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Solis L, Van Coillie S, Bonham JR, Hauck F, Hammarström L, Staal FJT, Lim B, Pergent M, Prévot J. Newborn Screening Today and Tomorrow: A Brief Report from the International Primary Immunodeficiencies Congress. Int J Neonatal Screen 2024; 10:30. [PMID: 38651395 PMCID: PMC11036269 DOI: 10.3390/ijns10020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/25/2024] Open
Abstract
This article presents the report of the session on "Newborn Screening for Primary Immunodeficiencies-Now What?" organised during the International Primary Immunodeficiency Congress (IPIC) held in November 2023. This clinical conference was organised by the International Patient Organisation for Primary Immunodeficiencies (IPOPI), the global patient organisation advocating for primary immunodeficiencies (PIDs) in patients. The session aimed at exploring the advances in newborn screening (NBS) for severe combined immunodeficiency, starting with the common practice and inserting the discussion into the wider perspective of genomics whilst taking into consideration the ethical aspects of screening as well as incorporating families and the public into the discussions, so as to ensure that NBS for treatable rare disorders continues to be one of the major public health advances of the 20th century.
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Affiliation(s)
- Leire Solis
- IPOPI, BE-1050 Brussels, Belgium; (L.S.); (S.V.C.); (B.L.); (M.P.)
| | | | - James R. Bonham
- International Society of Neonatal Screening, Reigerskamp 273, 3607 HP Maarssen, The Netherlands;
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-Universität München, DE-80337 Munich, Germany;
| | - Lennart Hammarström
- Department of Medical Biophysics and Biochemistry, Karolinska Instituet, SE-17177 Stockholm, Sweden;
| | - Frank J. T. Staal
- Departments of Immunology and Pediatrics, Leiden University Medical School, 2300 RC Leiden, The Netherlands;
| | - Bruce Lim
- IPOPI, BE-1050 Brussels, Belgium; (L.S.); (S.V.C.); (B.L.); (M.P.)
| | - Martine Pergent
- IPOPI, BE-1050 Brussels, Belgium; (L.S.); (S.V.C.); (B.L.); (M.P.)
| | - Johan Prévot
- IPOPI, BE-1050 Brussels, Belgium; (L.S.); (S.V.C.); (B.L.); (M.P.)
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Castiello MC, Di Verniere M, Draghici E, Fontana E, Penna S, Sereni L, Zecchillo A, Minuta D, Uva P, Zahn M, Gil-Farina I, Annoni A, Iaia S, Ott de Bruin LM, Notarangelo LD, Pike-Overzet K, Staal FJT, Villa A, Capo V. Partial correction of immunodeficiency by lentiviral vector gene therapy in mouse models carrying Rag1 hypomorphic mutations. Front Immunol 2023; 14:1268620. [PMID: 38022635 PMCID: PMC10679457 DOI: 10.3389/fimmu.2023.1268620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Recombination activating genes (RAG) 1 and 2 defects are the most frequent form of severe combined immunodeficiency (SCID). Patients with residual RAG activity have a spectrum of clinical manifestations ranging from Omenn syndrome to delayed-onset combined immunodeficiency, often associated with granulomas and/or autoimmunity (CID-G/AI). Lentiviral vector (LV) gene therapy (GT) has been proposed as an alternative treatment to the standard hematopoietic stem cell transplant and a clinical trial for RAG1 SCID patients recently started. However, GT in patients with hypomorphic RAG mutations poses additional risks, because of the residual endogenous RAG1 expression and the general state of immune dysregulation and associated inflammation. Methods In this study, we assessed the efficacy of GT in 2 hypomorphic Rag1 murine models (Rag1F971L/F971L and Rag1R972Q/R972Q), exploiting the same LV used in the clinical trial encoding RAG1 under control of the MND promoter. Results and discussion Starting 6 weeks after transplant, GT-treated mice showed a decrease in proportion of myeloid cells and a concomitant increase of B, T and total white blood cells. However, counts remained lower than in mice transplanted with WT Lin- cells. At euthanasia, we observed a general redistribution of immune subsets in tissues, with the appearance of mature recirculating B cells in the bone marrow. In the thymus, we demonstrated correction of the block at double negative stage, with a modest improvement in the cortical/medullary ratio. Analysis of antigenspecific IgM and IgG serum levels after in vivo challenge showed an amelioration of antibody responses, suggesting that the partial immune correction could confer a clinical benefit. Notably, no overt signs of autoimmunity were detected, with B-cell activating factor decreasing to normal levels and autoantibodies remaining stable after GT. On the other hand, thymic enlargement was frequently observed, although not due to vector integration and insertional mutagenesis. In conclusion, our work shows that GT could partially alleviate the combined immunodeficiency of hypomorphic RAG1 patients and that extensive efficacy and safety studies with alternative models are required before commencing RAG gene therapy in thesehighly complex patients.
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Affiliation(s)
- Maria Carmina Castiello
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Martina Di Verniere
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Elena Draghici
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Fontana
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Sara Penna
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Sereni
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Zecchillo
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Denise Minuta
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Uva
- Clinical Bioinformatics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | | | - Andrea Annoni
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Iaia
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lisa M. Ott de Bruin
- Willem-Alexander Children’s Hospital, Department of Pediatrics, Pediatric Stem Cell Transplantation Program, Leiden University Medical Center, Leiden, Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Anna Villa
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Valentina Capo
- San Raffaele-Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
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3
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Braams M, Pike-Overzet K, Staal FJT. The recombinase activating genes: architects of immune diversity during lymphocyte development. Front Immunol 2023; 14:1210818. [PMID: 37497222 PMCID: PMC10367010 DOI: 10.3389/fimmu.2023.1210818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
The mature lymphocyte population of a healthy individual has the remarkable ability to recognise an immense variety of antigens. Instead of encoding a unique gene for each potential antigen receptor, evolution has used gene rearrangements, also known as variable, diversity, and joining gene segment (V(D)J) recombination. This process is critical for lymphocyte development and relies on recombination-activating genes-1 (RAG1) and RAG2, here collectively referred to as RAG. RAG serves as powerful genome editing tools for lymphocytes and is strictly regulated to prevent dysregulation. However, in the case of dysregulation, RAG has been implicated in cases of cancer, autoimmunity and severe combined immunodeficiency (SCID). This review examines functional protein domains and motifs of RAG, describes advances in our understanding of the function and (dys)regulation of RAG, discuss new therapeutic options, such as gene therapy, for RAG deficiencies, and explore in vitro and in vivo methods for determining RAG activity and target specificity.
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Affiliation(s)
- Merijn Braams
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Leiden University Medical Centre, Leiden, Netherlands
- Department of Paediatrics, Leiden University Medical Centre, Leiden, Netherlands
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4
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Bastani S, Staal FJT, Canté-Barrett K. The quest for the holy grail: overcoming challenges in expanding human hematopoietic stem cells for clinical use. Stem Cell Investig 2023; 10:15. [PMID: 37457748 PMCID: PMC10345135 DOI: 10.21037/sci-2023-016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Hematopoietic stem cell (HSC) transplantation has been the golden standard for many hematological disorders. However, the number of HSCs obtained from several sources, including umbilical cord blood (UCB), often is insufficient for transplantation. For decades, maintaining or even expanding HSCs for therapeutic purposes has been a "holy grail" in stem cell biology. Different methods have been proposed to improve the efficiency of cell expansion and enhance homing potential such as co-culture with stromal cells or treatment with specific agents. Recent progress has shown that this is starting to become feasible using serum-free and well-defined media. Some of these protocols to expand HSCs along with genetic modification have been successfully applied in clinical trials and some others are studied in preclinical and clinical studies. However, the main challenges regarding ex vivo expansion of HSCs such as limited growth potential and tendency to differentiate in culture still need improvements. Understanding the biology of blood stem cells, their niche and signaling pathways has provided possibilities to regulate cell fate decisions and manipulate cells to optimize expansion of HSCs in vitro. Here, we review the plethora of HSC expansion protocols that have been proposed and indicate the current state of the art for their clinical application.
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Affiliation(s)
- Sepideh Bastani
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Kirsten Canté-Barrett
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
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5
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Guo N, Li N, Jia L, Jiang Q, Schreurs M, van Unen V, de Sousa Lopes SMC, Vloemans AA, Eggermont J, Lelieveldt B, Staal FJT, de Miranda NFCC, Pascutti MF, Koning F. Immune subset-committed proliferating cells populate the human foetal intestine throughout the second trimester of gestation. Nat Commun 2023; 14:1318. [PMID: 36899020 PMCID: PMC10006174 DOI: 10.1038/s41467-023-37052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The intestine represents the largest immune compartment in the human body, yet its development and organisation during human foetal development is largely unknown. Here we show the immune subset composition of this organ during development, by longitudinal spectral flow cytometry analysis of human foetal intestinal samples between 14 and 22 weeks of gestation. At 14 weeks, the foetal intestine is mainly populated by myeloid cells and three distinct CD3-CD7+ ILC, followed by rapid appearance of adaptive CD4+, CD8+ T and B cell subsets. Imaging mass cytometry identifies lymphoid follicles from week 16 onwards in a villus-like structure covered by epithelium and confirms the presence of Ki-67+ cells in situ within all CD3-CD7+ ILC, T, B and myeloid cell subsets. Foetal intestinal lymphoid subsets are capable of spontaneous proliferation in vitro. IL-7 mRNA is detected within both the lamina propria and the epithelium and IL-7 enhances proliferation of several subsets in vitro. Overall, these observations demonstrate the presence of immune subset-committed cells capable of local proliferation in the developing human foetal intestine, likely contributing to the development and growth of organized immune structures throughout most of the 2nd trimester, which might influence microbial colonization upon birth.
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Affiliation(s)
- Nannan Guo
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,State Key Laboratory of Zoonotic Diseases, Institute of Zoonoses, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Li Jia
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Qinyue Jiang
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Mette Schreurs
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | | | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - M Fernanda Pascutti
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
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6
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Cordes M, Pike-Overzet K, Van Den Akker EB, Staal FJT, Canté-Barrett K. Multi-omic analyses in immune cell development with lessons learned from T cell development. Front Cell Dev Biol 2023; 11:1163529. [PMID: 37091971 PMCID: PMC10118026 DOI: 10.3389/fcell.2023.1163529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Traditionally, flow cytometry has been the preferred method to characterize immune cells at the single-cell level. Flow cytometry is used in immunology mostly to measure the expression of identifying markers on the cell surface, but-with good antibodies-can also be used to assess the expression of intracellular proteins. The advent of single-cell RNA-sequencing has paved the road to study immune development at an unprecedented resolution. Single-cell RNA-sequencing studies have not only allowed us to efficiently chart the make-up of heterogeneous tissues, including their most rare cell populations, it also increasingly contributes to our understanding how different omics modalities interplay at a single cell resolution. Particularly for investigating the immune system, this means that these single-cell techniques can be integrated to combine and correlate RNA and protein data at the single-cell level. While RNA data usually reveals a large heterogeneity of a given population identified solely by a combination of surface protein markers, the integration of different omics modalities at a single cell resolution is expected to greatly contribute to our understanding of the immune system.
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Affiliation(s)
- Martijn Cordes
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Erik B. Van Den Akker
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, Netherlands
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, Netherlands
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Frank J. T. Staal,
| | - Kirsten Canté-Barrett
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, Netherlands
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Cordes M, Canté-Barrett K, van den Akker EB, Moretti FA, Kiełbasa SM, Vloemans SA, Garcia-Perez L, Teodosio C, van Dongen JJM, Pike-Overzet K, Reinders MJT, Staal FJT. Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multilineage development in the human thymus. Sci Immunol 2022; 7:eade0182. [DOI: 10.1126/sciimmunol.ade0182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
T cell development in the mouse thymus has been studied extensively, but less is known regarding T cell development in the human thymus. We used a combination of single-cell techniques and functional assays to perform deep immune profiling of human T cell development, focusing on the initial stages of prelineage commitment. We identified three thymus-seeding progenitor populations that also have counterparts in the bone marrow. In addition, we found that the human thymus physiologically supports the development of monocytes, dendritic cells, and NK cells, as well as limited development of B cells. These results are an important step toward monitoring and guiding regenerative therapies in patients after hematopoietic stem cell transplantation.
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Affiliation(s)
- Martijn Cordes
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Kirsten Canté-Barrett
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Netherlands
| | - Erik B. van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Federico A. Moretti
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Szymon M. Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Sandra A. Vloemans
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Laura Garcia-Perez
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC, USAL-CSIC-FICUS), Department of Medicine, University of Salamanca, Salamanca, Spain
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC, USAL-CSIC-FICUS), Department of Medicine, University of Salamanca, Salamanca, Spain
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Netherlands
- Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
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8
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Tajer P, Canté-Barrett K, Naber BAE, Vloemans SA, van Eggermond MCJA, van der Hoorn ML, Pike-Overzet K, Staal FJT. IL3 Has a Detrimental Effect on Hematopoietic Stem Cell Self-Renewal in Transplantation Settings. Int J Mol Sci 2022; 23:ijms232112736. [PMID: 36361533 PMCID: PMC9655151 DOI: 10.3390/ijms232112736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
The ex vivo expansion and maintenance of long-term hematopoietic stem cells (LT-HSC) is crucial for stem cell-based gene therapy. A combination of stem cell factor (SCF), thrombopoietin (TPO), FLT3 ligand (FLT3) and interleukin 3 (IL3) cytokines has been commonly used in clinical settings for the expansion of CD34+ from different sources, prior to transplantation. To assess the effect of IL3 on repopulating capacity of cultured CD34+ cells, we employed the commonly used combination of STF, TPO and FILT3 with or without IL3. Expanded cells were transplanted into NSG mice, followed by secondary transplantation. Overall, this study shows that IL3 leads to lower human cell engraftment and repopulating capacity in NSG mice, suggesting a negative effect of IL3 on HSC self-renewal. We, therefore, recommend omitting IL3 from HSC-based gene therapy protocols.
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Affiliation(s)
- Parisa Tajer
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Kirsten Canté-Barrett
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brigitta A. E. Naber
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Sandra A. Vloemans
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | | | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Correspondence:
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9
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Zlei M, Sidorov IA, Joosten SA, Heemskerk MHM, Myeni SK, Pothast CR, de Brouwer CS, Boomaars-van der Zanden AL, van Meijgaarden KE, Morales ST, Wessels E, Janse JJ, Goeman JJ, Cobbaert CM, Kroes ACM, Cannegieter SC, Roestenberg M, Visser LG, Kikkert M, Feltkamp MCW, Arbous SM, Staal FJT, Ottenhoff THM, van Dongen JJM, Roukens AHE, de Vries JJC. Immune Determinants of Viral Clearance in Hospitalised COVID-19 Patients: Reduced Circulating Naïve CD4+ T Cell Counts Correspond with Delayed Viral Clearance. Cells 2022; 11:cells11172743. [PMID: 36078151 PMCID: PMC9455062 DOI: 10.3390/cells11172743] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Virus-specific cellular and humoral responses are major determinants for protection from critical illness after SARS-CoV-2 infection. However, the magnitude of the contribution of each of the components to viral clearance remains unclear. Here, we studied the timing of viral clearance in relation to 122 immune parameters in 102 hospitalised patients with moderate and severe COVID-19 in a longitudinal design. Delayed viral clearance was associated with more severe disease and was associated with higher levels of SARS-CoV-2-specific (neutralising) antibodies over time, increased numbers of neutrophils, monocytes, basophils, and a range of pro-inflammatory cyto-/chemokines illustrating ongoing, partially Th2 dominating, immune activation. In contrast, early viral clearance and less critical illness correlated with the peak of neutralising antibodies, higher levels of CD4 T cells, and in particular naïve CD4+ T cells, suggesting their role in early control of SARS-CoV-2 possibly by proving appropriate B cell help. Higher counts of naïve CD4+ T cells also correlated with lower levels of MIF, IL-9, and TNF-beta, suggesting an indirect role in averting prolonged virus-induced tissue damage. Collectively, our data show that naïve CD4+ T cell play a critical role in rapid viral T cell control, obviating aberrant antibody and cytokine profiles and disease deterioration. These data may help in guiding risk stratification for severe COVID-19.
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Affiliation(s)
- Mihaela Zlei
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Igor A. Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mirjam H. M. Heemskerk
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Sebenzile K. Myeni
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Cilia R. Pothast
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Caroline S. de Brouwer
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Linda Boomaars-van der Zanden
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Krista E. van Meijgaarden
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Shessy T. Morales
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Els Wessels
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jacqueline J. Janse
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jelle J. Goeman
- Medical Statistics Section, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Aloys C. M. Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Suzanne C. Cannegieter
- Department of Clinical Epidemiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Meta Roestenberg
- Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Leonardus G. Visser
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mariet C. W. Feltkamp
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Sesmu M. Arbous
- Department of Clinical Epidemiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Intensive Care, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Anna H. E. Roukens
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jutte J. C. de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Correspondence:
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10
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Zbinden A, Canté-Barrett K, Pike-Overzet K, Staal FJT. Stem Cell-Based Disease Models for Inborn Errors of Immunity. Cells 2021; 11:cells11010108. [PMID: 35011669 PMCID: PMC8750661 DOI: 10.3390/cells11010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
The intrinsic capacity of human hematopoietic stem cells (hHSCs) to reconstitute myeloid and lymphoid lineages combined with their self-renewal capacity hold enormous promises for gene therapy as a viable treatment option for a number of immune-mediated diseases, most prominently for inborn errors of immunity (IEI). The current development of such therapies relies on disease models, both in vitro and in vivo, which allow the study of human pathophysiology in great detail. Here, we discuss the current challenges with regards to developmental origin, heterogeneity and the subsequent implications for disease modeling. We review models based on induced pluripotent stem cell technology and those relaying on use of adult hHSCs. We critically review the advantages and limitations of current models for IEI both in vitro and in vivo. We conclude that existing and future stem cell-based models are necessary tools for developing next generation therapies for IEI.
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11
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Schwarzer A, Talbot SR, Selich A, Morgan M, Schott JW, Dittrich-Breiholz O, Bastone AL, Weigel B, Ha TC, Dziadek V, Gijsbers R, Thrasher AJ, Staal FJT, Gaspar HB, Modlich U, Schambach A, Rothe M. Predicting genotoxicity of viral vectors for stem cell gene therapy using gene expression-based machine learning. Mol Ther 2021; 29:3383-3397. [PMID: 34174440 PMCID: PMC8636173 DOI: 10.1016/j.ymthe.2021.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/12/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022] Open
Abstract
Hematopoietic stem cell gene therapy is emerging as a promising therapeutic strategy for many diseases of the blood and immune system. However, several individuals who underwent gene therapy in different trials developed hematological malignancies caused by insertional mutagenesis. Preclinical assessment of vector safety remains challenging because there are few reliable assays to screen for potential insertional mutagenesis effects in vitro. Here we demonstrate that genotoxic vectors induce a unique gene expression signature linked to stemness and oncogenesis in transduced murine hematopoietic stem and progenitor cells. Based on this finding, we developed the surrogate assay for genotoxicity assessment (SAGA). SAGA classifies integrating retroviral vectors using machine learning to detect this gene expression signature during the course of in vitro immortalization. On a set of benchmark vectors with known genotoxic potential, SAGA achieved an accuracy of 90.9%. SAGA is more robust and sensitive and faster than previous assays and reliably predicts a mutagenic risk for vectors that led to leukemic severe adverse events in clinical trials. Our work provides a fast and robust tool for preclinical risk assessment of gene therapy vectors, potentially paving the way for safer gene therapy trials.
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Affiliation(s)
- Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Steven R Talbot
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Anton Selich
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Juliane W Schott
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | | | - Antonella L Bastone
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Bettina Weigel
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Teng Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Violetta Dziadek
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Rik Gijsbers
- Molecular Virology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Adrian J Thrasher
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Hubert B Gaspar
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ute Modlich
- Research Group for Gene Modification in Stem Cells, Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
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12
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Klaver-Flores S, Zittersteijn HA, Canté-Barrett K, Lankester A, Hoeben RC, Gonçalves MAFV, Pike-Overzet K, Staal FJT. Genomic Engineering in Human Hematopoietic Stem Cells: Hype or Hope? Front Genome Ed 2021; 2:615619. [PMID: 34713237 PMCID: PMC8525357 DOI: 10.3389/fgeed.2020.615619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Many gene editing techniques are developed and tested, yet, most of these are optimized for transformed cell lines, which differ from their primary cell counterparts in terms of transfectability, cell death propensity, differentiation capability, and chromatin accessibility to gene editing tools. Researchers are working to overcome the challenges associated with gene editing of primary cells, namely, at the level of improving the gene editing tool components, e.g., the use of modified single guide RNAs, more efficient delivery of Cas9 and RNA in the ribonucleoprotein of these cells. Despite these efforts, the low efficiency of proper gene editing in true primary cells is an obstacle that needs to be overcome in order to generate sufficiently high numbers of corrected cells for therapeutic use. In addition, many of the therapeutic candidate genes for gene editing are expressed in more mature blood cell lineages but not in the hematopoietic stem cells (HSCs), where they are tightly packed in heterochromatin, making them less accessible to gene editing enzymes. Bringing HSCs in proliferation is sometimes seen as a solution to overcome lack of chromatin access, but the induction of proliferation in HSCs often is associated with loss of stemness. The documented occurrences of off-target effects and, importantly, on-target side effects also raise important safety issues. In conclusion, many obstacles still remain to be overcome before gene editing in HSCs for gene correction purposes can be applied clinically. In this review, in a perspective way, we will discuss the challenges of researching and developing a novel genetic engineering therapy for monogenic blood and immune system disorders.
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Affiliation(s)
| | - Hidde A Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan Lankester
- Department of Pediatrics, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Manuel A F V Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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13
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de Roo JJD, Naber BAE, Vloemans SA, de Haas EFE, van der Laan AMA, Staal FJT. Flow Cytometry and Confocal Imaging Analysis of Low Wnt Expression in Axin2-mTurquoise2 Reporter Thymocytes. J Vis Exp 2021. [PMID: 34633363 DOI: 10.3791/62141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Measuring Wnt expression levels is essential when trying to identify or test new Wnt therapeutic targets. Previous studies have shown that canonical Wnt signaling operates via a dosage-driven mechanism, motivating the need to study and measure Wnt signaling in various cell types. Although several reporter models have been proposed to represent physiological Wnt expression, either the genetic context or the reporter protein highly influenced the validity, accuracy, and flexibility of these tools. This paper describes methods for acquiring and analyzing data obtained with the Axin2-mTurquoise2 mouse Wnt reporter model, which contains a mutated Axin2em1Fstl allele. This model facilitates the study of endogenous canonical Wnt signaling in individual cells over a wide range of Wnt activity. This protocol describes how to fully appreciate Axin2-mTurquoise2 reporter activity using cell population analysis of the hematopoietic system, combined with cell surface markers or β-catenin intracellular staining. These procedures serve as a base for implementation and reproduction in other tissues or cells of interest. By combining fluorescence-activated cell sorting and confocal imaging, distinct canonical Wnt expression levels can be visualized. The recommended measurement and analysis strategies provide quantitative data on the fluorescent expression levels for precise assessment of canonical Wnt signaling. These methods will be useful for researchers who want to use the Axin2-mTurquise2 model for canonical Wnt expression patterns.
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14
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Moirangthem RD, Ma K, Lizot S, Cordesse A, Olivré J, de Chappedelaine C, Joshi A, Cieslak A, Tchen J, Cagnard N, Asnafi V, Rausell A, Simons L, Zuber J, Taghon T, Staal FJT, Pflumio F, Six E, Cavazzana M, Lagresle-Peyrou C, Soheili T, André I. A DL-4- and TNFα-based culture system to generate high numbers of nonmodified or genetically modified immunotherapeutic human T-lymphoid progenitors. Cell Mol Immunol 2021; 18:1662-1676. [PMID: 34117371 PMCID: PMC8245454 DOI: 10.1038/s41423-021-00706-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Several obstacles to the production, expansion and genetic modification of immunotherapeutic T cells in vitro have restricted the widespread use of T-cell immunotherapy. In the context of HSCT, delayed naïve T-cell recovery contributes to poor outcomes. A novel approach to overcome the major limitations of both T-cell immunotherapy and HSCT would be to transplant human T-lymphoid progenitors (HTLPs), allowing reconstitution of a fully functional naïve T-cell pool in the patient thymus. However, it is challenging to produce HTLPs in the high numbers required to meet clinical needs. Here, we found that adding tumor necrosis factor alpha (TNFα) to a DL-4-based culture system led to the generation of a large number of nonmodified or genetically modified HTLPs possessing highly efficient in vitro and in vivo T-cell potential from either CB HSPCs or mPB HSPCs through accelerated T-cell differentiation and enhanced HTLP cell cycling and survival. This study provides a clinically suitable cell culture platform to generate high numbers of clinically potent nonmodified or genetically modified HTLPs for accelerating immune recovery after HSCT and for T-cell-based immunotherapy (including CAR T-cell therapy).
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Affiliation(s)
- Ranjita Devi Moirangthem
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Kuiying Ma
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Sabrina Lizot
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Anne Cordesse
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Juliette Olivré
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Corinne de Chappedelaine
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Akshay Joshi
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Agata Cieslak
- grid.412134.10000 0004 0593 9113Laboratory of Onco-Hematology, AP-HP, Hôpital Necker-Enfants Malades., Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Institut Necker-Enfants Malades (INEM), INSERM UMR 1151, Paris, France
| | - John Tchen
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Nicolas Cagnard
- grid.508487.60000 0004 7885 7602Plateforme Bio-informatique, Université Paris Descartes, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, France
| | - Vahid Asnafi
- grid.412134.10000 0004 0593 9113Laboratory of Onco-Hematology, AP-HP, Hôpital Necker-Enfants Malades., Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Institut Necker-Enfants Malades (INEM), INSERM UMR 1151, Paris, France
| | - Antonio Rausell
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Clinical Bioinformatics, INSERM UMR 1163, Paris, France
| | - Laura Simons
- grid.412134.10000 0004 0593 9113Department of Biotherapy Clinical Investigation Center, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Julien Zuber
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France ,grid.412134.10000 0004 0593 9113Department of Adult Kidney Transplantation, AP-HP, Hôpital Necker, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium ,grid.5342.00000 0001 2069 7798Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Frank J. T. Staal
- grid.10419.3d0000000089452978Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Françoise Pflumio
- grid.7429.80000000121866389Team Niche and Cancer in Hematopoiesis, Université de Paris and Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Emmanuelle Six
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Marina Cavazzana
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France ,grid.412134.10000 0004 0593 9113Department of Biotherapy Clinical Investigation Center, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Chantal Lagresle-Peyrou
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France ,grid.412134.10000 0004 0593 9113Department of Biotherapy Clinical Investigation Center, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Tayebeh Soheili
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
| | - Isabelle André
- grid.508487.60000 0004 7885 7602Université de Paris, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Paris, France
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15
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Garcia-Perez L, van Roon L, Schilham MW, Lankester AC, Pike-Overzet K, Staal FJT. Combining Mobilizing Agents with Busulfan to Reduce Chemotherapy-Based Conditioning for Hematopoietic Stem Cell Transplantation. Cells 2021; 10:cells10051077. [PMID: 33946560 PMCID: PMC8147230 DOI: 10.3390/cells10051077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/24/2021] [Indexed: 02/06/2023] Open
Abstract
In the context of hematopoietic stem cell (HSC) transplantation, conditioning with myelo- and immune-ablative agents is used to eradicate the patient’s diseased cells, generate space in the marrow and suppress immune reactions prior to the infusion of donor HSCs. While conditioning is required for effective and long-lasting HSC engraftment, currently used regimens are also associated with short and long-term side effects on extramedullary tissues and even mortality. Particularly in patients with severe combined immunodeficiency (SCID), who are generally less than 1-year old at the time of transplantation and often suffer from existing comorbidities. There is a pressing need for development of alternative, less toxic conditioning regimens. Hence, we here aimed to improve efficacy of currently used myeloablative protocols by combining busulfan with stem-cell niche-directed therapeutic agents (G-CSF or plerixafor) that are approved for clinical use in stem cell mobilization. T, B and myeloid cell recovery was analyzed in humanized NSG mice after different conditioning regimens. Increasing levels of human leukocyte chimerism were observed in a busulfan dose-dependent manner, showing comparable immune recovery as with total body irradiation in CD34-transplanted NSG mice. Notably, a better T cell reconstitution compared to TBI was observed after busulfan conditioning not only in NSG mice but also in SCID mouse models. Direct effects of reducing the stem cell compartment in the bone marrow were observed after G-CSF and plerixafor administration, as well as in combination with low doses of busulfan. Unfortunately, these direct effects on the stem population in the bone marrow were not reflected in increased human chimerism or immune recovery after CD34 transplantation in NSG mice. These results indicate moderate potential of reduced conditioning regimens for clinical use relevant for all allogeneic transplants.
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Affiliation(s)
- Laura Garcia-Perez
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.G.-P.); (L.v.R.); (K.P.-O.)
| | - Lieke van Roon
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.G.-P.); (L.v.R.); (K.P.-O.)
| | - Marco W. Schilham
- Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.W.S.); (A.C.L.)
| | - Arjan C. Lankester
- Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.W.S.); (A.C.L.)
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.G.-P.); (L.v.R.); (K.P.-O.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.G.-P.); (L.v.R.); (K.P.-O.)
- Correspondence:
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16
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Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells 2021; 10:1074. [PMID: 33946533 PMCID: PMC8147249 DOI: 10.3390/cells10051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
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Affiliation(s)
- Veronica Della Chiara
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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17
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Khatri I, Staal FJT, van Dongen JJM. Corrigendum: Blocking of the High-Affinity Interaction-Synapse Between SARS-CoV-2 Spike and Human ACE2 Proteins Likely Requires Multiple High-Affinity Antibodies: An Immune Perspective. Front Immunol 2021; 12:659375. [PMID: 33936092 PMCID: PMC8080062 DOI: 10.3389/fimmu.2021.659375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/26/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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18
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Zittersteijn HA, Harteveld CL, Klaver-Flores S, Lankester AC, Hoeben RC, Staal FJT, Gonçalves MAFV. A Small Key for a Heavy Door: Genetic Therapies for the Treatment of Hemoglobinopathies. Front Genome Ed 2021; 2:617780. [PMID: 34713239 PMCID: PMC8525365 DOI: 10.3389/fgeed.2020.617780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Throughout the past decades, the search for a treatment for severe hemoglobinopathies has gained increased interest within the scientific community. The discovery that ɤ-globin expression from intact HBG alleles complements defective HBB alleles underlying β-thalassemia and sickle cell disease, has provided a promising opening for research directed at relieving ɤ-globin repression mechanisms and, thereby, improve clinical outcomes for patients. Various gene editing strategies aim to reverse the fetal-to-adult hemoglobin switch to up-regulate ɤ-globin expression through disabling either HBG repressor genes or repressor binding sites in the HBG promoter regions. In addition to these HBB mutation-independent strategies involving fetal hemoglobin (HbF) synthesis de-repression, the expanding genome editing toolkit is providing increased accuracy to HBB mutation-specific strategies encompassing adult hemoglobin (HbA) restoration for a personalized treatment of hemoglobinopathies. Moreover, besides genome editing, more conventional gene addition strategies continue under investigation to restore HbA expression. Together, this research makes hemoglobinopathies a fertile ground for testing various innovative genetic therapies with high translational potential. Indeed, the progressive understanding of the molecular clockwork underlying the hemoglobin switch together with the ongoing optimization of genome editing tools heightens the prospect for the development of effective and safe treatments for hemoglobinopathies. In this context, clinical genetics plays an equally crucial role by shedding light on the complexity of the disease and the role of ameliorating genetic modifiers. Here, we cover the most recent insights on the molecular mechanisms underlying hemoglobin biology and hemoglobinopathies while providing an overview of state-of-the-art gene editing platforms. Additionally, current genetic therapies under development, are equally discussed.
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Affiliation(s)
- Hidde A. Zittersteijn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis L. Harteveld
- Department of Human and Clinical Genetics, The Hemoglobinopathies Laboratory, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arjan C. Lankester
- Department of Pediatrics, Stem Cell Transplantation Program, Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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19
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Jridi I, Canté-Barrett K, Pike-Overzet K, Staal FJT. Inflammation and Wnt Signaling: Target for Immunomodulatory Therapy? Front Cell Dev Biol 2021; 8:615131. [PMID: 33614624 PMCID: PMC7890028 DOI: 10.3389/fcell.2020.615131] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Wnt proteins comprise a large family of highly conserved glycoproteins known for their role in development, cell fate specification, tissue regeneration, and tissue homeostasis. Aberrant Wnt signaling is linked to developmental defects, malignant transformation, and carcinogenesis as well as to inflammation. Mounting evidence from recent research suggests that a dysregulated activation of Wnt signaling is involved in the pathogenesis of chronic inflammatory diseases, such as neuroinflammation, cancer-mediated inflammation, and metabolic inflammatory diseases. Recent findings highlight the role of Wnt in the modulation of inflammatory cytokine production, such as NF-kB signaling and in innate defense mechanisms as well as in the bridging of innate and adaptive immunity. This sparked the development of novel therapeutic treatments against inflammatory diseases based on Wnt modulation. Here, we summarize the role and function of the Wnt pathway in inflammatory diseases and focus on Wnt signaling as underlying master regulator of inflammation that can be therapeutically targeted.
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Affiliation(s)
- Imen Jridi
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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Garcia-Perez L, van Eggermond MCJA, Maietta E, van der Hoorn MLP, Pike-Overzet K, Staal FJT. A Novel Branched DNA-Based Flowcytometric Method for Single-Cell Characterization of Gene Therapy Products and Expression of Therapeutic Genes. Front Immunol 2021; 11:607991. [PMID: 33584681 PMCID: PMC7876092 DOI: 10.3389/fimmu.2020.607991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 11/13/2022] Open
Abstract
Many preclinical and clinical studies of hematopoietic stem cell-based gene therapy (GT) are based on the use of lentiviruses as the vector of choice. Assessment of the vector titer and transduction efficiency of the cell product is critical for these studies. Efficacy and safety of the modified cell product are commonly determined by assessing the vector copy number (VCN) using qPCR. However, this optimized and well-established method in the GT field is based on bulk population averages, which can lead to misinterpretation of the actual VCN per transduced cell. Therefore, we introduce here a single cell-based method that allows to unmask cellular heterogeneity in the GT product, even when antibodies are not available. We use Invitrogen's flow cytometry-based PrimeFlow™ RNA Assay with customized probes to determine transduction efficiency of transgenes of interest, promoter strength, and the cellular heterogeneity of murine and human stem cells. The assay has good specificity and sensitivity to detect the transgenes, as shown by the high correlations between PrimeFlow™-positive cells and the VCN. Differences in promoter strengths can readily be detected by differences in percentages and fluorescence intensity. Hence, we show a customizable method that allows to determine the number of transduced cells and the actual VCN per transduced cell in a GT product. The assay is suitable for all therapeutic genes for which antibodies are not available or too cumbersome for routine flow cytometry. The method also allows co-staining of surface markers to analyze differential transduction efficiencies in subpopulations of target cells.
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Affiliation(s)
- Laura Garcia-Perez
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - Elisa Maietta
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
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21
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Canté-Barrett K, Staal FJT. An adequate human T cell repertoire from a single T cell progenitor: Lessons from an experiment of nature. EBioMedicine 2020; 60:103015. [PMID: 32977163 PMCID: PMC7516063 DOI: 10.1016/j.ebiom.2020.103015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/17/2022] Open
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22
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Khatri I, Staal FJT, van Dongen JJM. Blocking of the High-Affinity Interaction-Synapse Between SARS-CoV-2 Spike and Human ACE2 Proteins Likely Requires Multiple High-Affinity Antibodies: An Immune Perspective. Front Immunol 2020; 11:570018. [PMID: 33042151 PMCID: PMC7527437 DOI: 10.3389/fimmu.2020.570018] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
The pandemic of Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 has induced global eagerness to develop vaccines and therapeutics for treating COVID-19, including neutralizing antibodies. To develop effective therapeutic antibodies against SARS-CoV-2, it is critical to understand the interaction between viral and host's proteins. The human ACE2 (hACE2) protein is the crucial target for the SARS-CoV's Spike protein that allows the virus to adhere to host epithelial cells. X-ray crystal structures and biophysical properties of protein-protein interactions reveal a large interaction surface with high binding-affinity between SARS-CoV-2 and hACE2 (18 interactions), at least 15-fold stronger than between SARS-CoV-1 and hACE2 (eight interactions). This suggests that antibodies against CoV-1 infection might not be very efficient against CoV-2. Furthermore, interspecies comparisons indicate that ACE2 proteins of man and cat are far closer than dog, ferret, mouse, and rat with significant differences in binding-affinity between Spike and ACE2 proteins. This strengthens the notion of productive SARS-CoV-2 transmission between felines and humans and that classical animal models are not optimally suited for evaluating therapeutic antibodies. The large interaction surface with strong affinity between SARS-CoV-2 and hACE2 (dG-12.4) poses a huge challenge to develop reliable antibody therapy that truly blocks SARS-CoV-2 adherence and infection. We gauge that single antibodies against single epitopes might not sufficiently interfere with the strong interaction-synapse between Spike and hACE2 proteins. Instead, appropriate combinations of high-affinity neutralizing antibodies against different epitopes might be needed, preferably of IgA-class for optimal and prolonged activity at epithelial layers of respiratory and intestine tracts.
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Affiliation(s)
- Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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23
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Garcia-Perez L, Famili F, Cordes M, Brugman M, van Eggermond M, Wu H, Chouaref J, Granado DSL, Tiemessen MM, Pike-Overzet K, Daxinger L, Staal FJT. Functional definition of a transcription factor hierarchy regulating T cell lineage commitment. Sci Adv 2020; 6:eaaw7313. [PMID: 32789164 PMCID: PMC7400773 DOI: 10.1126/sciadv.aaw7313] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 06/17/2020] [Indexed: 05/02/2023]
Abstract
T cell factor 1 (Tcf1) is the first T cell-specific protein induced by Notch signaling in the thymus, leading to the activation of two major target genes, Gata3 and Bcl11b. Tcf1 deficiency results in partial arrests in T cell development, high apoptosis, and increased development of B and myeloid cells. Phenotypically, seemingly fully T cell-committed thymocytes with Tcf1 deficiency have promiscuous gene expression and an altered epigenetic profile and can dedifferentiate into more immature thymocytes and non-T cells. Restoring Bcl11b expression in Tcf1-deficient cells rescues T cell development but does not strongly suppress the development of non-T cells; in contrast, expressing Gata3 suppresses their development but does not rescue T cell development. Thus, T cell development is controlled by a minimal transcription factor network involving Notch signaling, Tcf1, and the subsequent division of labor between Bcl11b and Gata3, thereby ensuring a properly regulated T cell gene expression program.
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Affiliation(s)
- Laura Garcia-Perez
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Farbod Famili
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Martijn Cordes
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Martijn Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Marja van Eggermond
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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24
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Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P. Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis. Cell Metab 2020; 31:862-877.e14. [PMID: 32268117 DOI: 10.1016/j.cmet.2020.03.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 01/22/2023]
Abstract
Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor angiogenesis and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcriptomes. By single-cell RNA sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference predicted that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. ECs displayed metabolic transcriptome heterogeneity during cell-cycle progression and in quiescence. Hypothesizing that conserved genes are important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome-scale metabolic modeling, and gene expression meta-analysis in cross-species datasets, followed by in vitro and in vivo validation, to identify SQLE and ALDH18A1 as previously unknown metabolic angiogenic targets.
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Affiliation(s)
- Katerina Rohlenova
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Melissa García-Caballero
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Abhishek Subramanian
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Kim D Falkenberg
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp 2610, Belgium; Center for Oncological Research, University of Antwerp, Antwerp 2000, Belgium
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Federico Taverna
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Andreas Pircher
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Shawez Khan
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Steve Stegen
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Aging, KU Leuven, Leuven 3000, Belgium
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frank J T Staal
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Rene J Mclaughlin
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | | | - Nadine Ectors
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Tobias K Karakach
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Geert Carmeliet
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Aging, KU Leuven, Leuven 3000, Belgium
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
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25
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Goveia J, Rohlenova K, Taverna F, Treps L, Conradi LC, Pircher A, Geldhof V, de Rooij LPMH, Kalucka J, Sokol L, García-Caballero M, Zheng Y, Qian J, Teuwen LA, Khan S, Boeckx B, Wauters E, Decaluwé H, De Leyn P, Vansteenkiste J, Weynand B, Sagaert X, Verbeken E, Wolthuis A, Topal B, Everaerts W, Bohnenberger H, Emmert A, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Impens F, Lagani V, Vinckier S, Mazzone M, Schoonjans L, Dewerchin M, Eelen G, Karakach TK, Yang H, Wang J, Bolund L, Lin L, Thienpont B, Li X, Lambrechts D, Luo Y, Carmeliet P. An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates. Cancer Cell 2020; 37:421. [PMID: 32183954 DOI: 10.1016/j.ccell.2020.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Themeli M, Chhatta A, Boersma H, Prins HJ, Cordes M, de Wilt E, Farahani AS, Vandekerckhove B, van der Burg M, Hoeben RC, Staal FJT, Mikkers HMM. iPSC-Based Modeling of RAG2 Severe Combined Immunodeficiency Reveals Multiple T Cell Developmental Arrests. Stem Cell Reports 2020; 14:300-311. [PMID: 31956083 PMCID: PMC7013232 DOI: 10.1016/j.stemcr.2019.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022] Open
Abstract
RAG2 severe combined immune deficiency (RAG2-SCID) is a lethal disorder caused by the absence of functional T and B cells due to a differentiation block. Here, we generated induced pluripotent stem cells (iPSCs) from a RAG2-SCID patient to study the nature of the T cell developmental blockade. We observed a strongly reduced capacity to differentiate at every investigated stage of T cell development, from early CD7−CD5− to CD4+CD8+. The impaired differentiation was accompanied by an increase in CD7−CD56+CD33+ natural killer (NK) cell-like cells. T cell receptor D rearrangements were completely absent in RAG2SCID cells, whereas the rare T cell receptor B rearrangements were likely the result of illegitimate rearrangements. Repair of RAG2 restored the capacity to induce T cell receptor rearrangements, normalized T cell development, and corrected the NK cell-like phenotype. In conclusion, we succeeded in generating an iPSC-based RAG2-SCID model, which enabled the identification of previously unrecognized disorder-related T cell developmental roadblocks. RAG2-SCID cells show impaired differentiation at several stages of T cell development RAG2-SCID T and NK cells fail to undergo legitimate RAG-driven TCR rearrangements RAG2-SCID cells exhibit a skewed differentiation toward NK cell-like cells RAG2-SCID phenotype is rescued by gene correction
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Affiliation(s)
- Maria Themeli
- Department of Hematology, Amsterdam UMC, Location VUmc, Cancer Center Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Amiet Chhatta
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Hester Boersma
- Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Henk Jan Prins
- Department of Hematology, Amsterdam UMC, Location VUmc, Cancer Center Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Martijn Cordes
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Edwin de Wilt
- Department of Clinical Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Aïda Shahrabi Farahani
- Department of Hematology, Amsterdam UMC, Location VUmc, Cancer Center Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Bart Vandekerckhove
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent 9000, Belgium
| | - Mirjam van der Burg
- Department of Immunology, Erasmus Medical Center, Rotterdam 3015 GE, The Netherlands
| | - Rob C Hoeben
- Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Harald M M Mikkers
- Department of Cell & Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands; LUMC hiPSC Hotel, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands.
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27
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Goveia J, Rohlenova K, Taverna F, Treps L, Conradi LC, Pircher A, Geldhof V, de Rooij LPMH, Kalucka J, Sokol L, García-Caballero M, Zheng Y, Qian J, Teuwen LA, Khan S, Boeckx B, Wauters E, Decaluwé H, De Leyn P, Vansteenkiste J, Weynand B, Sagaert X, Verbeken E, Wolthuis A, Topal B, Everaerts W, Bohnenberger H, Emmert A, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Impens F, Lagani V, Vinckier S, Mazzone M, Schoonjans L, Dewerchin M, Eelen G, Karakach TK, Yang H, Wang J, Bolund L, Lin L, Thienpont B, Li X, Lambrechts D, Luo Y, Carmeliet P. An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates. Cancer Cell 2020; 37:21-36.e13. [PMID: 31935371 DOI: 10.1016/j.ccell.2019.12.001] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/30/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022]
Abstract
Heterogeneity of lung tumor endothelial cell (TEC) phenotypes across patients, species (human/mouse), and models (in vivo/in vitro) remains poorly inventoried at the single-cell level. We single-cell RNA (scRNA)-sequenced 56,771 endothelial cells from human/mouse (peri)-tumoral lung and cultured human lung TECs, and detected 17 known and 16 previously unrecognized phenotypes, including TECs putatively regulating immune surveillance. We resolved the canonical tip TECs into a known migratory tip and a putative basement-membrane remodeling breach phenotype. Tip TEC signatures correlated with patient survival, and tip/breach TECs were most sensitive to vascular endothelial growth factor blockade. Only tip TECs were congruent across species/models and shared conserved markers. Integrated analysis of the scRNA-sequenced data with orthogonal multi-omics and meta-analysis data across different human tumors, validated by functional analysis, identified collagen modification as a candidate angiogenic pathway.
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Affiliation(s)
- Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Katerina Rohlenova
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Federico Taverna
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Andreas Pircher
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Melissa García-Caballero
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Junbin Qian
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Shawez Khan
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Els Wauters
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium
| | - Herbert Decaluwé
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Paul De Leyn
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Johan Vansteenkiste
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Xavier Sagaert
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Erik Verbeken
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Albert Wolthuis
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Baki Topal
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Wouter Everaerts
- Laboratory for Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium; Department of Urology, University Hospitals Leuven, Leuven 3000, Belgium
| | | | - Alexander Emmert
- Department of Thoracic and Cardiovascular Surgery, University Medical Center, Göttingen 37075, Germany
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frank J T Staal
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Rene J Mclaughlin
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Francis Impens
- VIB Proteomics Core and VIB Center for Medical Biotechnology, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, Tbilisi 0162, Georgia; Gnosis Data Analysis PC, Heraklion GR-700 13, Greece
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Tobias K Karakach
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China; Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
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28
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Cordes M, Pike-Overzet K, van Eggermond M, Vloemans S, Baert MR, Garcia-Perez L, Staal FJT, Reinders MJT, van den Akker EB. ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data. Bioinformatics 2019; 36:btz804. [PMID: 31665245 PMCID: PMC7703782 DOI: 10.1093/bioinformatics/btz804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/29/2019] [Accepted: 10/24/2019] [Indexed: 11/29/2022] Open
Abstract
SUMMARY An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions. AVAILABILITY R-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martijn Cordes
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marja van Eggermond
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Vloemans
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Miranda R Baert
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura Garcia-Perez
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Erik B van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
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29
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Tajer P, Pike-Overzet K, Arias S, Havenga M, Staal FJT. Ex Vivo Expansion of Hematopoietic Stem Cells for Therapeutic Purposes: Lessons from Development and the Niche. Cells 2019; 8:cells8020169. [PMID: 30781676 PMCID: PMC6407064 DOI: 10.3390/cells8020169] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/13/2019] [Indexed: 12/21/2022] Open
Abstract
Expansion of hematopoietic stem cells (HSCs) for therapeutic purposes has been a “holy grail” in the field for many years. Ex vivo expansion of HSCs can help to overcome material shortage for transplantation purposes and genetic modification protocols. In this review, we summarize improved understanding in blood development, the effect of niche and conservative signaling pathways on HSCs in mice and humans, and also advances in ex vivo culturing protocols of human HSCs with cytokines or small molecule compounds. Different expansion protocols have been tested in clinical trials. However, an optimal condition for ex vivo expansion of human HSCs still has not been found yet. Translating and implementing new findings from basic research (for instance by using genetic modification of human HSCs) into clinical protocols is crucial to improve ex vivo expansion and eventually boost stem cell gene therapy.
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Affiliation(s)
- Parisa Tajer
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
| | - Sagrario Arias
- Batavia Biosciences, Zernikedreef 16, 2333 CL Leiden, The Netherlands.
| | - Menzo Havenga
- Batavia Biosciences, Zernikedreef 16, 2333 CL Leiden, The Netherlands.
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, L3-Q Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
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30
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Staal FJT, Aiuti A, Cavazzana M. Autologous Stem-Cell-Based Gene Therapy for Inherited Disorders: State of the Art and Perspectives. Front Pediatr 2019; 7:443. [PMID: 31737588 PMCID: PMC6834641 DOI: 10.3389/fped.2019.00443] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/11/2019] [Indexed: 12/14/2022] Open
Abstract
Gene therapy using patient's own stem cells is rapidly becoming an alternative to allogeneic stem cell transplantation, especially when suitably compatible donors cannot be found. The advent of efficient virus-based methods for delivering therapeutic genes has enabled the development of genetic medicines for inherited disorders of the immune system, hemoglobinopathies, and a number of devastating metabolic diseases. Here, we briefly review the state of the art in the field, including gene editing approaches. A growing number of pediatric diseases can be successfully cured by hematopoietic stem-cell-based gene therapy.
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Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, Netherlands
| | - Alessandro Aiuti
- Paediatric Immunohematology Unit, San Raffaele Telethon Institute for Gene Therapy, IRCCS, San Raffaele Scientific Institute, Milan, Italy.,Vita Salute, San Raffaele University, Milan, Italy
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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31
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Staal FJT. Cell intrinsic regulation of external hematopoietic stem cell stress. Stem Cell Investig 2018; 5:16. [PMID: 29984225 DOI: 10.21037/sci.2018.05.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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32
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Mansour MR, He S, Li Z, Lobbardi R, Abraham BJ, Hug C, Rahman S, Leon TE, Kuang YY, Zimmerman MW, Blonquist T, Gjini E, Gutierrez A, Tang Q, Garcia-Perez L, Pike-Overzet K, Anders L, Berezovskaya A, Zhou Y, Zon LI, Neuberg D, Fielding AK, Staal FJT, Langenau DM, Sanda T, Young RA, Look AT. JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia. J Exp Med 2018; 215:1929-1945. [PMID: 29941549 PMCID: PMC6028512 DOI: 10.1084/jem.20170484] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 03/14/2018] [Accepted: 05/30/2018] [Indexed: 01/14/2023] Open
Abstract
A substantial subset of patients with T cell acute lymphoblastic leukemia (T-ALL) develops resistance to steroids and succumbs to their disease. JDP2 encodes a bZIP protein that has been implicated as a T-ALL oncogene from insertional mutagenesis studies in mice, but its role in human T-ALL pathogenesis has remained obscure. Here we show that JDP2 is aberrantly expressed in a subset of T-ALL patients and is associated with poor survival. JDP2 is required for T-ALL cell survival, as its depletion by short hairpin RNA knockdown leads to apoptosis. Mechanistically, JDP2 regulates prosurvival signaling through direct transcriptional regulation of MCL1. Furthermore, JDP2 is one of few oncogenes capable of initiating T-ALL in transgenic zebrafish. Notably, thymocytes from rag2:jdp2 transgenic zebrafish express high levels of mcl1 and demonstrate resistance to steroids in vivo. These studies establish JDP2 as a novel oncogene in high-risk T-ALL and implicate overexpression of MCL1 as a mechanism of steroid resistance in JDP2-overexpressing cells.
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Affiliation(s)
- Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, England, UK
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Zhaodong Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Riadh Lobbardi
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | | | - Clemens Hug
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Sunniyat Rahman
- Department of Haematology, University College London Cancer Institute, London, England, UK
| | - Theresa E Leon
- Department of Haematology, University College London Cancer Institute, London, England, UK
| | - You-Yi Kuang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Traci Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Evisa Gjini
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alejandro Gutierrez
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
| | - Qin Tang
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Laura Garcia-Perez
- Department of Immunohematology, Leiden University Medical Center, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology, Leiden University Medical Center, Leiden, Netherlands
| | - Lars Anders
- Whitehead Institute for Biomedical Research, Cambridge, MA
| | - Alla Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Yi Zhou
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
| | - Leonard I Zon
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Adele K Fielding
- Department of Haematology, University College London Cancer Institute, London, England, UK
| | - Frank J T Staal
- Department of Immunohematology, Leiden University Medical Center, Leiden, Netherlands
| | - David M Langenau
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA
- Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, Singapore
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
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33
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Osugui L, de Roo JJ, de Oliveira VC, Sodré ACP, Staal FJT, Popi AF. B-1 cells and B-1 cell precursors prompt different responses to Wnt signaling. PLoS One 2018; 13:e0199332. [PMID: 29928002 PMCID: PMC6013157 DOI: 10.1371/journal.pone.0199332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/05/2018] [Indexed: 11/17/2022] Open
Abstract
Recently several studies demonstrated a role for the Wnt pathway in lymphocyte development and self-renewal of hematopoietic stem cells (HSCs). B-1 cells constitute a separate lineage of B lymphocytes, originating during fetal hematopoiesis, expressing lymphoid and myeloid markers and possessing self-renewal ability, similar to early hematopoietic progenitors and HSCs. A plethora of studies have shown an important role for the evolutionary conserved Wnt pathway in the biology of HSCs and T lymphocyte development. Our previous data demonstrated abundant expression of Wnt pathway components by B-1 cells, including Wnt ligands and receptors. Here we report that the canonical Wnt pathway is activated in B-1 cell precursors, but not in mature B-1 cells. However, both B-1 precursors and B-1 cells are able to respond to Wnt ligands in vitro. Canonical Wnt activity promotes proliferation of B-1 cells, while non-canonical Wnt signals induce the expansion of B-1 precursors. Interestingly, using a co-culture system with OP9 cells, Wnt3a stimulus supported the generation of B-1a cells. Taking together, these results indicate that B-1 cells and their progenitors are differentially responsive to Wnt ligands, and that the balance of activation of canonical and non-canonical Wnt signaling may regulate the maintenance and differentiation of different B-1 cell subsets.
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Affiliation(s)
- Lika Osugui
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jolanda J de Roo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Vivian Cristina de Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Clara Pires Sodré
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Ana Flavia Popi
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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34
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Famili F, Brugman MH, Taskesen E, Naber BEA, Fodde R, Staal FJT. High Levels of Canonical Wnt Signaling Lead to Loss of Stemness and Increased Differentiation in Hematopoietic Stem Cells. Stem Cell Reports 2017; 6:652-659. [PMID: 27167156 PMCID: PMC4939829 DOI: 10.1016/j.stemcr.2016.04.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/25/2022] Open
Abstract
Canonical Wnt signaling regulates the self-renewal of most if not all stem cell systems. In the blood system, the role of Wnt signaling has been the subject of much debate but there is consensus that high Wnt signals lead to loss of reconstituting capacity. To better understand this phenomenon, we have taken advantage of a series of hypomorphic mutant Apc alleles resulting in a broad range of Wnt dosages in hematopoietic stem cells (HSCs) and performed whole-genome gene expression analyses. Gene expression profiling and functional studies show that HSCs with APC mutations lead to high Wnt levels, enhanced differentiation, and diminished proliferation but have no effect on apoptosis, collectively leading to loss of stemness. Thus, we provide mechanistic insight into the role of APC mutations and Wnt signaling in HSC biology. As Wnt signals are explored in various in vivo and ex vivo expansion protocols for HSCs, our findings also have clinical ramifications.
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Affiliation(s)
- Farbod Famili
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, the Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, the Netherlands
| | - Erdogan Taskesen
- Department of Clinical Genetics, VU University, 1081 Amsterdam, the Netherlands
| | - Brigitta E A Naber
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, the Netherlands
| | - Riccardo Fodde
- Department of Pathology, Erasmus Medical Center, 3000 Rotterdam, the Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 Leiden, the Netherlands.
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35
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de Roo JJD, Breukel C, Chhatta AR, Linssen MM, Vloemans SA, Salvatori D, Mikkers HMM, Verbeek SJ, Staal FJT. Axin2-mTurquoise2: A novel reporter mouse model for the detection of canonical Wnt signalling. Genesis 2017; 55. [PMID: 28875532 DOI: 10.1002/dvg.23068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 01/08/2023]
Abstract
The canonical Wnt signalling pathway has been implicated in organogenesis and self-renewal of essentially all stem cell systems. In vivo reporter systems are crucial to assess the role of Wnt signalling in the biology and pathology of stem cell systems. We set out to develop a Turquoise (TQ) fluorescent protein based Wnt reporter. We used a CRISPR-Cas9 approach to insert a TQ fluorescent protein encoding gene into the general Wnt target gene Axin2, thereby establishing a Wnt reporter mouse similar to previously generated Wnt reporter mice but with the mTurquoise2 gene instead of E. coli-β-galactosidase (LacZ). The use of mTurquoise2 is especially important in organ systems in which cells need to a be alive for further experimentation such as in vitro activation or transplantation studies. We here report successful generation of Axin2-TQ mice and show that cells from these mice faithfully respond to Wnt signals. High Wnt signals were detected in the intestinal crypts, a classical Wnt signalling site in vivo, and by flow cytometry in the thymus. These mice are an improved tool to further elucidate the role of Wnt signalling in vivo.
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Affiliation(s)
- Jolanda J D de Roo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, The Netherlands
| | - Cor Breukel
- Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Amiet R Chhatta
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, The Netherlands.,Department of Molecular Cell Biology, Leiden University Medical Center, The Netherlands
| | - Margot M Linssen
- Department of Central Laboratory Animal Facility, Leiden University Medical Center, The Netherlands
| | - Sandra A Vloemans
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, The Netherlands
| | - Daniela Salvatori
- Department of Central Laboratory Animal Facility, Leiden University Medical Center, The Netherlands
| | - Harald M M Mikkers
- Department of Molecular Cell Biology, Leiden University Medical Center, The Netherlands
| | - Sjef J Verbeek
- Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, The Netherlands
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36
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Rahman S, Magnussen M, León TE, Farah N, Li Z, Abraham BJ, Alapi KZ, Mitchell RJ, Naughton T, Fielding AK, Pizzey A, Bustraan S, Allen C, Popa T, Pike-Overzet K, Garcia-Perez L, Gale RE, Linch DC, Staal FJT, Young RA, Look AT, Mansour MR. Activation of the LMO2 oncogene through a somatically acquired neomorphic promoter in T-cell acute lymphoblastic leukemia. Blood 2017; 129:3221-3226. [PMID: 28270453 PMCID: PMC5472898 DOI: 10.1182/blood-2016-09-742148] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/22/2017] [Indexed: 01/17/2023] Open
Abstract
Somatic mutations within noncoding genomic regions that aberrantly activate oncogenes have remained poorly characterized. Here we describe recurrent activating intronic mutations of LMO2, a prominent oncogene in T-cell acute lymphoblastic leukemia (T-ALL). Heterozygous mutations were identified in PF-382 and DU.528 T-ALL cell lines in addition to 3.7% of pediatric (6 of 160) and 5.5% of adult (9 of 163) T-ALL patient samples. The majority of indels harbor putative de novo MYB, ETS1, or RUNX1 consensus binding sites. Analysis of 5'-capped RNA transcripts in mutant cell lines identified the usage of an intermediate promoter site, with consequential monoallelic LMO2 overexpression. CRISPR/Cas9-mediated disruption of the mutant allele in PF-382 cells markedly downregulated LMO2 expression, establishing clear causality between the mutation and oncogene dysregulation. Furthermore, the spectrum of CRISPR/Cas9-derived mutations provides important insights into the interconnected contributions of functional transcription factor binding. Finally, these mutations occur in the same intron as retroviral integration sites in gene therapy-induced T-ALL, suggesting that such events occur at preferential sites in the noncoding genome.
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Affiliation(s)
- Sunniyat Rahman
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Michael Magnussen
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Theresa E León
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Nadine Farah
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Zhaodong Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Krisztina Z Alapi
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Rachel J Mitchell
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Tom Naughton
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Adele K Fielding
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Arnold Pizzey
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Sophia Bustraan
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Christopher Allen
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Teodora Popa
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Karin Pike-Overzet
- Department of Immunohematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laura Garcia-Perez
- Department of Immunohematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rosemary E Gale
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - David C Linch
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Frank J T Staal
- Department of Immunohematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA; and
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Children's Hospital, Boston, MA
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
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Canté-Barrett K, Mendes RD, Li Y, Vroegindeweij E, Pike-Overzet K, Wabeke T, Langerak AW, Pieters R, Staal FJT, Meijerink JPP. Loss of CD44 dim Expression from Early Progenitor Cells Marks T-Cell Lineage Commitment in the Human Thymus. Front Immunol 2017; 8:32. [PMID: 28163708 PMCID: PMC5247458 DOI: 10.3389/fimmu.2017.00032] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
Human T-cell development is less well studied than its murine counterpart due to the lack of genetic tools and the difficulty of obtaining cells and tissues. Here, we report the transcriptional landscape of 11 immature, consecutive human T-cell developmental stages. The changes in gene expression of cultured stem cells on OP9-DL1 match those of ex vivo isolated murine and human thymocytes. These analyses led us to define evolutionary conserved gene signatures that represent pre- and post-αβ T-cell commitment stages. We found that loss of dim expression of CD44 marks human T-cell commitment in early CD7+CD5+CD45dim cells, before the acquisition of CD1a surface expression. The CD44−CD1a− post-committed thymocytes have initiated in frame T-cell receptor rearrangements that are accompanied by loss of capacity to differentiate toward myeloid, B- and NK-lineages, unlike uncommitted CD44dimCD1a− thymocytes. Therefore, loss of CD44 represents a previously unrecognized human thymocyte stage that defines the earliest committed T-cell population in the thymus.
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Affiliation(s)
- Kirsten Canté-Barrett
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Rui D Mendes
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital , Rotterdam , Netherlands
| | - Yunlei Li
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital , Rotterdam , Netherlands
| | - Eric Vroegindeweij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands
| | - Tamara Wabeke
- Department of Immunology, Erasmus Medical Center , Rotterdam , Netherlands
| | - Anton W Langerak
- Department of Immunology, Erasmus Medical Center , Rotterdam , Netherlands
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden , Netherlands
| | - Jules P P Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands; Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, Netherlands
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38
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Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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39
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Wiekmeijer AS, Pike-Overzet K, Brugman MH, van Eggermond MCJA, Cordes M, de Haas EFE, Li Y, Oole E, van IJcken WFJ, Egeler RM, Meijerink JP, Staal FJT. Overexpression of LMO2 causes aberrant human T-Cell development in vivo by three potentially distinct cellular mechanisms. Exp Hematol 2016; 44:838-849.e9. [PMID: 27302866 DOI: 10.1016/j.exphem.2016.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/01/2016] [Indexed: 02/08/2023]
Abstract
Overexpression of LMO2 is known to be one of the causes of T-cell acute lymphoblastic leukemia (T-ALL) development; however, the mechanisms behind its oncogenic activity are incompletely understood. LMO2-overexpressing transgenic mouse models suggest an accumulation of immature T-cell progenitors in the thymus as the main preleukemic event. The effects of LMO2 overexpression on human T-cell development in vivo are unknown. Here, we report studies of a humanized mouse model transplanted with LMO2-transduced human hematopoietic stem/progenitor cells. The effects of LMO2 overexpression were confined to the T-cell lineage; however, initially, multipotent cells were transduced. Three effects of LMO2 on human T-cell development were observed: (1) a block at the double-negative/immature single-positive stage, (2) an accumulation of CD4(+)CD8(+) double-positive CD3(-) cells, and (3) an altered CD8/CD4 ratio with enhanced peripheral T lymphocytes. Microarray analysis of sorted double-positive cells overexpressing LMO2 led to the identification of an LMO2 gene set that clustered with human T-ALL patient samples of the described "proliferative" cluster. In this article, we demonstrate previously unrecognized mechanisms by which LMO2 alters human T-cell development in vivo; these mechanisms correlate with human T-ALL leukemogenesis.
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Affiliation(s)
- Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marja C J A van Eggermond
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn Cordes
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Edwin F E de Haas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Yunlei Li
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Edwin Oole
- Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - R Maarten Egeler
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands; Division of Hematology/Oncology, Hospital for Sick Children/University of Toronto, Toronto, Canada
| | - Jules P Meijerink
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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40
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Staal FJT, Chhatta A, Mikkers H. Caught in a Wnt storm: Complexities of Wnt signaling in hematopoiesis. Exp Hematol 2016; 44:451-7. [PMID: 27016274 DOI: 10.1016/j.exphem.2016.03.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/10/2023]
Abstract
The Wnt signaling pathway is an evolutionary conserved pathway that is involved in the development of almost every organ system in the body and provides self-renewal signals for most, if not all, adult stem cell systems. In recent years, this pathway has been studied by various research groups working on hematopoietic stem cells, resulting in contradicting conclusions. Here, we discuss and interpret the results of these studies and propose that Wnt dosage, the source of hematopoietic stem cells, and interactions with other pathways explain these disparate results.
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Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands; Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Amiet Chhatta
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands; Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Harald Mikkers
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands; Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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41
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Abstract
Zebrafish is gaining increased popularity as a model organism to study stem cell biology. It also is widely used as model system to visualize human leukemic stem cells. However, xenotransplantation of primary human stem/progenitor cells has not been described. Here, we use casper pigmentation mutant fish that are transparent crossed to fli-GFP transgenic fish as recipients of red labeled human CD34(+) cells. We have investigated various conditions and protocols with the aim to monitor and visualize the fate of transplanted human CD34(+) cells. We here report successful use of casper mutant zebrafish embryos for the direct monitoring of human hematopoietic stem cell transplantation, differentiation, and trafficking in vivo.
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Affiliation(s)
- Frank J T Staal
- 1 Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, the Netherlands
| | - Herman P Spaink
- 2 Department of Molecular Cell Biology, Institute of Biology Leiden, Leiden University , Leiden, the Netherlands
| | - Willem E Fibbe
- 1 Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, the Netherlands
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42
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Staal FJT, Wiekmeijer AS, Brugman MH, Pike-Overzet K. The functional relationship between hematopoietic stem cells and developing T lymphocytes. Ann N Y Acad Sci 2016; 1370:36-44. [PMID: 26773328 DOI: 10.1111/nyas.12995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In contrast to all other blood and immune cells, T lymphocytes do not develop in the bone marrow (BM), but in the specialized microenvironment provided by the thymus. Similar to the other lineages, however, all T cells arise from multipotent hematopoietic stem cells (HSCs) that reside in the BM. Not all HSCs give rise to T cells; but how many and what kind of developmental checkpoints are located along this intricate differentiation path is the subject of intense research. Traditionally, this process has been studied almost exclusively using mouse cells, but recent advances in immunodeficient mouse models, high-speed cell sorting, lentiviral transduction protocols, and deep sequencing techniques have allowed these questions to be addressed using human cells. Here we review the process of thymic seeding by BM-derived cells and T cell commitment in humans, discussing recent insights into the clonal composition of the thymus and the definition of developmental checkpoints, on the basis of insights from human severe combined immunodeficiency patients.
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Affiliation(s)
- Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
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43
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Famili F, Naber BAE, Vloemans S, de Haas EFE, Tiemessen MM, Staal FJT. Discrete roles of canonical and non-canonical Wnt signaling in hematopoiesis and lymphopoiesis. Cell Death Dis 2015; 6:e1981. [PMID: 26583322 PMCID: PMC4670932 DOI: 10.1038/cddis.2015.326] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/30/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022]
Abstract
The mechanisms that regulate proliferation, fate decisions and differentiation of hematopoietic stem cells (HSC) and thymic stem cells are highly complex. Several signaling pathways including Wnt signaling have important roles during these processes. Both canonical and non-canonical Wnt signaling are important in normal and malignant hematopoiesis and lymphoid development, yet their precise roles are controversial. In a side-by-side comparison, we investigated the roles of the canonical and non-canonical Wnt pathway in hematopoiesis and thymopoiesis. As complete loss-of-function models for non-canonical Wnt signaling are not yet available and highly complex for canonical Wnt signaling, we decided to use a gain-of-function approach. To this end, Wnt3a and Wn5a, two well-known prototypical canonical and non-canonical Wnt ligands were produced in hematopoiesis supporting stromal assays. High levels of Wnt3a signaling blocked T-cell development at early stages, whereas intermediate levels accelerated T-cell development. In contrast, Wnt5a signaling prompted apoptosis in developing thymocytes, without affecting differentiation at a particular stage. To explore the role of Wnt3a and Wnt5a in vivo, we transduced HSCs isolated from fetal liver, transduced with Wnt3a and Wnt5a vectors, and performed reconstitution assays in irradiated C57Bl/6 mice. Wnt3a overexpression led to increased lymphopoiesis, whereas Wnt5a augments myelopoiesis in the bone marrow (BM) and spleen. Thus, the canonical and non-canonical Wnt signaling have discrete roles in hematopoiesis and thymopoiesis, and understanding their right dose of action is crucial for prospective translational applications.
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Affiliation(s)
- F Famili
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | - B A E Naber
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | - S Vloemans
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | - E F E de Haas
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | - M M Tiemessen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | - F J T Staal
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
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44
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Redeker A, Welten SPM, Baert MRM, Vloemans SA, Tiemessen MM, Staal FJT, Arens R. The Quantity of Autocrine IL-2 Governs the Expansion Potential of CD8+ T Cells. J Immunol 2015; 195:4792-801. [PMID: 26453748 DOI: 10.4049/jimmunol.1501083] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/11/2015] [Indexed: 01/05/2023]
Abstract
Adequate responsiveness of CD8(+) T cell populations is of utmost importance for the efficacy of many vaccines and immunotherapeutic strategies against intracellular pathogens and cancer. In this study, we show in mouse models that the relative number of IL-2-producing cells within Ag-specific CD8(+) T cell populations predicts the population expansion capacity upon challenge. We further demonstrate that IL-2 producers constitute the best responding subset. Notably, we show that elevated production of IL-2 by CD8(+) T cells results in concomitant improved population expansion capacity and immunity. The amount of IL-2 produced on a per-cell basis essentially connects directly to the superior CD8(+) T cell population expansion. Together, our findings identified that autocrine IL-2 production operates in a dose-dependent fashion to facilitate the expansion potential of Ag-specific CD8(+) T cell populations, which may instigate ways to augment therapies depending on fit CD8(+) T cells.
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Affiliation(s)
- Anke Redeker
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Suzanne P M Welten
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Miranda R M Baert
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Sandra A Vloemans
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Machteld M Tiemessen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
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45
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Wiekmeijer AS, Pike-Overzet K, IJspeert H, Brugman MH, Wolvers-Tettero ILM, Lankester AC, Bredius RGM, van Dongen JJM, Fibbe WE, Langerak AW, van der Burg M, Staal FJT. Identification of checkpoints in human T-cell development using severe combined immunodeficiency stem cells. J Allergy Clin Immunol 2015; 137:517-526.e3. [PMID: 26441229 DOI: 10.1016/j.jaci.2015.08.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) represents congenital disorders characterized by a deficiency of T cells caused by arrested development in the thymus. Yet the nature of these developmental blocks has remained elusive because of the difficulty of taking thymic biopsy specimens from affected children. OBJECTIVE We sought to identify the stages of arrest in human T-cell development caused by various major types of SCID. METHODS We performed transplantation of SCID CD34(+) bone marrow stem/progenitor cells into an optimized NSG xenograft mouse model, followed by detailed phenotypic and molecular characterization using flow cytometry, immunoglobulin and T-cell receptor spectratyping, and deep sequencing of immunoglobulin heavy chain (IGH) and T-cell receptor δ (TRD) loci. RESULTS Arrests in T-cell development caused by mutations in IL-7 receptor α (IL7RA) and IL-2 receptor γ (IL2RG) were observed at the most immature thymocytes much earlier than expected based on gene expression profiling of human thymocyte subsets and studies with corresponding mouse mutants. T-cell receptor rearrangements were functionally required at the CD4(-)CD8(-)CD7(+)CD5(+) stage given the developmental block and extent of rearrangements in mice transplanted with Artemis-SCID cells. The xenograft model used is not informative for adenosine deaminase-SCID, whereas hypomorphic mutations lead to less severe arrests in development. CONCLUSION Transplanting CD34(+) stem cells from patients with SCID into a xenograft mouse model provides previously unattainable insight into human T-cell development and functionally identifies the arrest in thymic development caused by several SCID mutations.
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Affiliation(s)
- Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Arjan C Lankester
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robbert G M Bredius
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Willem E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.
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46
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Taskesen E, Staal FJT, Reinders MJT. An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in acute myeloid leukemia. BMC Bioinformatics 2015; 16 Suppl 4:S4. [PMID: 25734857 PMCID: PMC4347618 DOI: 10.1186/1471-2105-16-s4-s4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number of genes of the WNT pathway are analyzed by using either gene expression or DNA-methylation profiles for the identification of prognostic markers and potential candidate targets for drug therapy. It is known that mRNA expression is controlled by DNA-methylation and that specific patterns can infer the ability to differentiate biological differences, thus a combined analysis using all WNT annotated genes could provide more insight in the WNT signaling. Approach We created a computational approach that integrates gene expression and DNA promoter methylation profiles. The approach represents the continuous gene expression and promoter methylation profiles with nine discrete mutually exclusive scenarios. The scenario representation allows for a refinement of patient groups by a more powerful statistical analysis, and the construction of a co-expression network. We focused on 268 WNT annotated signaling genes that are derived from the molecular signature database. Results Using the scenarios we identified seven prognostic markers for overall survival and event-free survival. Three genes are novel prognostic markers; two with favorable outcome (PSMD2, PPARD) and one with unfavorable outcome (XPNPEP). The remaining four genes (LEF1, SFRP2, RUNX1, and AXIN2) were previously identified but we could refine the patient groups. Three AML risk groups were further analyzed and the co-expression network showed that only the good risk group harbors frequent promoter hypermethylation and significantly correlated interactions with proteasome family members. Conclusion Our results provide novel insights in WNT signaling in AML, we discovered new and previously identified prognostic markers and a refinement of the patient groups.
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47
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Tiemessen MM, Baert MRM, Kok L, van Eggermond MCJA, van den Elsen PJ, Arens R, Staal FJT. T Cell factor 1 represses CD8+ effector T cell formation and function. J Immunol 2014; 193:5480-7. [PMID: 25355919 DOI: 10.4049/jimmunol.1303417] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Wnt-responsive transcription factor T cell factor 1 (Tcf1) is well known for its role in thymic T cell development and the formation of memory CD8(+) T cells. However, its role in the initial phases of CD8(+) T effector cell formation has remained unexplored. We report that high levels of Wnt signaling and Tcf1 are operational in naive and memory CD8(+) T cells, whereas Wnt signaling and Tcf1 were low in effector CD8(+) T cells. CD8(+) T cells deficient in Tcf1 produce IFN-γ more rapidly, coinciding with increased demethylation of the IFN-γ enhancer and higher expression of the transcription factors Tbet and Blimp1. Moreover, virus-specific Tcf1(-/-) CD8(+) T cells show accelerated expansion in acute infection, which is associated with increased IFN-γ and TNF production and lower viral load. Genetic complementation experiments with various Tcf1 isoforms indicate that Tcf1 dosage and protein stability are critical in suppressing IFN-γ production. Isoforms lacking the β-catenin binding domain are equally effective in inhibiting CD8(+) effector T cell formation. Thus, Tcf1 functions as a repressor of CD8(+) effector T cell formation in a β-catenin/Wnt-independent manner.
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Affiliation(s)
- Machteld M Tiemessen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Miranda R M Baert
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Lianne Kok
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Marja C J A van Eggermond
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Peter J van den Elsen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC/Leiden, the Netherlands
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Beisner J, Teltschik Z, Ostaff MJ, Tiemessen MM, Staal FJT, Wang G, Gersemann M, Perminow G, Vatn MH, Schwab M, Stange EF, Wehkamp J. TCF-1-mediated Wnt signaling regulates Paneth cell innate immune defense effectors HD-5 and -6: implications for Crohn's disease. Am J Physiol Gastrointest Liver Physiol 2014; 307:G487-98. [PMID: 24994854 DOI: 10.1152/ajpgi.00347.2013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Wnt signaling regulates small intestinal stem cell maintenance and Paneth cell differentiation. In patients with ileal Crohn's disease (CD), a decrease of Paneth cell α-defensins has been observed that is partially caused by impaired TCF-4 and LRP6 function. Here we show reduced expression of the Wnt signaling effector TCF-1 (also known as TCF-7) in patients with ileal CD. Reporter gene assays and in vitro promoter binding analysis revealed that TCF-1 activates α-defensin HD-5 and HD-6 transcription in cooperation with β-catenin and that activation is mediated by three distinct TCF binding sites. EMSA analysis showed binding of TCF-1 to the respective motifs. In ileal CD patients, TCF-1 mRNA expression levels were significantly reduced. Moreover, we found specifically reduced expression of active TCF-1 mRNA isoforms. Tcf-1 knockout mice exhibited reduced cryptdin expression in the jejunum, which was not consistently seen at other small intestinal locations. Our data provide evidence that TCF-1-mediated Wnt signaling is disturbed in small intestinal CD, which might contribute to the observed barrier dysfunction in the disease.
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Affiliation(s)
- Julia Beisner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Zora Teltschik
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Maureen J Ostaff
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Machteld M Tiemessen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Guoxing Wang
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Michael Gersemann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; Department of Pediatrics, Akershus University Hospital, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Gori Perminow
- Department of Pediatrics, Akershus University Hospital, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Morten H Vatn
- University of Oslo, Epigen, Faculty Division Akershus University Hospital and Medical Clinic, Gastroenterology, Oslo University Hospital, Rikshospitalet, Oslo, Norway; and
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany; Department of Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, University Hospital, Tuebingen, Germany
| | - Eduard F Stange
- Department of Gastroenterology, Robert Bosch Hospital, Stuttgart, Germany
| | - Jan Wehkamp
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany; Department of Gastroenterology, Robert Bosch Hospital, Stuttgart, Germany;
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Wiekmeijer AS, Pike-Overzet K, Brugman MH, Salvatori DCF, Egeler RM, Bredius RGM, Fibbe WE, Staal FJT. Sustained Engraftment of Cryopreserved Human Bone Marrow CD34(+) Cells in Young Adult NSG Mice. Biores Open Access 2014; 3:110-6. [PMID: 24940562 PMCID: PMC4048975 DOI: 10.1089/biores.2014.0008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are defined by their ability to repopulate the bone marrow of myeloablative conditioned and/or (lethally) irradiated recipients. To study the repopulating potential of human HSCs, murine models have been developed that rely on the use of immunodeficient mice that allow engraftment of human cells. The NSG xenograft model has emerged as the current standard for this purpose allowing for engraftment and study of human T cells. Here, we describe adaptations to the original NSG xenograft model that can be readily implemented. These adaptations encompass use of adult mice instead of newborns and a short ex vivo culture. This protocol results in robust and reproducible high levels of lympho-myeloid engraftment. Immunization of recipient mice with relevant antigen resulted in specific antibody formation, showing that both T cells and B cells were functional. In addition, bone marrow cells from primary recipients exhibited repopulating ability following transplantation into secondary recipients. Similar results were obtained with cryopreserved human bone marrow samples, thus circumventing the need for fresh cells and allowing the use of patient derived bio-bank samples. Our findings have implications for use of this model in fundamental stem cell research, immunological studies in vivo and preclinical evaluations for HSC transplantation, expansion, and genetic modification.
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Affiliation(s)
- Anna-Sophia Wiekmeijer
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, The Netherlands
| | - Karin Pike-Overzet
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, The Netherlands
| | - Martijn H Brugman
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, The Netherlands
| | - Daniela C F Salvatori
- Central Laboratory Animal Facility, Leiden University Medical Center , Leiden, The Netherlands
| | - R Maarten Egeler
- Department of Pediatrics, Leiden University Medical Center , Leiden, The Netherlands . ; Division of Hematology/Oncology, Hospital for Sick Children/University of Toronto , Toronto, Canada
| | - Robbert G M Bredius
- Department of Pediatrics, Leiden University Medical Center , Leiden, The Netherlands
| | - Willem E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, The Netherlands
| | - Frank J T Staal
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center , Leiden, The Netherlands
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50
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van der Weerd K, van Hagen PM, Schrijver B, Heuvelmans SJWM, Hofland LJ, Swagemakers SMA, Bogers AJJC, Dik WA, Visser TJ, van Dongen JJM, van der Lelij AJ, Staal FJT. Thyrotropin acts as a T-cell developmental factor in mice and humans. Thyroid 2014; 24:1051-61. [PMID: 24635198 DOI: 10.1089/thy.2013.0396] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Using gene expression profiling, we detected differential thyrotropin receptor (TSH-R) expression during human T-cell development in the thymus. This expression pattern indicated a potential role for the TSH-R within the thymus, independent of its function in the thyroid gland. Here, we demonstrate that TSH-R expression is thymus-specific within the immune system. TSH was able to bind and activate the TSH-R present on thymocytes, thereby activating calcium signaling and cyclic adenosine monophosphate signaling pathways. Mice lacking functional TSH-R expression (hyt/hyt mice) were shown to have lower frequencies of DP and SP thymocytes compared to their heterozygous littermates. Moreover, addition of TSH to co-cultures of human thymocytes enhanced T-cell development. Thus, TSH acts as a previously unrecognized growth factor for developing T cells, with potential clinical use to enhance thymic output and thereby the functional T-cell repertoire in the periphery. The direct effects of TSH on thymocytes may also explain the thus far enigmatic thymic hyperplasia in Graves' disease.
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Affiliation(s)
- Kim van der Weerd
- 1 Department of Immunology, Erasmus University Medical Center , Rotterdam, The Netherlands
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