progenitors and their niche sense and respond to infectious stress. Exp Hematol 2015; 44:92-100. [PMID: 26646990 DOI: 10.1016/j.exphem.2015.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/18/2015] [Accepted: 11/21/2015] [Indexed: 12/20/2022]
Abstract
Hematopoietic stem/progenitor cells (HSPCs) play important roles in fighting systemic infection as they supply immune cells in a demand-adapted manner. Various mechanisms govern HSPC responses to infection, including cytokine signaling, niche function, and direct sensing of pathogen-derived molecules by HSPCs themselves. Here we review recent advances in our understanding of HSPC responses to infection and also consider newly identified STING-mediated machinery recognizing bacteria-derived cyclic dinucleotides.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Toshio Suda
- Cancer Science Institute, National University of Singapore, Singapore
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
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11
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Development of a diverse human T-cell repertoire despite stringent restriction of hematopoietic clonality in the thymus. Proc Natl Acad Sci U S A 2015; 112:E6020-7. [PMID: 26483497 DOI: 10.1073/pnas.1519118112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The fate and numbers of hematopoietic stem cells (HSC) and their progeny that seed the thymus constitute a fundamental question with important clinical implications. HSC transplantation is often complicated by limited T-cell reconstitution, especially when HSC from umbilical cord blood are used. Attempts to improve immune reconstitution have until now been unsuccessful, underscoring the need for better insight into thymic reconstitution. Here we made use of the NOD-SCID-IL-2Rγ(-/-) xenograft model and lentiviral cellular barcoding of human HSCs to study T-cell development in the thymus at a clonal level. Barcoded HSCs showed robust (>80% human chimerism) and reproducible myeloid and lymphoid engraftment, with T cells arising 12 wk after transplantation. A very limited number of HSC clones (<10) repopulated the xenografted thymus, with further restriction of the number of clones during subsequent development. Nevertheless, T-cell receptor rearrangements were polyclonal and showed a diverse repertoire, demonstrating that a multitude of T-lymphocyte clones can develop from a single HSC clone. Our data imply that intrathymic clonal fitness is important during T-cell development. As a consequence, immune incompetence after HSC transplantation is not related to the transplantation of limited numbers of HSC but to intrathymic events.
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12
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Hematopoietic stem cells: concepts, definitions, and the new reality. Blood 2015; 125:2605-13. [PMID: 25762175 DOI: 10.1182/blood-2014-12-570200] [Citation(s) in RCA: 345] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/03/2015] [Indexed: 12/25/2022] Open
Abstract
Hematopoietic stem cell (HSC) research took hold in the 1950s with the demonstration that intravenously injected bone marrow cells can rescue irradiated mice from lethality by reestablishing blood cell production. Attempts to quantify the cells responsible led to the discovery of serially transplantable, donor-derived, macroscopic, multilineage colonies detectable on the spleen surface 1 to 2 weeks posttransplant. The concept of self-renewing multipotent HSCs was born, but accompanied by perplexing evidence of great variability in the outcomes of HSC self-renewal divisions. The next 60 years saw an explosion in the development and use of more refined tools for assessing the behavior of prospectively purified subsets of hematopoietic cells with blood cell-producing capacity. These developments have led to the formulation of increasingly complex hierarchical models of hematopoiesis and a growing list of intrinsic and extrinsic elements that regulate HSC cycling status, viability, self-renewal, and lineage outputs. More recent examination of these properties in individual, highly purified HSCs and analyses of their perpetuation in clonally generated progeny HSCs have now provided definitive evidence of linearly transmitted heterogeneity in HSC states. These results anticipate the need and use of emerging new technologies to establish models that will accommodate such pluralistic features of HSCs and their control mechanisms.
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13
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Babovic S, Eaves CJ. Hierarchical organization of fetal and adult hematopoietic stem cells. Exp Cell Res 2014; 329:185-91. [DOI: 10.1016/j.yexcr.2014.08.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/02/2014] [Indexed: 02/06/2023]
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14
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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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15
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Naik SH, Schumacher TN, Perié L. Cellular barcoding: a technical appraisal. Exp Hematol 2014; 42:598-608. [PMID: 24996012 DOI: 10.1016/j.exphem.2014.05.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 12/29/2022]
Abstract
Cellular barcoding involves the tagging of individual cells of interest with unique genetic heritable identifiers or barcodes and is emerging as a powerful tool to address individual cell fates on a large scale. However, as with many new technologies, diverse technical and analytical challenges have emerged. Here, we review those challenges and highlight both the power and limitations of cellular barcoding. We then illustrate the contribution of cellular barcoding to the understanding of hematopoiesis and outline the future potential of this technology.
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Affiliation(s)
- Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Ton N Schumacher
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Leïla Perié
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.
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16
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Pollock JD, Wu DY, Satterlee JS. Molecular neuroanatomy: a generation of progress. Trends Neurosci 2014; 37:106-23. [PMID: 24388609 PMCID: PMC3946666 DOI: 10.1016/j.tins.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 11/22/2022]
Abstract
The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.
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Affiliation(s)
- Jonathan D Pollock
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA.
| | - Da-Yu Wu
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - John S Satterlee
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
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17
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Determining Lineage Pathways from Cellular Barcoding Experiments. Cell Rep 2014; 6:617-24. [DOI: 10.1016/j.celrep.2014.01.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/09/2013] [Accepted: 01/14/2014] [Indexed: 11/21/2022] Open
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18
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Cornils K, Thielecke L, Hüser S, Forgber M, Thomaschewski M, Kleist N, Hussein K, Riecken K, Volz T, Gerdes S, Glauche I, Dahl A, Dandri M, Roeder I, Fehse B. Multiplexing clonality: combining RGB marking and genetic barcoding. Nucleic Acids Res 2014; 42:e56. [PMID: 24476916 PMCID: PMC3985654 DOI: 10.1093/nar/gku081] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.
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Affiliation(s)
- Kerstin Cornils
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany, Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden 01307, Germany, ALS Automated Lab Solutions GmbH, Jena 07747, Germany, Department of Neuropathology, Hannover Medical School, Institute of Pathology, Hannover 30625, Germany, Department of Internal Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany, Deep Sequencing Group SFB 655, Biotechnology Center, Technische Universität Dresden, Dresden 01307, Germany
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19
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Bystrykh LV, de Haan G, Verovskaya E. Barcoded vector libraries and retroviral or lentiviral barcoding of hematopoietic stem cells. Methods Mol Biol 2014; 1185:345-360. [PMID: 25062640 DOI: 10.1007/978-1-4939-1133-2_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cellular barcoding is a relatively recent technique aimed at clonal analysis of a proliferating cell population of any kind. The method was shown to be particularly successful in monitoring clonal contributions of hematopoietic stem cells (HSCs). An essential step of the method is retroviral or lentiviral labeling of the hematopoietic cells. The unique feature of the method is the generation of a vector library containing specific artificial DNA tags, generally known as barcodes. The library must satisfy multiple essential requirements. Importantly, considering the number of possible variations within the barcode sequence, the actual size of the barcoded vector library, and the number of clonogenic (stem) cells in the given experiment should be in ratios far from saturation. Excessive bias in barcodes frequencies must be avoided, and the library size must be assessed prior to the sequencing analysis. The final sequencing results must undergo statistical filtering. If all requirements are met, the method ensures profound sensitivity and accuracy for monitoring of the clonal fluctuations in a wide range of biological experiments.
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Affiliation(s)
- Leonid V Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antoninus Deusinglaan 1, Building 3226, 9713 AV, Groningen, The Netherlands,
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20
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Analysis of the clonal growth and differentiation dynamics of primitive barcoded human cord blood cells in NSG mice. Blood 2013; 122:3129-37. [PMID: 24030380 DOI: 10.1182/blood-2013-06-508432] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Human cord blood (CB) offers an attractive source of cells for clinical transplants because of its rich content of cells with sustained repopulating ability in spite of an apparent deficiency of cells with rapid reconstituting ability. Nevertheless, the clonal dynamics of nonlimiting CB transplants remain poorly understood. To begin to address this question, we exposed CD34+ CB cells to a library of barcoded lentiviruses and used massively parallel sequencing to quantify the clonal distributions of lymphoid and myeloid cells subsequently detected in sequential marrow aspirates obtained from 2 primary NOD/SCID-IL2Rγ(-/-) mice, each transplanted with ∼10(5) of these cells, and for another 6 months in 2 secondary recipients. Of the 196 clones identified, 68 were detected at 4 weeks posttransplant and were often lympho-myeloid. The rest were detected later, after variable periods up to 13 months posttransplant, but with generally increasing stability throughout time, and they included clones in which different lineages were detected. However, definitive evidence of individual cells capable of generating T-, B-, and myeloid cells, for over a year, and self-renewal of this potential was also obtained. These findings highlight the caveats and utility of this model to analyze human hematopoietic stem cell control in vivo.
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