1
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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2
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Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D. Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites. Nat Microbiol 2024; 9:228-240. [PMID: 38172619 DOI: 10.1038/s41564-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France.
| | - Gael A Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Eloi Littner
- Sorbonne Université, Collège Doctoral, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Jean Cury
- Université Paris-Saclay, Inria, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Orsay, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Théophile Niault
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Delphine Lapaillerie
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
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3
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Canales-Herrerias P, Crickx E, Broketa M, Sokal A, Chenon G, Azzaoui I, Vandenberghe A, Perima A, Iannascoli B, Richard-Le Goff O, Castrillon C, Mottet G, Sterlin D, Robbins A, Michel M, England P, Millot GA, Eyer K, Baudry J, Mahevas M, Bruhns P. High-affinity autoreactive plasma cells disseminate through multiple organs in patients with immune thrombocytopenic purpura. J Clin Invest 2022; 132:153580. [PMID: 35503254 PMCID: PMC9197514 DOI: 10.1172/jci153580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
The major therapeutic goal for immune thrombocytopenic purpura (ITP) is to restore normal platelet counts using drugs to promote platelet production or by interfering with mechanisms responsible for platelet destruction. Eighty percent of patients with ITP possess anti–integrin αIIbβ3 IgG autoantibodies that cause platelet opsonization and phagocytosis. The spleen is considered the primary site of autoantibody production by autoreactive B cells and platelet destruction. The immediate failure in approximately 50% of patients to recover a normal platelet count after anti-CD20 rituximab-mediated B cell depletion and splenectomy suggests that autoreactive, rituximab-resistant, IgG-secreting B cells (IgG-SCs) reside in other anatomical compartments. We analyzed more than 3,300 single IgG-SCs from spleen, bone marrow, and/or blood of 27 patients with ITP, revealing high interindividual variability in affinity for αIIbβ3, with variations over 3 logs. IgG-SC dissemination and range of affinities were, however, similar for each patient. Longitudinal analysis of autoreactive IgG-SCs upon treatment with the anti-CD38 mAb daratumumab demonstrated variable outcomes, from complete remission to failure with persistence of high-affinity anti–αIIbβ3 IgG-SCs in the bone marrow. This study demonstrates the existence and dissemination of high-affinity autoreactive plasma cells in multiple anatomical compartments of patients with ITP that may cause the failure of current therapies.
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Affiliation(s)
| | - Etienne Crickx
- INSERM U1151/CNRS UMS8253, Institut Necker-Enfants Malades, Paris, France
| | - Matteo Broketa
- Department of Immunology, Institut Pasteur, Paris, France
| | - Aurélien Sokal
- INSERM U1151/CNRS UMS8253, Institut Necker-Enfants Malades, Paris, France
| | - Guilhem Chenon
- Laboratoire Colloïdes et Matériaux Divisés (LCMD), ESPCI, Paris, France
| | - Imane Azzaoui
- Service de Médecine Interne, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, Paris, France
| | - Alexis Vandenberghe
- Service de Médecine Interne, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Est Créteil, Paris, France
| | - Angga Perima
- Department of Immunology, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Ailsa Robbins
- Department of Internal Medicine, Infectious Diseases, and Clinical Immunolo, Robert Debré Hospital, Reims University Hospitals, Reims, France
| | - Marc Michel
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Créteil, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Gael A Millot
- Hub Bioinformatique et Biostatistique, Institut Pasteur, Paris, France
| | - Klaus Eyer
- Laboratory for Functional Immune Repertoire Analysis, ETH Zurich, Zurich, Switzerland
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés (LCMD), ESPCI, Paris, France
| | - Matthieu Mahevas
- INSERM U1151/CNRS UMS8253, Institut Necker-Enfants Malades, Paris, France
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4
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Menegatti S, Guillemot V, Latis E, Yahia-Cherbal H, Mittermüller D, Rouilly V, Mascia E, Rosine N, Koturan S, Millot GA, Leloup C, Duffy D, Gleizes A, Hacein-Bey-Abina S, Sellam J, Berenbaum F, Miceli-Richard C, Dougados M, Bianchi E, Rogge L. Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo. Ann Rheum Dis 2020; 80:475-486. [PMID: 33268443 PMCID: PMC7958106 DOI: 10.1136/annrheumdis-2020-218304] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Objectives Antitumour necrosis factor (TNF) therapy has revolutionised treatment of several chronic inflammatory diseases, including spondyloarthritis (SpA). However, TNF inhibitors (TNFi) are not effective in all patients and the biological basis for treatment failure remains unknown. We have analysed induced immune responses to define the mechanism of action of TNF blockers in SpA and to identify immunological correlates of responsiveness to TNFi. Methods Immune responses to microbial and pathway-specific stimuli were analysed in peripheral blood samples from 80 patients with axial SpA before and after TNFi treatment, using highly standardised whole-blood stimulation assays. Cytokines and chemokines were measured in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, and gene expression was monitored using nCounter assays. Results Anti-TNF therapy induced profound changes in patients’ innate immune responses. TNFi action was selective, and had only minor effects on Th1/Th17 immunity. Modular transcriptional repertoire analysis identified prostaglandin E2 synthesis and signalling, leucocyte recirculation, macrophage polarisation, dectin and interleukin (IL)-1 signalling, as well as the nuclear factor kappa B (NF-kB) transcription factor family as key pathways targeted by TNF blockers in vivo. Analysis of induced immune responses before treatment initiation revealed that expression of molecules associated with leucocyte adhesion and invasion, chemotaxis and IL-1 signalling are correlated with therapeutic responses to anti-TNF. Conclusions We show that TNFi target multiple immune cell pathways that cooperate to resolve inflammation. We propose that immune response profiling provides new insight into the biology of TNF-blocker action in patients and can identify signalling pathways associated with therapeutic responses to biological therapies.
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Affiliation(s)
- Silvia Menegatti
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Vincent Guillemot
- Bioinformatics and Biostatistics Hub-Département de Biologie Computationelle, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Eleonora Latis
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hanane Yahia-Cherbal
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Daniela Mittermüller
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | | | - Elena Mascia
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | - Nicolas Rosine
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Surya Koturan
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gael A Millot
- Bioinformatics and Biostatistics Hub-Département de Biologie Computationelle, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Claire Leloup
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Institut Pasteur, Translational Immunology Laboratory, Department of Immunology, Paris, France
| | - Aude Gleizes
- Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France.,UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | - Salima Hacein-Bey-Abina
- Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France.,UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Jérémie Sellam
- Sorbonne Université, Service de Rhumatologie, Hôpital Saint-Antoine, AP-HP, Paris, France.,Centre de Recherche Saint-Antoine, INSERM UMR_S 938, Paris, France
| | - Francis Berenbaum
- Sorbonne Université, Service de Rhumatologie, Hôpital Saint-Antoine, AP-HP, Paris, France.,Centre de Recherche Saint-Antoine, INSERM UMR_S 938, Paris, France
| | - Corinne Miceli-Richard
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Paris Descartes University, Rheumatology Department, Cochin Hospital, AP-HP, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Maxime Dougados
- Paris Descartes University, Rheumatology Department, Cochin Hospital, AP-HP, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France.,INSERM U1153 Clinical Epidemiology and Biostatistics, PRES Sorbonne Paris-Cité, Paris, France
| | - Elisabetta Bianchi
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Lars Rogge
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France .,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
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5
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Balbino B, Herviou P, Godon O, Stackowicz J, Goff ORL, Iannascoli B, Sterlin D, Brûlé S, Millot GA, Harris FM, Voronina VA, Nadeau KC, Macdonald LE, Murphy AJ, Bruhns P, Reber LL. The anti-IgE mAb omalizumab induces adverse reactions by engaging Fcγ receptors. J Clin Invest 2020; 130:1330-1335. [PMID: 31770111 DOI: 10.1172/jci129697] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/13/2019] [Indexed: 01/07/2023] Open
Abstract
Omalizumab is an anti-IgE monoclonal antibody (mAb) approved for the treatment of severe asthma and chronic spontaneous urticaria. Use of omalizumab is associated with reported side effects ranging from local skin inflammation at the injection site to systemic anaphylaxis. To date, the mechanisms through which omalizumab induces adverse reactions are still unknown. Here, we demonstrated that immune complexes formed between omalizumab and IgE can induce both skin inflammation and anaphylaxis through engagement of IgG receptors (FcγRs) in FcγR-humanized mice. We further developed an Fc-engineered mutant version of omalizumab, and demonstrated that this mAb is equally potent as omalizumab at blocking IgE-mediated allergic reactions, but does not induce FcγR-dependent adverse reactions. Overall, our data indicate that omalizumab can induce skin inflammation and anaphylaxis by engaging FcγRs, and demonstrate that Fc-engineered versions of the mAb could be used to reduce such adverse reactions.
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Affiliation(s)
- Bianca Balbino
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,Sorbonne Université, Paris, France
| | - Pauline Herviou
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Ophélie Godon
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Julien Stackowicz
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,Sorbonne Université, Paris, France
| | - Odile Richard-Le Goff
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Bruno Iannascoli
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Delphine Sterlin
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,Assistance Publique-Hôpitaux de Paris, La Pitié-Salpêtrière, Département d'Immunologie, Paris, France
| | - Sébastien Brûlé
- Plateforme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Gael A Millot
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Faith M Harris
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | | | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, California, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Stanford University, California, USA
| | | | | | - Pierre Bruhns
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Laurent L Reber
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,Center for Physiopathology of Toulouse-Purpan (CPTP), UMR 1043, University of Toulouse, INSERM CNRS, Toulouse France
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6
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Monteiro AN, Bouwman P, Kousholt AN, Eccles DM, Millot GA, Masson JY, Schmidt MK, Sharan SK, Scully R, Wiesmüller L, Couch F, Vreeswijk MPG. Variants of uncertain clinical significance in hereditary breast and ovarian cancer genes: best practices in functional analysis for clinical annotation. J Med Genet 2020; 57:509-518. [PMID: 32152249 DOI: 10.1136/jmedgenet-2019-106368] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/28/2019] [Accepted: 12/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Alvaro N Monteiro
- Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Peter Bouwman
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arne N Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Diana M Eccles
- Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Gael A Millot
- Hub-DBC, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Shyam K Sharan
- National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Ralph Scully
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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7
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Sanchez David RY, Combredet C, Najburg V, Millot GA, Beauclair G, Schwikowski B, Léger T, Camadro JM, Jacob Y, Bellalou J, Jouvenet N, Tangy F, Komarova AV. LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses. Sci Signal 2019; 12:eaar3993. [PMID: 31575732 DOI: 10.1126/scisignal.aar3993] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) RIG-I, MDA5, and LGP2 stimulate inflammatory and antiviral responses by sensing nonself RNA molecules produced during viral replication. Here, we investigated how LGP2 regulates the RIG-I- and MDA5-dependent induction of type I interferon (IFN) signaling and showed that LGP2 interacted with different components of the RNA-silencing machinery. We identified a direct protein-protein interaction between LGP2 and the IFN-inducible, double-stranded RNA binding protein PACT. The LGP2-PACT interaction was mediated by the regulatory C-terminal domain of LGP2 and was necessary for inhibiting RIG-I-dependent responses and for amplifying MDA5-dependent responses. We described a point mutation within LGP2 that disrupted the LGP2-PACT interaction and led to the loss of LGP2-mediated regulation of RIG-I and MDA5 signaling. These results suggest a model in which the LGP2-PACT interaction regulates the inflammatory responses mediated by RIG-I and MDA5 and enables the cellular RNA-silencing machinery to coordinate with the innate immune response.
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Affiliation(s)
- Raul Y Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Ecole doctorale B3MI/Paris7, Paris, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Gael A Millot
- Hub de Bioinformatique et Biostatistique-C3BI, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Guillaume Beauclair
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Benno Schwikowski
- Systems Biology Laboratory and USR 3756, Institut Pasteur and CNRS, Paris, France
| | - Thibaut Léger
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jean-Michel Camadro
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Université Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Yves Jacob
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
| | - Jacques Bellalou
- Platform of Recombinant Proteins in Prokaryotic Cells, Institut Pasteur, 75015, CNRS UMR 3528, Paris, France
| | - Nolwenn Jouvenet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
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8
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Golmard L, Castéra L, Krieger S, Moncoutier V, Abidallah K, Tenreiro H, Laugé A, Tarabeux J, Millot GA, Nicolas A, Laé M, Abadie C, Berthet P, Polycarpe F, Frébourg T, Elan C, de Pauw A, Gauthier-Villars M, Buecher B, Stern MH, Stoppa-Lyonnet D, Vaur D, Houdayer C. Contribution of germline deleterious variants in the RAD51 paralogs to breast and ovarian cancers. Eur J Hum Genet 2017; 25:1345-1353. [PMID: 29255180 DOI: 10.1038/s41431-017-0021-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) have recently been involved in breast and ovarian cancer predisposition: RAD51B, RAD51C, and RAD51D in ovarian cancer, RAD51B and XRCC2 in breast cancer. The aim of this study was to estimate the contribution of deleterious variants in the five RAD51 paralogs to breast and ovarian cancers. The five RAD51 paralog genes were analyzed by next-generation sequencing technologies in germline DNA from 2649 consecutive patients diagnosed with breast and/or ovarian cancer. Twenty-one different deleterious variants were identified in the RAD51 paralogs in 30 patients: RAD51B (n = 4), RAD51C (n = 12), RAD51D (n = 7), XRCC2 (n = 2), and XRCC3 (n = 5). The overall deleterious variant rate was 1.13% (95% confidence interval (CI): 0.72-1.55%) (30/2649), including 15 variants in breast cancer only cases (15/2063; 0.73% (95% CI: 0.34-1.11%)) and 15 variants in cases with at least one ovarian cancer (15/570; 2.63% (95% CI: 1.24-4.02%)). This study is the first evaluation of the five RAD51 paralogs in breast and ovarian cancer predisposition and it demonstrates that deleterious variants can be present in breast cancer only cases. Moreover, this is the first time that XRCC3 deleterious variants have been identified in breast and ovarian cancer cases.
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Affiliation(s)
- Lisa Golmard
- Department of Tumour Biology, Institut Curie, Paris, 75005, France. .,Inserm U830, Institut Curie, Paris, 75005, France.
| | - Laurent Castéra
- Department of Cancer Biology and Genetics, CCC François Baclesse, Caen, 14000, France.,Inserm U1079, Normandy Center for Genomic and Personalized Medicine, Rouen, 76183, France
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, CCC François Baclesse, Caen, 14000, France.,Inserm U1079, Normandy Center for Genomic and Personalized Medicine, Rouen, 76183, France.,University of Caen, Normandie, 14032, France
| | | | | | | | - Anthony Laugé
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | - Julien Tarabeux
- Department of Tumour Biology, Institut Curie, Paris, 75005, France.,Inserm U830, Institut Curie, Paris, 75005, France
| | - Gael A Millot
- Institut Curie, PSL Research University, CNRS UMR3244, Paris, 75005, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR3244, Paris, 75005, France
| | - André Nicolas
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | - Marick Laé
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | - Caroline Abadie
- Department of Genetics, Centre Hospitalo-Universitaire, Rennes, 35033, France
| | - Pascaline Berthet
- Department of Genetics, Centre François Baclesse, Caen, 14000, France
| | | | - Thierry Frébourg
- Inserm U1079, Normandy Center for Genomic and Personalized Medicine, Rouen, 76183, France.,Department of Genetics, Centre Hospitalo-Universitaire, Rouen, 76000, France.,University of Rouen, IRIB, Rouen, 76183, France
| | - Camille Elan
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | - Antoine de Pauw
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | | | - Bruno Buecher
- Department of Tumour Biology, Institut Curie, Paris, 75005, France
| | - Marc-Henri Stern
- Department of Tumour Biology, Institut Curie, Paris, 75005, France.,Inserm U830, Institut Curie, Paris, 75005, France.,Institut Curie, PSL Research University, Paris, 75005, France
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, Institut Curie, Paris, 75005, France.,Inserm U830, Institut Curie, Paris, 75005, France.,Paris Descartes University, Sorbonne Paris Cité, Paris, 75006, France
| | - Dominique Vaur
- Department of Cancer Biology and Genetics, CCC François Baclesse, Caen, 14000, France.,Inserm U1079, Normandy Center for Genomic and Personalized Medicine, Rouen, 76183, France
| | - Claude Houdayer
- Department of Tumour Biology, Institut Curie, Paris, 75005, France.,Inserm U830, Institut Curie, Paris, 75005, France.,Paris Descartes University, Sorbonne Paris Cité, Paris, 75006, France
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9
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Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MPG, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JNM, Carvalho MA, Brody LC, Sharan SK, Monteiro AN. BRCA1 Circos: a visualisation resource for functional analysis of missense variants. J Med Genet 2015; 52:224-30. [PMID: 25643705 PMCID: PMC4392196 DOI: 10.1136/jmedgenet-2014-102766] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/29/2014] [Accepted: 12/05/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.
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Affiliation(s)
- Ankita Jhuraney
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- University of South Florida Cancer Biology PhD Program, Tampa, Florida, USA
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Randall C Johnson
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Bailey Kessing
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Renato S Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Phillip Whiley
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Hôpital René Huguenin, Paris, France
| | - Gael A Millot
- Institut Curie, Université Pierre et Marie Curie, Paris, France
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago, Spain
| | - Nicolas Coquelle
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Alvaro Galli
- Instituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | | | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tuya Pal
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Simon Thomas
- Salisbury District Hospital, Salisbury, Wiltshire, UK
| | - Maxime Vallée
- International Agency for Research on Cancer, Lyon, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Marcelo A Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Shyam K Sharan
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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10
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Gay S, Lachages AM, Millot GA, Courbet S, Letessier A, Debatisse M, Brison O. Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions. EMBO Rep 2010; 11:698-704. [PMID: 20671737 DOI: 10.1038/embor.2010.112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 12/25/2022] Open
Abstract
In eukaryotes, only a fraction of replication origins fire at each S phase. Local histone acetylation was proposed to control firing efficiency of origins, but conflicting results were obtained. We report that local histone acetylation does not reflect origin efficiencies along the adenosine monophosphate deaminase 2 locus in mammalian fibroblasts. Reciprocally, modulation of origin efficiency does not affect acetylation. However, treatment with a deacetylase inhibitor changes the initiation pattern. We demonstrate that this treatment alters pyrimidine biosynthesis and decreases fork speed, which recruits latent origins. Our findings reconcile results that seemed inconsistent and reveal an unsuspected effect of deacetylase inhibitors on replication dynamics.
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Affiliation(s)
- Sophie Gay
- Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248 Paris, France
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11
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Coppo P, Wolf M, Veyradier A, Bussel A, Malot S, Millot GA, Daubin C, Bordessoule D, Pène F, Mira JP, Heshmati F, Maury E, Guidet B, Boulanger E, Galicier L, Parquet N, Vernant JP, Rondeau E, Azoulay E, Schlemmer B. Prognostic value of inhibitory anti-ADAMTS13 antibodies in adult-acquired thrombotic thrombocytopenic purpura. Br J Haematol 2006; 132:66-74. [PMID: 16371021 DOI: 10.1111/j.1365-2141.2005.05837.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to assess the prognostic value of inhibitory anti-ADAMTS13 antibodies in thrombotic thrombocytopenic purpura (TTP), we performed a multicentre prospective study of 33 adult patients with idiopathic acquired TTP. Patients were treated with high-dose plasma infusion and therapeutic plasma exchange. Patients without (group 1, n = 12) and with (group 2, n = 21) detectable inhibitory anti-ADAMTS13 antibodies were compared for clinical presentation, treatment and outcome. Both groups were comparable for clinical presentation. All patients in group 1 achieved a sustained complete remission within a median of 7 d [95% confidence interval (CI), 4-18], which required a median plasma volume of 235 ml/kg (range, 131-1251). In group 2, 17 patients achieved a durable complete remission within a median of 23 d (95% CI, 11-32) (P = 0.001). Median plasma volume was 718 ml/kg (range, 219-3107) (P = 0.02). In group 2, there was a trend for more episodes of flare-up than in group 1 (13 vs. 3, respectively, P = 0.07). Four patients, all from group 2, died (P = not significant). The relapse rate was comparable between both groups. We suggest that TTP with detectable inhibitory anti-ADAMTS13 antibodies displays a worse prognosis, relative to a delayed platelet count recovery, a higher plasma volume requirement to achieve complete remission, and a trend for more frequent episodes of flare-up.
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Affiliation(s)
- P Coppo
- Service d'Hématologie et de Thérapie Cellulaire, Faculté de Médecine Paris VI, Hôpital Saint-Antoine, Paris.
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12
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Millot GA, Svinarchuk F, Lacout C, Vainchenker W, Dumenil D. The granulocyte colony-stimulating factor receptor supports erythroid differentiation in the absence of the erythropoietin receptor or Stat5. Br J Haematol 2001; 112:449-58. [PMID: 11167846 DOI: 10.1046/j.1365-2141.2001.02591.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To evaluate the functional conservation of signal transduction mechanisms between haematopoietic receptors and to characterize the molecules activated in this phenomenon, we introduced granulocyte colony-stimulating factor receptor (G-CSFR) cDNA into mouse fetal liver cells using a retroviral vector. In semi-solid medium assays, G-CSFR-infected cells gave rise to all types of colonies [granulocyte-macrophage (GM), megakaryocyte (MK) and mixed lineage (GEMM) colony-forming units (CFU) and erythroid burst-forming units (BFU-E)] in the presence of G-CSF alone. The direct effect of G-CSF on erythroid differentiation of G-CSFR-transduced erythroid progenitors was demonstrated by the development of erythroid colonies using G-CSFR-expressing Lin- cells cloned at one cell per well in liquid culture in the presence of G-CSF. Interestingly, while Stat5, but not Stat3, was activated in erythroid cells in response to erythropoietin (EPO), both were activated in erythroid and granulocytic cells stimulated by G-CSF. Furthermore, G-CSF induced the growth of erythroid colonies from G-CSFR-expressing fetal liver cells from EPO receptor-/- (EPO-R-/-) or Stat5a-/- Stat5b-/- mice, demonstrating that erythroid differentiation can occur in the absence of EPO-R or Stat5. These data show that forced expression of G-CSFR allows G-CSF-dependent multilineage proliferation and differentiation of haematopoietic progenitors and rescues EPO-R-/- erythroid cells. While G-CSF induces Stat5 activation in G-CSFR-expressing erythroid cells, this activation is not necessary for the terminal erythroid differentiation induced by G-CSF.
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Affiliation(s)
- G A Millot
- INSERM U362, Laboratoire Hématopoïèse et Cellules Souches, Institut Gustave Roussy, Villejuif, France
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