1
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Alaterre E, Ovejero S, Bret C, Dutrieux L, Sika D, Fernandez Perez R, Espéli M, Fest T, Cogné M, Martin-Subero JI, Milpied P, Cavalli G, Moreaux J. Integrative single-cell chromatin and transcriptome analysis of human plasma cell differentiation. Blood 2024; 144:496-509. [PMID: 38643512 DOI: 10.1182/blood.2023023237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/23/2024] Open
Abstract
ABSTRACT Plasma cells (PCs) are highly specialized cells representing the end stage of B-cell differentiation. We have shown that PC differentiation can be reproduced in vitro using elaborate culture systems. The molecular changes occurring during PC differentiation are recapitulated in this in vitro differentiation model. However, a major challenge exists to decipher the spatiotemporal epigenetic and transcriptional programs that drive the early stages of PC differentiation. We combined single cell (sc) RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with high throughput sequencing (scATAC-seq) to decipher the trajectories involved in PC differentiation. ScRNA-seq experiments revealed a strong heterogeneity of the preplasmablastic and plasmablastic stages. Among genes that were commonly identified using scATAC-seq and scRNA-seq, we identified several transcription factors with significant stage specific potential importance in PC differentiation. Interestingly, differentially accessible peaks characterizing the preplasmablastic stage were enriched in motifs of BATF3, FOS and BATF, belonging to activating protein 1 (AP-1) transcription factor family that may represent key transcriptional nodes involved in PC differentiation. Integration of transcriptomic and epigenetic data at the single cell level revealed that a population of preplasmablasts had already undergone epigenetic remodeling related to PC profile together with unfolded protein response activation and are committed to differentiate in PC. These results and the supporting data generated with our in vitro PC differentiation model provide a unique resource for the identification of molecular circuits that are crucial for early and mature PC maturation and biological functions. These data thus provide critical insights into epigenetic- and transcription-mediated reprogramming events that sustain PC differentiation.
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Affiliation(s)
- Elina Alaterre
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
| | - Sara Ovejero
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | - Caroline Bret
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | - Laure Dutrieux
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
| | - Dassou Sika
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
| | | | - Marion Espéli
- INSERM U1160 EMiLy, Institut de Recherche Saint-Louis, Université Paris-Cité, Paris, France
| | - Thierry Fest
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, Team B_DEVIL, UMR_S1236, Rennes, France
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire, Rennes, France
| | - Michel Cogné
- Institut National de La Santé et de La Recherche Médicale, Unité Mixte de Recherche U1236, Université de Rennes, Etablissement Français Du Sang Bretagne, Rennes, France
- Centre Hospitalier Universitaire de Rennes, Suivi Immunologique des Thérapies Innovantes, Pôle Biologie, Rennes, France
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Pierre Milpied
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Giacomo Cavalli
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
| | - Jérôme Moreaux
- Institute of Human Genetics, Unité Mixte de Recherche, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- University of Montpellier, UFR Medicine, Montpellier, France
- Institut Universitaire de France, Paris, France
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2
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Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [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] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
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Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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3
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Cousu C, Mulot E, De Smet A, Formichetti S, Lecoeuche D, Ren J, Muegge K, Boulard M, Weill JC, Reynaud CA, Storck S. Germinal center output is sustained by HELLS-dependent DNA-methylation-maintenance in B cells. Nat Commun 2023; 14:5695. [PMID: 37709749 PMCID: PMC10502085 DOI: 10.1038/s41467-023-41317-3] [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] [Received: 02/20/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
HELLS/LSH (Helicase, Lymphoid Specific) is a SNF2-like chromatin remodelling protein involved in DNA methylation. Its loss-of-function in humans causes humoral immunodeficiency, called ICF4 syndrome (Immunodeficiency, Centromeric Instability, Facial anomalies). Here we show by our newly generated B-cell-specific Hells conditional knockout mouse model that HELLS plays a pivotal role in T-dependent B-cell responses. HELLS deficiency induces accelerated decay of germinal center (GC) B cells and impairs the generation of high affinity memory B cells and circulating antibodies. Mutant GC B cells undergo dramatic DNA hypomethylation and massive de-repression of evolutionary recent retrotransposons, which surprisingly does not directly affect their survival. Instead, they prematurely upregulate either memory B cell markers or the transcription factor ATF4, which is driving an mTORC1-dependent metabolic program typical of plasma cells. Treatment of wild type mice with a DNMT1-specific inhibitor phenocopies the accelerated kinetics, thus pointing towards DNA-methylation maintenance by HELLS being a crucial mechanism to fine-tune the GC transcriptional program and enable long-lasting humoral immunity.
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Affiliation(s)
- Clara Cousu
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Eléonore Mulot
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Annie De Smet
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Sara Formichetti
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), 00015, Monterotondo, Italy
- Joint PhD degree program, European Molecular Biology Laboratory and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Damiana Lecoeuche
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Jianke Ren
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
- NHC Key Lab of Reproduction Regulation,Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Matthieu Boulard
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), 00015, Monterotondo, Italy
| | - Jean-Claude Weill
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Claude-Agnès Reynaud
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France
| | - Sébastien Storck
- Université Paris Cité, CNRS UMR 8253, INSERM U1151, Institut Necker Enfants Malades, F-75015, Paris, France.
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4
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Boast B, Goel S, González-Granado LI, Niemela J, Stoddard J, Edwards ESJ, Seneviratne S, Spensberger D, Quesada-Espinosa JF, Allende LM, McDonnell J, Haseley A, Lesmana H, Walkiewicz MA, Muhammad E, Bosco JJ, Fleisher TA, Cohen S, Holland SM, van Zelm MC, Enders A, Kuehn HS, Rosenzweig SD. TCF3 haploinsufficiency defined by immune, clinical, gene-dosage, and murine studies. J Allergy Clin Immunol 2023; 152:736-747. [PMID: 37277074 PMCID: PMC10527523 DOI: 10.1016/j.jaci.2023.05.017] [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] [Received: 03/22/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND TCF3 is a transcription factor contributing to early lymphocyte differentiation. Germline monoallelic dominant negative and biallelic loss-of-function (LOF) null TCF3 mutations cause a fully penetrant severe immunodeficiency. We identified 8 individuals from 7 unrelated families with monoallelic LOF TCF3 variants presenting with immunodeficiency with incomplete clinical penetrance. OBJECTIVE We sought to define TCF3 haploinsufficiency (HI) biology and its association with immunodeficiency. METHODS Patient clinical data and blood samples were analyzed. Flow cytometry, Western blot analysis, plasmablast differentiation, immunoglobulin secretion, and transcriptional activity studies were conducted on individuals carrying TCF3 variants. Mice with a heterozygous Tcf3 deletion were analyzed for lymphocyte development and phenotyping. RESULTS Individuals carrying monoallelic LOF TCF3 variants showed B-cell defects (eg, reduced total, class-switched memory, and/or plasmablasts) and reduced serum immunoglobulin levels; most but not all presented with recurrent but nonsevere infections. These TCF3 LOF variants were either not transcribed or translated, resulting in reduced wild-type TCF3 protein expression, strongly suggesting HI pathophysiology for the disease. Targeted RNA sequencing analysis of T-cell blasts from TCF3-null, dominant negative, or HI individuals clustered away from healthy donors, implying that 2 WT copies of TCF3 are needed to sustain a tightly regulated TCF3 gene-dosage effect. Murine TCF3 HI resulted in a reduction of circulating B cells but overall normal humoral immune responses. CONCLUSION Monoallelic LOF TCF3 mutations cause a gene-dosage-dependent reduction in wild-type protein expression, B-cell defects, and a dysregulated transcriptome, resulting in immunodeficiency. Tcf3+/- mice partially recapitulate the human phenotype, underscoring the differences between TCF3 in humans and mice.
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Affiliation(s)
- Brigette Boast
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Shubham Goel
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Luis I González-Granado
- Department of Pediatrics, Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), School of Medicine, Complutense University, Madrid, Spain
| | - Julie Niemela
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Emily S J Edwards
- Department of Immunology, Monash University, and The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia
| | - Sandali Seneviratne
- Centre for Personalised Immunology and Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Dominik Spensberger
- ANU Gene Targeting Facility, Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | | - Luis M Allende
- Department of Immunology, Hospital 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - John McDonnell
- Department of Pediatric Allergy and Immunology, Cleveland Clinic, Cleveland, Ohio
| | - Alexandria Haseley
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Harry Lesmana
- Center for Personalized Genetic Healthcare, Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio; Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Cleveland Clinic, Cleveland, Ohio
| | - Magdalena A Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Emad Muhammad
- Hematology Laboratory, Carmel Medical Center, Haifa, Spain
| | - Julian J Bosco
- Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, Australia
| | - Thomas A Fleisher
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Shai Cohen
- Allergy and Clinical Immunology Service, Department of Internal Medicine B, Lin and Carmel Medical Center, The Technion, Israel Institute of Technology, Haifa, Israel
| | - Steven M Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Menno C van Zelm
- Department of Immunology, Monash University, and The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, Australia; Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, Australia
| | - Anselm Enders
- Centre for Personalised Immunology and Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Md.
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Haas M, Fest T. Final step of B-cell differentiation into plasmablasts; the right time to activate plasma cell PIM2 kinase. Immunol Lett 2023; 258:45-50. [PMID: 37207916 DOI: 10.1016/j.imlet.2023.05.006] [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: 01/16/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
The differentiation of B cells into antibody-secreting plasma cells is a complex process that involves extensive changes in morphology, lifespan, and cellular metabolism to support the high rates of antibody production. During the final stage of differentiation, B cells undergo significant expansion of their endoplasmic reticulum and mitochondria, which induces cellular stress and may lead to cell death in absence of effective inhibition of the apoptotic pathway. These changes are tightly regulated at transcriptional and epigenetic levels, as well as at post-translational level, with protein modifications playing a critical role in the process of cellular modification and adaptation. Our recent research has highlighted the pivotal role of the serine/threonine kinase PIM2 in B cell differentiation, from commitment stage to plasmablast and maintenance of expression in mature plasma cells. PIM2 has been shown to promote cell cycle progression during the final stage of differentiation and to inhibit Caspase 3 activation, raising the threshold for apoptosis. In this review, we examine the key molecular mechanisms controlled by PIM2 that contribute to plasma cell development and maintenance.
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Affiliation(s)
- Marion Haas
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, Team B_DEVIL, UMR_S1236, Rennes, France; Laboratoire d'Hématologie, Centre Hospitalier Universitaire, Rennes, France
| | - Thierry Fest
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, Team B_DEVIL, UMR_S1236, Rennes, France; Laboratoire d'Hématologie, Centre Hospitalier Universitaire, Rennes, France.
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6
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The cellular biology of plasma cells: Unmet challenges and opportunities. Immunol Lett 2023; 254:6-12. [PMID: 36646289 DOI: 10.1016/j.imlet.2023.01.005] [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: 11/06/2022] [Revised: 12/27/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Plasma cells and the antibodies they secrete are paramount for protection against infection but can also be implicated in diseases including autoantibody-mediated disease and multiple myeloma. Plasma cell terminal differentiation relies on a transcriptional switch and on important morphological changes. The cellular and molecular mechanisms underlying these processes are partly understood and how plasma cells manage to survive for long periods of time while secreting large quantities of antibodies remains unclear. In this review we aim to put in perspective what is known about plasma cell cellular biology to highlight the challenges faced by this field of research but also to illustrate how new opportunities may arise from the study of the fundamental mechanisms sustaining plasma cell survival and function.
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7
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Boothby MR, Brookens SK, Raybuck AL, Cho SH. Supplying the trip to antibody production-nutrients, signaling, and the programming of cellular metabolism in the mature B lineage. Cell Mol Immunol 2022; 19:352-369. [PMID: 34782762 PMCID: PMC8591438 DOI: 10.1038/s41423-021-00782-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID pandemic has refreshed and expanded recognition of the vital role that sustained antibody (Ab) secretion plays in our immune defenses against microbes and of the importance of vaccines that elicit Ab protection against infection. With this backdrop, it is especially timely to review aspects of the molecular programming that govern how the cells that secrete Abs arise, persist, and meet the challenge of secreting vast amounts of these glycoproteins. Whereas plasmablasts and plasma cells (PCs) are the primary sources of secreted Abs, the process leading to the existence of these cell types starts with naive B lymphocytes that proliferate and differentiate toward several potential fates. At each step, cells reside in specific microenvironments in which they not only receive signals from cytokines and other cell surface receptors but also draw on the interstitium for nutrients. Nutrients in turn influence flux through intermediary metabolism and sensor enzymes that regulate gene transcription, translation, and metabolism. This review will focus on nutrient supply and how sensor mechanisms influence distinct cellular stages that lead to PCs and their adaptations as factories dedicated to Ab secretion. Salient findings of this group and others, sometimes exhibiting differences, will be summarized with regard to the journey to a distinctive metabolic program in PCs.
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Affiliation(s)
- Mark R Boothby
- Department of Pathology, Microbiology & Immunology, Molecular Pathogenesis Division, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department of Medicine, Rheumatology & Immunology Division, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Cancer Biology Program, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Institute of Infection, Inflammation, and Immunology, Nashville, TN, 37232, USA.
| | - Shawna K Brookens
- Department of Pathology, Microbiology & Immunology, Molecular Pathogenesis Division, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Cancer Biology Program, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ariel L Raybuck
- Department of Pathology, Microbiology & Immunology, Molecular Pathogenesis Division, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sung Hoon Cho
- Department of Pathology, Microbiology & Immunology, Molecular Pathogenesis Division, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute of Infection, Inflammation, and Immunology, Nashville, TN, 37232, USA
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8
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Pivotal role of PIM2 kinase in plasmablast generation and plasma cell survival, opening new treatment options in myeloma. Blood 2022; 139:2316-2337. [PMID: 35108359 DOI: 10.1182/blood.2021014011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
The differentiation of B cells into plasmablasts (PBs) and then plasma cells (PCs) is associated with extensive cell reprogramming and new cell functions. By using specific inhibition strategies (including a novel morpholino RNA antisense approach), we found that early, sustained upregulation of the proviral integrations of Moloney virus 2 (PIM2) kinase is a pivotal event during human B cell in vitro differentiation and then continues in mature normal and malignant PCs in the bone marrow. In particular, PIM2 sustained the G1/S transition by acting on CDC25A and p27Kip1 and hindering caspase 3-driven apoptosis through BAD phosphorylation and cytoplasmic stabilization of p21Cip1. In PCs, interleukin-6 triggered PIM2 expression, resulting in anti-apoptotic effects on which malignant PCs were particularly dependent. In multiple myeloma, pan-PIM and MCL1 inhibitors displayed synergistic activity. Our results highlight a cell-autonomous function that links kinase activity to the PBs' newly acquired secretion ability and the adaptability observed in both normal and malignant PCs, and finally should prompt the reconsideration of PIM2 as a therapeutic target in multiple myeloma.
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9
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Chen HY, Hsu M, Lio CWJ. Micro but mighty-Micronutrients in the epigenetic regulation of adaptive immune responses. Immunol Rev 2022; 305:152-164. [PMID: 34820863 PMCID: PMC8766944 DOI: 10.1111/imr.13045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 01/03/2023]
Abstract
Micronutrients are essential small molecules required by organisms in minute quantity for survival. For instance, vitamins and minerals, the two major categories of micronutrients, are central for biological processes such as metabolism, cell replication, differentiation, and immune response. Studies estimated that around two billion humans worldwide suffer from micronutrient deficiencies, also known as "hidden hunger," linked to weakened immune responses. While micronutrients affect the immune system at multiple levels, recent studies showed that micronutrients potentially impact the differentiation and function of immune cells as cofactors for epigenetic enzymes, including the 2-oxoglutarate-dependent dioxygenase (2OGDD) family involved in histone and DNA demethylation. Here, we will first provide an overview of the role of DNA methylation in T cells and B cells, followed by the micronutrients ascorbate (vitamin C) and iron, two critical cofactors for 2OGDD. We will discuss the emerging evidence of these micronutrients could regulate adaptive immune response by influencing epigenetic remodeling.
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Affiliation(s)
| | | | - Chan-Wang Jerry Lio
- Corresponding author: Chan-Wang Jerry Lio (), Address: 460 W 12 Ave, Columbus, Ohio, USA 43064, Tel: (614)-247-5337
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10
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Santamaria K, Desmots F, Leonard S, Caron G, Haas M, Delaloy C, Chatonnet F, Rossille D, Pignarre A, Monvoisin C, Seffals M, Lamaison C, Cogné M, Tarte K, Fest T. Committed Human CD23-Negative Light-Zone Germinal Center B Cells Delineate Transcriptional Program Supporting Plasma Cell Differentiation. Front Immunol 2021; 12:744573. [PMID: 34925321 PMCID: PMC8674954 DOI: 10.3389/fimmu.2021.744573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
B cell affinity maturation occurs in the germinal center (GC). Light-zone (LZ) GC B cells (BGC-cells) interact with follicular dendritic cells (FDCs) and compete for the limited, sequential help from T follicular helper cells needed to escape from apoptosis and complete their differentiation. The highest-affinity LZ BGC-cells enter the cell cycle and differentiate into PCs, following a dramatic epigenetic reorganization that induces transcriptome changes in general and the expression of the PRDM1 gene in particular. Human PC precursors are characterized by the loss of IL-4/STAT6 signaling and the absence of CD23 expression. Here, we studied the fate of human LZ BGC-cells as a function of their CD23 expression. We first showed that CD23 expression was restricted to the GC LZ, where it was primarily expressed by FDCs; less than 10% of tonsil LZ BGC-cells were positive. Sorted LZ BGC-cells left in culture and stimulated upregulated CD23 expression but were unable to differentiate into PCs – in contrast to cells that did not upregulate CD23 expression. An in-depth analysis (including single-cell gene expression) showed that stimulated CD23-negative LZ BGC-cells differentiated into plasmablasts and time course of gene expression changes delineates the transcriptional program that sustains PC differentiation. In particular, we identified a B cell proliferation signature supported by a transient MYC gene expression. Overall, the CD23 marker might be of value in answering questions about the differentiation of normal BGC-cells and allowed us to propose an instructive LZ BGC-cells maturation and fate model.
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Affiliation(s)
- Kathleen Santamaria
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France
| | - Fabienne Desmots
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Simon Leonard
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Gersende Caron
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Marion Haas
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Céline Delaloy
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France
| | - Fabrice Chatonnet
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Delphine Rossille
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Amandine Pignarre
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Céline Monvoisin
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France
| | - Marine Seffals
- University of Rennes 1, UMS Biosit, H2P2 Platform, Rennes, France
| | - Claire Lamaison
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France
| | - Michel Cogné
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Karin Tarte
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
| | - Thierry Fest
- UMR 1236, University of Rennes 1, INSERM, Établissement Français du Sang Bretagne, Rennes, France.,Pôle de Biologie, Rennes University Medical Center, Rennes, France
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11
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Large-scale DNA demethylation occurs in proliferating ovarian granulosa cells during mouse follicular development. Commun Biol 2021; 4:1334. [PMID: 34824385 PMCID: PMC8617273 DOI: 10.1038/s42003-021-02849-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
During ovarian follicular development, granulosa cells proliferate and progressively differentiate to support oocyte maturation and ovulation. To determine the underlying links between proliferation and differentiation in granulosa cells, we determined changes in 1) the expression of genes regulating DNA methylation and 2) DNA methylation patterns, histone acetylation levels and genomic DNA structure. In response to equine chorionic gonadotropin (eCG), granulosa cell proliferation increased, DNA methyltransferase (DNMT1) significantly decreased and Tet methylcytosine dioxygenase 2 (TET2) significantly increased in S-phase granulosa cells. Comprehensive MeDIP-seq analyses documented that eCG treatment decreased methylation of promoter regions in approximately 40% of the genes in granulosa cells. The expression of specific demethylated genes was significantly increased in association with specific histone modifications and changes in DNA structure. These epigenetic processes were suppressed by a cell cycle inhibitor. Based on these results, we propose that the timing of sequential epigenetic events is essential for progressive, stepwise changes in granulosa cell differentiation.
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12
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Delaloy C, Schuh W, Jäck HM, Bonaud A, Espéli M. Single cell resolution of Plasma Cell fate programming in health and disease. Eur J Immunol 2021; 52:10-23. [PMID: 34694625 DOI: 10.1002/eji.202149216] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/14/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022]
Abstract
Long considered a homogeneous population dedicated to antibody secretion, plasma cell phenotypic and functional heterogeneity is increasingly recognised. Plasma cells were first segregated based on their maturation level, but the complexity of this subset might well be underestimated by this simple dichotomy. Indeed, in the last decade new functions have been attributed to plasma cells including but not limited to cytokine secretion. However, a proper characterization of plasma cell heterogeneity has remained elusive partly due to technical issues and cellular features that are specific to this cell type. Cell intrinsic and cell extrinsic signals could be at the origin of this heterogeneity. Recent advances in technologies like single cell RNA-seq, ATAC-seq or ChIP-seq on low cell numbers helped to elucidate the fate decision in other cell lineages and similar approaches could be implemented to evaluate the heterogeneous fate of activated B cells in health and disease. Here, we summarized published work shedding some lights on the stimuli and genetic program shaping B cell terminal differentiation at the single cell level in mice and men. We also discuss the fate and heterogeneity of plasma cells during immune responses, vaccination and in the frame of human plasma cell disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Céline Delaloy
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, LabEx IGO, 2 Av du Pr Léon Bernard, Rennes, 35043, France.,French Germinal Center Club, French Society for Immunology (SFI), Paris, 75015, France
| | - Wolfgang Schuh
- Division of Molecular Immunology, Department of Internal Medicine III, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine III, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany
| | - Amélie Bonaud
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris, F-75010, France.,OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Hôpital Saint-Louis, Paris, France
| | - Marion Espéli
- French Germinal Center Club, French Society for Immunology (SFI), Paris, 75015, France.,Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris, F-75010, France.,OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Hôpital Saint-Louis, Paris, France
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13
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Derrien J, Guérin-Charbonnel C, Gaborit V, Campion L, Devic M, Douillard E, Roi N, Avet-Loiseau H, Decaux O, Facon T, Mallm JP, Eils R, Munshi NC, Moreau P, Herrmann C, Magrangeas F, Minvielle S. The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability. Genome Med 2021; 13:127. [PMID: 34372935 PMCID: PMC8351364 DOI: 10.1186/s13073-021-00938-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background Cancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective. Methods Here, we performed an analysis of 42 MM samples from 21 patients by using enhanced reduced representation bisulfite sequencing (eRRBS). We combined several metrics of epigenetic heterogeneity to analyze DNA methylation heterogeneity in MM patients. Results We show that MM is characterized by the continuous accumulation of stochastic methylation at the promoters of development-related genes. High combinatorial entropy change is associated with poor outcomes in our pilot study and depends predominantly on partially methylated domains (PMDs). These PMDs, which represent the major source of inter- and intrapatient DNA methylation heterogeneity in MM, are linked to other key epigenetic aberrations, such as CpG island (CGI)/transcription start site (TSS) hypermethylation and H3K27me3 redistribution as well as 3D organization alterations. In addition, transcriptome analysis revealed that intratumor methylation heterogeneity was associated with low-level expression and high variability. Conclusions We propose that disrupted DNA methylation in MM is responsible for high epigenetic and transcriptomic instability allowing tumor cells to adapt to environmental changes by tapping into a pool of evolutionary trajectories. Supplementary Information The online version contains supplementary material available at (10.1186/s13073-021-00938-3).
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Affiliation(s)
- Jennifer Derrien
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France
| | - Catherine Guérin-Charbonnel
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Institut de Cancérologie de l'Ouest, Nantes-Saint Herblain, France
| | - Victor Gaborit
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,LS2N, CNRS, Université de Nantes, Nantes, France
| | - Loïc Campion
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Institut de Cancérologie de l'Ouest, Nantes-Saint Herblain, France
| | - Magali Devic
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Centre Hospitalier Universitaire, Nantes, France
| | - Elise Douillard
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Centre Hospitalier Universitaire, Nantes, France
| | - Nathalie Roi
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Centre Hospitalier Universitaire, Nantes, France
| | - Hervé Avet-Loiseau
- Institut Universitaire du Cancer, CHU, Centre de Recherche en Cancérologie de Toulouse, INSERM 1037, Toulouse, France
| | | | | | - Jan-Philipp Mallm
- Research Group Genome Organization & Function, DKFZ, and BioQuant Heidelberg, Heidelberg, 69120, Germany
| | - Roland Eils
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, 69120, Germany.,Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt- Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Berlin Institute of Health (BIH), Center for Digital Health, Anna-Louisa-Karsch-Strasse 2, Berlin, 10178, Germany
| | - Nikhil C Munshi
- Dana-Farber Cancer Institute, Harvard Medical School, LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Boston, MA, United States
| | - Philippe Moreau
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Centre Hospitalier Universitaire, Nantes, France
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, 69120, Germany
| | - Florence Magrangeas
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France.,Centre Hospitalier Universitaire, Nantes, France
| | - Stéphane Minvielle
- Université de Nantes, CNRS, INSERM, CRCINA, Nantes, F-44000, France. .,Centre Hospitalier Universitaire, Nantes, France.
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14
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Plasmablasts derive from CD23- activated B cells after the extinction of IL-4/STAT6 signaling and IRF4 induction. Blood 2021; 137:1166-1180. [PMID: 33150420 DOI: 10.1182/blood.2020005083] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 10/19/2020] [Indexed: 01/07/2023] Open
Abstract
The terminal differentiation of B cells into antibody-secreting cells (ASCs) is a critical component of adaptive immune responses. However, it is a very sensitive process, and dysfunctions lead to a variety of lymphoproliferative neoplasias including germinal center-derived lymphomas. To better characterize the late genomic events that drive the ASC differentiation of human primary naive B cells, we used our in vitro differentiation system and a combination of RNA sequencing and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC sequencing). We discovered 2 mechanisms that drive human terminal B-cell differentiation. First, after an initial response to interleukin-4 (IL-4), cells that were committed to an ASC fate downregulated the CD23 marker and IL-4 signaling, whereas cells that maintained IL-4 signaling did not differentiate. Second, human CD23- cells also increased IRF4 protein to levels required for ASC differentiation, but they did that independently of the ubiquitin-mediated degradation process previously described in mice. Finally, we showed that CD23- cells carried the imprint of their previous activated B-cell status, were precursors of plasmablasts, and had a phenotype similar to that of in vivo preplasmablasts. Altogether, our results provide an unprecedented genomic characterization of the fate decision between activated B cells and plasmablasts, which provides new insights into the pathological mechanisms that drive lymphoma biology.
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15
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Zhang F, Chen S, Yang T, Ao H, Zhai L, Li Q, Xing K, Liu Y, Liu H, Yu Y, Wang C. Novel DNA methylation markers of PRRSV-specific antibodies and their intergenerational transmission from pregnant sows to piglets. Gene 2021; 801:145831. [PMID: 34274485 DOI: 10.1016/j.gene.2021.145831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 01/11/2023]
Abstract
The main strategy for preventing porcine reproductive and respiratory syndrome (PRRS) is vaccination. However, current commercial porcine reproductive and respiratory syndrome virus (PRRSV) vaccines have limited effectiveness and may even cause infections in pigs. The identification of stable molecular markers associated with immune responses to PRRSV vaccination in pigs provides a new approach for PRRS prevention. DNA methylation, the most stable epigenetic molecular marker related to PRRSV vaccination, has not been investigated. In the current research, we used whole genome bisulfite sequencing (WGBS) to investigate DNA methylation in pregnant sows that received PRRSV vaccination and their piglets with high and low PRRSV-specific antibody levels. By performing methylation data analysis and basing on our previous transcriptomic studies, we identified several differentially methylated genes (DMGs) that are involved in the pathways of inflammatory and immune responses. Among the DMGs, ISG15, MX1, SERPINE1, GNG11 and IFIT3 were common hub genes in the two generations. MX1 and GNG11 were located in quantitative trait loci related with PRRSV antibody titer and PRRSV susceptibility, respectively. These results suggest that PRRSV vaccination in sows induces DNA methylation changes in genes and DNA methylation changes occur through intergenerational transmission. The novel DNA methylation markers and target genes observed in our study provide new insights into the molecular mechanisms of immune responses to PRRSV vaccination across two pig generations.
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Affiliation(s)
- Fengxia Zhang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China; Innovation Team of Pig Health Breeding, Institute of Animal Husbandry and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Siqian Chen
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Ting Yang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hong Ao
- The State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Zhai
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Qianjun Li
- Innovation Team of Pig Health Breeding, Institute of Animal Husbandry and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yibing Liu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Huatao Liu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, China.
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16
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Li J, Li L, Sun X, Deng T, Huang G, Li X, Xie Z, Zhou Z. Role of Tet2 in Regulating Adaptive and Innate Immunity. Front Cell Dev Biol 2021; 9:665897. [PMID: 34222235 PMCID: PMC8247589 DOI: 10.3389/fcell.2021.665897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Accumulated evidence indicates that epigenetic modifications play central roles in gene expression regulation and participate in developing many autoimmune and autoinflammatory diseases. Mechanistically, epigenetic modifications act as a bridge between environmental and cellular factors and susceptibility genes. DNA methylation is a critical epigenetic modification that is regulated by ten-eleven translocation (TET) enzymes. Accumulating evidence has revealed that TET family proteins function as gene regulators and antitumor drug targets mainly because of their ability to oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Recently, the effect of Tet2, an essential TET protein, on the development of autoimmune diseases has been explored. In this review, we summarize the current understanding of Tet2 in immune response regulation, clarify the mechanisms of Tet2 in B and T cell differentiation and function, and discuss the opposing effects of Tet2 on inflammatory gene expression in the immune system to provide new potential therapeutic targets for related 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, 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
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, 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, 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, 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, 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, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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17
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Patterson DG, Kania AK, Zuo Z, Scharer CD, Boss JM. Epigenetic gene regulation in plasma cells. Immunol Rev 2021; 303:8-22. [PMID: 34010461 DOI: 10.1111/imr.12975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Humoral immunity provides protection from pathogenic infection and is mediated by antibodies following the differentiation of naive B cells (nBs) to antibody-secreting cells (ASCs). This process requires substantial epigenetic and transcriptional rewiring to ultimately repress the nB program and replace it with one conducive to ASC physiology and function. Notably, these reprogramming events occur within the framework of cell division. Efforts to understand the relationship of cell division with reprogramming and ASC differentiation in vivo have uncovered the timing and scope of reprogramming, as well as key factors that influence these events. Herein, we discuss the unique physiology of ASC and how nBs undergo epigenetic and genome architectural reorganization to acquire the necessary functions to support antibody production. We also discuss the stage-wise manner in which reprogramming occurs across cell divisions and how key molecular determinants can influence B cell fate outcomes.
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Affiliation(s)
- Dillon G Patterson
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Anna K Kania
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Zhihong Zuo
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Xiangya School of Medicine, Central South University, Changsha, China
| | | | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
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18
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Lemarié M, Chatonnet F, Caron G, Fest T. Early Emergence of Adaptive Mechanisms Sustaining Ig Production: Application to Antibody Therapy. Front Immunol 2021; 12:671998. [PMID: 33995412 PMCID: PMC8117215 DOI: 10.3389/fimmu.2021.671998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 01/13/2023] Open
Abstract
Antibody therapy, where artificially-produced immunoglobulins (Ig) are used to treat pathological conditions such as auto-immune diseases and cancers, is a very innovative and competitive field. Although substantial efforts have been made in recent years to obtain specific and efficient antibodies, there is still room for improvement especially when considering a precise tissular targeting or increasing antigen affinity. A better understanding of the cellular and molecular steps of terminal B cell differentiation, in which an antigen-activated B cell becomes an antibody secreting cell, may improve antibody therapy. In this review, we use our recently published data about human B cell differentiation, to show that the mechanisms necessary to adapt a metamorphosing B cell to its new secretory function appear quite early in the differentiation process i.e., at the pre-plasmablast stage. After characterizing the molecular pathways appearing at this stage, we will focus on recent findings about two main processes involved in antibody production: unfolded protein response (UPR) and endoplasmic reticulum (ER) stress. We’ll show that many genes coding for factors involved in UPR and ER stress are induced at the pre-plasmablast stage, sustaining our hypothesis. Finally, we propose to use this recently acquired knowledge to improve productivity of industrialized therapeutic antibodies.
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Affiliation(s)
- Maud Lemarié
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, UMR_S1236, Rennes, France
| | - Fabrice Chatonnet
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, UMR_S1236, Rennes, France.,Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire, Rennes, France
| | - Gersende Caron
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, UMR_S1236, Rennes, France.,Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire, Rennes, France
| | - Thierry Fest
- Université de Rennes 1, INSERM, Établissement Français du Sang de Bretagne, UMR_S1236, Rennes, France.,Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire, Rennes, France
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19
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Kassambara A, Herviou L, Ovejero S, Jourdan M, Thibaut C, Vikova V, Pasero P, Elemento O, Moreaux J. RNA-sequencing data-driven dissection of human plasma cell differentiation reveals new potential transcription regulators. Leukemia 2021; 35:1451-1462. [PMID: 33824465 PMCID: PMC8102200 DOI: 10.1038/s41375-021-01234-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Plasma cells (PCs) play an important role in the adaptive immune system through a continuous production of antibodies. We have demonstrated that PC differentiation can be modeled in vitro using complex multistep culture systems reproducing sequential differentiation process occurring in vivo. Here we present a comprehensive, temporal program of gene expression data encompassing human PC differentiation (PCD) using RNA sequencing (RNA-seq). Our results reveal 6374 differentially expressed genes classified into four temporal gene expression patterns. A stringent pathway enrichment analysis of these gene clusters highlights known pathways but also pathways largely unknown in PCD, including the heme biosynthesis and the glutathione conjugation pathways. Additionally, our analysis revealed numerous novel transcriptional networks with significant stage-specific overexpression and potential importance in PCD, including BATF2, BHLHA15/MIST1, EZH2, WHSC1/MMSET, and BLM. We have experimentally validated a potent role for BLM in regulating cell survival and proliferation during human PCD. Taken together, this RNA-seq analysis of PCD temporal stages helped identify coexpressed gene modules with associated up/downregulated transcription regulator genes that could represent major regulatory nodes for human PC maturation. These data constitute a unique resource of human PCD gene expression programs in support of future studies for understanding the underlying mechanisms that control PCD.
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Affiliation(s)
- Alboukadel Kassambara
- Department of Biological Hematology, CHU Montpellier, Montpellier, France.,IGH, CNRS, University of Montpellier, Montpellier, France
| | - Laurie Herviou
- IGH, CNRS, University of Montpellier, Montpellier, France
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France.,IGH, CNRS, University of Montpellier, Montpellier, France
| | - Michel Jourdan
- IGH, CNRS, University of Montpellier, Montpellier, France
| | | | | | | | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France. .,IGH, CNRS, University of Montpellier, Montpellier, France. .,University of Montpellier, UFR Medicine, Montpellier, France. .,Institut Universitaire de France (IUF), Paris, France.
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20
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Rogers KJ, Vijay R, Butler NS. Anti-malarial humoral immunity: the long and short of it. Microbes Infect 2021; 23:104807. [PMID: 33684519 DOI: 10.1016/j.micinf.2021.104807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 12/17/2022]
Abstract
Humoral immunity is critical for limiting Plasmodium parasite infections and the severity of malaria. Naturally acquired immunity against malaria occurs inefficiently and protection is relatively short-lived. Here we review recent advances and explore emerging hypotheses regarding the molecular and cellular pathways that regulate Plasmodium parasite-specific B cell responses and durable anti-malarial humoral immunity.
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Affiliation(s)
- Kai J Rogers
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Rahul Vijay
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Noah S Butler
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, The University of Iowa, Iowa City, IA, USA.
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21
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Zouali M. DNA methylation signatures of autoimmune diseases in human B lymphocytes. Clin Immunol 2020; 222:108622. [PMID: 33188932 DOI: 10.1016/j.clim.2020.108622] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Accepted: 11/07/2020] [Indexed: 12/15/2022]
Abstract
B lymphocytes play key roles in adaptive and innate immunity. In autoimmune diseases, their participation in disease instigation and/or progression has been demonstrated in both experimental models and clinical trials. Recent epigenetic investigations of human B lymphocyte subsets revealed the importance of DNA methylation in exquisitely regulating the cellular activation and differentiation programs. This review discusses recent advances on the potential of DNA methylation to shape events that impart generation of plasma cells and memory B cells, providing novel insight into homeostatic regulation of the immune system. In parallel, epigenetic profiling of B cells from patients with systemic or organo-specific autoimmune diseases disclosed distinctive differential methylation regions that, in some cases, could stratify patients from controls. Development of tools for editing DNA methylation in the mammalian genome could be useful for future functional studies of epigenetic regulation by offering the possibility to edit locus-specific methylation, with potential translational applications.
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Affiliation(s)
- Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, No. 91, Xueshi Road, North District, Taichung City, Taïwan 404, Taichung, Taiwan.
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22
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Khoenkhoen S, Ádori M, Pedersen GK, Karlsson Hedestam GB. Flow Cytometry-Based Protocols for the Analysis of Human Plasma Cell Differentiation. Front Immunol 2020; 11:571321. [PMID: 33133085 PMCID: PMC7550473 DOI: 10.3389/fimmu.2020.571321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/28/2020] [Indexed: 12/02/2022] Open
Abstract
Humoral immunity is established after differentiation of antigen-specific B cells into plasma cells (PCs) that produce antibodies of relevant specificities. Defects in the development, activation, or differentiation of B cells severely compromises the immune response. Primary immunodeficiencies are often characterized by hypogammaglobulinemia and the inability to mount effective antigen-specific antibody responses, resulting in increased susceptibility to infections. After IgA deficiency, which is most often asymptomatic, common variable immunodeficiency (CVID) is the most prevalent symptomatic primary immunodeficiency, but in most cases the underlying genetic causes are unknown or their roles in disease pathogenesis are poorly understood. In this study, we developed a protocol for in vitro stimulation of primary human B cells for subsequent analyses of PC differentiation and antibody production. With this approach, we were able to detect a population of CD38+ IRF4+ Blimp-1+ cells committed to PC fate and IgG production, including when starting from cryopreserved samples. The application of functional assays to characterize PC differentiation and possible defects therein in B cells from patients suffering from primary antibody deficiencies with late B cell defects could increase our understanding of the disease pathophysiology and underlying mechanisms.
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Affiliation(s)
- Sharesta Khoenkhoen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Monika Ádori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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23
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The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. ACTA ACUST UNITED AC 2020; 1:1066-1081. [PMID: 34079956 DOI: 10.1038/s43018-020-00131-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.
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24
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Xue VW, Chung JYF, Córdoba CAG, Cheung AHK, Kang W, Lam EWF, Leung KT, To KF, Lan HY, Tang PMK. Transforming Growth Factor-β: A Multifunctional Regulator of Cancer Immunity. Cancers (Basel) 2020. [PMID: 33114183 DOI: 10.3390/cancers12113099.pmid:33114183;pmcid:pmc7690808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Transforming growth factor-β (TGF-β) was originally identified as an anti-tumour cytokine. However, there is increasing evidence that it has important roles in the tumour microenvironment (TME) in facilitating cancer progression. TGF-β actively shapes the TME via modulating the host immunity. These actions are highly cell-type specific and complicated, involving both canonical and non-canonical pathways. In this review, we systemically update how TGF-β signalling acts as a checkpoint regulator for cancer immunomodulation. A better appreciation of the underlying pathogenic mechanisms at the molecular level can lead to the discovery of novel and more effective therapeutic strategies for cancer.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Jeff Yat-Fai Chung
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Cristina Alexandra García Córdoba
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Alvin Ho-Kwan Cheung
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Kam-Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hui-Yao Lan
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Patrick Ming-Kuen Tang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong 999077, China
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25
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Transforming Growth Factor-β: A Multifunctional Regulator of Cancer Immunity. Cancers (Basel) 2020; 12:cancers12113099. [PMID: 33114183 PMCID: PMC7690808 DOI: 10.3390/cancers12113099] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Transforming growth factor beta (TGF-β) is a multifunctional cytokine that can restrict cancer onset but also promote cancer progression at late stages of cancer. The ability of TGF-β in producing diverse and sometimes opposing effects relies on its potential to control different cellular signalling and gene expression in distinct cell types, and environmental settings. The tumour promoting role of TGF-β is primarily mediated through its effects on the local tumour microenvironment (TME) of the cancer cells. In this review, we discuss the most recent research on the role and regulation of TGF-β, with a specific focus on its functions on promoting cancer progression through targeting different immune cells in the TME as well as its therapeutic perspectives. Abstract Transforming growth factor-β (TGF-β) was originally identified as an anti-tumour cytokine. However, there is increasing evidence that it has important roles in the tumour microenvironment (TME) in facilitating cancer progression. TGF-β actively shapes the TME via modulating the host immunity. These actions are highly cell-type specific and complicated, involving both canonical and non-canonical pathways. In this review, we systemically update how TGF-β signalling acts as a checkpoint regulator for cancer immunomodulation. A better appreciation of the underlying pathogenic mechanisms at the molecular level can lead to the discovery of novel and more effective therapeutic strategies for cancer.
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26
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Lio CWJ, Huang SCC. Circles of Life: linking metabolic and epigenetic cycles to immunity. Immunology 2020; 161:165-174. [PMID: 32418209 DOI: 10.1111/imm.13207] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolites are the essential substrates for epigenetic modification enzymes to write or erase the epigenetic blueprint in cells. Hence, the availability of nutrients and activity of metabolic pathways strongly influence the enzymatic function. Recent studies have shed light on the choreography between metabolome and epigenome in the control of immune cell differentiation and function, with a major focus on histone modifications. Yet, despite its importance in gene regulation, DNA methylation and its relationship with metabolism is relatively unclear. In this review, we will describe how the metabolic flux can influence epigenetic networks in innate and adaptive immune cells, with a focus on the DNA methylation cycle and the metabolites S-adenosylmethionine and α-ketoglutarate. Future directions will be discussed for this rapidly emerging field.
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Affiliation(s)
- Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA.,Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Stanley Ching-Cheng Huang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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27
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Snyder AD, Ochs SD, Johnson BE, Sulentic CEW. Aryl hydrocarbon receptor-induced activation of the human IGH hs1.2 enhancer: Mutational analysis of putative regulatory binding motifs. Mol Immunol 2020; 120:164-178. [PMID: 32146146 DOI: 10.1016/j.molimm.2020.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/31/2019] [Accepted: 02/06/2020] [Indexed: 11/25/2022]
Abstract
The human hs1.2 enhancer within the Ig heavy chain gene (IGH) is polymorphic and associated with a number of autoimmune diseases. The polymorphic region is characterized by tandem repeats of an ∼53-bp invariant sequence containing possible binding sites for several transcription factors. Our previous studies suggest the human hs1.2 enhancer is sensitive to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and high affinity ligand of the aryl hydrocarbon receptor (AhR). TCDD induced hs1.2 enhancer activity in an AhR-dependent manner and the number of invariant sequences influenced the magnitude of activity. To better understand the regulation of human hs1.2 enhancer activity, the objective of the current study was to utilize mutational analysis and luciferase reporter constructs to evaluate the contribution of putative transcription factor binding sites to overall hs1.2 enhancer activity and modulation by TCDD. Basal and LPS-induced activity of the hs1.2 enhancer appeared to be most affected by mutation of sites outside of the invariant sequence or deletion of the entire invariant sequence; whereas sites influencing the effect of TCDD were dependent on the cellular activation state (i.e. unstimulated vs. LPS stimulation) and relatively independent of the putative AhR binding site within the invariant sequence. These results suggest that AhR activation affects human hs1.2 activity through an as yet undetermined non-canonical pathway. A better understanding regarding the role of the hs1.2 enhancer in human Ig expression and how AhR ligands modulate its activity may lead to insights into overall Ig regulation and mechanisms of dysfunction.
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Affiliation(s)
- Andrew D Snyder
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Sharon D Ochs
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Brooke E Johnson
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States
| | - Courtney E W Sulentic
- Department of Pharmacology & Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, OH, 45435, United States.
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28
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Chatonnet F, Pignarre A, Sérandour AA, Caron G, Avner S, Robert N, Kassambara A, Laurent A, Bizot M, Agirre X, Prosper F, Martin-Subero JI, Moreaux J, Fest T, Salbert G. The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation. Haematologica 2020; 105:774-783. [PMID: 31221779 PMCID: PMC7049362 DOI: 10.3324/haematol.2019.222133] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/19/2019] [Indexed: 01/16/2023] Open
Abstract
Cell identity relies on the cross-talk between genetics and epigenetics and their impact on gene expression. Oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) is the first step of an active DNA demethylation process occurring mainly at enhancers and gene bodies and, as such, participates in processes governing cell identity in normal and pathological conditions. Although genetic alterations are well documented in multiple myeloma (MM), epigenetic alterations associated with this disease have not yet been thoroughly analyzed. To gain insight into the biology of MM, genome-wide 5hmC profiles were obtained and showed that regions enriched in this modified base overlap with MM enhancers and super enhancers and are close to highly expressed genes. Through the definition of a MM-specific 5hmC signature, we identified FAM72D as a poor prognostic gene located on 1q21, a region amplified in high risk myeloma. We further uncovered that FAM72D functions as part of the FOXM1 transcription factor network controlling cell proliferation and survival and we evidenced an increased sensitivity of cells expressing high levels of FOXM1 and FAM72 to epigenetic drugs targeting histone deacetylases and DNA methyltransferases.
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Affiliation(s)
- Fabrice Chatonnet
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Amandine Pignarre
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Aurélien A Sérandour
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Nantes, France
- Institut de Cancérologie de l'Ouest, Site René-Gauducheau, Saint-Herblain, France
| | - Gersende Caron
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Stéphane Avner
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | | | - Audrey Laurent
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Maud Bizot
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Xabier Agirre
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | | | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- IGH, CNRS, Univ Montpellier, France
| | - Thierry Fest
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Gilles Salbert
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
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29
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Zhang Y, Good-Jacobson KL. Epigenetic regulation of B cell fate and function during an immune response. Immunol Rev 2019; 288:75-84. [PMID: 30874352 DOI: 10.1111/imr.12733] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/17/2018] [Indexed: 12/18/2022]
Abstract
The humoral immune response requires coordination of molecular programs to mediate differentiation into unique B cell subsets that help clear the infection and form immune memory. Epigenetic modifications are crucial for ensuring that the appropriate genes are transcribed or repressed during B cell differentiation. Recent studies have illuminated the changes in DNA methylation and histone post-translational modifications that accompany the formation of germinal center and antibody-secreting cells during an immune response. In particular, the B cell subset-specific expression and function of DNA methyltransferases and histone-modifying complexes that mediate epigenome changes have begun to be unravelled. This review will discuss the recent advances in this field, as well as highlight critical questions about the relationship between epigenetic regulation and B cell fate and function that are yet to be answered.
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Affiliation(s)
- Yan Zhang
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kim L Good-Jacobson
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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30
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Dalloul I, Boyer F, Dalloul Z, Pignarre A, Caron G, Fest T, Chatonnet F, Delaloy C, Durandy A, Jeannet R, Lereclus E, Boutouil H, Aldigier JC, Péron S, Le Noir S, Cook-Moreau J, Cogné M. Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues. PLoS Genet 2019; 15:e1007721. [PMID: 31199803 PMCID: PMC6594652 DOI: 10.1371/journal.pgen.1007721] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 06/26/2019] [Accepted: 05/14/2019] [Indexed: 12/24/2022] Open
Abstract
B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin (Ig) genes by activation-induced deaminase (AID). AID promotes affinity maturation of Ig variable regions and class switch recombination (CSR) in mature B lymphocytes. In the IgH locus, these processes are under control of the 3' regulatory region (3'RR) super-enhancer, a region demonstrated in the mouse to be both transcribed and itself targeted by AID-mediated recombination. Alternatively to CSR, IgH deletions joining Sμ to "like-switch" DNA repeats that flank the 3' super-enhancer can thus accomplish so-called "locus suicide recombination" (LSR) in mouse B-cells. Using an optimized LSR-seq high throughput method, we now show that AID-mediated LSR is evolutionarily conserved and also actively occurs in humans, providing an activation-induced cell death pathway in multiple conditions of B-cell activation. LSR either focuses on the functional IgH allele or is bi-allelic, and its signature is mainly detected when LSR is ongoing while it vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells. Highly diversified breakpoints are distributed either within the upstream (3'RR1) or downstream (3'RR2) copies of the IgH 3' super-enhancer and all conditions activating CSR in vitro also seem to trigger LSR although TLR ligation appeared the most efficient. Molecular analysis of breakpoints and junctions confirms that LSR is AID-dependent and reveals junctional sequences somehow similar to CSR junctions but with increased usage of microhomologies.
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Affiliation(s)
- Iman Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - François Boyer
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Zeinab Dalloul
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Gersende Caron
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | - Thierry Fest
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Céline Delaloy
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
| | | | - Robin Jeannet
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Emilie Lereclus
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Hend Boutouil
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | | | - Sophie Péron
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Sandrine Le Noir
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
| | - Jeanne Cook-Moreau
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
| | - Michel Cogné
- CNRS UMR 7276 / INSERM U1262, Université de Limoges, Limoges, France
- INSERM U1236, Université de Rennes; EFS Bretagne, Rennes, France
- MC and JCM co-directed this work
- * E-mail: (MC); (JCM)
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31
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Schoeler K, Aufschnaiter A, Messner S, Derudder E, Herzog S, Villunger A, Rajewsky K, Labi V. TET enzymes control antibody production and shape the mutational landscape in germinal centre B cells. FEBS J 2019; 286:3566-3581. [PMID: 31120187 PMCID: PMC6851767 DOI: 10.1111/febs.14934] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022]
Abstract
Upon activation by antigen, B cells form germinal centres where they clonally expand and introduce affinity-enhancing mutations into their B-cell receptor genes. Somatic mutagenesis and class switch recombination (CSR) in germinal centre B cells are initiated by the activation-induced cytidine deaminase (AID). Upon germinal centre exit, B cells differentiate into antibody-secreting plasma cells. Germinal centre maintenance and terminal fate choice require transcriptional reprogramming that associates with a substantial reconfiguration of DNA methylation patterns. Here we examine the role of ten-eleven-translocation (TET) proteins, enzymes that facilitate DNA demethylation and promote a permissive chromatin state by oxidizing 5-methylcytosine, in antibody-mediated immunity. Using a conditional gene ablation strategy, we show that TET2 and TET3 guide the transition of germinal centre B cells to antibody-secreting plasma cells. Optimal AID expression requires TET function, and TET2 and TET3 double-deficient germinal centre B cells show defects in CSR. However, TET2/TET3 double-deficiency does not prevent the generation and selection of high-affinity germinal centre B cells. Rather, combined TET2 and TET3 loss-of-function in germinal centre B cells favours C-to-T and G-to-A transition mutagenesis, a finding that may be of significance for understanding the aetiology of B-cell lymphomas evolving in conditions of reduced TET function.
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Affiliation(s)
- Katia Schoeler
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Andreas Aufschnaiter
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Simon Messner
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Emmanuel Derudder
- Institute for Biomedical Aging Research, University of Innsbruck, Austria
| | - Sebastian Herzog
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
| | - Andreas Villunger
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Klaus Rajewsky
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
| | - Verena Labi
- Division of Developmental Immunology, Biocenter, Medical University of Innsbruck, Austria
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32
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Willis SN, Nutt SL. New players in the gene regulatory network controlling late B cell differentiation. Curr Opin Immunol 2019; 58:68-74. [DOI: 10.1016/j.coi.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
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33
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Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman R, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature 2019; 569:576-580. [PMID: 31092926 PMCID: PMC6533116 DOI: 10.1038/s41586-019-1198-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy2,3. The CLL epigenome is also an important disease-defining feature4,5, and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations6. However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously. Here, to measure the epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced-representation bisulfite sequencing to B cells from healthy donors and patients with CLL. We observed that the common clonal origin of CLL results in a consistently increased epimutation rate, with low variability in the cell-to-cell epimutation rate. By contrast, variable epimutation rates across healthy B cells reflect diverse evolutionary ages across the trajectory of B cell differentiation, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed us to reconstruct lineages at high-resolution with single-cell data, and to apply this directly to patient samples. The CLL lineage tree shape revealed earlier branching and longer branch lengths than in normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. Integration of single-cell bisulfite sequencing analysis with single-cell transcriptomes and genotyping confirmed that genetic subclones mapped to distinct clades, as inferred solely on the basis of epimutation information. Finally, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells that were preferentially expelled from the lymph node after treatment, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts the lineage history of CLL and its evolution with therapy.
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Affiliation(s)
- Federico Gaiti
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ryan Matthew Brand
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Steven Kothen-Hill
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Rafael Schulman
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | - Davide Risso
- Weill Cornell Medicine, New York, NY, 10021, USA,Department of Statistical Sciences, University of Padova, Padova, 35121, Italy
| | - Kyu-Tae Kim
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kevin Y. Huang
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | | | | | - Nathaniel D. Omans
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Evan Biederstedt
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lili Wang
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA,Beckman Research Institute, City of Hope, Monrovia, CA, 91016, USA
| | | | | | - Martin J. Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine J. Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Dan A. Landau
- New York Genome Center, New York, NY, 10013, USA,Weill Cornell Medicine, New York, NY, 10021, USA,Corresponding author: Dan A. Landau, MD, PhD, Weill Cornell Medicine, Belfer Research Building, 413 East 69th Street, New York, NY 10021,
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34
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Del Pino-Molina L, Rodríguez-Ubreva J, Torres Canizales J, Coronel-Díaz M, Kulis M, Martín-Subero JI, van der Burg M, Ballestar E, López-Granados E. Impaired CpG Demethylation in Common Variable Immunodeficiency Associates With B Cell Phenotype and Proliferation Rate. Front Immunol 2019; 10:878. [PMID: 31105700 PMCID: PMC6492528 DOI: 10.3389/fimmu.2019.00878] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/05/2019] [Indexed: 01/01/2023] Open
Abstract
Common Variable Immunodeficiency (CVID) is characterized by impaired antibody production and poor terminal differentiation of the B cell compartment, yet its pathogenesis is still poorly understood. We first reported the occurrence of epigenetic alterations in CVID by high-throughput methylation analysis in CVID-discordant monozygotic twins. Data from a recent whole DNA methylome analysis throughout different stages of normal B cell differentiation allowed us to design a new experimental approach. We selected CpG sites for analysis based on two criteria: one, CpGs with potential association with the transcriptional status of relevant genes for B cell activation and differentiation; and two, CpGs that undergo significant demethylation from naïve to memory B cells in healthy individuals. DNA methylation was analyzed by bisulfite pyrosequencing of specific CpG sites in sorted naïve and memory B cell subsets from CVID patients and healthy donors. We observed impaired demethylation in two thirds of the selected CpGs in CVID memory B cells, in genes that govern B cell-specific processes or participate in B cell signaling. The degree of demethylation impairment associated with the extent of the memory B cell reduction. The impaired demethylation in such functionally relevant genes as AICDA in switched memory B cells correlated with a lower proliferative rate. Our new results reinforce the hypothesis of altered demethylation during B cell differentiation as a contributing pathogenic mechanism to the impairment of B cell function and maturation in CVID. In particular, deregulated epigenetic control of AICDA could play a role in the defective establishment of a post-germinal center B cell compartment in CVID.
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Affiliation(s)
- Lucía Del Pino-Molina
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Juan Torres Canizales
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - María Coronel-Díaz
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo López-Granados
- Lymphocyte Pathophysiology in Immunodeficiencies Group, Department of Clinical Immunology, IdiPAZ Institute for Health Research, University Hospital La Paz, Madrid, Spain
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35
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EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation. Leukemia 2019; 33:2047-2060. [PMID: 30755708 PMCID: PMC6756037 DOI: 10.1038/s41375-019-0392-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/09/2018] [Accepted: 01/11/2019] [Indexed: 12/13/2022]
Abstract
Plasma cells (PCs) play a major role in the defense of the host organism against pathogens. We have shown that PC generation can be modeled using multi-step culture systems that reproduce the sequential cell differentiation occurring in vivo. Using this unique model, we investigated the role of EZH2 during PC differentiation (PCD) using H3K27me3 and EZH2 ChIP-binding profiles. We then studied the effect of the inhibition of EZH2 enzymatic activity to understand how EZH2 regulates the key functions involved in PCD. EZH2 expression significantly increases in preplasmablasts with H3K27me3 mediated repression of genes involved in B cell and plasma cell identity. EZH2 was also found to be recruited to H3K27me3-free promoters of transcriptionally active genes known to regulate cell proliferation. Inhibition the catalytic activity of EZH2 resulted in B to PC transcriptional changes associated with PC maturation induction, as well as higher immunoglobulin secretion. Altogether, our data suggest that EZH2 is involved in the maintenance of preplasmablast transitory immature proliferative state that supports their amplification.
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36
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Paczkowska J, Soloch N, Bodnar M, Kiwerska K, Janiszewska J, Vogt J, Domanowska E, Martin-Subero JI, Ammerpohl O, Klapper W, Marszalek A, Siebert R, Giefing M. Expression of ELF1, a lymphoid ETS domain-containing transcription factor, is recurrently lost in classical Hodgkin lymphoma. Br J Haematol 2019; 185:79-88. [PMID: 30681722 DOI: 10.1111/bjh.15757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 01/06/2023]
Abstract
Loss of B cell-specific transcription factors (TFs) and the resulting loss of B-cell phenotype of Hodgkin and Reed-Sternberg (HRS) cells is a hallmark of classical Hodgkin lymphoma (cHL). Here we have analysed two members of ETS domain containing TFs, ELF1 and ELF2, regarding (epi)genomic changes as well as gene and protein expression. We observed absence or lower levels of ELF1 protein in HRS cells of 31/35 (89%) cases compared to the bystander cells and significant (P < 0·01) downregulation of the gene on mRNA as well as protein level in cHL compared to non-cHL cell lines. However, no recurrent loss of ELF2 protein was observed. Moreover, ELF1 was targeted by heterozygous deletions combined with hypermethylation of the remaining allele(s) in 4/7 (57%) cell lines. Indeed, DNA hypermethylation (range 95-99%, mean 98%) detected in the vicinity of the ELF1 transcription start site was found in all 7/7 (100%) cHL cell lines. Similarly, 5/18 (28%) analysed primary biopsies carried heterozygous deletions of the gene. We demonstrate that expression of ELF1 is impaired in cHL through genetic and epigenetic alterations, and thus, it may represent an additional member of a TF network whose downregulation contributes to the loss of B-cell phenotype of HRS cells.
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Affiliation(s)
- Julia Paczkowska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Natalia Soloch
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Science, Poznan, Poland
| | - Katarzyna Kiwerska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Tumour Pathology, Greater Poland Cancer Centre, Poznan, Poland
| | | | - Julia Vogt
- Institute of Human Genetics, Ulm University & Ulm University Medical Centre, Ulm, Germany
| | - Ewa Domanowska
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - José I Martin-Subero
- Insitut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University & Ulm University Medical Centre, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Wolfram Klapper
- Department of Pathology, Hematopathology Section and Lymph Node Registry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andrzej Marszalek
- Department of Tumour Pathology and Prophylaxis, Poznan University of Medical Sciences & Greater Poland Cancer Centre, Poznan, Poland
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Centre, Ulm, Germany.,Institute of Human Genetics, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Institute of Human Genetics, Christian-Albrechts-University Kiel, Kiel, Germany
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37
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Hoque SAM, Kawai T, Zhu Z, Shimada M. Mitochondrial Protein Turnover Is Critical for Granulosa Cell Proliferation and Differentiation in Antral Follicles. J Endocr Soc 2018; 3:324-339. [PMID: 30652133 PMCID: PMC6330174 DOI: 10.1210/js.2018-00329] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/27/2018] [Indexed: 12/28/2022] Open
Abstract
Granulosa cell (GC) proliferation is essential for follicular development. FSH is a key factor in GC proliferation, and a continuous supply of high levels of ATP is necessary for cell proliferation. However, genes encoding proteins of the glycolytic pathways are poorly expressed in GCs. Therefore, we hypothesized that mitochondrial gene expression and protein synthesis play a primary role in ATP production during GC proliferation. To test this hypothesis, we performed an in vivo study of GCs collected from 23-day-old mice ovaries with or without equine chorionic gonadotropin (eCG) priming. It was observed that mitochondrial activity with membrane potential, expression of protein-coding genes (Nd1-6, Cytb, Atpase6,8) and transcription-related genes (Polrmt, Tfam, Tfb2m), copy number of mitochondrial (mt-)DNA, and protein synthesis were increased in GCs after 24 hours of eCG injection and mostly maintained elevated up to 48 hours. Therefore, we performed in vitro culture of GCs in DMEM medium supplemented with FSH, testosterone, and serum and containing different glucose concentrations with or without d-chloramphenicol (CRP) for 24 hours. GC proliferation and ATP production were observed to be independent of glucose concentration. Furthermore, FSH-induced mitochondrial activity with membrane potential, ATP content, BrdU-incorporated cell proliferation, intensity of mt-ND1 and mt-ND6 proteins, and expressions of marker genes for proliferation and differentiation were significantly decreased by CRP treatment. These results revealed the crucial role of mitochondria in the supply of ATP and the necessity of mitochondrial gene expression and protein synthesis in not only the proliferation but also the differentiation of GCs during follicular development.
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Affiliation(s)
- S A Masudul Hoque
- Laboratory of Reproductive Endocrinology, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.,Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tomoko Kawai
- Laboratory of Reproductive Endocrinology, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Zhendong Zhu
- Laboratory of Reproductive Endocrinology, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.,College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Masayuki Shimada
- Laboratory of Reproductive Endocrinology, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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38
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Insight into origins, mechanisms, and utility of DNA methylation in B-cell malignancies. Blood 2018; 132:999-1006. [PMID: 30037886 DOI: 10.1182/blood-2018-02-692970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding how tumor cells fundamentally alter their identity is critical to identify specific vulnerabilities for use in precision medicine. In B-cell malignancy, knowledge of genetic changes has resulted in great gains in our understanding of the biology of tumor cells, impacting diagnosis, prognosis, and treatment. Despite this knowledge, much remains to be explained as genetic events do not completely explain clinical behavior and outcomes. Many patients lack recurrent driver mutations, and said drivers can persist in nonmalignant cells of healthy individuals remaining cancer-free for decades. Epigenetics has emerged as a valuable avenue to further explain tumor phenotypes. The epigenetic landscape is the software that powers and stabilizes cellular identity by abridging a broad genome into the essential information required per cell. A genome-level view of B-cell malignancies reveals complex but recurrent epigenetic patterns that define tumor types and subtypes, permitting high-resolution classification and novel insight into tumor-specific mechanisms. Epigenetic alterations are guided by distinct cellular processes, such as polycomb-based silencing, transcription, signaling pathways, and transcription factor activity, and involve B-cell-specific aspects, such as activation-induced cytidine deaminase activity and germinal center-specific events. Armed with a detailed knowledge of the epigenetic events that occur across the spectrum of B-cell differentiation, B-cell tumor-specific aberrations can be detected with improved accuracy and serve as a model for identification of tumor-specific events in cancer. Insight gained through recent efforts may prove valuable in guiding the use of both epigenetic- and nonepigenetic-based therapies.
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39
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Barwick BG, Scharer CD, Martinez RJ, Price MJ, Wein AN, Haines RR, Bally APR, Kohlmeier JE, Boss JM. B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation. Nat Commun 2018; 9:1900. [PMID: 29765016 PMCID: PMC5953949 DOI: 10.1038/s41467-018-04234-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/10/2018] [Indexed: 12/22/2022] Open
Abstract
B cells provide humoral immunity by differentiating into antibody-secreting plasma cells, a process that requires cellular division and is linked to DNA hypomethylation. Conversely, little is known about how de novo deposition of DNA methylation affects B cell fate and function. Here we show that genetic deletion of the de novo DNA methyltransferases Dnmt3a and Dnmt3b (Dnmt3-deficient) in mouse B cells results in normal B cell development and maturation, but increased cell activation and expansion of the germinal center B cell and plasma cell populations upon immunization. Gene expression is mostly unaltered in naive and germinal center B cells, but dysregulated in Dnmt3-deficient plasma cells. Differences in gene expression are proximal to Dnmt3-dependent DNA methylation and chromatin changes, both of which coincide with E2A and PU.1-IRF composite-binding motifs. Thus, de novo DNA methylation limits B cell activation, represses the plasma cell chromatin state, and regulates plasma cell differentiation.
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Affiliation(s)
- Benjamin G Barwick
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, 1701 Uppergate Drive, WCI 4060 C, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Ryan J Martinez
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Medicine, Emory University School of Medicine, 1648 Pierce Dr. NE, Atlanta, GA, 30307, USA
| | - Madeline J Price
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Alexander N Wein
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Robert R Haines
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Alexander P R Bally
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
- Department of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, 954 Gatewood Rd NE, Suite 3052, Atlanta, GA, 30329, USA
| | - Jacob E Kohlmeier
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Rd., Rm 3001, Atlanta, GA, 30322, USA.
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Lejart A, Salbert G, Huet S. Cytosine hydroxymethylation by TET enzymes: From the control of gene expression to the regulation of DNA repair mechanisms, and back. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Bagacean C, Le Dantec C, Berthou C, Tempescul A, Saad H, Bordron A, Zdrenghea M, Cristea V, Douet-Guilbert N, Renaudineau Y. Combining cytogenetic and epigenetic approaches in chronic lymphocytic leukemia improves prognosis prediction for patients with isolated 13q deletion. Clin Epigenetics 2017; 9:122. [PMID: 29209431 PMCID: PMC5704505 DOI: 10.1186/s13148-017-0422-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/17/2017] [Indexed: 11/10/2022] Open
Abstract
Background Both defective DNA methylation and active DNA demethylation processes are emerging as important risk factors in chronic lymphocytic leukemia (CLL). However, associations between 5-cytosine epigenetic markers and the most frequent chromosomal abnormalities detected in CLL remain to be established. Methods CLL patients were retrospectively classified into a cytogenetic low-risk group (isolated 13q deletion), an intermediate-risk group (normal karyotype or trisomy 12), and a high-risk group (11q deletion, 17p deletion, or complex karyotype [≥ 3 breakpoints]). The two 5-cytosine derivatives, 5-methylcytosine (5-mCyt) and 5-hydroxymethylcytosine (5-hmCyt), were tested by ELISA (n = 60), while real-time quantitative PCR was used for determining transcriptional expression levels of DNMT and TET (n = 24). Results By using global DNA methylation/demethylation levels, in the low-risk disease group, two subgroups with significantly different clinical outcomes have been identified (median treatment-free survival [TFS] 45 versus > 120 months for 5-mCyt, p = 0.0008, and 63 versus > 120 months for 5-hmCyt, p = 0.04). A defective 5-mCyt status was further associated with a higher percentage of 13q deleted nuclei (> 80%), thus suggesting an acquired process. When considering the cytogenetic intermediate/high-risk disease groups, an association of 5-mCyt status with lymphocytosis (p = 0.0008) and the lymphocyte doubling time (p = 0.04) but not with TFS was observed, as well as a reduction of DNMT3A, TET1, and TET2 transcripts. Conclusions Combining cytogenetic studies with 5-mCyt assessment adds accuracy to CLL patients’ prognoses and particularly for those with 13q deletion as a sole cytogenetic abnormality.
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Affiliation(s)
- Cristina Bagacean
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France.,"Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Christelle Le Dantec
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Christian Berthou
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Adrian Tempescul
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Anne Bordron
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France
| | - Mihnea Zdrenghea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Yves Renaudineau
- U1227 B lymphocytes and autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, networks IC-CGO and REpiCGO from "Canceropole Grand Ouest", Brest, France.,Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, BP 824, 29609 Brest, France
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CD8 + T Lymphocyte Self-Renewal during Effector Cell Determination. Cell Rep 2017; 17:1773-1782. [PMID: 27829149 DOI: 10.1016/j.celrep.2016.10.032] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/03/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022] Open
Abstract
Selected CD8+ T cells must divide, produce differentiated effector cells, and self-renew, often repeatedly. We now show that silencing expression of the transcription factor TCF1 marks loss of self-renewal by determined effector cells and that this requires cell division. In acute infections, the first three CD8+ T cell divisions produce daughter cells with unequal proliferative signaling but uniform maintenance of TCF1 expression. The more quiescent initial daughter cells resemble canonical central memory cells. The more proliferative, effector-prone cells from initial divisions can subsequently undergo division-dependent production of a TCF1-negative effector daughter cell along with a self-renewing TCF1-positive daughter cell, the latter also contributing to the memory cell pool upon resolution of infection. Self-renewal in the face of effector cell determination may promote clonal amplification and memory cell formation in acute infections, sustain effector regeneration during persistent subclinical infections, and be rate limiting, but remediable, in chronic active infections and cancer.
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Hipp N, Symington H, Pastoret C, Caron G, Monvoisin C, Tarte K, Fest T, Delaloy C. IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression. Nat Commun 2017; 8:1443. [PMID: 29129929 PMCID: PMC5682283 DOI: 10.1038/s41467-017-01475-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/19/2017] [Indexed: 01/23/2023] Open
Abstract
Plasma cell differentiation is a tightly regulated process that requires appropriate T cell helps to reach the induction threshold. To further understand mechanisms by which T cell inputs regulate B cell fate decision, we investigate the minimal IL-2 stimulation for triggering human plasma cell differentiation in vitro. Here we show that the timed repression of BACH2 through IL-2-mediated ERK/ELK1 signalling pathway directs plasma cell lineage commitment. Enforced BACH2 repression in activated B cells unlocks the plasma cell transcriptional program and induces their differentiation into immunoglobulin M-secreting cells. RNA-seq and ChIP-seq results further identify BACH2 target genes involved in this process. An active regulatory region within the BACH2 super-enhancer, under ELK1 control and differentially regulated upon B-cell activation and cellular divisions, helps integrate IL-2 signal. Our study thus provides insights into the temporal regulation of BACH2 and its targets for controlling the differentiation of human naive B cells. T cells help B cells to differentiate into antibody-producing plasma cells. Here the authors show that T cells produce interleukin-2 to activate ERK/ELK1 and suppress BACH2 expression by modulating the BACH2 super-enhancer, thereby altering BACH2 downstream transcription programs for plasma cell differentiation.
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Affiliation(s)
- Nicolas Hipp
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France
| | - Hannah Symington
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France
| | - Cédric Pastoret
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France.,Laboratoire d'Hématologie, Centre Hospitalier Universitaire (CHU) Rennes, 2 rue Henri Le Guilloux, 35033, Rennes Cedex 9, France
| | - Gersende Caron
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France.,Laboratoire d'Hématologie, Centre Hospitalier Universitaire (CHU) Rennes, 2 rue Henri Le Guilloux, 35033, Rennes Cedex 9, France
| | - Céline Monvoisin
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France
| | - Karin Tarte
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France.,Laboratoire d'Immunologie, Thérapie Cellulaire et Hématopoïèse (ITeCH), Centre Hospitalier Universitaire (CHU) Rennes, 2 rue Henri Le Guilloux, 35033, Rennes Cedex 9, France
| | - Thierry Fest
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France. .,Laboratoire d'Hématologie, Centre Hospitalier Universitaire (CHU) Rennes, 2 rue Henri Le Guilloux, 35033, Rennes Cedex 9, France.
| | - Céline Delaloy
- UMR U1236, Université de Rennes 1, INSERM, Etablissement Français du Sang (EFS) de Bretagne, Equipe labellisée Ligue contre le Cancer, Labex IGO, 2 Av du Pr Léon Bernard, 35043, Rennes, France.
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Charting the dynamic epigenome during B-cell development. Semin Cancer Biol 2017; 51:139-148. [PMID: 28851627 DOI: 10.1016/j.semcancer.2017.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The epigenetic landscape undergoes a widespread modulation during embryonic development and cell differentiation. Within the hematopoietic system, B cells are perhaps the cell lineage with a more dynamic DNA methylome during their maturation process, which involves approximately one third of all the CpG sites of the genome. Although each B-cell maturation step displays its own DNA methylation fingerprint, the DNA methylome is more extensively modified in particular maturation transitions. These changes are gradually accumulated in specific chromatin environments as cell differentiation progresses and reflect different features and functional states of B cells. Promoters and enhancers of B-cell transcription factors acquire activation-related epigenetic marks and are sequentially expressed in particular maturation windows. These transcription factors further reconfigure the epigenetic marks and activity state of their target sites to regulate the expression of genes related to B-cell functions. Together with this observation, extensive DNA methylation changes in areas outside gene regulatory elements such as hypomethylation of heterochromatic regions and hypermethylation of CpG-rich regions, also take place in mature B cells, which intriguingly have been described as hallmarks of cancer. This process starts in germinal center B cells, a highly proliferative cell type, and becomes particularly apparent in long-lived cells such as memory and plasma cells. Overall, the characterization of the DNA methylome during B-cell differentiation not only provides insights into the complex epigenetic network of regulatory elements that mediate the maturation process but also suggests that late B cells also passively accumulate epigenetic changes related to cell proliferation and longevity.
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Valor LM, Rodríguez-Bayona B, Ramos-Amaya AB, Brieva JA, Campos-Caro A. The transcriptional profiling of human in vivo-generated plasma cells identifies selective imbalances in monoclonal gammopathies. PLoS One 2017; 12:e0183264. [PMID: 28817638 PMCID: PMC5560601 DOI: 10.1371/journal.pone.0183264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Plasma cells (PC) represent the heterogeneous final stage of the B cells (BC) differentiation process. To characterize the transition of BC into PC, transcriptomes from human naïve BC were compared to those of three functionally-different subsets of human in vivo-generated PC: i) tonsil PC, mainly consisting of early PC; ii) PC released to the blood after a potent booster-immunization (mostly cycling plasmablasts); and, iii) bone marrow CD138+ PC that represent highly mature PC and include the long-lived PC compartment. This transcriptional transition involves subsets of genes related to key processes for PC maturation: the already known protein processing, apoptosis and homeostasis, and of new discovery including histones, macromolecule assembly, zinc-finger transcription factors and neuromodulation. This human PC signature is partially reproduced in vitro and is conserved in mouse. Moreover, the present study identifies genes that define PC subtypes (e.g., proliferation-associated genes for circulating PC and transcriptional-related genes for tonsil and bone marrow PC) and proposes some putative transcriptional regulators of the human PC signatures (e.g., OCT/POU, XBP1/CREB, E2F, among others). Finally, we also identified a restricted imbalance of the present PC transcriptional program in monoclonal gammopathies that correlated with PC malignancy.
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Affiliation(s)
- Luis M. Valor
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Beatriz Rodríguez-Bayona
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Ana B. Ramos-Amaya
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - José A. Brieva
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
| | - Antonio Campos-Caro
- Unidad de Investigación, Hospital Universitario Puerta del Mar and Instituto de Investigación e Innovación en Ciencias Biomédicas de Cádiz (INiBICA), Cádiz, Spain
- * E-mail:
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Tsuchida Y, Sumitomo S, Ishigaki K, Suzuki A, Kochi Y, Tsuchiya H, Ota M, Komai T, Inoue M, Morita K, Okamura T, Yamamoto K, Fujio K. TGF-β3 Inhibits Antibody Production by Human B Cells. PLoS One 2017; 12:e0169646. [PMID: 28052118 PMCID: PMC5215424 DOI: 10.1371/journal.pone.0169646] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022] Open
Abstract
TGF-β is a pleotropic cytokine involved in various biological processes. Of the three isoforms of TGF-β, TGF-β1 has long been recognized as an important inhibitory cytokine in the immune system and has been reported to inhibit B cell function in both mice and humans. Recently, it has been suggested that TGF-β3 may play an important role in the regulation of immune system in mice. Murine CD4+CD25-LAG3+ regulatory T cells suppress B cell function through the production of TGF-β3, and it has been reported that TGF-β3 is therapeutic in a mouse model of systemic lupus erythematosus. The effect of TGF-β3 on human B cells has not been reported, and we herein examined the effect of TGF-β3 on human B cells. TGF-β3 suppressed B cell survival, proliferation, differentiation into plasmablasts, and antibody secretion. Although the suppression of human B cells by TGF-β1 has long been recognized, the precise mechanism for the suppression of B cell function by TGF-β1 remains elusive; therefore, we examined the effect of TGF-β1 and β3 on pathways important in B cell activation and differentiation. TGF-β1 and TGF-β3 inhibited some of the key molecules of the cell cycle, as well as transcription factors important in B cell differentiation into antibody secreting cells such as IRF4, Blimp-1, and XBP1. TGF-β1 and β3 also inhibited B cell receptor signaling. Our results suggest that TGF-β3 modifying therapy might be therapeutic in autoimmune diseases with B cell dysregulation in humans.
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Affiliation(s)
- Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shuji Sumitomo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiko Komai
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mariko Inoue
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kaoru Morita
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Max Planck-The University of Tokyo Center for Integrative Inflammology, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Jiang Z, Xu W, Dan G, Liu Y, Xiong J. P53 and Murine Double Mimute 2 (MDM2) Expression Changes and Significance in Different Types of Endometrial Lesions. Med Sci Monit 2016; 22:4786-4793. [PMID: 27924072 PMCID: PMC5158131 DOI: 10.12659/msm.898616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Endometrial lesions are common in obstetrics and gynecology, including endometrial polyps, uterine adenomyosis, and malignant endometrial adenocarcinoma. Endometrial lesions seriously affect women’s health, fertility, quality of life, and life safety. As a pro-apoptosis gene, p53 is considered to be closely related with human tumors. Murine double mimute 2 (MDM2) is an oncogene that can promote tumor occurrence and development. P53 and MDM2 expression and significance in different types of endometrial lesions have not been fully elucidated. Material/Methods Normal endometrium, endometrial polyps, uterine adenomyosis, and endometrial adenocarcinoma tissue samples were collected. Real-time PCR was used to detect p53 and MDM2 mRNA expression. Immunohistochemical staining and Western blot analysis were applied to test p53 and MDM2 protein expression. Their correlation with clinical staging of endometrial adenocarcinoma was analyzed. Results P53 and MDM2 mRNA and protein expression were significantly elevated in the endometrial polyps group and the endometrial adenocarcinoma group compared with the normal control group (P<0.05). Their levels increased more obviously in endometrial adenocarcinoma compared with endometrial polyps (P<0.05). P53 and MDM2 mRNA and protein expression were slightly enhanced in uterine adenomyosis compared with normal controls, but this difference lacked statistical significance (P>0.05). P53 and MDM2 mRNA and protein level showed a positive correlation. Significantly higher expression of p53 or MDM2 was observed in patients with stage III compared to those in patients with stage II. Higher expression was also observed in patients with stage II than in patients with stage I. Conclusions P53 and MDM2 mRNA and protein were elevated in endometrial polyps and endometrial adenocarcinoma and their expressions were correlated with clinical staging of endometrial adenocarcinoma. They can promote cancer occurrence and development, and can be treated to assist diagnosis and provide a reference for treatment.
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Affiliation(s)
- Zhongyong Jiang
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Wanqing Xu
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Gang Dan
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Yuan Liu
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
| | - Jie Xiong
- Department of Clinical Laboratory, Chengdu Military General Hospital, Chengdu Military District, Chengdu, Sichuan, China (mainland)
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Nish SA, Zens KD, Kratchmarov R, Lin WHW, Adams WC, Chen YH, Yen B, Rothman NJ, Bhandoola A, Xue HH, Farber DL, Reiner SL. CD4+ T cell effector commitment coupled to self-renewal by asymmetric cell divisions. J Exp Med 2016; 214:39-47. [PMID: 27923906 PMCID: PMC5206501 DOI: 10.1084/jem.20161046] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/06/2016] [Accepted: 11/10/2016] [Indexed: 12/24/2022] Open
Abstract
Nish et al. report that production of a fully committed Th1 effector cell occurs during an asymmetric cell division wherein the other daughter cell remains memory cell–like. Unequal transmission of metabolic signaling may be the driver of this regenerative behavior. Upon infection, an activated CD4+ T cell produces terminally differentiated effector cells and renews itself for continued defense. In this study, we show that differentiation and self-renewal arise as opposing outcomes of sibling CD4+ T cells. After influenza challenge, antigen-specific cells underwent several divisions in draining lymph nodes (LN; DLNs) while maintaining expression of TCF1. After four or five divisions, some cells silenced, whereas some cells maintained TCF1 expression. TCF1-silenced cells were T helper 1–like effectors and concentrated in the lungs. Cells from earliest divisions were memory-like and concentrated in nondraining LN. TCF1-expressing cells from later divisions in the DLN could self-renew, clonally yielding a TCF1-silenced daughter cell as well as a sibling cell maintaining TCF1 expression. Some TCF1-expressing cells in DLNs acquired an alternative, follicular helper-like fate. Modeled differentiation experiments in vitro suggested that unequal PI3K/mechanistic target of rapamycin signaling drives intraclonal cell fate heterogeneity. Asymmetric division enables self-renewal to be coupled to production of differentiated CD4+ effector T cells during clonal selection.
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Affiliation(s)
- Simone A Nish
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Kyra D Zens
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Surgery, Columbia University Medical Center, New York, NY 10032
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Wen-Hsuan W Lin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - William C Adams
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Yen-Hua Chen
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Bonnie Yen
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Nyanza J Rothman
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Avinash Bhandoola
- T-Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Hai-Hui Xue
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032.,Department of Surgery, Columbia University Medical Center, New York, NY 10032
| | - Steven L Reiner
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032 .,Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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50
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Tekpli X, Urbanucci A, Hashim A, Vågbø CB, Lyle R, Kringen MK, Staff AC, Dybedal I, Mills IG, Klungland A, Staerk J. Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells. Epigenetics Chromatin 2016; 9:21. [PMID: 27252783 PMCID: PMC4888655 DOI: 10.1186/s13072-016-0070-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/20/2016] [Indexed: 01/01/2023] Open
Abstract
Background Hematopoietic stem cell renewal and differentiation are regulated through epigenetic processes. The conversion of 5-methylcytosine into 5-hydroxymethylcytosine (5hmC) by ten-eleven-translocation enzymes provides new insights into the epigenetic regulation of gene expression during development. Here, we studied the potential gene regulatory role of 5hmC during human hematopoiesis. Results We used reduced representation of 5-hydroxymethylcytosine profiling (RRHP) to characterize 5hmC distribution in CD34+ cells, CD4+ T cells, CD19+ B cells, CD14+ monocytes and granulocytes. In all analyzed blood cell types, the presence of 5hmC at gene bodies correlates positively with gene expression, and highest 5hmC levels are found around transcription start sites of highly expressed genes. In CD34+ cells, 5hmC primes for the expression of genes regulating myeloid and lymphoid lineage commitment. Throughout blood cell differentiation, intragenic 5hmC is maintained at genes that are highly expressed and required for acquisition of the mature blood cell phenotype. Moreover, in CD34+ cells, the presence of 5hmC at enhancers associates with increased binding of RUNX1 and FLI1, transcription factors essential for hematopoiesis. Conclusions Our study provides a comprehensive genome-wide overview of 5hmC distribution in human hematopoietic cells and new insights into the epigenetic regulation of gene expression during human hematopoiesis. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0070-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xavier Tekpli
- Nordic European Molecular Laboratory (EMBL) Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, P.O. Box 1137, 0318 Oslo, Norway ; Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway
| | - Alfonso Urbanucci
- Nordic European Molecular Laboratory (EMBL) Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, P.O. Box 1137, 0318 Oslo, Norway ; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Adnan Hashim
- Nordic European Molecular Laboratory (EMBL) Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, P.O. Box 1137, 0318 Oslo, Norway
| | - Cathrine B Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Robert Lyle
- Department of Medical Genetics, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Marianne K Kringen
- Department of Pharmacology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Anne Cathrine Staff
- Department of Obstetrics and Gynecology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Ingunn Dybedal
- Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Ian G Mills
- Nordic European Molecular Laboratory (EMBL) Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, P.O. Box 1137, 0318 Oslo, Norway ; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway ; PCUK Movember Centre of Excellence, CCRCB, Queen's University, Belfast, UK
| | - Arne Klungland
- Clinic for Diagnostics and Intervention, Institute of Medical Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway ; Norwegian Center for Stem Cell Research, University of Oslo, Oslo, Norway
| | - Judith Staerk
- Nordic European Molecular Laboratory (EMBL) Partnership, Centre for Molecular Medicine Norway, University of Oslo, Blindern, P.O. Box 1137, 0318 Oslo, Norway ; Department of Haematology, Oslo University Hospital, Oslo, Norway ; Norwegian Center for Stem Cell Research, University of Oslo, Oslo, Norway
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