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The splenic T cell receptor repertoire during an immune response against a complex antigen: Expanding private clones accumulate in the high and low copy number region. PLoS One 2022; 17:e0273264. [PMID: 36001559 PMCID: PMC9401120 DOI: 10.1371/journal.pone.0273264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Large cellular antigens comprise a variety of different epitopes leading to a T cell response of extreme diversity. Therefore, tracking such a response by next generation sequencing of the T cell receptor (TCR) in order to identify common TCR properties among the expanding T cells represents an enormous challenge. In the present study we adapted a set of established indices to elucidate alterations in the TCR repertoire regarding sequence similarities between TCRs including VJ segment usage and diversity of nucleotide coding of a single TCR. We combined the usage of these indices with a new systematic splitting strategy regarding the copy number of the extracted clones to divide the repertoire into multiple fractions for separate analysis. We implemented this new analytic approach using the splenic TCR repertoire following immunization with sheep red blood cells (SRBC) in mice. As expected, early after immunization presumably antigen-specific clones accumulated in high copy number fractions, but at later time points similar accumulation of specific clones occurred within the repertoire fractions of lowest copy number. For both repertoire regions immunized animals could reliably be distinguished from control in a classification approach, demonstrating the robustness of the two effects at the individual level. The direction in which the indices shifted after immunization revealed that for both the early and the late effect alterations in repertoire parameters were caused by antigen-specific private clones displacing non-specific public clones. Taken together, tracking antigen-specific clones by their displacement of average TCR repertoire characteristics in standardized repertoire fractions ensures that our analytical approach is fairly independent from the antigen in question and thus allows the in-depth characterization of a variety of immune responses.
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Tune C, Hahn J, Autenrieth SE, Meinhardt M, Pagel R, Schampel A, Schierloh LK, Kalies K, Westermann J. Sleep restriction prior to antigen exposure does not alter the T cell receptor repertoire but impairs germinal center formation during a T cell-dependent B cell response in murine spleen. Brain Behav Immun Health 2021; 16:100312. [PMID: 34589803 PMCID: PMC8474616 DOI: 10.1016/j.bbih.2021.100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Abstract
It is well known that sleep promotes immune functions. In line with this, a variety of studies in animal models and humans have shown that sleep restriction following an antigen challenge dampens the immune response on several levels which leads to e.g. worsening of disease outcome and reduction of vaccination efficiency, respectively. However, the inverse scenario with sleep restriction preceding an antigen challenge is only investigated in a few animal models where it has been shown to reduce antigen uptake and presentation as well as pathogen clearance and survival rates. Here, we use injection of sheep red blood cells to investigate the yet unknown effect on a T cell-dependent B cell response in a well-established mouse model. We found that 6 h of sleep restriction prior to the antigen challenge does not impact the T cell reaction including the T cell receptor repertoire but dampens the development of germinal centers which correlates with reduced antigen-specific antibody titer indicating an impaired B cell response. These changes concerned a functionally more relevant level than those found in the same experimental model with the inverse scenario when sleep restriction followed the antigen challenge. Taken together, our findings showed that the outcome of the T cell-dependent B cell response is indeed impacted by sleep restriction prior to the antigen challenge which highlights the clinical significance of this scenario and the need for further investigations in humans, for example concerning the effect of sleep restriction preceding a vaccination.
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Key Words
- Antigen presentation
- BCZ, B cell zone
- CCL, C–C motif ligand
- CCR, C–C motif receptor
- CD, cluster of differentiation
- CIITA, class II major histocompatibility complex transactivator
- CXCL, C-X-C motif ligand
- FDR, false discovery rate
- GC, germinal center
- Germinal center
- IFN, interferon
- IL, interleukin
- IgG, Immunglobulin G
- MHC-II, major histocompatibility complex II
- Mouse
- RP, red pulp
- SD, standard deviation
- SLO, secondary lymphoid organ
- SRBC, sheep red blood cells
- Sheep red blood cells
- Sleep deprivation
- Spleen
- T cell-dependent B cell response
- TCR, T cell receptor
- TCR-R, T cell receptor repertoire
- TCZ, T cell zone
- Tfh, follicular T helper cells
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Affiliation(s)
- Cornelia Tune
- Institute of Anatomy, University of Luebeck, Germany
| | - Julia Hahn
- Department of Internal Medicine II, University of Tuebingen, Germany
| | | | | | - Rene Pagel
- Institute of Anatomy, University of Luebeck, Germany
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Niebuhr M, Belde J, Fähnrich A, Serge A, Irla M, Ellebrecht CT, Hammers CM, Bieber K, Westermann J, Kalies K. Receptor repertoires of murine follicular T helper cells reveal a high clonal overlap in separate lymph nodes in autoimmunity. eLife 2021; 10:70053. [PMID: 34402793 PMCID: PMC8370764 DOI: 10.7554/elife.70053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Follicular T helper cells (Tfh) are a specialized subset of CD4 effector T cells that are crucial for germinal center (GC) reactions and for selecting B cells to undergo affinity maturation. Despite this central role for humoral immunity, only few data exist about their clonal distribution when multiple lymphoid organs are exposed to the same antigen (Ag) as it is the case in autoimmunity. Here, we used an autoantibody-mediated disease model of the skin and injected one auto-Ag into the two footpads of the same mouse and analyzed the T cell receptor (TCR)β sequences of Tfh located in GCs of both contralateral draining lymph nodes. We found that over 90% of the dominant GC-Tfh clonotypes were shared in both lymph nodes but only transiently. The initially dominant Tfh clonotypes especially declined after establishment of chronic disease while GC reaction and autoimmune disease continued. Our data demonstrates a dynamic behavior of Tfh clonotypes under autoimmune conditions and emphasizes the importance of the time point for distinguishing auto-Ag-specific Tfh clonotypes from potential bystander activated ones.
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Affiliation(s)
- Markus Niebuhr
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Julia Belde
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Arnauld Serge
- Laboratoire Adhésion et Inflammation, Inserm U1067 CNRS, Aix-Marseille Université, Marseille, France
| | - Magali Irla
- Centre d'Immunologie de Marseille Luminy (CIML), INSERM U1104, Aix-Marseille Université UM2, Marseille, France
| | - Christoph T Ellebrecht
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Pennsylvania, Philadelphia, United States
| | - Christoph M Hammers
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
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Ohigashi I, Frantzeskakis M, Jacques A, Fujimori S, Ushio A, Yamashita F, Ishimaru N, Yin D, Cam M, Kelly MC, Awasthi P, Takada K, Takahama Y. The thymoproteasome hardwires the TCR repertoire of CD8+ T cells in the cortex independent of negative selection. J Exp Med 2021; 218:211763. [PMID: 33555295 PMCID: PMC7873839 DOI: 10.1084/jem.20201904] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/27/2020] [Accepted: 01/06/2021] [Indexed: 01/01/2023] Open
Abstract
The thymoproteasome expressed specifically in thymic cortical epithelium optimizes the generation of CD8+ T cells; however, how the thymoproteasome contributes to CD8+ T cell development is unclear. Here, we show that the thymoproteasome shapes the TCR repertoire directly in cortical thymocytes before migration to the thymic medulla. We further show that the thymoproteasome optimizes CD8+ T cell production independent of the thymic medulla; independent of additional antigen-presenting cells, including medullary thymic epithelial cells and dendritic cells; and independent of apoptosis-mediated negative selection. These results indicate that the thymoproteasome hardwires the TCR repertoire of CD8+ T cells with cortical positive selection independent of negative selection in the thymus.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Melina Frantzeskakis
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Alison Jacques
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sayumi Fujimori
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Aya Ushio
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Fusano Yamashita
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Da Yin
- Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Margaret Cam
- Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael C Kelly
- Single Cell Analysis Facility, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Parirokh Awasthi
- Transgenic Mouse Model Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kensuke Takada
- Laboratory of Molecular Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Effects of sleep on the splenic milieu in mice and the T cell receptor repertoire recruited into a T cell dependent B cell response. Brain Behav Immun Health 2020; 5:100082. [PMID: 34589857 PMCID: PMC8474558 DOI: 10.1016/j.bbih.2020.100082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
Sleep is known to improve immune function ranging from cell distribution in the naïve state to elevated antibody titers after an immune challenge. The underlying mechanisms still remain unclear, partially because most studies have focused on the analysis of blood only. Hence, we investigated the effects of sleep within the spleen in female C57BL/6J mice with normal sleep compared to short-term sleep-deprived animals both in the naïve state and after an antigen challenge. Lack of sleep decreased the expression of genes associated with immune cell recruitment into and antigen presentation within the spleen both in the naïve state and during a T cell dependent B cell response directed against sheep red blood cells (SRBC). However, neither T cell proliferation nor formation of SRBC-specific antibodies was affected. In addition, the T cell receptor repertoire recruited into the immune response within seven days was not influenced by sleep deprivation. Thus, sleep modulated the molecular milieu within the spleen whereas we could not detect corresponding changes in the primary immune response against SRBC. Further studies will show whether sleep influences the secondary immune response against SRBC or the development of the B cell receptor repertoire, and how this can be compared to other antigens. Sleep deprivation (SD) decreases expression of genes involved in T cell function. SD induces those changes in the milieu of both lymph nodes and spleen. SD dampens the expression of several genes in the spleen during an immune response. SD does not alter the T cell receptor repertoire recruited into the immune response.
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Key Words
- Antigen presentation
- BCZ, B cell zone
- CCL, C–C motif ligand
- CCR, C–C motif receptor
- CD, cluster of differentiation
- CIITA, class II major histocompatibility complex transactivator
- CXCL, C-X-C motif ligand
- FDR, false discovery rate
- GC, germinal center
- IFN, interferon
- IL, interleukin
- Lymphocyte migration
- MHC-II, major histocompatibility complex II
- SD, sleep deprivation
- SLO, secondary lymphoid organ
- SRBC, sheep red blood cells
- Sheep red blood cells
- Sleep deprivation
- T cell dependent B cell Response
- T cell receptor repertoire
- TCR, T cell receptor
- TCR-R, T cell receptor repertoire
- TCZ, T cell zone
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