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Ni Y, You G, Gong Y, Su X, Du Y, Wang X, Ding X, Fu Q, Zhang M, Cheng T, Lan Y, Liu B, Liu C. Human yolk sac-derived innate lymphoid-biased multipotent progenitors emerge prior to hematopoietic stem cell formation. Dev Cell 2024:S1534-5807(24)00388-5. [PMID: 38996461 DOI: 10.1016/j.devcel.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024]
Abstract
Hematopoietic stem cell (HSC)-independent lymphopoiesis has been elucidated in murine embryos. However, our understanding regarding human embryonic counterparts remains limited. Here, we demonstrated the presence of human yolk sac-derived lymphoid-biased progenitors (YSLPs) expressing CD34, IL7R, LTB, and IRF8 at Carnegie stage 10, much earlier than the first HSC emergence. The number and lymphopoietic potential of these progenitors were both significantly higher in the yolk sac than the embryo proper at this early stage. Importantly, single-cell/bulk culture and CITE-seq have elucidated the tendency of YSLP to differentiate into innate lymphoid cells and dendritic cells. Notably, lymphoid progenitors in fetal liver before and after HSC seeding displayed distinct transcriptional features, with the former closely resembling those of YSLPs. Overall, our data identified the origin, potential, and migratory dynamics of innate lymphoid-biased multipotent progenitors in human yolk sac before HSC emergence, providing insights for understanding the stepwise establishment of innate immune system in humans.
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Affiliation(s)
- Yanli Ni
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Guoju You
- School of Medicine, Tsinghua University, Beijing 100080, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Xiaoyu Su
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang 212013, China
| | - Yuan Du
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Xiaoshuang Wang
- Department of Biochemistry and Molecular Biology, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Xiaochen Ding
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Qingfeng Fu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Man Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China
| | - Tao Cheng
- Department of Biochemistry and Molecular Biology, State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Yu Lan
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing 100071, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650031, China; Department of Physiology and Pathophysiology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
| | - Chen Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
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2
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Wang Y, Riaz F, Wang W, Pu J, Liang Y, Wu Z, Pan S, Song J, Yang L, Zhang Y, Wu H, Han F, Tang J, Wang X. Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome. Front Immunol 2024; 15:1289492. [PMID: 38510251 PMCID: PMC10950951 DOI: 10.3389/fimmu.2024.1289492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.
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Affiliation(s)
- Yanqing Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Farooq Riaz
- Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Wei Wang
- Department of Radiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jincheng Pu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanyuan Liang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhenzhen Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengnan Pan
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiamin Song
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lufei Yang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Youwei Zhang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huihong Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Han
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianping Tang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuan Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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3
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Popravko A, Mackintosh L, Dzierzak E. A life-time of hematopoietic cell function: ascent, stability, and decline. FEBS Lett 2024. [PMID: 38439688 DOI: 10.1002/1873-3468.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Aging is a set of complex processes that occur temporally and continuously. It is generally a unidirectional progression of cellular and molecular changes occurring during the life stages of cells, tissues and ultimately the whole organism. In vertebrate organisms, this begins at conception from the first steps in blastocyst formation, gastrulation, germ layer differentiation, and organogenesis to a continuum of embryonic, fetal, adolescent, adult, and geriatric stages. Tales of the "fountain of youth" and songs of being "forever young" are dominant ideas informing us that growing old is something science should strive to counteract. Here, we discuss the normal life stages of the blood system, particularly the historical recognition of its importance in the early growth stages of vertebrates, and what this means with respect to progressive gain and loss of hematopoietic function in the adult.
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Affiliation(s)
- Anna Popravko
- Institute for Regeneration and Repair, University of Edinburgh, UK
| | - Lorna Mackintosh
- Institute for Regeneration and Repair, University of Edinburgh, UK
| | - Elaine Dzierzak
- Institute for Regeneration and Repair, University of Edinburgh, UK
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4
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Alhaj Hussen K, Chabaane E, Nelson E, Lekiashvili S, Diop S, Keita S, Evrard B, Lardenois A, Delord M, Verhoeyen E, Cornils K, Kasraian Z, Macintyre EA, Cumano A, Garrick D, Goodhardt M, Andrieu GP, Asnafi V, Chalmel F, Canque B. Multimodal cartography of human lymphopoiesis reveals B and T/NK/ILC lineages are subjected to differential regulation. iScience 2023; 26:107890. [PMID: 37766969 PMCID: PMC10520540 DOI: 10.1016/j.isci.2023.107890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The developmental cartography of human lymphopoiesis remains incompletely understood. Here, we establish a multimodal map demonstrating that lymphoid specification follows independent direct or stepwise hierarchic routes converging toward the emergence of newly characterized CD117lo multi-lymphoid progenitors (MLPs) that undergo a proliferation arrest before entering the CD127- (NK/ILC/T) or CD127+ (B) lymphoid pathways. While the differentiation of CD127- early lymphoid progenitors is mainly driven by Flt3 signaling, emergence of their CD127+ counterparts is regulated cell-intrinsically and depends exclusively on the divisional history of their upstream precursors, including hematopoietic stem cells. Further, transcriptional mapping of differentiation trajectories reveals that whereas myeloid granulomonocytic lineages follow continuous differentiation pathways, lymphoid trajectories are intrinsically discontinuous and characterized by sequential waves of cell proliferation allowing pre-commitment amplification of lymphoid progenitor pools. Besides identifying new lymphoid specification pathways and regulatory checkpoints, our results demonstrate that NK/ILC/T and B lineages are under fundamentally distinct modes of regulation. (149 words).
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Affiliation(s)
- Kutaiba Alhaj Hussen
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Service de Biochimie, Université de Paris Saclay, Hôpital Paul Brousse, AP-HP, Villejuif, Paris, France
| | - Emna Chabaane
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Elisabeth Nelson
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Shalva Lekiashvili
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Samuel Diop
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Seydou Keita
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Bertrand Evrard
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Aurélie Lardenois
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Marc Delord
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Els Verhoeyen
- CIRI, International Center for Infectiology Research, Université de Lyon, INSERM U1111, Lyon, France
- Centre Mediterranéen de Médecine Moléculaire (C3M), INSERM U1065, Nice, France
| | - Kerstin Cornils
- Division of Pediatric Stem Cell Transplantation and Immunology, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf and Research Institute Children’s Cancer Center, Hamburg, Germany
| | - Zeinab Kasraian
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Elizabeth A. Macintyre
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
| | - David Garrick
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Michele Goodhardt
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Guillaume P. Andrieu
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Frederic Chalmel
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bruno Canque
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
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5
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MacNabb BW, Rothenberg EV. Speed and navigation control of thymocyte development by the fetal T-cell gene regulatory network. Immunol Rev 2023; 315:171-196. [PMID: 36722494 PMCID: PMC10771342 DOI: 10.1111/imr.13190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
T-cell differentiation is a tightly regulated developmental program governed by interactions between transcription factors (TFs) and chromatin landscapes and affected by signals received from the thymic stroma. This process is marked by a series of checkpoints: T-lineage commitment, T-cell receptor (TCR)β selection, and positive and negative selection. Dynamically changing combinations of TFs drive differentiation along the T-lineage trajectory, through mechanisms that have been most extensively dissected in adult mouse T-lineage cells. However, fetal T-cell development differs from adult in ways that suggest that these TF mechanisms are not fully deterministic. The first wave of fetal T-cell differentiation occurs during a unique developmental window during thymic morphogenesis, shows more rapid kinetics of differentiation with fewer rounds of cell division, and gives rise to unique populations of innate lymphoid cells (ILCs) and invariant γδT cells that are not generated in the adult thymus. As the characteristic kinetics and progeny biases are cell-intrinsic properties of thymic progenitors, the differences could be based on distinct TF network circuitry within the progenitors themselves. Here, we review recent single-cell transcriptome data that illuminate the TF networks involved in T-cell differentiation in the fetal and adult mouse thymus.
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Affiliation(s)
- Brendan W MacNabb
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California, USA
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6
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Bomfim BCM, Azevedo-Silva J, Caminha G, Santos JPR, Pelajo-Machado M, de Paula Ayres-Silva J. Lectin-based carbohydrate profile of megakaryocytes in murine fetal liver during development. Sci Rep 2023; 13:6729. [PMID: 37185919 PMCID: PMC10130079 DOI: 10.1038/s41598-023-32863-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
Hematopoiesis is the process by which blood cells are generated. During embryonic development, these cells migrate through different organs until they reach the bone marrow, their definitive place in adulthood. Around E10.5, the fetal liver starts budding from the gut, where first hematopoietic cells arrive and expand. Hematopoietic cell migration occurs through cytokine stimulation, receptor expression, and glycosylation patterns on the cell surface. In addition, carbohydrates can modulate different cell activation states. For this reason, we aimed to characterize and quantify fetal megakaryocytic cells in mouse fetal liver according to their glycan residues at different gestational ages through lectins. Mouse fetuses between E11.5 and E18.5 were formalin-fixed and, paraffin-embedded, for immunofluorescence analysis using confocal microscopy. The results showed that the following sugar residues were expressed in proliferating and differentiating megakaryocytes in the fetal liver at different gestational ages: α-mannose, α-glucose, galactose, GlcNAc, and two types of complex oligosaccharides. Megakaryocytes also showed three proliferation waves during liver development at E12.5, E14.5, and E18.5. Additionally, the lectins that exhibited high and specific pattern intensities at liver capsules and vessels were shown to be a less time-consuming and robust alternative alternative to conventional antibodies for displaying liver structures such as capsules and vessels, as well as for megakaryocyte differentiation in the fetal liver.
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Affiliation(s)
| | - Jessyca Azevedo-Silva
- Laboratory of Pathology, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Giulia Caminha
- Laboratory of Pathology, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | | | - Marcelo Pelajo-Machado
- Laboratory of Pathology, Oswaldo Cruz Institute - Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
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7
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Liu C, Omilusik K, Toma C, Kurd NS, Chang JT, Goldrath AW, Wang W. Systems-level identification of key transcription factors in immune cell specification. PLoS Comput Biol 2022; 18:e1010116. [PMID: 36156073 PMCID: PMC9536753 DOI: 10.1371/journal.pcbi.1010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/06/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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8
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The immune landscape of human thymic epithelial tumors. Nat Commun 2022; 13:5463. [PMID: 36115836 PMCID: PMC9482639 DOI: 10.1038/s41467-022-33170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Human thymic epithelial tumors (TET) are common malignancies in the anterior mediastinum with limited biological understanding. Here we show, by single cell analysis of the immune landscape, that the developmental pattern of intra-tumoral T-cells identify three types within TETs. We characterize the developmental alterations and TCR repertoires of tumor-infiltrating T cells in the context of the distinguishing epithelial tumor cell types. We demonstrate that a subset of tumor cells, featuring medullary thymic epithelial cell (TEC) phenotype and marked by KRT14/GNB3 expression, accumulate in type 1 TETs, while T-cell positive selection is inhibited. Type 2 TETs are dominated by CCL25+ cortical TEC-like cells that appear to promote T-cell positive selection. Interestingly, the CHI3L1+ medullary TEC-like cells that are the characteristic feature of type 3 TETs don’t seem to support T-cell development, however, they may induce a tissue-resident CD8+ T cell response. In summary, our work suggests that the molecular subtype of epithelial tumour cells in TETs determine their tumour immune microenvironment, thus GNB3 and CHI3L1 might predict the immunological behavior and hence prognosis of these tumours. Thymic epithelial tumours represent a heterogenous group of malignancies with varied immune cell infiltration and prognosis. Here authors systematically analyze the phenotypes of both epithelial and immune cells that form these tumours, and identify three major subtypes with different T cell involvement that might affect prognosis.
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9
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Murine fetal bone marrow does not support functional hematopoietic stem and progenitor cells until birth. Nat Commun 2022; 13:5403. [PMID: 36109585 PMCID: PMC9477881 DOI: 10.1038/s41467-022-33092-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
While adult bone marrow (BM) hematopoietic stem and progenitor cells (HSPCs) and their extrinsic regulation is well studied, little is known about the composition, function, and extrinsic regulation of the first HSPCs to enter the BM during development. Here, we functionally interrogate murine BM HSPCs from E15.5 through P0. Our work reveals that fetal BM HSPCs are present by E15.5, but distinct from the HSPC pool seen in fetal liver, both phenotypically and functionally, until near birth. We also generate a transcriptional atlas of perinatal BM HSPCs and the BM niche in mice across ontogeny, revealing that fetal BM lacks HSPCs with robust intrinsic stem cell programs, as well as niche cells supportive of HSPCs. In contrast, stem cell programs are preserved in neonatal BM HSPCs, which reside in a niche expressing HSC supportive factors distinct from those seen in adults. Collectively, our results provide important insights into the factors shaping hematopoiesis during this understudied window of hematopoietic development. Relatively little is known about the first hematopoietic stem and progenitor cells to arrive in the fetal bone marrow. Here they characterize the frequency, function, and molecular identity of fetal BM HSPCs and their bone marrow niche, and show that most BM HSPCs have little hematopoietic function until birth.
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10
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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11
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Abstract
A high diversity of αβ T cell receptors (TCRs), capable of recognizing virtually any pathogen but also self-antigens, is generated during T cell development in the thymus. Nevertheless, a strict developmental program supports the selection of a self-tolerant T cell repertoire capable of responding to foreign antigens. The steps of T cell selection are controlled by cortical and medullary stromal niches, mainly composed of thymic epithelial cells and dendritic cells. The integration of important cues provided by these specialized niches, including (a) the TCR signal strength induced by the recognition of self-peptide-MHC complexes, (b) costimulatory signals, and (c) cytokine signals, critically controls T cell repertoire selection. This review discusses our current understanding of the signals that coordinate positive selection, negative selection, and agonist selection of Foxp3+ regulatory T cells. It also highlights recent advances that have unraveled the functional diversity of thymic antigen-presenting cell subsets implicated in T cell selection.
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Affiliation(s)
- Magali Irla
- Centre d'Immunologie de Marseille-Luminy (CIML), CNRS, INSERM, Aix-Marseille Université, Marseille, France;
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12
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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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13
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Liu C, Gong Y, Zhang H, Yang H, Zeng Y, Bian Z, Xin Q, Bai Z, Zhang M, He J, Yan J, Zhou J, Li Z, Ni Y, Wen A, Lan Y, Hu H, Liu B. Delineating spatiotemporal and hierarchical development of human fetal innate lymphoid cells. Cell Res 2021; 31:1106-1122. [PMID: 34239074 PMCID: PMC8486758 DOI: 10.1038/s41422-021-00529-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Whereas the critical roles of innate lymphoid cells (ILCs) in adult are increasingly appreciated, their developmental hierarchy in early human fetus remains largely elusive. In this study, we sorted human hematopoietic stem/progenitor cells, lymphoid progenitors, putative ILC progenitor/precursors and mature ILCs in the fetal hematopoietic, lymphoid and non-lymphoid tissues, from 8 to 12 post-conception weeks, for single-cell RNA-sequencing, followed by computational analysis and functional validation at bulk and single-cell levels. We delineated the early phase of ILC lineage commitment from hematopoietic stem/progenitor cells, which mainly occurred in fetal liver and intestine. We further unveiled interleukin-3 receptor as a surface marker for the lymphoid progenitors in fetal liver with T, B, ILC and myeloid potentials, while IL-3RA- lymphoid progenitors were predominantly B-lineage committed. Notably, we determined the heterogeneity and tissue distribution of each ILC subpopulation, revealing the proliferating characteristics shared by the precursors of each ILC subtype. Additionally, a novel unconventional ILC2 subpopulation (CRTH2- CCR9+ ILC2) was identified in fetal thymus. Taken together, our study illuminates the precise cellular and molecular features underlying the stepwise formation of human fetal ILC hierarchy with remarkable spatiotemporal heterogeneity.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Han Zhang
- Department of Blood Transfusion, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhilei Bian
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Qian Xin
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Man Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jing Yan
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Aiqing Wen
- Department of Blood Transfusion, Daping Hospital, Army Military Medical University, Chongqing, China.
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Hongbo Hu
- Center for Immunology and Hematology, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University. Collaboration and Innovation Center for Biotherapy, Chengdu, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
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14
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Shin SB, McNagny KM. ILC-You in the Thymus: A Fresh Look at Innate Lymphoid Cell Development. Front Immunol 2021; 12:681110. [PMID: 34025680 PMCID: PMC8136430 DOI: 10.3389/fimmu.2021.681110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/20/2021] [Indexed: 01/20/2023] Open
Abstract
The discovery of innate lymphoid cells (ILCs) has revolutionized our understanding of innate immunity and immune cell interactions at epithelial barrier sites. Their presence and maintenance are critical for modulating immune homeostasis, responding to injury or infection, and repairing damaged tissues. To date, ILCs have been defined by a set of transcription factors, surface antigens and cytokines, and their functions resemble those of three major classes of helper T cell subsets, Th1, Th2 and Th17. Despite this, the lack of antigen-specific surface receptors and the notion that ILCs can develop in the absence of the thymic niche have clearly set them apart from the T-cell lineage and promulgated a dogma that ILCs develop directly from progenitors in the bone marrow. Interestingly however, emerging studies have challenged the BM-centric view of adult ILC development and suggest that ILCs could arise neonatally from developing T cell progenitors. In this review, we discuss ILC development in parallel to T-cell development and summarize key findings that support a T-cell-centric view of ILC ontogeny.
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Affiliation(s)
- Samuel B Shin
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Kelly M McNagny
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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15
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Rothenberg EV. Single-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human. Exp Hematol 2021; 95:1-12. [PMID: 33454362 PMCID: PMC8018899 DOI: 10.1016/j.exphem.2020.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023]
Abstract
T-Cell development is a major branch of lymphoid development and a key output of hematopoiesis, especially in early life, but the molecular requirements for T-cell potential have remained obscure. Considerable advances have now been made toward solving this problem through single-cell transcriptome studies, interfaced with in vitro differentiation assays that monitor potential efficiently at the single-cell level. This review focuses on a series of recent reports studying mouse and human early T-cell precursors, both in the developing fetus and in stringently purified postnatal samples of intrathymic and prethymic T-lineage precursors. Cross-comparison of results reveals a robustly conserved core program in mouse and human, but with some informative and provocative variations between species and between ontogenic states. Repeated findings are the multipotent progenitor regulatory signature of thymus-seeding cells and the proximity of the T-cell program to dendritic cell programs, especially to plasmacytoid dendritic cells in humans.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA.
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16
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Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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17
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Elsaid R, Meunier S, Burlen-Defranoux O, Soares-da-Silva F, Perchet T, Iturri L, Freyer L, Vieira P, Pereira P, Golub R, Bandeira A, Perdiguero EG, Cumano A. A wave of bipotent T/ILC-restricted progenitors shapes the embryonic thymus microenvironment in a time-dependent manner. Blood 2021; 137:1024-1036. [PMID: 33025012 PMCID: PMC8065239 DOI: 10.1182/blood.2020006779] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
During embryonic development, multiple waves of hematopoietic progenitors with distinct lineage potential are differentially regulated in time and space. Two different waves of thymic progenitors colonize the fetal thymus where they contribute to thymic organogenesis and homeostasis. The origin, the lineage differentiation potential of the first wave, and their relative contribution in shaping the thymus architecture, remained, however, unclear. Here, we show that the first wave of thymic progenitors comprises a unique population of bipotent T and innatel lymphoid cells (T/ILC), generating a lymphoid tissue inducer cells (LTi's), in addition to invariant Vγ5+ T cells. Transcriptional analysis revealed that innate lymphoid gene signatures and, more precisely, the LTi-associated transcripts were expressed in the first, but not in the second, wave of thymic progenitors. Depletion of early thymic progenitors in a temporally controlled manner showed that the progeny of the first wave is indispensable for the differentiation of autoimmune regulator-expressing medullary thymic epithelial cells (mTECs). We further show that these progenitors are of strict hematopoietic stem cell origin, despite the overlap between lymphopoiesis initiation and the transient expression of lymphoid-associated transcripts in yolk sac (YS) erythromyeloid-restricted precursors. Our work highlights the relevance of the developmental timing on the emergence of different lymphoid subsets, required for the establishment of a functionally diverse immune system.
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Affiliation(s)
- Ramy Elsaid
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sylvain Meunier
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Odile Burlen-Defranoux
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Francisca Soares-da-Silva
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Instituto de Investigação e Inovação em Saúde (I3S) and
- Instituto Nacional de Engenharia Biomédica (INEB), Universidade do Porto, Porto, Portugal
| | - Thibaut Perchet
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Lorea Iturri
- Macrophages and Endothelial Cells Group, Development and Stem Cell Biology Department, Institut Pasteur, Paris, France; and
- Cellule Pasteur, University Pierre et Marie Curie (UPMC), Paris, France
| | - Laina Freyer
- Macrophages and Endothelial Cells Group, Development and Stem Cell Biology Department, Institut Pasteur, Paris, France; and
| | - Paulo Vieira
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Pablo Pereira
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Rachel Golub
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Antonio Bandeira
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Elisa Gomez Perdiguero
- Macrophages and Endothelial Cells Group, Development and Stem Cell Biology Department, Institut Pasteur, Paris, France; and
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
- Unité 1223, INSERM, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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18
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Deng Y, Chen H, Zeng Y, Wang K, Zhang H, Hu H. Leaving no one behind: tracing every human thymocyte by single-cell RNA-sequencing. Semin Immunopathol 2021; 43:29-43. [PMID: 33449155 DOI: 10.1007/s00281-020-00834-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/22/2020] [Indexed: 02/05/2023]
Abstract
The thymus is the primary organ for T-cell development, providing an essential microenvironment consisting of the appropriate cytokine milieu and specialized stromal cells. Thymus-seeding progenitors from circulation immigrate into the thymus and undergo the stepwise T-cell specification, commitment, and selection processes. The transcriptional factors, epigenetic regulators, and signaling pathways involved in the T-cell development have been intensively studied using mouse models. Despite our growing knowledge of T-cell development, major questions remain unanswered regarding the ontogeny and early events of T-cell development at the fetal stage, especially in humans. The recently developed single-cell RNA-sequencing technique provides an ideal tool to investigate the heterogeneity of T-cell precursors and the molecular mechanisms underlying the divergent fates of certain T-cell precursors at the single-cell level. In this review, we aim to summarize the current progress of the study on human thymus organogenesis and thymocyte and thymic epithelial cell development, which is to shed new lights on developing novel strategies for in vitro T-cell regeneration and thymus rejuvenation.
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Affiliation(s)
- Yujun Deng
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Chen
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China.,State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Keyue Wang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Huiyuan Zhang
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology and State Key Laboratory of Biotherapy, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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19
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Tsiouplis NJ, Bailey DW, Chiou LF, Wissink FJ, Tsagaratou A. TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease. Front Cell Dev Biol 2021; 8:623948. [PMID: 33520997 PMCID: PMC7843795 DOI: 10.3389/fcell.2020.623948] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.
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Affiliation(s)
- Nikolas James Tsiouplis
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - David Wesley Bailey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States
| | - Lilly Felicia Chiou
- University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States
| | - Fiona Jane Wissink
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States.,University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States.,University of North Carolina Department of Genetics, Chapel Hill, NC, United States.,University of North Carolina Department of Microbiology and Immunology, Chapel Hill, NC, United States
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20
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Liu C, Lan Y, Liu B, Zhang H, Hu H. T Cell Development: Old Tales Retold By Single-Cell RNA Sequencing. Trends Immunol 2021; 42:165-175. [PMID: 33446417 DOI: 10.1016/j.it.2020.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Mammalian T cell development initiates from the migration of hematopoietic progenitors to the thymus, which undergo cell proliferation, T-lineage specification and commitment, as well as positive and negative selection. These processes are precisely controlled at multiple levels and have been intensively studied using gene-modified animal models and in vitro coculture systems. However, several long-standing questions, including the characterization of the rare but crucial progenitors/precursors and the molecular mechanisms underlying their fate decision, have been dampened because of cell scarcity and lack of appropriate techniques. Single-cell RNA sequencing (scRNA-seq) makes it possible to investigate and resolve some of these questions, leading to new remarkable progress in identifying and characterizing early thymic progenitors and delineating the refined developmental trajectories of conventional and unconventional T cells.
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Affiliation(s)
- Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China; State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Huiyuan Zhang
- Department of Rheumatology and Immunology, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
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21
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Keita S, Canque B, Alhaj Hussen K. Modeling Human Fetal Hematopoiesis in Humanized Mice. Methods Mol Biol 2021; 2308:225-233. [PMID: 34057726 DOI: 10.1007/978-1-0716-1425-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Due to difficulties to access primary human bone marrow samples and age or donor effects, human hematopoiesis has long remained far less well characterized than in the mouse. Despite recent progresses in single-cell RNA profiling only little is known as to phenotype, function and developmental trajectories of human lymphomyeloid progenitors and precursors. This is especially true regarding the developmental architecture of the lymphoid lineage which has been the subject of persistent controversies over the past decades. Here, we describe an original approach of in vivo modeling of human fetal hematopoiesis immunodeficient NSG mice engrafted with neonatal CD34+ hematopoietic progenitor cells (HPCs) allowing for rapid identification and isolation of lymphomyeloid developmental intermediates.
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Affiliation(s)
- Seydou Keita
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Bruno Canque
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France.
| | - Kutaiba Alhaj Hussen
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Service d'Hématologie Biologique, Hôpital Tenon, Hôpitaux Universitaires de l'Est Parisien, Assistance Publique Hôpitaux de Paris, Paris, France
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22
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Abstract
The spleen is the second major reservoir of B cells in the adult. In the spleen, cells, generated in the bone marrow, are selected, mature, and become part of the peripheral B-cell pool. Murine spleen comprises several B-cell subsets representing various maturation stages and/or cell functions. The spleen is a complex lymphoid organ organized into two main structures with different functions: the red and white pulp. The red pulp is flowed with blood while the white pulp is organized in primary follicles, with a B-cell area composed of follicular B cells and a T-cell area surrounding a periarterial lymphatic sheath. The frontier between the red and white pulp is defined as the marginal zone (MZ) and contains the MZ B cells. Because B cells, localized in different areas, are characterized by distinct expression levels of B-cell receptor (BCR) and of other surface markers, splenic B-cell subsets can be easily identified and purified by flow cytometry analyses and fluorescence-activated cell sorting (FACS).Here, we will focus on MZ B cells and on their precursors, giving some experimental hints to identify, generate, and isolate these cells. We will combine the use of FACS analysis and confocal microscopy to visualize MZ B cells in cell suspensions and in tissue sections, respectively. We will also give some clues to analyze B-cell repertoire on isolated MZ-B cells.
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23
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Golub R. The Notch signaling pathway involvement in innate lymphoid cell biology. Biomed J 2020; 44:133-143. [PMID: 33863682 PMCID: PMC8178581 DOI: 10.1016/j.bj.2020.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The role of Notch in the immune system was first described in the late 90s. Reports revealed that Notch is one of the most conserved developmental pathways involved in diverse biological processes such as the development, differentiation, survival and functions of many immune populations. Here, we provide an extended view of the pleiotropic effects of the Notch signaling on the innate lymphoid cell (ILC) biology. We review the current knowledge on Notch signaling in the regulation of ILC differentiation, plasticity and functions in diverse tissue types and at both the fetal and adult developmental stages. ILCs are early responder cells that secrete a large panel of cytokines after stimulation. By controlling the abundance of ILCs and the specificity of their release, the Notch pathway is also implicated in the regulation of their functions. The Notch pathway is therefore an important player in both ILC cell fate decision and ILC immune response.
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Affiliation(s)
- Rachel Golub
- Unit of Lymphocytes and Immunity, Department of Immunology, Institut Pasteur, Paris, France.
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Liedtke S, Korschgen L, Korn J, Duppers A, Kogler G. GMP-grade CD34 + selection from HLA-homozygous licensed cord blood units and short-term expansion under European ATMP regulations. Vox Sang 2020; 116:123-135. [PMID: 32687634 DOI: 10.1111/vox.12978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND Based on a synergistic consortium, the cord blood (CB) bank Düsseldorf was responsible for the selection of HLA-homozygous (HLA-h) donors, contacting/re-consenting the mothers, Good Manufacturing Practice (GMP)-grade CD34+ enrichment, followed by short-term expansion of CD34+ cells and qualification of the resulting CD34+ population as advanced therapy medicinal product (ATMP)-starting material. Among 20 639 licensed Düsseldorf cord blood units (CBUs), 139 potential HLA-h donors were identified with the most frequent 10 German haplotypes. 100% of the donors were contacted, and for 47·5%, consent was obtained. HLA-A, -B, -C, -DR, -DQ and -DP were determined by sequencing. METHODS Thawing/washing of the CBUs was performed in the presence of Volulyte/HSA with Sepax® , CD34+ selection by automated CliniMACS® -system (Miltenyi), expansion with qualified GMP-grade cytokines and media in the GMP facility. RESULTS Here, we specify minimal criteria (≥5 x 105 viable CD34+ -count, ≥80% CD34+ -purity and ≥70% viability) and confirm that n = 10 CB units (max storage time 16 years) could be qualified for an ATMP starting material. The mean fold change expansion of isolated CD34+ cells at Day 3/4 (d3/4) was 3·38 ± 3·02 with a mean purity of 86·90 ± 10·38% and a high viability of 96·07 ± 4·72%. CONCLUSION As of March 2019, approval was obtained by the Bezirksregierung Düsseldorf for the GMP-compliant production. The production of HLA-homozygous expanded CD34+ cells from cryopreserved CB under European ATMP regulations presented here describes the successful clinical translation and implementation of a qualified manufacturing process. This approach considers the main obstacle of rejection of transplanted cells (due to the immunological HLA barrier) by preselection of HLA-homozygous transplants.
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Affiliation(s)
- Stefanie Liedtke
- Institute of Transplantation Diagnostics and Cell Therapeutics, José Carreras Stem Cell Bank, University Clinic, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Lutz Korschgen
- Institute of Transplantation Diagnostics and Cell Therapeutics, José Carreras Stem Cell Bank, University Clinic, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Janine Korn
- Institute of Transplantation Diagnostics and Cell Therapeutics, José Carreras Stem Cell Bank, University Clinic, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Almuth Duppers
- Institute of Transplantation Diagnostics and Cell Therapeutics, José Carreras Stem Cell Bank, University Clinic, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Gesine Kogler
- Institute of Transplantation Diagnostics and Cell Therapeutics, José Carreras Stem Cell Bank, University Clinic, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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25
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Iwanami N, Takeshita K, Lawir DF, Suetake I, Tajima S, Sikora K, Trancoso I, ÓMeara C, Siamishi I, Takahama Y, Furutani-Seiki M, Kondoh H, Yonezawa Y, Schorpp M, Boehm T. Epigenetic Protection of Vertebrate Lymphoid Progenitor Cells by Dnmt1. iScience 2020; 23:101260. [PMID: 32585597 PMCID: PMC7322073 DOI: 10.1016/j.isci.2020.101260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/28/2020] [Accepted: 06/08/2020] [Indexed: 11/27/2022] Open
Abstract
DNA methylation is a universal epigenetic mechanism involved in regulation of gene expression and genome stability. The DNA maintenance methylase DNMT1 ensures that DNA methylation patterns are faithfully transmitted to daughter cells during cell division. Because loss of DNMT1 is lethal, a pan-organismic analysis of DNMT1 function is lacking. We identified new recessive dnmt1 alleles in medaka and zebrafish and, guided by the structures of mutant proteins, generated a recessive variant of mouse Dnmt1. Each of the three missense mutations studied here distorts the catalytic pocket and reduces enzymatic activity. Because all three DNMT1 mutant animals are viable, it was possible to examine their phenotypes throughout life. The consequences of genome-wide hypomethylation of DNA of somatic tissues in the Dnmt1 mutants are surprisingly mild but consistently affect the development of the lymphoid lineage. Our findings indicate that developing lymphocytes in vertebrates are sensitive to perturbations of DNA maintenance methylation. Genetic screens identified recessive viable missense alleles of dnmt1 in teleosts A viable mouse Dnmt1 mutant generated by structure-guided precision mutagenesis Missense mutations distort the catalytic pocket and reduce enzymatic activity DNA hypomethylation consistently affects development of the lymphoid lineage
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Affiliation(s)
- Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
| | | | - Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Katarzyna Sikora
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Connor ÓMeara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Makoto Furutani-Seiki
- Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi 755-8505, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
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26
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Elsaid R, Yang J, Cumano A. The influence of space and time on the establishment of B cell identity. Biomed J 2019; 42:209-217. [PMID: 31627863 PMCID: PMC6818146 DOI: 10.1016/j.bj.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/21/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023] Open
Abstract
During embryonic development multiple waves of hematopoietic progenitors with distinct lineage potential are differentially regulated in time and space. Consistent with this view, some specialized lymphocytes emerge during a limited time-window in embryogenesis and migrate to the tissues where they contribute to organogenesis and to tissue homeostasis. These cells are not constantly produced by bone marrow derived hematopoietic stem cells but are maintained in tissues and self-renew throughout life. These particular cell subsets are produced from lymphoid restricted progenitors only found in the first days of fetal liver hematopoietic activity. Growing evidence of the heterogeneity and layered organization of the hematopoietic system is leading to a common view that some lymphocyte subsets are functionally different because they follow distinct developmental programs and emerge from distinct waves of lymphoid progenitors. However, understanding the influence of developmental origin and the relative contribution of local microenvironment on the development of these specialized lymphocyte subsets needs further analysis. In this review, we discuss how different pathways followed by developing B cells during ontogeny may contribute to the diverse functions.
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Affiliation(s)
- Ramy Elsaid
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Junjie Yang
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; CNBG Company, China
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, U1223, INSERM, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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