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Mhanna V, Barennes P, Vantomme H, Fourcade G, Coatnoan N, Six A, Klatzmann D, Mariotti-Ferrandiz E. Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice. Cell Rep Methods 2024; 4:100753. [PMID: 38614088 PMCID: PMC11045977 DOI: 10.1016/j.crmeth.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/28/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
Abstract
Accurate characterization and comparison of T cell receptor (TCR) repertoires from small biological samples present significant challenges. The main challenge is the low material input, which compromises the quality of bulk sequencing and hinders the recovery of sufficient TCR sequences for robust analyses. We aimed to address this limitation by implementing a strategic approach to pool homologous biological samples. Our findings demonstrate that such pooling indeed enhances the TCR repertoire coverage, particularly for cell subsets of constrained sizes, and enables accurate comparisons of TCR repertoires at different levels of complexity across T cell subsets with different sizes. This methodology holds promise for advancing our understanding of T cell repertoires in scenarios where sample size constraints are a prevailing concern.
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Affiliation(s)
- Vanessa Mhanna
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Hélène Vantomme
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Gwladys Fourcade
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - Nicolas Coatnoan
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), 75005 Paris, France; Institut Universitaire de France, France.
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Quiniou V, Barennes P, Mhanna V, Stys P, Vantomme H, Zhou Z, Martina F, Coatnoan N, Barbie M, Pham HP, Clémenceau B, Vie H, Shugay M, Six A, Brandao B, Mallone R, Mariotti-Ferrandiz E, Klatzmann D. Human thymopoiesis produces polyspecific CD8 + α/β T cells responding to multiple viral antigens. eLife 2023; 12:81274. [PMID: 36995951 PMCID: PMC10063231 DOI: 10.7554/elife.81274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
T-cell receptors (TCRs) are formed by stochastic gene rearrangements, theoretically generating >1019 sequences. They are selected during thymopoiesis, which releases a repertoire of about 108 unique TCRs per individual. How evolution shaped a process that produces TCRs that can effectively handle a countless and evolving set of infectious agents is a central question of immunology. The paradigm is that a diverse enough repertoire of TCRs should always provide a proper, though rare, specificity for any given need. Expansion of such rare T cells would provide enough fighters for an effective immune response and enough antigen-experienced cells for memory. We show here that human thymopoiesis releases a large population of clustered CD8+ T cells harboring α/β paired TCRs that (i) have high generation probabilities and (ii) a preferential usage of some V and J genes, (iii) which CDR3 are shared between individuals, and (iv) can each bind and be activated by multiple unrelated viral peptides, notably from EBV, CMV, and influenza. These polyspecific T cells may represent a first line of defense that is mobilized in response to infections before a more specific response subsequently ensures viral elimination. Our results support an evolutionary selection of polyspecific α/β TCRs for broad antiviral responses and heterologous immunity.
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Affiliation(s)
- Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Vanessa Mhanna
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Paul Stys
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
| | - Helene Vantomme
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Federica Martina
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Nicolas Coatnoan
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Michele Barbie
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | | | - Béatrice Clémenceau
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Henri Vie
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russian Federation
| | - Adrien Six
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
| | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | | | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
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3
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Castro R, Magadán S, Jouneau L, Mhana V, Pham HP, Mariotti-Ferrandiz E, Six A, Huetz F, Boudinot P. Clonotypic IgH Response against Systemic Viral infection in Pronephros and Spleen of a Teleost Fish. J Immunol 2022; 208:2573-2582. [PMID: 35577368 DOI: 10.4049/jimmunol.2200088] [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] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Upon infection, B lymphocytes develop clonal responses. In teleost fish, which lack lymph nodes, the kinetics and location of B cell responses remain poorly characterized. Fish pronephros is the site of B cell differentiation and the main niche for persistence of plasma cells. In this study, we undertook the analysis of the rainbow trout IgHμ repertoire in this critical tissue for humoral adaptive immunity after primary immunization and boost with a rhabdovirus, the viral hemorrhagic septicemia virus (VHSV). We used a barcoded 5' RACE-cDNA sequencing approach to characterize modifications of the IgHμ repertoire, including VH usage in expressed V(D)J rearrangements, clonal diversity, and clonotype sharing between individual fish and treatments. In the pronephros, our approach quantified the clonotype frequency across the whole IgH repertoire (i.e., with all VH), measuring the frequency of Ag-responding clonotypes. Viral infection led to extensive modifications of the pronephros B cell repertoire, implicating several VH subgroups after primary infection. In contrast, only modest changes in repertoire persisted 5 mo later, including VHSV-specific public expansions. The IgM public response implicating IgHV1-18 and JH5, previously described in spleen, was confirmed in pronephros in all infected fish, strongly correlated to the response. However, the distribution of top clonotypes showed that pronephros and spleen B cells constitute distinct compartments with different IgH repertoires. Unexpectedly, after boost, the frequency of anti-VHSV clonotypes decreased both in pronephros and spleen, raising questions about B cell circulation. A better monitoring of B cell response kinetics in lymphoid tissues will be an essential step to understand B memory and plasmocyte formation mechanisms in fish.
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Affiliation(s)
- Rosario Castro
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadán
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra, Spain
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Vanessa Mhana
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | - Hang-Phuong Pham
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | | | - Adrien Six
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | - François Huetz
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR 1222 INSERM, Paris, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France;
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Dérian N, Pham HP, Nehar-Belaid D, Tchitchek N, Klatzmann D, Eric V, Six A. The Tsallis generalized entropy enhances the interpretation of transcriptomics datasets. PLoS One 2022; 17:e0266618. [PMID: 35446844 PMCID: PMC9022844 DOI: 10.1371/journal.pone.0266618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background
Identifying differentially expressed genes between experimental conditions is still the gold-standard approach to interpret transcriptomic profiles. Alternative approaches based on diversity measures have been proposed to complement the interpretation of such datasets but are only used marginally.
Methods
Here, we reinvestigated diversity measures, which are commonly used in ecology, to characterize mice pregnancy microenvironments based on a public transcriptome dataset. Mainly, we evaluated the Tsallis entropy function to explore the potential of a collection of diversity measures for capturing relevant molecular event information.
Results
We demonstrate that the Tsallis entropy function provides additional information compared to the traditional diversity indices, such as the Shannon and Simpson indices. Depending on the relative importance given to the most abundant transcripts based on the Tsallis entropy function parameter, our approach allows appreciating the impact of biological stimulus on the inter-individual variability of groups of samples. Moreover, we propose a strategy for reducing the complexity of transcriptome datasets using a maximation of the beta diversity.
Conclusions
We highlight that a diversity-based analysis is suitable for capturing complex molecular events occurring during physiological events. Therefore, we recommend their use through the Tsallis entropy function to analyze transcriptomics data in addition to differential expression analyses.
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Affiliation(s)
- Nicolas Dérian
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | | | - Djamel Nehar-Belaid
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America
| | - Nicolas Tchitchek
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Vicaut Eric
- APHP, Hôpitaux Saint-Louis Lariboisière, Univ Paris 07, Unité de recherche clinique, UMR 942, Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR-S 959, Immunology-Immunopathology- Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
- * E-mail:
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5
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Jeger-Madiot R, Vaineau R, Heredia M, Tchitchek N, Bertrand L, Pereira M, Konza O, Gouritin B, Hoareau-Coudert B, Corneau A, Blanc C, Savier E, Buffet P, Six A, Klatzmann D, Moris A, Graff-Dubois S. Naive and memory CD4 + T cell subsets can contribute to the generation of human Tfh cells. iScience 2022; 25:103566. [PMID: 34984326 PMCID: PMC8693005 DOI: 10.1016/j.isci.2021.103566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/07/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022] Open
Abstract
CD4+ T follicular helper cells (Tfh) promote B cell maturation and antibody production in secondary lymphoid organs. By using an innovative culture system based on splenocyte stimulation, we studied the dynamics of naive and memory CD4+ T cells during the generation of a Tfh cell response. We found that both naive and memory CD4+ T cells can acquire phenotypic and functional features of Tfh cells. Moreover, we show here that the transition of memory as well as naive CD4+ T cells into the Tfh cell profile is supported by the expression of pro-Tfh genes, including transcription factors known to orchestrate Tfh cell development. Using this culture system, we provide pieces of evidence that HIV infection differentially alters these newly identified pathways of Tfh cell generation. Such diversity in pathways of Tfh cell generation offers a new framework for the understanding of Tfh cell responses in physiological and pathological contexts.
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Affiliation(s)
- Raphaël Jeger-Madiot
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France
| | - Romain Vaineau
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Maud Heredia
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France
| | - Nicolas Tchitchek
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Lisa Bertrand
- Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Mathias Pereira
- Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Océane Konza
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Bruno Gouritin
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | | | - Aurélien Corneau
- Sorbonne Université, INSERM UMS037 PASS, Cytometry facility (CyPS), Paris, France
| | - Catherine Blanc
- Sorbonne Université, INSERM UMS037 PASS, Cytometry facility (CyPS), Paris, France
| | - Eric Savier
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pitie-Salpetriere Hospital, Department of Hepato-Biliary and Pancreatic Surgery and Liver Transplantation, Paris, France.,Sorbonne Université, INSERM, St Antoine Research Center CRSA, Paris, France
| | - Pierre Buffet
- Université de Paris, INSERM, UMRS 1134, Biologie Intégrée du Globule Rouge, Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Arnaud Moris
- Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Stéphanie Graff-Dubois
- Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,Sorbonne Université, INSERM, CNRS, Center for Immunology and Microbial Infections, Paris, France.,Sorbonne Université, INSERM UMS037 PASS, Cytometry facility (CyPS), Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Pitie-Salpetriere Hospital, Department of Hepato-Biliary and Pancreatic Surgery and Liver Transplantation, Paris, France
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6
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Mhanna V, Fourcade G, Barennes P, Quiniou V, Pham HP, Ritvo PG, Brimaud F, Gouritin B, Churlaud G, Six A, Mariotti-Ferrandiz E, Klatzmann D. Impaired Activated/Memory Regulatory T Cell Clonal Expansion Instigates Diabetes in NOD Mice. Diabetes 2021; 70:976-985. [PMID: 33479057 DOI: 10.2337/db20-0896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022]
Abstract
Regulatory T cell (Treg) insufficiency licenses the destruction of insulin-producing pancreatic β-cells by autoreactive effector T cells (Teffs), causing spontaneous autoimmune diabetes in NOD mice. We investigated the contribution to diabetes of the T-cell receptor (TCR) repertoires of naive regulatory T cells (nTregs), activated/memory Tregs (amTregs), and CD4+ Teffs from prediabetic NOD mice and normal C57BL/6 (B6) mice. NOD mice amTreg and Teff repertoire diversity was unexpectedly higher than that of B6 mice. This was due to the presence of highly expanded clonotypes in B6 amTregs and Teffs that were largely lost in their NOD counterparts. Interleukin-2 (IL-2) administration to NOD mice restored such amTreg clonotype expansions and prevented diabetes development. In contrast, IL-2 administration only led to few or no clonotype expansions in nTregs and Teffs, respectively. Noteworthily, IL-2-expanded amTreg and nTreg clonotypes were markedly enriched in islet-antigen specific TCRs. Altogether, our results highlight the link between a reduced clonotype expansion within the activated Treg repertoire and the development of an autoimmune disease. They also indicate that the repertoire of amTregs is amenable to rejuvenation by IL-2.
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Affiliation(s)
- Vanessa Mhanna
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Gwladys Fourcade
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Pierre Barennes
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Valentin Quiniou
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Hang P Pham
- Statistics Department, ILTOO Pharma, Paris, France
| | - Paul-Gydeon Ritvo
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Faustine Brimaud
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Bruno Gouritin
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Guillaume Churlaud
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Adrien Six
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | | | - David Klatzmann
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
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7
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Waldschmitt N, Kitamoto S, Secher T, Zacharioudaki V, Boulard O, Floquet E, Delacre M, Lamas B, Pham HP, Six A, Richard ML, Dagorn JC, Eberl G, Langella P, Chatel JM, Ryffel B, Iovanna JL, Poulin LF, Sokol H, Kamada N, Chamaillard M. The regenerating family member 3 β instigates IL-17A-mediated neutrophil recruitment downstream of NOD1/2 signalling for controlling colonisation resistance independently of microbiota community structure. Gut 2019; 68:1190-1199. [PMID: 30279238 DOI: 10.1136/gutjnl-2018-316757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/08/2018] [Accepted: 08/29/2018] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Loss of the Crohn's disease predisposing NOD2 gene results in an intestinal microenvironment conducive for colonisation by attaching-and-effacing enteropathogens. However, it remains elusive whether it relies on the intracellular recruitment of the serine-threonine kinase RIPK2 by NOD2, a step that is required for its activation of the transcription factor NF-κB. DESIGN Colonisation resistance was evaluated in wild type and mutant mice, as well as in ex-germ-free (ex-GF) mice which were colonised either with faeces from Ripk2-deficient mice or with bacteria with similar preferences for carbohydrates to those acquired by the pathogen. The severity of the mucosal pathology was quantified at several time points postinfection by using a previously established scoring. The community resilience in response to infection was evaluated by 16S ribosomal RNA gene sequence analysis. The control of pathogen virulence was evaluated by monitoring the secretion of Citrobacter-specific antibody response in the faeces. RESULTS Primary infection was similarly outcompeted in ex-GF Ripk2-deficient and control mice, demonstrating that the susceptibility to infection resulting from RIPK2 deficiency cannot be solely attributed to specific microbiota community structures. In contrast, delayed clearance of Citrobacter rodentium and exacerbated histopathology were preceded by a weakened propensity of intestinal macrophages to afford innate lymphoid cell activation. This tissue protection unexpectedly required the regenerating family member 3β by instigating interleukin (IL) 17A-mediated neutrophil recruitment to the intestine and subsequent phosphorylation of signal transducer and activator of transcription 3. CONCLUSIONS These results unveil a previously unrecognised mechanism that efficiently protects from colonisation by diarrhoeagenic bacteria early in infection.
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Affiliation(s)
- Nadine Waldschmitt
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Sho Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Thomas Secher
- INEM, Orléans University, CNRS UMR 7355, F-45071, Orléans, France
| | - Vassiliki Zacharioudaki
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Olivier Boulard
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Emilie Floquet
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Myriam Delacre
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Bruno Lamas
- Laboratoire des Biomolécules (LBM), SorbonneUniversités, UPMC Univ. Paris 06, École normale supérieure, PSL ResearchUniversity, CNRS, INSERM, APHP, Paris, France.,Commensals and Probiotics-Host Interactions Laboratory, INRA, UMR1319Micalis & AgroParisTech, Jouy-en-Josas, France
| | - Hang-Phuong Pham
- ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France
| | - Adrien Six
- Department of Immunology-Immunopathology-Immunotherapy (I3), Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS959, Paris, France
| | - Mathias L Richard
- Commensals and Probiotics-Host Interactions Laboratory, INRA, UMR1319Micalis & AgroParisTech, Jouy-en-Josas, France
| | - Jean-Charles Dagorn
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Université, Inserm U1068, CNRS UMR 7258 and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Gérard Eberl
- Microenvironment and Immunity Unit, Institut Pasteur, Paris, France
| | - Philippe Langella
- Commensals and Probiotics-Host Interactions Laboratory, INRA, UMR1319Micalis & AgroParisTech, Jouy-en-Josas, France
| | - Jean-Marc Chatel
- Commensals and Probiotics-Host Interactions Laboratory, INRA, UMR1319Micalis & AgroParisTech, Jouy-en-Josas, France
| | - Bernhard Ryffel
- INEM, Orléans University, CNRS UMR 7355, F-45071, Orléans, France
| | - Juan Lucio Iovanna
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Université, Inserm U1068, CNRS UMR 7258 and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Lionel F Poulin
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
| | - Harry Sokol
- Laboratoire des Biomolécules (LBM), SorbonneUniversités, UPMC Univ. Paris 06, École normale supérieure, PSL ResearchUniversity, CNRS, INSERM, APHP, Paris, France.,Commensals and Probiotics-Host Interactions Laboratory, INRA, UMR1319Micalis & AgroParisTech, Jouy-en-Josas, France.,Department of Gastroenterology, Saint Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mathias Chamaillard
- CIIL - Centre d'Infection et d'Immunité de Lille, Université de Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204, F-59000, Lille, France
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8
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Tsitoura E, Kazazi D, Oz-Arslan D, Sever EA, Khalili S, Vassilaki N, Aslanoglou E, Dérian N, Six A, Sezerman OU, Klatzmann D, Mavromara P. Comparison of Dendritic Cell Activation by Virus-Based Vaccine Delivery Vectors Emphasizes the Transcriptional Downregulation of the Oxidative Phosphorylation Pathway. Hum Gene Ther 2019; 30:429-445. [PMID: 30351174 DOI: 10.1089/hum.2018.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antigen delivery platforms based on engineered viruses or virus-like particles are currently developed as vaccines against infectious diseases. As the interaction of vaccines with dendritic cells (DCs) shapes the immunological response, we compared the interaction of a range of virus-based vectors and virus-like particles with DCs in a murine model of systemic administration and transcriptome analyses of splenic DCs. The transcriptome profiles of DCs separated the vaccine vectors into two distinct groups characterized by high- and low-magnitude differential gene expression, which strongly correlated with (1) the surface expression of costimulatory molecules CD40, CD83, and CD86 on DCs, and (2) antigen-specific T-cell responses. Pathway analysis using PANOGA (Pathway and Network-Oriented GWAS Analysis) revealed that the JAK/STAT pathway was significantly activated by both groups of vaccines. In contrast, the oxidative phosphorylation pathway was significantly downregulated only by the high-magnitude DC-stimulating vectors. A gene signature including exclusively chemokine-, cytokine-, and receptor-related genes revealed a vector-specific pattern. Overall, this in vivo DC stimulation model demonstrated a strong relationship between the levels of induced DC maturation and the intensity of T-cell-specific immune responses with a distinct cytokine/chemokine profile, metabolic shifting, and cell surface expression of maturation markers. It could represent an important tool for vaccine design.
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Affiliation(s)
- Eliza Tsitoura
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Dorothea Kazazi
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Devrim Oz-Arslan
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
- 2 Department of Biophysics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Elif Arik Sever
- 3 Department of Biostatistics and Medical Informatics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Shirin Khalili
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Niki Vassilaki
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Elina Aslanoglou
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Nicolas Dérian
- 4 Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- 5 AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Adrien Six
- 4 Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- 5 AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Osman Ugur Sezerman
- 3 Department of Biostatistics and Medical Informatics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - David Klatzmann
- 4 Sorbonne Université, INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- 5 AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Penelope Mavromara
- 1 Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
- 6 Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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9
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Lamas B, Michel ML, Waldschmitt N, Pham HP, Zacharioudaki V, Dupraz L, Delacre M, Natividad JM, Costa GD, Planchais J, Sovran B, Bridonneau C, Six A, Langella P, Richard ML, Chamaillard M, Sokol H. Card9 mediates susceptibility to intestinal pathogens through microbiota modulation and control of bacterial virulence. Gut 2018; 67:1836-1844. [PMID: 28790160 DOI: 10.1136/gutjnl-2017-314195] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/19/2017] [Accepted: 07/23/2017] [Indexed: 01/14/2023]
Abstract
OBJECTIVE In association with innate and adaptive immunity, the microbiota controls the colonisation resistance against intestinal pathogens. Caspase recruitment domain 9 (CARD9), a key innate immunity gene, is required to shape a normal gut microbiota. Card9-/- mice are more susceptible to the enteric mouse pathogen Citrobacter rodentium that mimics human infections with enteropathogenic and enterohaemorrhagic Escherichia coli. Here, we examined how CARD9 controls C. rodentium infection susceptibility through microbiota-dependent and microbiota-independent mechanisms. DESIGN C. rodentium infection was assessed in conventional and germ-free (GF) wild-type (WT) and Card9-/- mice. To explore the impact of Card9-/-microbiota in infection susceptibility, GF WT mice were colonised with WT (WT→GF) or Card9-/- (Card9-/- →GF) microbiota before C. rodentium infection. Microbiota composition was determined by 16S rDNA gene sequencing. Inflammation severity was determined by histology score and lipocalin level. Microbiota-host immune system interactions were assessed by quantitative PCR analysis. RESULTS CARD9 controls pathogen virulence in a microbiota-independent manner by supporting a specific humoral response. Higher susceptibility to C. rodentium-induced colitis was observed in Card9-/- →GF mice. The microbiota of Card9-/- mice failed to outcompete the monosaccharide-consuming C. rodentium, worsening the infection severity. A polysaccharide-enriched diet counteracted the ecological advantage of C. rodentium and the defective pathogen-specific antibody response in Card9-/- mice. CONCLUSIONS CARD9 modulates the susceptibility to intestinal infection by controlling the pathogen virulence in a microbiota-dependent and microbiota-independent manner. Genetic susceptibility to intestinal pathogens can be overridden by diet intervention that restores humoural immunity and a competing microbiota.
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Affiliation(s)
- Bruno Lamas
- Sorbonne University - Université Pierre et Marie Curie (UPMC), Paris, France.,Avenir Team Gut Microbiota and Immunity, Equipe de Recherche Labélisée (ERL) 1157, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Unité Mixte de Recherche (UMR) 7203, Centre National de Recherche Scientifique (CNRS), Paris, France.,Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France.,Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Marie-Laure Michel
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Nadine Waldschmitt
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France.,INSERM U1019, Team 11, Equipe FRM, INSERM, Lille, France
| | | | - Vassiliki Zacharioudaki
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France.,INSERM U1019, Team 11, Equipe FRM, INSERM, Lille, France
| | - Louise Dupraz
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Myriam Delacre
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France.,INSERM U1019, Team 11, Equipe FRM, INSERM, Lille, France
| | - Jane M Natividad
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Gregory Da Costa
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Julien Planchais
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Bruno Sovran
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Chantal Bridonneau
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Adrien Six
- Department of Immunology-Immunopathology-Immunotherapy, Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMRS959, Paris, France
| | - Philippe Langella
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Mathias L Richard
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Mathias Chamaillard
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France.,INSERM U1019, Team 11, Equipe FRM, INSERM, Lille, France
| | - Harry Sokol
- Sorbonne University - Université Pierre et Marie Curie (UPMC), Paris, France.,Avenir Team Gut Microbiota and Immunity, Equipe de Recherche Labélisée (ERL) 1157, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Unité Mixte de Recherche (UMR) 7203, Centre National de Recherche Scientifique (CNRS), Paris, France.,Laboratoire de BioMolécules (LBM), Centre Hospitalo-Universitaire (CHU) Saint-Antoine 27 rue de Chaligny, Paris, France.,Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, Jouy en Josas, France.,Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique-Hopitaux de Paris, UPMC, Paris, France
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10
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Magadan S, Jouneau L, Puelma Touzel M, Marillet S, Chara W, Six A, Quillet E, Mora T, Walczak AM, Cazals F, Sunyer O, Fillatreau S, Boudinot P. Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination. Front Immunol 2018; 9:2115. [PMID: 30319606 PMCID: PMC6170628 DOI: 10.3389/fimmu.2018.02115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/28/2018] [Indexed: 11/13/2022] Open
Abstract
Vaccination induces “public” antibody clonotypes common to all individuals of a species, that may mediate universal protection against pathogens. Only few studies tried to trace back the origin of these public B-cell clones. Here we used Illumina sequencing and computational modeling to unveil the mechanisms shaping the structure of the fish memory antibody response against an attenuated Viral Hemorrhagic Septicemia rhabdovirus. After vaccination, a persistent memory response with a public VH5JH5 IgM component was composed of dominant antibodies shared among all individuals. The rearrangement model showed that these public junctions occurred with high probability indicating that they were already favored before vaccination due to the recombination process, as shown in mammals. In addition, these clonotypes were in the naïve repertoire associated with larger similarity classes, composed of junctions differing only at one or two positions by amino acids with comparable properties. The model showed that this property was due to selective processes exerted between the recombination and the naive repertoire. Finally, our results showed that public clonotypes greatly expanded after vaccination displayed several VDJ junctions differing only by one or two amino acids with similar properties, highlighting a convergent response. The fish public memory antibody response to a virus is therefore shaped at three levels: by recombination biases, by selection acting on the formation of the pre-vaccination repertoire, and by convergent selection of functionally similar clonotypes during the response. We also show that naive repertoires of IgM and IgT have different structures and sharing between individuals, due to selection biases. In sum, our comparative approach identifies three conserved features of the antibody repertoire associated with public memory responses. These features were already present in the last common ancestors of fish and mammals, while other characteristics may represent species-specific solutions.
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Affiliation(s)
- Susana Magadan
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luc Jouneau
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France
| | - Maximilian Puelma Touzel
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, and École Normale Supérieure (PSL), Paris, France
| | - Simon Marillet
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France.,Université Côte d'Azur and INRIA, Sophia Antipolis, France
| | - Wahiba Chara
- Sorbonne Université, INSERM, UMR S 959, Immunology-Immunopathology -Immunotherapy (I3), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR S 959, Immunology-Immunopathology -Immunotherapy (I3), Paris, France
| | - Edwige Quillet
- INRA, Génétique Animale et Biologie Intégrative, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, UPMC and Ecole Normale Supérieure, PSL, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, and École Normale Supérieure (PSL), Paris, France
| | | | - Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Simon Fillatreau
- INEM, INSERM U1151/CNRS UMR8253, Institut Necker-Enfants Malades, Faculté de Médecine Paris Descartes, Paris, France.,Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants Malades, Paris, France
| | - Pierre Boudinot
- INRA, Virologie et Immunologie Moléculaires, Université Paris-Saclay, Jouy-en-Josas, France
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11
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Lorenzon R, Mariotti-Ferrandiz E, Aheng C, Ribet C, Toumi F, Pitoiset F, Chaara W, Derian N, Johanet C, Drakos I, Harris S, Amselem S, Berenbaum F, Benveniste O, Bodaghi B, Cacoub P, Grateau G, Amouyal C, Hartemann A, Saadoun D, Sellam J, Seksik P, Sokol H, Salem JE, Vicaut E, Six A, Rosenzwajg M, Bernard C, Klatzmann D. Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol. BMJ Open 2018; 8:e021037. [PMID: 30166293 PMCID: PMC6119447 DOI: 10.1136/bmjopen-2017-021037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 07/02/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Autoimmune and autoinflammatory diseases (AIDs) represent a socioeconomic burden as the second cause of chronic illness in Western countries. In this context, the TRANSIMMUNOM clinical protocol is designed to revisit the nosology of AIDs by combining basic, clinical and information sciences. Based on classical and systems biology analyses, it aims to uncover important phenotypes that cut across diagnostic groups so as to discover biomarkers and identify novel therapeutic targets. METHODS AND ANALYSIS TRANSIMMUNOM is an observational clinical protocol that aims to cross-phenotype a set of 19 AIDs, six related control diseases and healthy volunteers . We assembled a multidisciplinary cohort management team tasked with (1) selecting informative biological (routine and omics type) and clinical parameters to be captured, (2) standardising the sample collection and shipment circuit, (3) selecting omics technologies and benchmarking omics data providers, (4) designing and implementing a multidisease electronic case report form and an omics database and (5) implementing supervised and unsupervised data analyses. ETHICS AND DISSEMINATION The study was approved by the institutional review board of Pitié-Salpêtrière Hospital (ethics committee Ile-De-France 48-15) and done in accordance with the Declaration of Helsinki and good clinical practice. Written informed consent is obtained from all participants before enrolment in the study. TRANSIMMUNOM's project website provides information about the protocol (https://www.transimmunom.fr/en/) including experimental set-up and tool developments. Results will be disseminated during annual scientific committees appraising the project progresses and at national and international scientific conferences. DISCUSSION Systems biology approaches are increasingly implemented in human pathophysiology research. The TRANSIMMUNOM study applies such approach to the pathophysiology of AIDs. We believe that this translational systems immunology approach has the potential to provide breakthrough discoveries for better understanding and treatment of AIDs. TRIAL REGISTRATION NUMBER NCT02466217; Pre-results.
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Affiliation(s)
- Roberta Lorenzon
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Caroline Aheng
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Claire Ribet
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Ferial Toumi
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Fabien Pitoiset
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Wahiba Chaara
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Derian
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Catherine Johanet
- Immunology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UFR 967, Sorbonne Université, Paris, France
| | - Iannis Drakos
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Sophie Harris
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
| | - Serge Amselem
- Laboratoire de génétique, UMR S933, Sorbonne Université, INSERM, Paris, France
| | - Francis Berenbaum
- Rheumatology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S938, Sorbonne Université, INSERM, Paris, France
| | - Olivier Benveniste
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR 974, Sorbonne Université, Paris, France
| | - Bahram Bodaghi
- Département Hospitalo-Universitaire Vision and Handicaps ‘ViewMaintain’, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Patrice Cacoub
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Gilles Grateau
- Internal Medicine Department, Tenon Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S933, Sorbonne Université, INSERM, Paris, France
| | - Chloe Amouyal
- Diabetology Department, Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - Agnes Hartemann
- Diabetology Department, Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, Île-de-France, France
| | - David Saadoun
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Internal Medicine and Clinical Immunology Department, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jeremie Sellam
- Rheumatology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- UMR S938, Sorbonne Université, INSERM, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- GRC-UPMC 03, Sorbonne Université, Paris, France
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- GRC-UPMC 03, Sorbonne Université, Paris, France
| | - Joe-Elie Salem
- CIC-1421, Pharmacology Department, INSERM, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Vicaut
- Unité de recherche clinique, UMR 942, Saint-Louis Lariboisière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Adrien Six
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Michelle Rosenzwajg
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Claude Bernard
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - David Klatzmann
- Immunology, Immunopathology, Immunotherapy (i3), Sorbonne Université, INSERM, Paris, France
- Biotherapy (CIC-BTi) and Inflammation, Immunopathology, Biotherapy Department (i2B), Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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12
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Chaara W, Gonzalez-Tort A, Florez LM, Klatzmann D, Mariotti-Ferrandiz E, Six A. RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy. Front Immunol 2018; 9:1038. [PMID: 29868003 PMCID: PMC5962720 DOI: 10.3389/fimmu.2018.01038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 01/02/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to proper use of these data. Here, we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high-sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; and (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modeling of the highly complex nature of TCR repertoires.
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Affiliation(s)
- Wahiba Chaara
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Ariadna Gonzalez-Tort
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Laura-Maria Florez
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
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13
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Six A, Bocheux A, Charra F, Mathevet F, Kreher D, Attias AJ. 2D self-assembly of phenylene-vinylene tectons at the liquid-highly oriented pyrolytic graphite interface: from chain length effects to anisotropic guest-host dynamics. Nanotechnology 2017; 28:025602. [PMID: 27922835 DOI: 10.1088/1361-6528/28/2/025602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we report the synthesis and characterization of a series of new phenylene-vinylene tectons. The study by scanning tunneling microscopy of their supramolecular self-assembly at the interface between a phenyloctane solution and highly oriented pyrolytic graphite demonstrates that variation of concentration and length of alkyl chains led to the formation of different networks, a compact one and a nanoporous one, with a fine control of the lattice parameters. The study of guest-host properties of the nanoporous network revealed a selectivity toward guest compounds according to their shape and size. Moreover, the statistical analysis of pore-to-pore guest dynamics evidences an anisotropic diffusion process.
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Affiliation(s)
- A Six
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 8232, Institut Parisien de Chimie Moléculaire, Université Pierre et Marie Curie, 4 Place Jussieu, F-75005 Paris, France
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14
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Hamel Y, Mauvais FX, Pham HP, Kratzer R, Marchi C, Barilleau É, Waeckel-Enée E, Arnoux JB, Hartemann A, Cordier C, Mégret J, Rocha B, de Lonlay P, Beltrand J, Six A, Robert JJ, van Endert P. A unique CD8(+) T lymphocyte signature in pediatric type 1 diabetes. J Autoimmun 2016; 73:54-63. [PMID: 27318739 DOI: 10.1016/j.jaut.2016.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 06/01/2016] [Accepted: 06/08/2016] [Indexed: 12/16/2022]
Abstract
Human type 1 diabetes results from a destructive auto-reactive immune response in which CD8(+) T lymphocytes play a critical role. Given the intense ongoing efforts to develop immune intervention to prevent and/or cure the disease, biomarkers suitable for prediction of disease risk and progress, as well as for monitoring of immunotherapy are required. We undertook separate multi-parameter analyses of single naïve and activated/memory CD8(+) T lymphocytes from pediatric and adult patients, with the objective of identifying cellular profiles associated with onset of type 1 diabetes. We observe global perturbations in gene and protein expression and in the abundance of T cell populations characterizing pediatric but not adult patients, relative to age-matched healthy individuals. Pediatric diabetes is associated with a unique population of CD8(+) T lymphocytes co-expressing effector (perforin, granzyme B) and regulatory (transforming growth factor β, interleukin-10 receptor) molecules. This population persists after metabolic normalization and is especially abundant in children with high titers of auto-antibodies to glutamic acid decarboxylase and with elevated HbA1c values. These findings highlight striking differences between pediatric and adult type 1 diabetes, indicate prolonged large-scale perturbations in the CD8(+) T cell compartment in the former, and suggest that CD8(+)CD45RA(-) T cells co-expressing effector and regulatory factors are of interest as biomarkers in pediatric type 1 diabetes.
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Affiliation(s)
- Yamina Hamel
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - François-Xavier Mauvais
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Hang-Phuong Pham
- Sorbonne Universités, UPMC Université Paris 6, 75015 Paris, France; Institut National de la Sante et de la Recherche Médicale, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), 75013 Paris, France
| | - Roland Kratzer
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Christophe Marchi
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Émilie Barilleau
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Emmanuelle Waeckel-Enée
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Jean-Baptiste Arnoux
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre de référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Agnès Hartemann
- Université Pierre & Marie Curie, IHU ICAN, 75013 Paris, France; Service de Diabétologie, Hôpital de la Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris, 75013 Paris, France
| | - Corinne Cordier
- Institut National de la Sante et de la Recherche Médicale, US24, 75015 Paris, France; Centre National de la Recherche Scientifique, UMS3633, 75015 Paris, France
| | - Jerome Mégret
- Institut National de la Sante et de la Recherche Médicale, US24, 75015 Paris, France; Centre National de la Recherche Scientifique, UMS3633, 75015 Paris, France
| | - Benedita Rocha
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France
| | - Pascale de Lonlay
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre de référence des Maladies Héréditaires du Métabolisme, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France; Institut Imagine, Institut National de la Sante et de la Recherche Médicale, Unité 1163, 75015 Paris, France
| | - Jacques Beltrand
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Endocrinologie, Gynécologie et Diabétologie Pédiatrique, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Adrien Six
- Sorbonne Universités, UPMC Université Paris 6, 75015 Paris, France; Institut National de la Sante et de la Recherche Médicale, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), 75013 Paris, France
| | - Jean-Jacques Robert
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Endocrinologie, Gynécologie et Diabétologie Pédiatrique, Hôpital Necker, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Peter van Endert
- Institut National de la Sante et de la Recherche Médicale, Unité 1151, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de médecine, 75015 Paris, France; Centre National de la Recherche Scientifique, UMR8253, 75015 Paris, France.
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15
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Dérian N, Bellier B, Pham HP, Tsitoura E, Kazazi D, Huret C, Mavromara P, Klatzmann D, Six A. Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses. PLoS Comput Biol 2016; 12:e1004801. [PMID: 26998760 PMCID: PMC4801398 DOI: 10.1371/journal.pcbi.1004801] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 02/08/2016] [Indexed: 01/19/2023] Open
Abstract
Systems biology offers promising approaches for identifying response-specific signatures to vaccination and assessing their predictive value. Here, we designed a modelling strategy aiming to predict the quality of late T-cell responses after vaccination from early transcriptome analysis of dendritic cells. Using standardized staining with tetramer, we first quantified antigen-specific T-cell expansion 5 to 10 days after vaccination with one of a set of 41 different vaccine vectors all expressing the same antigen. Hierarchical clustering of the responses defined sets of high and low T cell response inducers. We then compared these responses with the transcriptome of splenic dendritic cells obtained 6 hours after vaccination with the same vectors and produced a random forest model capable of predicting the quality of the later antigen-specific T-cell expansion. The model also successfully predicted vector classification as low or strong T-cell response inducers of a novel set of vaccine vectors, based on the early transcriptome results obtained from spleen dendritic cells, whole spleen and even peripheral blood mononuclear cells. Finally, our model developed with mouse datasets also accurately predicted vaccine efficacy from literature-mined human datasets. Vaccines are designed to elicit effective immune responses against antigens. The various vector platforms used in vaccine development are diverse and complex, rendering the selection of promising vaccines vector challenging. We have designed a modeling strategy that predicts the propensity of vaccine vectors to elicit strong late T-cell responses using transcriptome material obtained 6 hours after vaccination. Our model, designed with mouse datasets, also predicted vector efficacy from mined human data. Thus, molecular signatures obtained 6 hours after vaccination can predict vaccine efficacy at 2 weeks post vaccination, which should help in vaccine development.
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Affiliation(s)
- Nicolas Dérian
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
| | - Bertrand Bellier
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
| | - Hang Phuong Pham
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
| | - Eliza Tsitoura
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Dorothea Kazazi
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Christophe Huret
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
| | - Penelope Mavromara
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - David Klatzmann
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
- * E-mail: (DK); (AS)
| | - Adrien Six
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology, Immunopathology, Immunotherapy, Paris, France
- AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, Paris, France
- INSERM, UMRS 959, "Immunology, Immunopathology, Immunotherapy", Paris, France
- * E-mail: (DK); (AS)
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16
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Zeidan MJ, Saadoun D, Garrido M, Klatzmann D, Six A, Cacoub P. Behçet's disease physiopathology: a contemporary review. Auto Immun Highlights 2016; 7:4. [PMID: 26868128 PMCID: PMC4751097 DOI: 10.1007/s13317-016-0074-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022]
Abstract
Behçet’s disease, also known as the Silk Road Disease, is a rare systemic vasculitis disorder of unknown etiology. Recurrent attacks of acute inflammation characterize Behçet’s disease. Frequent oral aphthous ulcers, genital ulcers, skin lesions and ocular lesions are the most common manifestations. Inflammation is typically self-limiting in time and relapsing episodes of clinical manifestations represent a hallmark of Behçet’s disease. Other less frequent yet severe manifestations that have a major prognostic impact involve the eyes, the central nervous system, the main large vessels and the gastrointestinal tract. Behçet’s disease has a heterogeneous onset and is associated with significant morbidity and premature mortality. This study presents a current immunological review of the disease and provides a synopsis of clinical aspects and treatment options.
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Affiliation(s)
- Mohamad J Zeidan
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France
- INSERM, UMR_S 959, 75013, Paris, France
- CNRS, FRE3632, 75005, Paris, France
| | - David Saadoun
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France
- INSERM, UMR_S 959, 75013, Paris, France
- CNRS, FRE3632, 75005, Paris, France
- Department of Internal Medicine and Clinical Immunology, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, 83 Boulevard de l'Hôpital, 75013, Paris, France
| | - Marlene Garrido
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France
- INSERM, UMR_S 959, 75013, Paris, France
- CNRS, FRE3632, 75005, Paris, France
| | - David Klatzmann
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France
- INSERM, UMR_S 959, 75013, Paris, France
- CNRS, FRE3632, 75005, Paris, France
| | - Adrien Six
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France
- INSERM, UMR_S 959, 75013, Paris, France
- CNRS, FRE3632, 75005, Paris, France
| | - Patrice Cacoub
- Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Sorbonne Universités, UPMC Univ Paris 06, UMR 7211, 75005, Paris, France.
- INSERM, UMR_S 959, 75013, Paris, France.
- CNRS, FRE3632, 75005, Paris, France.
- Department of Internal Medicine and Clinical Immunology, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, 83 Boulevard de l'Hôpital, 75013, Paris, France.
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17
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Colineau L, Rouers A, Yamamoto T, Xu Y, Urrutia A, Pham HP, Cardinaud S, Samri A, Dorgham K, Coulon PG, Cheynier R, Hosmalin A, Oksenhendler E, Six A, Kelleher AD, Zaunders J, Koup RA, Autran B, Moris A, Graff-Dubois S. HIV-Infected Spleens Present Altered Follicular Helper T Cell (Tfh) Subsets and Skewed B Cell Maturation. PLoS One 2015; 10:e0140978. [PMID: 26501424 PMCID: PMC4621058 DOI: 10.1371/journal.pone.0140978] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/16/2015] [Indexed: 12/27/2022] Open
Abstract
Follicular helper T (Tfh) cells within secondary lymphoid organs control multiple steps of B cell maturation and antibody (Ab) production. HIV-1 infection is associated with an altered B cell differentiation and Tfh isolated from lymph nodes of HIV-infected (HIV+) individuals provide inadequate B cell help in vitro. However, the mechanisms underlying this impairment of Tfh function are not fully defined. Using a unique collection of splenocytes, we compared the frequency, phenotype and transcriptome of Tfh subsets in spleens from HIV negative (HIV-) and HIV+ subjects. We observed an increase of CXCR5+PD-1highCD57-Tfh and germinal center (GC) CD57+ Tfh in HIV+ spleens. Both subsets showed a reduced mRNA expression of the transcription factor STAT-3, co-stimulatory, regulatory and signal transduction molecules as compared to HIV- spleens. Similarly, Foxp3 expressing follicular regulatory T (Tfr) cells were increased, suggesting sustained GC reactions in chronically HIV+ spleens. As a consequence, GC B cell populations were expanded, however, complete maturation into memory B cells was reduced in HIV+ spleens where we evidenced a compromised production of B cell-activating cytokines such as IL-4 and IL-10. Collectively our data indicate that, although Tfh proliferation and GC reactions seem to be ongoing in HIV-infected spleens, Tfh “differentiation” and expression of costimulatory molecules is skewed with a profound effect on B cell maturation.
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Affiliation(s)
- Lucie Colineau
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
| | - Angeline Rouers
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
| | - Takuya Yamamoto
- Immunology Laboratory, Vaccine research center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, United States of America
| | - Yin Xu
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Alejandra Urrutia
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
| | - Hang-Phuong Pham
- Sorbonne Universités UPMC Université Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
- INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
- CNRS, FRE3632, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
| | - Sylvain Cardinaud
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
| | - Assia Samri
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - Karim Dorgham
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - Pierre-Grégoire Coulon
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
| | - Rémi Cheynier
- INSERM, U1016, Institut Cochin, Paris, France
- CNRS, UMR8104, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Anne Hosmalin
- INSERM, U1016, Institut Cochin, Paris, France
- CNRS, UMR8104, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- AP-HP, Hôpital Cochin, Paris, France
| | - Eric Oksenhendler
- Université Paris Diderot, Assistance Publique-Hôpitaux de Paris, Département d’Immunologie Clinique, Hôpital Saint-Louis, Paris, France
| | - Adrien Six
- Sorbonne Universités UPMC Université Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
- INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
- CNRS, FRE3632, Immunology-Immunopathology-Immunotherapy (I3), Paris, France
| | - Anthony D. Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - John Zaunders
- St. Vincent's Centre for Applied Medical Research, St. Vincent's Hospital, Sydney, Australia
| | - Richard A. Koup
- Immunology Laboratory, Vaccine research center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, United States of America
| | - Brigitte Autran
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - Arnaud Moris
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- AP-HP, Hôpital Pitié-Salpêtière, Department of Immunology, Paris, France
| | - Stéphanie Graff-Dubois
- Sorbonne Universités, UPMC Université Paris 06, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- INSERM, U1135, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- CNRS, ERL 8255, Center for Immunology and Microbial Infections—CIMI-Paris, Paris, France
- * E-mail:
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18
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Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, Richard ML, Fargier E, Le Guern ME, Langella P, Sokol H. Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice. ISME J 2015. [PMID: 26218241 DOI: 10.1038/ismej.2015.127] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Studying host-microbiota interactions are fundamental to understanding the mechanisms involved in intestinal homeostasis and inflammation. In this work, we analyzed these interactions in mice that were mono-associated with six microorganisms that are representative of inflammatory bowel disease (IBD)-associated dysbiosis: the bacteria Bacteroides thetaiotaomicron, adhesive-invasive Escherichia coli (AIEC), Ruminococcus gnavus and Roseburia intestinalis; a yeast used as a probiotic drug, Saccharomyces boulardii CNCM I-745; and another yeast, Candida albicans. Extensive ex vivo analyses including colon transcriptomics, histology, immune response, bile acid metabolism and short-chain fatty acid production were studied. We showed that B. thetaiotaomicron had the highest impact on the immune system because it was almost able to recapitulate the effects of the entire conventional microbiota and notably induced Treg pathways. Furthermore, these analyses uncovered the effects of E. coli AIEC LF82 on indoleamine 2,3-dioxygenase expression and of S. boulardii CNCM I-745 on angiogenesis. These results were confirmed in vitro in human cell lines. Finally, our results suggested that R. gnavus has major effects on metabolism, and notably on tryptophan metabolism. This work therefore reveals that microorganisms with a potential role in intestinal homeostasis and inflammation have specific impacts on the host, and it suggests several tracks to follow to understand intestinal homeostasis and IBD pathogenesis better, providing new insights to identify novel therapeutic targets.
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Affiliation(s)
- Thomas W Hoffmann
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Hang-Phuong Pham
- ILTOO Pharma, Institut du Cerveau et de Moelle Epinière, Hôpital Pitié Salpêtrière, Paris, France
| | - Chantal Bridonneau
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Camille Aubry
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Bruno Lamas
- ERL INSERM U 1157/UMR7203, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie (UPMC), Paris, France
| | | | - Marco Moroldo
- INRA, UMR1313 GABI/CRB GADIE, Jouy en Josas, France.,AgroParisTech, UMR1313 GABI, Jouy en Josas, France
| | - Dominique Rainteau
- ERL INSERM U 1157/UMR7203, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie (UPMC), Paris, France
| | - Nicolas Lapaque
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Adrien Six
- Sorbonne Universités, UPMC Université Paris 06, INSERM UMR_S 959, CNRS FRE 3632, Immunology, Immunopathology, Immunotherapy (I3), Paris, France
| | - Mathias L Richard
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Emilie Fargier
- Biocodex, Centre Recherche et Développement, Compiègne, France
| | | | - Philippe Langella
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France
| | - Harry Sokol
- INRA, UMR1319 MICALIS, Jouy en Josas, France.,AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France.,ERL INSERM U 1157/UMR7203, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie (UPMC), Paris, France.,AgroParisTech, UMR1313 GABI, Jouy en Josas, France.,Service de Gastroentérologie et Nutrition, Hôpital Saint-Antoine, Assistance Publique Hôpitaux de Paris et Université Paris 6, Paris, France
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Vlková V, Štěpánek I, Hrušková V, Šenigl F, Mayerová V, Šrámek M, Šímová J, Bieblová J, Indrová M, Hejhal T, Dérian N, Klatzmann D, Six A, Reiniš M. Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes. Oncotarget 2015; 5:6923-35. [PMID: 25071011 PMCID: PMC4196173 DOI: 10.18632/oncotarget.2222] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Downregulation of MHC class I expression on tumour cells, a common mechanism by which tumour cells can escape from specific immune responses, can be associated with coordinated silencing of antigen-presenting machinery genes. The expression of these genes can be restored by IFNγ. In this study we documented association of DNA demethylation of selected antigen-presenting machinery genes located in the MHC genomic locus (TAP-1, TAP-2, LMP-2, LMP-7) upon IFNγ treatment with MHC class I upregulation on tumour cells in several MHC class I-deficient murine tumour cell lines (TC-1/A9, TRAMP-C2, MK16 and MC15). Our data also documented higher methylation levels in these genes in TC-1/A9 cells, as compared to their parental MHC class I-positive TC-1 cells. IFNγ-mediated DNA demethylation was relatively fast in comparison with demethylation induced by DNA methyltransferase inhibitor 5-azacytidine, and associated with increased histone H3 acetylation in the promoter regions of APM genes. Comparative transcriptome analysis in distinct MHC class I-deficient cell lines upon their treatment with either IFNγ or epigenetic agents revealed that a set of genes, significantly enriched for the antigen presentation pathway, was regulated in the same manner. Our data demonstrate that IFNγ acts as an epigenetic modifier when upregulating the expression of antigen-presenting machinery genes.
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Affiliation(s)
- Veronika Vlková
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Ivan Štěpánek
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Veronika Hrušková
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Filip Šenigl
- Department of Viral and Cellular Genetics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Veronika Mayerová
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Martin Šrámek
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Jana Šímová
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Jana Bieblová
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Marie Indrová
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Tomáš Hejhal
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
| | - Nicolas Dérian
- UPMC Univ Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy & Département Hospitalo-Universitaire (DHU) Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - David Klatzmann
- UPMC Univ Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy & Département Hospitalo-Universitaire (DHU) Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Adrien Six
- UPMC Univ Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy & Département Hospitalo-Universitaire (DHU) Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Milan Reiniš
- Department of Tumour Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v. v. i., Prague
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20
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Bergot AS, Chaara W, Ruggiero E, Mariotti-Ferrandiz E, Dulauroy S, Schmidt M, von Kalle C, Six A, Klatzmann D. TCR sequences and tissue distribution discriminate the subsets of naïve and activated/memory Treg cells in mice. Eur J Immunol 2015; 45:1524-34. [PMID: 25726757 DOI: 10.1002/eji.201445269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/08/2015] [Accepted: 02/24/2015] [Indexed: 12/12/2022]
Abstract
Analyses of the regulatory T (Treg) cell TCR repertoire should help elucidate the nature and diversity of their cognate antigens and thus how Treg cells protect us from autoimmune diseases. We earlier identified CD44(hi) CD62L(low) activated/memory (am) Treg cells as a Treg-cell subset with a high turnover and possible self-specificity. We now report that amTreg cells are predominantly distributed in lymph nodes (LNs) draining deep tissues. Multivariate analyses of CDR3 spectratyping first revealed that amTreg TCR repertoire is different from that of naïve Treg cells (nTreg cells) and effector T (Teff) cells. Furthermore, in deep- versus superficial LNs, TCR-β deep sequencing further revealed diversified nTreg-cell and amTreg-cell repertoires, although twofold less diverse than that of Teff cells, and with repertoire richness significantly lower in deep-LN versus superficial-LN Treg cells. Importantly, expanded clonotypes were mostly detected in deep-LN amTreg cells, some accounting for 20% of the repertoire. Strikingly, these clonotypes were absent from nTreg cells, but found at low frequency in Teff cells. Our results, obtained in nonmanipulated mice, indicate different antigenic targets for naïve and amTreg cells and that amTreg cells are self-specific. The data we present are consistent with an instructive component in Treg-cell differentiation.
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Affiliation(s)
- Anne-Sophie Bergot
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Wahiba Chaara
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Eliana Ruggiero
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - Sophie Dulauroy
- CNRS, URA 1961 UPMC, Immunophysiopathologie Infectieuse, Institut Pasteur, Paris, France
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Adrien Six
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
| | - David Klatzmann
- Sorbonne Universités, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,INSERM, UMRS 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy and Département Hospitalo-Universitaire Inflammation-Immunopathology-Biotherapy (i2B), Paris, France
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21
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Rosenzwajg M, Churlaud G, Mallone R, Six A, Dérian N, Chaara W, Lorenzon R, Long SA, Buckner JH, Afonso G, Pham HP, Hartemann A, Yu A, Pugliese A, Malek TR, Klatzmann D. Low-dose interleukin-2 fosters a dose-dependent regulatory T cell tuned milieu in T1D patients. J Autoimmun 2015; 58:48-58. [PMID: 25634360 DOI: 10.1016/j.jaut.2015.01.001] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 12/26/2014] [Accepted: 01/05/2015] [Indexed: 12/13/2022]
Abstract
Most autoimmune diseases (AID) are linked to an imbalance between autoreactive effector T cells (Teffs) and regulatory T cells (Tregs). While blocking Teffs with immunosuppression has long been the only therapeutic option, activating/expanding Tregs may achieve the same objective without the toxicity of immunosuppression. We showed that low-dose interleukin-2 (ld-IL-2) safely expands/activates Tregs in patients with AID, such HCV-induced vasculitis and Type 1 Diabetes (T1D). Here we analyzed the kinetics and dose-relationship of IL-2 effects on immune responses in T1D patients. Ld-IL-2 therapy induced a dose-dependent increase in CD4(+)Foxp3(+) and CD8(+)Foxp3(+) Treg numbers and proportions, the duration of which was markedly dose-dependent. Tregs expressed enhanced levels of activation markers, including CD25, GITR, CTLA-4 and basal pSTAT5, and retained a 20-fold higher sensitivity to IL-2 than Teff and NK cells. Plasma levels of regulatory cytokines were increased in a dose-dependent manner, while cytokines linked to Teff and Th17 inflammatory cells were mostly unchanged. Global transcriptome analyses showed a dose-dependent decrease in immune response signatures. At the highest dose, Teff responses against beta-cell antigens were suppressed in all 4 patients tested. These results inform of broader changes induced by ld-IL-2 beyond direct effects on Tregs, and relevant for further development of ld-IL-2 for therapy and prevention of T1D, and other autoimmune and inflammatory diseases.
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Affiliation(s)
- Michelle Rosenzwajg
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - Guillaume Churlaud
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - Roberto Mallone
- Inserm, U1016, Institut Cochin, Immunology of Diabetes Team, DeAR Lab, F-75014, Paris, France; CNRS, UMR8104, F-75014, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, F-75014, Paris, France; AP-HP, Hôpital Cochin-Port Royal, Diabetology Department, F-75014, Paris, France
| | - Adrien Six
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - Nicolas Dérian
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - Wahiba Chaara
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - Roberta Lorenzon
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France
| | - S Alice Long
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Jane H Buckner
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Georgia Afonso
- Inserm, U1016, Institut Cochin, Immunology of Diabetes Team, DeAR Lab, F-75014, Paris, France; CNRS, UMR8104, F-75014, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, F-75014, Paris, France; AP-HP, Hôpital Cochin-Port Royal, Diabetology Department, F-75014, Paris, France
| | - Hang-Phuong Pham
- ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, 75013, Paris, France
| | - Agnès Hartemann
- AP-HP, Hôpital Pitié-Salpêtrière, Diabetology, F-75651, Paris, France
| | - Aixin Yu
- The Diabetes Research Institute, University of Miami, Miami, FL, USA; Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Alberto Pugliese
- The Diabetes Research Institute, University of Miami, Miami, FL, USA; Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA; Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Thomas R Malek
- The Diabetes Research Institute, University of Miami, Miami, FL, USA; Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - David Klatzmann
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), F-75651, Paris, France; Sorbonne Université, UPMC Univ Paris 06, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France; Inserm, UMRS 959, Immunology-Immunopathology-Immunotherapy (I3), F-75005, Paris, France.
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22
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Pham HP, Dérian N, Chaara W, Bellier B, Klatzmann D, Six A. A novel strategy for molecular signature discovery based on independent component analysis. INT J DATA MIN BIOIN 2014; 9:277-304. [PMID: 25163169 DOI: 10.1504/ijdmb.2014.060052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microarray analysis often leads to either too large or too small numbers of gene candidates to allow meaningful identification of functional signatures. We aimed at overcoming this hurdle by combining two algorithms: i. Independent Component Analysis to extract statistically-based potential signatures. ii. Gene Set Enrichment Analysis to produce a score of enrichment with statistical significance of each potential signature. We have applied this strategy to identify regulatory T cell (Treg) molecular signatures from two experiments in mice, with cross-validation. These signatures can detect the -1% Treg in whole spleen. These findings demonstrate the relevance of our approach as a signature discovery tool.
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23
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Allenbach Y, Chaara W, Rosenzwajg M, Six A, Prevel N, Mingozzi F, Wanschitz J, Musset L, Charuel JL, Eymard B, Salomon B, Duyckaerts C, Maisonobe T, Dubourg O, Herson S, Klatzmann D, Benveniste O. Th1 response and systemic treg deficiency in inclusion body myositis. PLoS One 2014; 9:e88788. [PMID: 24594700 PMCID: PMC3942319 DOI: 10.1371/journal.pone.0088788] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 01/10/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Sporadic inclusion body myositis (sIBM), the most frequent myositis in elderly patients, is characterized by the presence muscle inflammation and degeneration. We aimed at characterizing immune responses and regulatory T cells, considered key players in the maintenance of peripheral immune tolerance, in sIBM. METHODS Serum and muscle tissue levels of 25 cytokines and phenotype of circulating immune cells were measured in 22 sIBM patients and compared with 22 healthy subjects. Cytokine data were analysed by unsupervised hierarchical clustering and principal components analysis. RESULTS Compared to healthy controls, sIBM patients had increased levels of Th-1 cytokines and chemokines such as IL-12 (261±138 pg/mL vs. 88±19 pg/mL; p<0.0001), CXCL-9 (186±12 pg/mL vs. 13±7 pg/mL; p<0.0001), and CXCL-10 (187±62 pg/mL vs. 13±6 pg/mL; p<0.0001). This was associated with an increased frequency of CD8+CD28- T cells (45.6±18.5% vs. 13.5±9.9%; p<0.0001), which were more prone to produce IFN-γ (45.6±18.5% vs. 13.5±9.9%; p<0.0001). sIBM patients also had a decreased frequency of circulating regulatory T cells (CD4+CD25+CD127lowFOXP3+, 6.9±1.7%; vs. 5.2±1.1%, p = 0.01), which displayed normal suppressor function and were also present in affected muscle. CONCLUSION sIBM patients present systemic immune activation with Th1 polarization involving the IFN-γ pathway and CD8+CD28- T cells associated with peripheral regulatory T cell deficiency.
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Affiliation(s)
- Yves Allenbach
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
- Internal Medicine Department 1, Centre de référence Maladie Neuromusculaire, Assistance Publique - Hôpitaux de Paris, Hôpital Pitié-Salpêtrière Paris, France
- * E-mail:
| | - Wahiba Chaara
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Michelle Rosenzwajg
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Adrien Six
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Nicolas Prevel
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Federico Mingozzi
- U974, Sorbonne Universités, Pierre and Marie Curie University, Paris 06, Paris, France
- U974, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Genethon, Evry, France
| | - Julia Wanschitz
- Department of Neurology, Innsbruck Medical University, Innsbruck, Austria
| | - Lucile Musset
- Department of immunochemistry, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University Paris 06, Paris, France
| | - Jean-Luc Charuel
- Department of immunochemistry, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University Paris 06, Paris, France
| | - Bruno Eymard
- Department of neurology, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University, Paris 06, Paris, France
| | - Benoit Salomon
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
| | - Charles Duyckaerts
- Department of neuropathology, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University Paris 06, Paris, France
| | - Thierry Maisonobe
- Department of neuropathology, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University Paris 06, Paris, France
| | - Odile Dubourg
- Department of neuropathology, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Pierre and Marie Curie University Paris 06, Paris, France
| | - Serge Herson
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
- Internal Medicine Department 1, Centre de référence Maladie Neuromusculaire, Assistance Publique - Hôpitaux de Paris, Hôpital Pitié-Salpêtrière Paris, France
| | - David Klatzmann
- Immunlogy-Immunopathology-Immunotherpapy (I3), Sorbonne Universités, Pierre and Marie Curie University Paris 06, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), Centre National de la Recherche Scientifique UMR 7211, Paris, France
- Immunlogy-Immunopathology-Immunotherpapy (I3), UMRS_959, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Olivier Benveniste
- Inflammation-Immunopathology-Biotherapy (i2B), Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
- Internal Medicine Department 1, Centre de référence Maladie Neuromusculaire, Assistance Publique - Hôpitaux de Paris, Hôpital Pitié-Salpêtrière Paris, France
- U974, Sorbonne Universités, Pierre and Marie Curie University, Paris 06, Paris, France
- U974, Institut National de la Santé et de la Recherche Médicale, Paris, France
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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Terrier B, Chaara W, Dufat L, Geri G, Rosenzwajg M, Musset L, Sène D, Saadoun D, Six A, Klatzmann D, Cacoub P. Serum biomarker signature identifies patients with B-cell non-Hodgkin lymphoma associated with cryoglobulinemia vasculitis in chronic HCV infection. Autoimmun Rev 2013; 13:319-26. [PMID: 24220267 DOI: 10.1016/j.autrev.2013.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 11/05/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) is associated with B-cell disorders, including mixed cryoglobulinemia (MC) and B-cell non-Hodgkin lymphoma (B-NHL). We hypothesized that combination of serum biomarkers could be used to identify B-NHL in HCV patients. METHODS We measured in 155 HCV infected patients, with and without MC and/or B-NHL, serum levels of eight markers previously described to be increased in patients with B-NHL, i.e. sCD22, sCD27, sIL-2Rα, sCD137, free-light chains of Ig (ratio κ/λ), heavy chains of Ig (ratio IgMκ/IgMλ), gammaglobulins and C4. We used a multiparametric analysis to determine a signature that identifies patients with overt B-NHL. RESULTS Serum levels were significantly different between patients without MC, patients with asymptomatic MC, patients with MC vasculitis and those with MC vasculitis and B-NHL for all biomarkers except for sCD137. Using multiparametric analysis, we identified a signature involving sCD27, sIL-2Rα, gammaglobulins and C4 levels associated with the presence of overt B-NHL in HCV-infected patients. This signature had a sensitivity of 100%, a specificity of 90%, and positive and negative predictive values of 97 and 100%, respectively for discriminating patients with overt B-NHL and those without B-NHL. CONCLUSION Our data indicate that serum biomarker signature allows identifying HCV-infected patients presenting with overt B-NHL.
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Affiliation(s)
- Benjamin Terrier
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France
| | - Wahiba Chaara
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; Department of Biotherapy, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - Laurent Dufat
- Department of Immunology, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - Guillaume Geri
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France
| | - Michelle Rosenzwajg
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France; Department of Immunology, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - Lucile Musset
- Department of Biotherapy, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - Damien Sène
- Department of Internal Medicine, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - David Saadoun
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France; Department of Internal Medicine, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France
| | - Adrien Six
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France
| | - David Klatzmann
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France
| | - Patrice Cacoub
- Département Hospitalo-Universitaire (I2B), UPMC Univ Paris 6, UMR 7211, F-75013 Paris, France; CNRS Centre National de la Recherche Scientifique, UMR 7211, F-75013 Paris, France; INSERM, UMRS959, F-75013 Paris, France; Department of Internal Medicine, Groupe Hospitalier Pitié-Salpétrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris 6, F-75013 Paris, France.
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26
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Thomas-Vaslin V, Six A, Ganascia JG, Bersini H. Dynamical and Mechanistic Reconstructive Approaches of T Lymphocyte Dynamics: Using Visual Modeling Languages to Bridge the Gap between Immunologists, Theoreticians, and Programmers. Front Immunol 2013; 4:300. [PMID: 24101919 PMCID: PMC3787330 DOI: 10.3389/fimmu.2013.00300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Dynamic modeling of lymphocyte behavior has primarily been based on populations based differential equations or on cellular agents moving in space and interacting each other. The final steps of this modeling effort are expressed in a code written in a programing language. On account of the complete lack of standardization of the different steps to proceed, we have to deplore poor communication and sharing between experimentalists, theoreticians and programmers. The adoption of diagrammatic visual computer language should however greatly help the immunologists to better communicate, to more easily identify the models similarities and facilitate the reuse and extension of existing software models. Since immunologists often conceptualize the dynamical evolution of immune systems in terms of “state-transitions” of biological objects, we promote the use of unified modeling language (UML) state-transition diagram. To demonstrate the feasibility of this approach, we present a UML refactoring of two published models on thymocyte differentiation. Originally built with different modeling strategies, a mathematical ordinary differential equation-based model and a cellular automata model, the two models are now in the same visual formalism and can be compared.
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Affiliation(s)
- Véronique Thomas-Vaslin
- UPMC Univ Paris 06, UMR7211, Immunology, Immunopathology, Immunotherapy (I3), Integrative Immunology , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) Integrative Immunology , Paris , France
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27
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Castro R, Takizawa F, Chaara W, Lunazzi A, Dang TH, Koellner B, Quillet E, Six A, Fischer U, Boudinot P. Contrasted TCRβ diversity of CD8+ and CD8- T cells in rainbow trout. PLoS One 2013; 8:e60175. [PMID: 23565199 PMCID: PMC3615082 DOI: 10.1371/journal.pone.0060175] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/23/2013] [Indexed: 12/18/2022] Open
Abstract
Teleost fish express highly diverse naive TCRβ (TRB) repertoires and mount strong public and private clonal responses upon infection with pathogens. Fish T cells express typical markers such as CD8, CD4-1 and CD4-2, CD3, CD28 and CTLA4. Fish CD8+ T cells have been shown to be responsible for antigen-specific cell-mediated cytotoxicity in in vitro systems using histo-compatible effector and target cells. We compare here the complexity of TRB repertoires between FACS sorted CD8+ and CD8− T cells from spleen and pronephros of rainbow trout. In contrast to human, while the TRB repertoire is highly diverse and polyclonal in CD8+ T cells of naïve fish, it appeared very different in CD8− lymphocytes with irregular CDR3 length distributions suggesting a dominance of activated clones already in naïve fish or the presence of non conventional T cells. After infection with a systemic virus, CD8+ T cells mount a typical response with significant skewing of CDR3 length profiles. The infection also induces significant modifications of the TRB repertoire expressed by the CD8− fraction, but for a different set of V/J combinations. In this fraction, the antiviral response results in an increase of the peak diversity of spectratypes. This unusual observation reflects the presence of a number of T cell expansions that rise the relative importance of minor peaks of the highly skewed distributions observed in unchallenged animals. These results suggest that the diversity of TRB expressed by CD8+ and CD8− αβ T cells may be subjected to different regulatory patterns in fish and in mammals.
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Affiliation(s)
- Rosario Castro
- Institut National de la Recherche Agronomique, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Fumio Takizawa
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Greifswald-Insel Riems, Germany
| | - Wahiba Chaara
- UPMC Univ Paris 06, UMR 7211, Paris, France
- Centre National de la Recherche Scientifique, UMR 7211, Paris, France
- Assistance Publique - Hôpitaux de Paris, Hopital Pitié Salpêtrière, Service de Biothérapie, Paris, France
| | - Aurélie Lunazzi
- Institut National de la Recherche Agronomique, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Thi Huong Dang
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Greifswald-Insel Riems, Germany
| | - Bernd Koellner
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Greifswald-Insel Riems, Germany
| | - Edwige Quillet
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Adrien Six
- UPMC Univ Paris 06, UMR 7211, Paris, France
- Centre National de la Recherche Scientifique, UMR 7211, Paris, France
| | - Uwe Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Greifswald-Insel Riems, Germany
- * E-mail: (UF); (PB)
| | - Pierre Boudinot
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Infectiology, Greifswald-Insel Riems, Germany
- * E-mail: (UF); (PB)
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28
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Fillatreau S, Six A, Magadan S, Castro R, Sunyer JO, Boudinot P. The astonishing diversity of Ig classes and B cell repertoires in teleost fish. Front Immunol 2013; 4:28. [PMID: 23408183 PMCID: PMC3570791 DOI: 10.3389/fimmu.2013.00028] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 01/24/2013] [Indexed: 12/17/2022] Open
Abstract
With lymphoid tissue anatomy different than mammals, and diverse adaptations to all aquatic environments, fish constitute a fascinating group of vertebrate to study the biology of B cell repertoires in a comparative perspective. Fish B lymphocytes express immunoglobulin (Ig) on their surface and secrete antigen-specific antibodies in response to immune challenges. Three antibody classes have been identified in fish, namely IgM, IgD, and IgT, while IgG, IgA, and IgE are absent. IgM and IgD have been found in all fish species analyzed, and thus seem to be primordial antibody classes. IgM and IgD are normally co-expressed from the same mRNA through alternative splicing, as in mammals. Tetrameric IgM is the main antibody class found in serum. Some species of fish also have IgT, which seems to exist only in fish and is specialized in mucosal immunity. IgM/IgD and IgT are expressed by two different sub-populations of B cells. The tools available to investigate B cell responses at the cellular level in fish are limited, but the progress of fish genomics has started to unravel a rich diversity of IgH and immunoglobulin light chain locus organization, which might be related to the succession of genome remodelings that occurred during fish evolution. Moreover, the development of deep sequencing techniques has allowed the investigation of the global features of the expressed fish B cell repertoires in zebrafish and rainbow trout, in steady state or after infection. This review provides a description of the organization of fish Ig loci, with a particular emphasis on their heterogeneity between species, and presents recent data on the structure of the expressed Ig repertoire in healthy and infected fish.
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Affiliation(s)
- Simon Fillatreau
- Deutsches Rheuma-Forschungszentrum, Leibniz Institute Berlin, Germany
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29
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Castro R, Jouneau L, Pham HP, Bouchez O, Giudicelli V, Lefranc MP, Quillet E, Benmansour A, Cazals F, Six A, Fillatreau S, Sunyer O, Boudinot P. Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection. PLoS Pathog 2013; 9:e1003098. [PMID: 23326228 PMCID: PMC3542120 DOI: 10.1371/journal.ppat.1003098] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/09/2012] [Indexed: 01/12/2023] Open
Abstract
Upon infection, B-lymphocytes expressing antibodies specific for the intruding pathogen develop clonal responses triggered by pathogen recognition via the B-cell receptor. The constant region of antibodies produced by such responding clones dictates their functional properties. In teleost fish, the clonal structure of B-cell responses and the respective contribution of the three isotypes IgM, IgD and IgT remain unknown. The expression of IgM and IgT are mutually exclusive, leading to the existence of two B-cell subsets expressing either both IgM and IgD or only IgT. Here, we undertook a comprehensive analysis of the variable heavy chain (VH) domain repertoires of the IgM, IgD and IgT in spleen of homozygous isogenic rainbow trout (Onchorhynchus mykiss) before, and after challenge with a rhabdovirus, the Viral Hemorrhagic Septicemia Virus (VHSV), using CDR3-length spectratyping and pyrosequencing of immunoglobulin (Ig) transcripts. In healthy fish, we observed distinct repertoires for IgM, IgD and IgT, respectively, with a few amplified μ and τ junctions, suggesting the presence of IgM- and IgT-secreting cells in the spleen. In infected animals, we detected complex and highly diverse IgM responses involving all VH subgroups, and dominated by a few large public and private clones. A lower number of robust clonal responses involving only a few VH were detected for the mucosal IgT, indicating that both IgM(+) and IgT(+) spleen B cells responded to systemic infection but at different degrees. In contrast, the IgD response to the infection was faint. Although fish IgD and IgT present different structural features and evolutionary origin compared to mammalian IgD and IgA, respectively, their implication in the B-cell response evokes these mouse and human counterparts. Thus, it appears that the general properties of antibody responses were already in place in common ancestors of fish and mammals, and were globally conserved during evolution with possible functional convergences.
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Affiliation(s)
- Rosario Castro
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
| | - Luc Jouneau
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
| | - Hang-Phuong Pham
- UPMC Univ Paris 06, UMR 7211, “Integrative Immunology” Team, Paris, France; CNRS, UMR 7211, “Immunology, Immunopathology, Immunotherapy,” Paris, France
| | - Olivier Bouchez
- UMR INRA 0444 Laboratoire de Génétique Cellulaire, GeT-PlaGe Core Facility, Castanet Tolosan, France
| | - Véronique Giudicelli
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire LIGM, IGH, UPR CNRS 1142 and Université Montpellier 2, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire LIGM, IGH, UPR CNRS 1142 and Université Montpellier 2, Montpellier, France
| | - Edwige Quillet
- Génétique Animale et Biologie Intégrative, INRA, Jouy-en-Josas, France
| | | | - Frédéric Cazals
- INRIA Sophia-Antipolis - Méditerranée, Algorithms-Biology-Structure, Sophia-Antipolis, France
| | - Adrien Six
- UPMC Univ Paris 06, UMR 7211, “Integrative Immunology” Team, Paris, France; CNRS, UMR 7211, “Immunology, Immunopathology, Immunotherapy,” Paris, France
| | - Simon Fillatreau
- Deutsches RheumaForschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Jouy-en-Josas, France
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30
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Buonocore F, Castro R, Randelli E, Lefranc MP, Six A, Kuhl H, Reinhardt R, Facchiano A, Boudinot P, Scapigliati G. Diversity, molecular characterization and expression of T cell receptor γ in a teleost fish, the sea bass (Dicentrarchus labrax, L). PLoS One 2012; 7:e47957. [PMID: 23133531 PMCID: PMC3485050 DOI: 10.1371/journal.pone.0047957] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/18/2012] [Indexed: 11/19/2022] Open
Abstract
Two lineages of T cells, expressing either the αβ T cell receptor (TR) or the γδ TR, exist in Gnathostomes. The latter type of T cells account for 1–10 % of T cells in blood and up to 30 % in the small intestine. They may recognize unconventional antigens (phosphorylated microbial metabolites, lipid antigens) without the need of major histocompatibility class I (MH1) or class II (MH2) presentation. In this work we have described cloning and structural characterization of TR -chain (TRG) from the teleost Dicentrarchus labrax. Further, by means of quantitative PCR analysis, we analyzed TRG expression levels both in poly I:C stimulated leukocytes in vitro, and following infection with betanodavirus in vivo. Two full length cDNAs relative to TRG, with the highest peptide and nucleotide identity with Japanese flounder, were identified. A multiple alignment analysis showed the conservation of peptides fundamental for TRG biological functions, and of the FGXG motif in the FR4 region, typical of most TR and immunoglobulin light chains. A 3D structure consisting of two domains mainly folded as beta strands with a sandwich architecture for each domain was also reported. TRG CDR3 of 8–18 AA in length and diversity in the TRG rearrangements expressed in thymus and intestine for a given V/C combination were evidenced by junction length spectratyping. TRG mRNA expression levels were high in basal conditions both in thymus and intestine, while in kidney and gut leukocytes they were up-regulated after in vitro stimulation by poly I:C. Finally, in juveniles the TRG expression levels were up-regulated in the head kidney and down-regulated in intestine after in vivo infection with betanodavirus. Overall, in this study the involvement of TRG-bearing T cells during viral stimulation was described for the first time, leading to new insights for the identification of T cell subsets in fish.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Rosario Castro
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Elisa Randelli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Marie-Paule Lefranc
- The International ImMunoGeneTics Information System®, Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, Centre National de la Recherche Scientifique and Université Montpellier 2, Montpellier, France
| | - Adrien Six
- Université Pierre et Marie Curie (Université Paris-06), Unité Mixte de Recherches 7211, “Integrative Immunology” Team, Paris, France
- Centre National Recherche Scientifique, Unité Mixte de Recherches, “Immunology, Immunopathology, Immunotherapy”, Paris, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Richard Reinhardt
- Genome Centre at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angelo Facchiano
- Laboratory of Bioinformatics and Computational Biology – National Research Council, Istitute of Sciences of Alimentation, Avellino, Italy
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
- * E-mail:
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Terrier B, Derian N, Schoindre Y, Chaara W, Geri G, Zahr N, Mariampillai K, Rosenzwajg M, Carpentier W, Musset L, Piette JC, Six A, Klatzmann D, Saadoun D, Patrice C, Costedoat-Chalumeau N. Restoration of regulatory and effector T cell balance and B cell homeostasis in systemic lupus erythematosus patients through vitamin D supplementation. Arthritis Res Ther 2012; 14:R221. [PMID: 23075451 PMCID: PMC3580532 DOI: 10.1186/ar4060] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 09/05/2012] [Indexed: 01/11/2023] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is a T and B cell-dependent autoimmune disease characterized by the appearance of autoantibodies, a global regulatory T cells (Tregs) depletion and an increase in Th17 cells. Recent studies have shown the multifaceted immunomodulatory effects of vitamin D, notably the expansion of Tregs and the decrease of Th1 and Th17 cells. A significant correlation between higher disease activity and lower serum 25-hydroxyvitamin D levels [25(OH)D] was also shown. Methods In this prospective study, we evaluated the safety and the immunological effects of vitamin D supplementation (100 000 IU of cholecalciferol per week for 4 weeks, followed by 100 000 IU of cholecalciferol per month for 6 months.) in 20 SLE patients with hypovitaminosis D. Results Serum 25(OH)D levels dramatically increased under vitamin D supplementation from 18.7±6.7 at day 0 to 51.4±14.1 (p<0.001) at 2 months and 41.5±10.1 ng/mL (p<0.001) at 6 months. Vitamin D was well tolerated and induced a preferential increase of naïve CD4+ T cells, an increase of regulatory T cells and a decrease of effector Th1 and Th17 cells. Vitamin D also induced a decrease of memory B cells and anti-DNA antibodies. No modification of the prednisone dosage or initiation of new immunosuppressant agents was needed in all patients. We did not observe SLE flare during the 6 months follow-up period. Conclusions This preliminary study suggests the beneficial role of vitamin D in SLE patients and needs to be confirmed in randomized controlled trials.
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Costa N, Pires AE, Gabriel AM, Goulart LF, Pereira C, Leal B, Queiros AC, Chaara W, Moraes-Fontes MF, Vasconcelos C, Ferreira C, Martins J, Bastos M, Santos MJ, Pereira MA, Martins B, Lima M, João C, Six A, Demengeot J, Fesel C. Broadened T-cell Repertoire Diversity in ivIg-treated SLE Patients is Also Related to the Individual Status of Regulatory T-cells. J Clin Immunol 2012; 33:349-60. [DOI: 10.1007/s10875-012-9816-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 10/02/2012] [Indexed: 12/14/2022]
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Bellais S, Six A, Fouet A, Longo M, Dmytruk N, Glaser P, Trieu-Cuot P, Poyart C. Capsular Switching in Group B Streptococcus CC17 Hypervirulent Clone: A Future Challenge for Polysaccharide Vaccine Development. J Infect Dis 2012; 206:1745-52. [DOI: 10.1093/infdis/jis605] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.
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Silva HM, Takenaka MCS, Moraes-Vieira PMM, Monteiro SM, Hernandez MO, Chaara W, Six A, Agena F, Sesterheim P, Barbé-Tuana FM, Saitovitch D, Lemos F, Kalil J, Coelho V. Preserving the B-cell compartment favors operational tolerance in human renal transplantation. Mol Med 2012; 18:733-43. [PMID: 22252714 DOI: 10.2119/molmed.2011.00281] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/10/2012] [Indexed: 12/18/2022] Open
Abstract
Transplanted individuals in operational tolerance (OT) maintain long-term stable graft function after completely stopping immunosuppression. Understanding the mechanisms involved in OT can provide valuable information about pathways to human transplantation tolerance. Here we report that operationally tolerant individuals display quantitative and functional preservation of the B-cell compartment in renal transplantation. OT exhibited normal numbers of circulating total B cells, naive, memory and regulatory B cells (Bregs) as well as preserved B-cell receptor repertoire, similar to healthy individuals. In addition, OT also displayed conserved capacity to activate the cluster of differentiation 40 (CD40)/signal transducer and activator of transcription 3 (STAT3) signaling pathway in Bregs, in contrast, with chronic rejection. Rather than expansion or higher activation, we show that the preservation of the B-cell compartment favors OT.
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Affiliation(s)
- Hernandez M Silva
- Laboratory of Immunology, Heart Institute-InCor, University of São Paulo Medical School, São Paulo, Brazil
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Blazewicz J, Borowski M, Chaara W, Kedziora P, Klatzmann D, Lukasiak P, Six A, Wojciechowski P. GeVaDSs - decision support system for novel Genetic Vaccine development process. BMC Bioinformatics 2012; 13:91. [PMID: 22574945 PMCID: PMC3531312 DOI: 10.1186/1471-2105-13-91] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 04/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The lack of a uniform way for qualitative and quantitative evaluation of vaccine candidates under development led us to set up a standardized scheme for vaccine efficacy and safety evaluation. We developed and implemented molecular and immunology methods, and designed support tools for immunization data storage and analyses. Such collection can create a unique opportunity for immunologists to analyse data delivered from their laboratories. RESULTS We designed and implemented GeVaDSs (Genetic Vaccine Decision Support system) an interactive system for efficient storage, integration, retrieval and representation of data. Moreover, GeVaDSs allows for relevant association and interpretation of data, and thus for knowledge-based generation of testable hypotheses of vaccine responses. CONCLUSIONS GeVaDSs has been tested by several laboratories in Europe, and proved its usefulness in vaccine analysis. Case study of its application is presented in the additional files. The system is available at: http://gevads.cs.put.poznan.pl/preview/(login: viewer, password: password).
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Affiliation(s)
- Jacek Blazewicz
- Institute of Computing Science, Poznań University of Technology, 60-965 Poznań, Poland.
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Abstract
Vaccines are the most effective tools to prevent infectious diseases and to minimize their impact on humans or animals. Despite the successful development of vaccines that are able to elicit potent and protective immune responses, the majority of vaccines have been so far developed empirically and mechanistic events leading to protective immune responses are often poorly understood. This hampers the development of new prophylactic as well as therapeutic vaccines for infectious diseases and cancer. Biological correlates of immune‐mediated protection are currently based on standard readout such as antibody titres and ELISPOT assays. The development of successful vaccines for difficult settings, such as infectious agents leading to chronic infection (HIV, HCV. . .) or cancer, calls for novel ‘readout systems’ or ‘correlates’ of immune‐mediated protection that would reliably predict immune responses to novel vaccines in vivo. Systems biology offers a new approach to vaccine design that is based upon understanding the molecular network mobilized by vaccination. Systems vaccinology approaches investigate more global correlates of successful vaccination, beyond the specific immune response to the antigens administered, providing new methods for measuring early vaccine efficacy and ultimately generating hypotheses for understanding the mechanisms that underlie successful immunogenicity. Using functional genomics, specific molecular signatures of individual vaccine can be identified and used as predictors of vaccination efficiency. The immune response to vaccination involves the coordinated induction of master transcription factors that leads to the development of a broad, polyfunctional and persistent immune response integrating all effector cells of the immune systems.
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Affiliation(s)
- Adrien Six
- UPMC Univ Paris 06, UMR 7211, F-75013 Paris, France.
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Pham HP, Manuel M, Petit N, Klatzmann D, Cohen-Kaminsky S, Six A, Marodon G. Half of the T-cell repertoire combinatorial diversity is genetically determined in humans and humanized mice. Eur J Immunol 2011; 42:760-70. [PMID: 22105329 DOI: 10.1002/eji.201141798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 10/26/2011] [Accepted: 11/17/2011] [Indexed: 01/04/2023]
Abstract
In humanized mice, the T-cell repertoire is derived from genetically identical human progenitors in distinct animals. Thus, careful comparison of the T-cell repertoires of humanized mice with those of humans may reveal the contribution of genetic determinism on T-cell repertoire formation. Here, we performed a comprehensive assessment of the distribution of V-J combinations of the human β chain of the T-cell receptor (hTRBV) in NOD.SCID.γc(-/-) (NSG) humanized mice. We observed that numerous V-J combinations were equally distributed in the thymus and in the periphery of humanized mice compared with human references. A global analysis of the data, comparing repertoire perturbation indices in humanized NSG mice and unrelated human PBMCs, reveals that 50% of the hTRBV families significantly overlapped. Using multivariate ranking and bootstrap analyses, we found that 18% of all possible V-J combinations contributed close to 50% of the expressed diversity, with significant over-representation of BV5-J1.1+1.2 and BV6-J1.1+1.2 rearrangements. Finally, comparison of CD3(-) and CD3(+) thymocyte repertoires indicated that the observed V-J combination overlap was already present before TCR-MHC selection in the thymus. Altogether, our results show that half of the T-cell repertoire combinatorial diversity in humans is genetically determined.
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Affiliation(s)
- Hang-Phuong Pham
- Hôpital La Pitié-Salpêtrière, UPMC Univ Paris 06, UMR 7211, Paris, France
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Terrier B, Geri G, Chaara W, Allenbach Y, Rosenzwajg M, Costedoat-Chalumeau N, Fouret P, Musset L, Benveniste O, Six A, Klatzmann D, Saadoun D, Cacoub P. Interleukin-21 modulates Th1 and Th17 responses in giant cell arteritis. ACTA ACUST UNITED AC 2011; 64:2001-11. [PMID: 22147555 DOI: 10.1002/art.34327] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Giant cell arteritis (GCA) is a large-vessel vasculitis of unknown origin. Recent findings indicate that at least 2 separate lineages of CD4+ T cells, Th1 and Th17 cells, participate in vascular inflammation. The pathways driving these T cell differentiations are incompletely understood, but may provide novel therapeutic targets. This study was undertaken to identify cytokines involved in the pathogenesis of GCA. METHODS Thirty GCA patients fulfilling the American College of Rheumatology criteria, with active disease or disease in remission, and 30 age-matched controls were included. Levels of 27 cytokines were determined in culture supernatants, and flow cytometric analysis of peripheral blood mononuclear cells (PBMCs) and immunohistochemical analysis of temporal artery samples were performed. RESULTS Multiparametric analysis of cytokines produced by PBMCs associated with GCA disease activity identified a signature involving interleukin-2 receptor (IL-2R), IL-12, interferon-γ (IFNγ), IL-17A, IL-21, and granulocyte-macrophage colony-stimulating factor (GM-CSF). An expansion of Th1 and Th17 cells and a decrease in Treg cells were observed in the peripheral blood of patients with active GCA. An expansion of IL-21-producing CD4+ T cells was also observed in patients with active GCA and correlated positively with Th17 and Th1 cell expansion. Immunohistochemical analysis revealed IFNγ, IL-17A, and IL-21 expression within inflammatory infiltrates. Stimulation of purified CD4+ T cells with IL-21 increased Th1 and Th17 cell frequencies and decreased FoxP3 expression. In contrast, blockade of IL-21 using IL-21R-Fc markedly decreased the production of IL-17A and IFNγ and increased FoxP3 expression. CONCLUSION Our findings indicate that IL-21 plays a critical role in modulating Th1 and Th17 responses and Treg cells in GCA, and might represent a potential target for novel therapy.
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Terrier B, Geri G, Chaara W, Allenbach Y, Rosenzwajg M, Costedoat-Chalumeau N, Fouret P, Benveniste O, Six A, Klatzmann D, Saadoun D, Cacoub P. L’interleukine-21 module les réponses lymphocytaires Th1 et Th17 au cours de la maladie de Horton. Rev Med Interne 2011. [DOI: 10.1016/j.revmed.2011.10.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Saadoun D, Rosenzwajg M, Joly F, Six A, Carrat F, Thibault V, Sene D, Cacoub P, Klatzmann D. Regulatory T-cell responses to low-dose interleukin-2 in HCV-induced vasculitis. N Engl J Med 2011; 365:2067-77. [PMID: 22129253 DOI: 10.1056/nejmoa1105143] [Citation(s) in RCA: 578] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Patients with vasculitis induced by the hepatitis C virus (HCV) have reduced levels of regulatory T cells (Tregs). Resolution of HCV infection correlates with cure of vasculitis and the recovery of Treg levels. We reasoned that interleukin-2, a cytokine that promotes Treg survival and function, could be beneficial for patients with vasculitis that is resistant to HCV therapy. METHODS We investigated the safety and immunologic effects of the administration of low-dose interleukin-2 in a prospective open-label, phase 1-phase 2a study. Ten patients with HCV-induced vasculitis that was refractory to conventional antiviral therapy, rituximab therapy, or both and who were not receiving glucocorticoid or immunosuppressant therapy, received one course of interleukin-2 (1.5 million IU per day) for 5 days, followed by three 5-day courses of 3 million IU per day at weeks 3, 6, and 9. Both the safety of the treatment and its effectiveness were evaluated, the latter by monitoring the Treg response and the clinical signs of HCV vasculitis. RESULTS No adverse events reached a level higher than grade 1. The treatment did not induce effector T-cell activation, vasculitis flare, or increased HCV viremia. We observed a reduction in cryoglobulinemia in 9 of 10 patients and improvement of vasculitis in 8 of 10. Administration of low-dose interleukin-2 was followed by an increase in the percentage of CD4+, CD25(high), forkhead box P3 (FOXP3+) Tregs [E(max) (maximum value)÷baseline value×100=420%] with potent suppressive activity in all subjects and by a concomitantly decreased proportion of marginal-zone B cells. Transcriptome studies of peripheral-blood mononuclear cells revealed that interleukin-2 induced a global attenuation of the signatures for inflammation and oxidative stress mediators. CONCLUSIONS The trial showed that low-dose interleukin-2 was not associated with adverse effects and led to Treg recovery and concomitant clinical improvement in patients with HCV-induced vasculitis, an autoimmune condition. (Funded by the French Agency for Research on AIDS and Viral Hepatitis [ANRS] and others; ClinicalTrials.gov number, NCT00574652.).
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Affiliation(s)
- David Saadoun
- Université Pierre et Marie Curie Université Paris 06, Paris, France
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Costa N, Pires AE, Gabriel AM, Goulart LF, Pereira C, Leal B, Queiros AC, Chaara W, Moraes-Fontes MF, Vasconcelos C, Ferreira C, Martins J, Bastos M, Santos MJ, Pereira MA, Martins B, Lima M, João C, Six A, Demengeot J, Fesel C. Active regulatory T-cells contribute to broadened T-cell repertoire diversity in ivIg-treated SLE patients. J Transl Med 2011. [PMCID: PMC3242290 DOI: 10.1186/1479-5876-9-s2-p6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Castro R, Bernard D, Lefranc MP, Six A, Benmansour A, Boudinot P. T cell diversity and TcR repertoires in teleost fish. Fish Shellfish Immunol 2011; 31:644-654. [PMID: 20804845 DOI: 10.1016/j.fsi.2010.08.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 08/17/2010] [Accepted: 08/22/2010] [Indexed: 05/29/2023]
Abstract
In vertebrates, the diverse and extended range of antigenic motifs is matched to large populations of lymphocytes. The concept of immune repertoire was proposed to describe this diversity of lymphocyte receptors--IG and TR--required for the recognition specificity. Immune repertoires have become useful tools to describe lymphocyte and receptor populations during the immune system development and in pathological situations. In teleosts, the presence of conventional T cells was first proposed to explain graft rejection and optimized specific antibody production. The discovery of TR genes definitely established the reality of conventional T cells in fish. The development of genomic and EST databases recently led to the description of several key T cell markers including CD4, CD8, CD3, CD28, CTLA4, as well as important cytokines, suggesting the existence of different T helper (Th) subtypes, similar to the mammalian Th1, Th2 and Th17. Over the last decade, repertoire studies have demonstrated that both public and private responses occur in fish as they do in mammals, and in vitro specific cytotoxicity assays have been established. While such typical features of T cells are similar in both fish and mammals, the structure of particular repertoires such as the one of gut intra-epithelial lymphocytes seems to be very different. Future studies will further reveal the particular characteristics of teleost T cell repertoires and adaptive responses.
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Affiliation(s)
- R Castro
- Virologie et Immunologie Moléculaires, INRA, 78352 Jouy-en-Josas, France
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Montaudouin C, Boucontet L, Mailhé-Lembezat MP, Mariotti-Ferrandiz ME, Louise A, Six A, Freitas AA, Garcia S. Endogenous TCR recombination in TCR Tg single RAG-deficient mice uncovered by robust in vivo T cell activation and selection. PLoS One 2010; 5:e10238. [PMID: 20454452 PMCID: PMC2861594 DOI: 10.1371/journal.pone.0010238] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/23/2010] [Indexed: 12/16/2022] Open
Abstract
Recombination activating gene (RAG)-deficient TCR (T Cell Receptor) Tg (transgenic) mice are routinely used as sources of monoclonal T cells. We found that after the transfer of T cells from a RAG-2-deficient 5CC7 TCR Tg mice into allogeneic hosts we recovered a population of T cells expressing diverse alphabeta-TCRs. In fact, in the thymus and spleen of the 5CC7 RAG-2-deficient donor mice, we detected rare T cells expressing non-Tg TCR chains. Similar observations were obtained using T cells from two other TCR transgenic strains, namely RAG-2-deficient aHY and RAG-1-deficient OT-1 mice. The sequences of the endogenous TCR transcripts suggested that gene recombination could occur, albeit quite inefficiently, in the RAG-deficient mice we used. In agreement, we evidenced rare TCR Valpha and Vbeta-chain transcripts in non-Tg RAG-2-deficient mice. Since in these non-Tg RAG-deficient mice no mature T cells could ever be found, our findings suggested a role for the TCR Tg in rescuing rare recombined endogenous chains. Robust T-cell activation by the allogeneic environment favored the selection and expansion of the rare cells expressing endogenous TCRs. Potential mechanisms involved in the recombination of the endogenous TCR chains in the different strains of RAG-deficient mice used, and in particular the possibility of RAG-1 hypomorphism due to an incomplete knocking out procedure, are discussed. Our findings have important experimental implications for studies using TCR-Tg RAG-deficient cells as monoclonal T cell populations.
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Affiliation(s)
- Caroline Montaudouin
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Laurent Boucontet
- Unité du Développement des Lymphocytes, Département d'Immunologie, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U668, Paris, France
| | - Marie-Pierre Mailhé-Lembezat
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Maria-Encarnita Mariotti-Ferrandiz
- Unité de Physiopathologie des Infections, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Anne Louise
- Plate-forme de Cytométrie, Département d'Immunologie, Institut Pasteur, Paris, France
| | - Adrien Six
- Unité de Physiopathologie des Infections, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Antonio A. Freitas
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
- * E-mail: (AAF); (SG)
| | - Sylvie Garcia
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
- * E-mail: (AAF); (SG)
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Blache C, Adriouch S, Calbo S, Drouot L, Dulauroy S, Arnoult C, Le Corre S, Six A, Seman M, Boyer O. Cutting Edge: CD4-Independent Development of Functional FoxP3+ Regulatory T Cells. J Immunol 2009; 183:4182-6. [DOI: 10.4049/jimmunol.0901678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Guillot-Delost M, Cheraï M, Hamel Y, Rosenzwajg M, Baillou C, Simonin G, Leclercq V, Mariotti-Ferrandiz ME, Six A, Bon-Durand V, Maury S, Salomon BL, Cohen JL, Klatzmann D, Lemoine FM. Clinical grade preparation of human natural regulatory T-cells encoding the thymidine kinase suicide gene as a safety gene: authors' reponse. J Gene Med 2009; 11:737-8. [DOI: 10.1002/jgm.1358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Abstract
The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as 'Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool.
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Affiliation(s)
- Z Granevitze
- The Robert H. Smith Institute of Plant Sciences & Genetics, The Hebrew University of Jerusalem, Faculty of Agriculture, Food and Environmental Quality Sciences, Rehovot 76100, Israel
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Guillot-Delost M, Cheraï M, Hamel Y, Rosenzwajg M, Baillou C, Simonin G, Leclercq V, Mariotti-Ferrandiz ME, Six A, Bon-Durand V, Maury S, Salomon BL, Cohen JL, Klatzmann D, Lemoine FM. Clinical-grade preparation of human natural regulatory T-cells encoding the thymidine kinase suicide gene as a safety gene. J Gene Med 2008; 10:834-46. [DOI: 10.1002/jgm.1220] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Berglund JP, Mariotti-Ferrandiz E, Rosmaraki E, Hall H, Cazenave PA, Six A, Höglund P. Erratum to “TCR repertoire dynamics in the pancreatic lymph nodes of non-obese diabetic (NOD) mice at the time of disease initiation” [Mol. Immunol. 45 (2008) 3059–3064]. Mol Immunol 2008. [DOI: 10.1016/j.molimm.2008.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Petrovic Berglund J, Petrovc Berglund J, Mariotti-Ferrandiz E, Rosmaraki E, Hall H, Cazenave PA, Six A, Höglund P. TCR repertoire dynamics in the pancreatic lymph nodes of non-obese diabetic (NOD) mice at the time of disease initiation. Mol Immunol 2008; 45:3059-64. [PMID: 18471883 DOI: 10.1016/j.molimm.2008.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/17/2022]
Abstract
Mouse T-cell development is unfinished at birth and continues during the first month of life, when T cells exit from the thymus and colonize secondary hematopoietic organs to build up a peripheral T-cell repertoire. T-cell responses against beta-cell-derived autoantigens are initiated in the pancreatic lymph nodes (PLN) of non-obese diabetic (NOD) mice during the same time period. We hypothesized that the combined effect of T-cell development and T-cell activation against tissue-specific antigens would create unique TCR repertoires in two different lymph node stations in NOD mice. To test this hypothesis, we determined the length distribution of the third complementarity-determining region (CDR3) of the TCR in the PLN and the inguinal lymph nodes (ILN) of 10, 14, 18 and 22-day-old NOD females. The analysis of all the BV genes revealed significant perturbations of the repertoire between days 10 and 22 but with no statistical differences between the PLN and ILN repertoires. In contrast, when a set of BV chains were amplified using BJ-specific primers, several unique TCR perturbations were observed in the PLN compared to the ILN. We propose that the TCR repertoire in peripheral lymph nodes of NOD mice develops dynamically between 10 and 22 days of age as a result of a developmental process. On top of that development, the local environment may fine-tune that repertoire, possibly by means of stimulation of T cells by tissue-specific antigens presented by local APC.
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Affiliation(s)
- Jelena Petrovic Berglund
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Box 280, S-171 77 Stockholm, Sweden
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