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Nakonechnaya TO, Moltedo B, Putintseva EV, Leyn S, Bolotin DA, Britanova OV, Shugay M, Chudakov DM. Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism. eLife 2024; 12:RP89382. [PMID: 38591522 PMCID: PMC11003740 DOI: 10.7554/elife.89382] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Suppressive function of regulatory T cells (Treg) is dependent on signaling of their antigen receptors triggered by cognate self, dietary, or microbial peptides presented on MHC II. However, it remains largely unknown whether distinct or shared repertoires of Treg TCRs are mobilized in response to different challenges in the same tissue or the same challenge in different tissues. Here we use a fixed TCRβ chain FoxP3-GFP mouse model to analyze conventional (eCD4) and regulatory (eTreg) effector TCRα repertoires in response to six distinct antigenic challenges to the lung and skin. This model shows highly 'digital' repertoire behavior with easy-to-track challenge-specific TCRα CDR3 clusters. For both eCD4 and eTreg subsets, we observe challenge-specific clonal expansions yielding homologous TCRα clusters within and across animals and exposure sites, which are also reflected in the draining lymph nodes but not systemically. Some CDR3 clusters are shared across cancer challenges, suggesting a response to common tumor-associated antigens. For most challenges, eCD4 and eTreg clonal response does not overlap. Such overlap is exclusively observed at the sites of certain tumor challenges, and not systematically, suggesting transient and local tumor-induced eCD4=>eTreg plasticity. This transition includes a dominant tumor-responding eCD4 CDR3 motif, as well as characteristic iNKT TCRα CDR3. In addition, we examine the homeostatic tissue residency of clonal eTreg populations by excluding the site of challenge from our analysis. We demonstrate that distinct CDR3 motifs are characteristic of eTreg cells residing in particular lymphatic tissues, regardless of the challenge. This observation reveals the tissue-resident, antigen-specific clonal Treg populations.
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Affiliation(s)
- Tatyana O Nakonechnaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Ekaterina V Putintseva
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Sofya Leyn
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Dmitry A Bolotin
- Institute of Translational Medicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Olga V Britanova
- Institute of Translational Medicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Mikhail Shugay
- Institute of Translational Medicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Dmitriy M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Central European Institute of TechnologyBrnoCzech Republic
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
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Ustiuzhanina MO, Streltsova MA, Timofeev ND, Kryukov MA, Chudakov DM, Kovalenko EI. Autologous T-Cell-Free Antigen Presentation System Unveils hCMV-Specific NK Cell Response. Cells 2024; 13:530. [PMID: 38534374 DOI: 10.3390/cells13060530] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
NK cells play a decisive role in controlling hCMV infection by combining innate and adaptive-like immune reactions. The hCMV-derived VMAPRTLFL (LFL) peptide is a potent activator of NKG2C+ NK cells. Proposed here is an autologous system of LFL stimulation without T lymphocytes and exogenous cytokines that allows us to evaluate NK-cell hCMV-specific responses in more native settings. In this model, we evaluated LFL-induced IFNγ production, focusing on signaling pathways and the degranulation and proliferation of NK cells orchestrated by microenvironment cytokine production and analyzed the transcriptome of expanded NK cells. NK cells of individuals having high anti-hCMV-IgG levels, in contrast to NK cells of hCMV-seronegative and low-positive donors, displayed increased IFNγ production and degranulation and activation levels and enhanced proliferation upon LFL stimulation. Cytokine profiles of these LFL-stimulated cultures demonstrated a proinflammatory shift. LFL-induced NK-cell IFNγ production was dependent on the PI3K and Ras/Raf/Mek signaling pathways, independently of cytokines. In hCMV-seropositive individuals, this model allowed obtaining NK-cell antigen-specific populations proliferating in response to LFL. The transcriptomic profile of these expanded NK cells showed increased adaptive gene expression and metabolic activation. The results complement the existing knowledge about hCMV-specific NK-cell response. This model may be further exploited for the identification and characterization of antigen-specific NK cells.
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Affiliation(s)
- Maria O Ustiuzhanina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria A Streltsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikita D Timofeev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim A Kryukov
- Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Central European Institute of Technology, Masaryk University, 60200 Brno, Czech Republic
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Elena I Kovalenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Bryushkova EA, Mushenkova NV, Turchaninova MA, Lukyanov DK, Chudakov DM, Serebrovskaya EO. B cell clonality in cancer. Semin Immunol 2024; 72:101874. [PMID: 38508089 DOI: 10.1016/j.smim.2024.101874] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/22/2024]
Abstract
Carcinogenesis in the process of long-term co-evolution of tumor cells and immune environment essentially becomes possible due to incorrect decisions made, remembered, and reproduced by the immune system at the level of clonal populations of antigen-specific T- and B-lymphocytes. Tumor-immunity interaction determines the nature of such errors and, consequently, delineates the possible ways of successful immunotherapeutic intervention. It is generally recognized that tumor-infiltrating B cells (TIL-B) can play both pro-tumor and anti-tumor roles. However, the exact mechanisms that determine the contribution of clonal B cell lineages with different specificities and functions remain largely unclear. This is due to the variability of cancer types, the molecular heterogeneity of tumor cells, and, to a large extent, the individual pattern of each immune response. Further progress requires detailed investigation of the functional properties and phenotypes of clonally heterogeneous B cells in relation to their antigenic specificities, which determine the functionality of both effector B lymphocytes and immunoglobulins produced in the tumor environment. Based on a real understanding of the role of clonal antigen-specific populations of B lymphocytes in the tumor microenvironment, we need to learn how to develop new methods of targeted immunotherapy, as well as adapt existing treatment options to the specific needs of different patients and patient subgroups. In this review, we will cover B cells functional diversity and their multifaceted roles in the tumor environment.
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Affiliation(s)
- E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, Moscow, Russia
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
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Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
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Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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Smirnova AO, Miroshnichenkova AM, Belyaeva LD, Kelmanson IV, Lebedev YB, Mamedov IZ, Chudakov DM, Komkov AY. Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity. Front Immunol 2023; 14:1245175. [PMID: 37744336 PMCID: PMC10513440 DOI: 10.3389/fimmu.2023.1245175] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.
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Affiliation(s)
- Anastasia O. Smirnova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Laima D. Belyaeva
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilya V. Kelmanson
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri B. Lebedev
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z. Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alexander Y. Komkov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
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Shcherbinin DS, Karnaukhov VK, Zvyagin IV, Chudakov DM, Shugay M. Large-scale template-based structural modeling of T-cell receptors with known antigen specificity reveals complementarity features. Front Immunol 2023; 14:1224969. [PMID: 37649481 PMCID: PMC10464843 DOI: 10.3389/fimmu.2023.1224969] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity. Methods Identification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R. Results Using the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues. Conclusion Our results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity.
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Affiliation(s)
- Dmitrii S. Shcherbinin
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Laboratory of Structural Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Vadim K. Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy M. Chudakov
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Center of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Mikhail Shugay
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Clement M, Ladell K, Miners KL, Marsden M, Chapman L, Cardus Figueras A, Scott J, Andrews R, Clare S, Kriukova VV, Lupyr KR, Britanova OV, Withers DR, Jones SA, Chudakov DM, Price DA, Humphreys IR. Inhibitory IL-10-producing CD4 + T cells are T-bet-dependent and facilitate cytomegalovirus persistence via coexpression of arginase-1. eLife 2023; 12:e79165. [PMID: 37440306 PMCID: PMC10344424 DOI: 10.7554/elife.79165] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/11/2023] [Indexed: 07/14/2023] Open
Abstract
Inhibitory CD4+ T cells have been linked with suboptimal immune responses against cancer and pathogen chronicity. However, the mechanisms that underpin the development of these regulatory cells, especially in the context of ongoing antigen exposure, have remained obscure. To address this knowledge gap, we undertook a comprehensive functional, phenotypic, and transcriptomic analysis of interleukin (IL)-10-producing CD4+ T cells induced by chronic infection with murine cytomegalovirus (MCMV). We identified these cells as clonally expanded and highly differentiated TH1-like cells that developed in a T-bet-dependent manner and coexpressed arginase-1 (Arg1), which promotes the catalytic breakdown of L-arginine. Mice lacking Arg1-expressing CD4+ T cells exhibited more robust antiviral immunity and were better able to control MCMV. Conditional deletion of T-bet in the CD4+ lineage suppressed the development of these inhibitory cells and also enhanced immune control of MCMV. Collectively, these data elucidated the ontogeny of IL-10-producing CD4+ T cells and revealed a previously unappreciated mechanism of immune regulation, whereby viral persistence was facilitated by the site-specific delivery of Arg1.
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Affiliation(s)
- Mathew Clement
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kelly L Miners
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Morgan Marsden
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Lucy Chapman
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Anna Cardus Figueras
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Jake Scott
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Robert Andrews
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Valeriia V Kriukova
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of KielKielGermany
| | - Ksenia R Lupyr
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of KielKielGermany
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - David R Withers
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Simon A Jones
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cell CenterAl MuntazahUnited Arab Emirates
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Ian R Humphreys
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Systems Immunity Research Institute, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
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8
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Friman V, Quinti I, Davydov AN, Shugay M, Farroni C, Engström E, Pour Akaber S, Barresi S, Mohamed A, Pulvirenti F, Milito C, Granata G, Giorda E, Ahlström S, Karlsson J, Marasco E, Marcellini V, Bocci C, Cascioli S, Scarsella M, Phad G, Tilevik A, Tartaglia M, Bemark M, Chudakov DM, Carsetti R, Grimsholm O. Defective peripheral B cell selection in common variable immune deficiency patients with autoimmune manifestations. Cell Rep 2023; 42:112446. [PMID: 37119135 DOI: 10.1016/j.celrep.2023.112446] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Common variable immune deficiency (CVID) is a heterogeneous disorder characterized by recurrent infections, low levels of serum immunoglobulins, and impaired vaccine responses. Autoimmune manifestations are common, but B cell central and peripheral selection mechanisms in CVID are incompletely understood. Here, we find that receptor editing, a measure of central tolerance, is increased in transitional B cells from CVID patients and that these cells have a higher immunoglobulin κ:λ ratio in CVID patients with autoimmune manifestations than in those with infection only. Contrariwise, the selection pressure in the germinal center on CD27bright memory B cells is decreased in CVID patients with autoimmune manifestations. Finally, functionally, T cell-dependent activation showed that naive B cells in CVID patients are badly equipped for activation and induction of mismatch repair genes. We conclude that central tolerance is functional whereas peripheral selection is defective in CVID patients with autoimmune manifestations, which could underpin the development of autoimmunity.
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Affiliation(s)
- Vanda Friman
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chiara Farroni
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Erik Engström
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shirin Pour Akaber
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Ahmed Mohamed
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Federica Pulvirenti
- Centre for Primary Immune Deficiency, AUO Policlinico Umberto I, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Granata
- Clinical and Research Department for Infectious Diseases, National Institute for Infectious Diseases L. Spallanzani (IRCCS), 00149 Rome, Italy
| | - Ezio Giorda
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sara Ahlström
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emiliano Marasco
- Division of Rheumatology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Chiara Bocci
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Simona Cascioli
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marco Scarsella
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ganesh Phad
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Brno, Czech Republic
| | - Rita Carsetti
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy; Unit of Diagnostic Immunology, Department of Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ola Grimsholm
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria; Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy.
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9
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Maiorova V, Mollaev MD, Vikhreva P, Chudakov DM, Kibardin A, Maschan MA, Larin S. Mutated Flt3Lg Provides Reduced Flt3 Recycling Compared to Wild-Type Flt3Lg and Retains the Specificity of Flt3Lg-Based CAR T-Cell Targeting in AML Models. Int J Mol Sci 2023; 24:ijms24087626. [PMID: 37108788 PMCID: PMC10146938 DOI: 10.3390/ijms24087626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
The cells of acute myeloid leukemia are defined by clonal growth and heterogenous immunophenotypes. Chimeric antigen receptors (CARs) commonly recognize molecular targets by single-chain antibody fragments (scFvs) specific to a tumor-associated antigen. However, ScFvs may form aggregates, thus stimulating tonic CAR T-cell activation and reducing CAR T-cell functioning in vivo. Harnessing natural ligands as recognition parts of CARs, specific targeting of membrane receptors can be achieved. Previously, we presented ligand-based Flt3-CAR T-cells targeting the Flt3 receptor. The extracellular part of Flt3-CAR consisted of full-size Flt3Lg. Meanwhile, upon recognition, Flt3-CAR may potentially activate Flt3, triggering proliferative signaling in blast cells. Moreover, the long-lasting presence of Flt3Lg may lead to Flt3 downregulation. In this paper, we present mutated Flt3Lg-based Flt3m-CAR ('m'-for 'mutant') T-cells targeting Flt3. The extracellular part of Flt3m-CAR consists of full-length Flt3Lg-L27P. We have determined that ED50 for recombinant Flt3Lg-L27P produced in CHO cells is at least 10-fold higher than for the wild-type Flt3Lg. We show that the mutation in the recognizing domain of Flt3m-CAR did not affect the specificity of Flt3m-CAR T-cells when compared to Flt3-CAR T-cells. Flt3m-CAR T-cells combine the specificity of ligand-receptor recognition with reduced Flt3Lg-L27P bioactivity, leading to potentially safer immunotherapy.
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Affiliation(s)
- Varvara Maiorova
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Murad D Mollaev
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
| | - Polina Vikhreva
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexey Kibardin
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
| | - Michael A Maschan
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
| | - Sergey Larin
- Dmitriy Rogachev National Medical Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
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10
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Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
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Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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11
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Stanevich OV, Alekseeva EI, Sergeeva M, Fadeev AV, Komissarova KS, Ivanova AA, Simakova TS, Vasilyev KA, Shurygina AP, Stukova MA, Safina KR, Nabieva ER, Garushyants SK, Klink GV, Bakin EA, Zabutova JV, Kholodnaia AN, Lukina OV, Skorokhod IA, Ryabchikova VV, Medvedeva NV, Lioznov DA, Danilenko DM, Chudakov DM, Komissarov AB, Bazykin GA. SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19. Nat Commun 2023; 14:149. [PMID: 36627290 PMCID: PMC9831376 DOI: 10.1038/s41467-022-34033-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Evolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin's lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.
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Affiliation(s)
| | | | - Maria Sergeeva
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Artem V Fadeev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Anna A Ivanova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Kirill A Vasilyev
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | | | - Marina A Stukova
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
| | - Elena R Nabieva
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Galya V Klink
- A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeny A Bakin
- First Pavlov State Medical University, Saint-Petersburg, Russia.,Bioinformatics Institute, Saint Petersburg, Russia
| | | | - Anastasia N Kholodnaia
- First Pavlov State Medical University, Saint-Petersburg, Russia.,City Hospital 31, Saint-Petersburg, Russia
| | - Olga V Lukina
- First Pavlov State Medical University, Saint-Petersburg, Russia
| | | | | | | | - Dmitry A Lioznov
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia.,First Pavlov State Medical University, Saint-Petersburg, Russia
| | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia. .,A.A. Kharkevich Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
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12
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Yang X, Garner LI, Zvyagin IV, Paley MA, Komech EA, Jude KM, Zhao X, Fernandes RA, Hassman LM, Paley GL, Savvides CS, Brackenridge S, Quastel MN, Chudakov DM, Bowness P, Yokoyama WM, McMichael AJ, Gillespie GM, Garcia KC. Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022; 612:771-777. [PMID: 36477533 PMCID: PMC10511244 DOI: 10.1038/s41586-022-05501-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.
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Affiliation(s)
- Xinbo Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lee I Garner
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivan V Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Michael A Paley
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina A Komech
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiang Zhao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn M Hassman
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Grace L Paley
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina S Savvides
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Max N Quastel
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dmitriy M Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Muscuoskeletal Science (NDORMS), Botnar Research Center, University of Oxford, Oxford, UK
| | - Wayne M Yokoyama
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Mukhina OA, Fomina DS, Parshin VV, Gushchin VA, Dolzhikova IV, Shchetinin AM, Chudakov DM, Alekseeva E, Korostin D, Bazykin GA, Klink G, Logunov DY, Lysenko MA. SARS-CoV-2 evolution in a patient with secondary B-cell immunodeficiency: A clinical case. Hum Vaccin Immunother 2022; 18:2101334. [PMID: 35914217 DOI: 10.1080/21645515.2022.2101334] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The article highlights the course of long-term SARS-CoV-2 infection in a patient with a secondary immunodeficiency developed with B-cell-depleting therapy of the underlying disease. Analysis of the intrapatient virus evolution revealed an inpatient S:G75A mutation that alters the 72GTNGTKR78 motif of the S-protein, with a possible role in binding to alternative cellular receptors. Therapy with a ready-made COVID-19-globulin preparation (native human immunoglobulin G (IgG) derived from the plasma of convalescent COVID-19-patients) resulted in rapid improvement of the patient's condition, fast, and stable elimination of the virus, and passive immunization of the patient for at least 30 days. The results suggest the use of products containing neutralizing antibodies opens new prospects for treatment algorithms for patients with persistent coronavirus infection, as well as for passive immunization schemes for patients with a presumably reduced specific response to vaccination.
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Affiliation(s)
- Olgo A Mukhina
- Moscow Healthcare Department, State Budgetary Healthcare Institution City Clinical Hospital, Moscow, Russia
| | - Daria S Fomina
- Moscow Healthcare Department, State Budgetary Healthcare Institution City Clinical Hospital, Moscow, Russia.,Federal State Autonomous Educational Institution of Higher Education First Moscow State Medical University named after I.M. Sechenov of the Ministry of Health of the Russian Federation, Sechenov University, Moscow, Russia
| | - Vasiliy V Parshin
- Moscow Healthcare Department, State Budgetary Healthcare Institution City Clinical Hospital, Moscow, Russia
| | - Vladimir A Gushchin
- Federal State Budgetary Institution "National Research Center for Epidemiology and Microbiology named after Honorary Academician N.-F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia.,Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Inna V Dolzhikova
- Federal State Budgetary Institution "National Research Center for Epidemiology and Microbiology named after Honorary Academician N.-F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexey M Shchetinin
- Federal State Budgetary Institution "National Research Center for Epidemiology and Microbiology named after Honorary Academician N.-F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Evgeniia Alekseeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitriy Korostin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Galya Klink
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Denis Yu Logunov
- Federal State Budgetary Institution "National Research Center for Epidemiology and Microbiology named after Honorary Academician N.-F. Gamaleya" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Maryana A Lysenko
- Moscow Healthcare Department, State Budgetary Healthcare Institution City Clinical Hospital, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
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14
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Mikelov AI, Alekseeva EI, Komech EA, Staroverov DB, Turchaninova MA, Shugay M, Chudakov DM, Bazykin GA, Zvyagin IV. Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires. eLife 2022; 11:79254. [PMID: 36107479 PMCID: PMC9525062 DOI: 10.7554/elife.79254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/08/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
The stability and plasticity of B cell-mediated immune memory ensures the ability to respond to the repeated challenges. We have analyzed the longitudinal dynamics of immunoglobulin heavy chain repertoires from memory B cells, plasmablasts, and plasma cells from the peripheral blood of generally healthy volunteers. We reveal a high degree of clonal persistence in individual memory B cell subsets, with inter-individual convergence in memory and antibody-secreting cells (ASCs). ASC clonotypes demonstrate clonal relatedness to memory B cells, and are transient in peripheral blood. We identify two clusters of expanded clonal lineages with differing prevalence of memory B cells, isotypes, and persistence. Phylogenetic analysis revealed signs of reactivation of persisting memory B cell-enriched clonal lineages, accompanied by new rounds of affinity maturation during proliferation and differentiation into ASCs. Negative selection contributes to both persisting and reactivated lineages, preserving the functionality and specificity of B cell receptors (BCRs) to protect against current and future pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | - Georgii A Bazykin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University
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15
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Lomakin YA, Zvyagin IV, Ovchinnikova LA, Kabilov MR, Staroverov DB, Mikelov A, Tupikin AE, Zakharova MY, Bykova NA, Mukhina VS, Favorov AV, Ivanova M, Simaniv T, Rubtsov YP, Chudakov DM, Zakharova MN, Illarioshkin SN, Belogurov AA, Gabibov AG. Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation. Front Immunol 2022; 13:803229. [PMID: 36052064 PMCID: PMC9425031 DOI: 10.3389/fimmu.2022.803229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundB lymphocytes play a pivotal regulatory role in the development of the immune response. It was previously shown that deficiency in B regulatory cells (Bregs) or a decrease in their anti-inflammatory activity can lead to immunological dysfunctions. However, the exact mechanisms of Bregs development and functioning are only partially resolved. For instance, only a little is known about the structure of their B cell receptor (BCR) repertoires in autoimmune disorders, including multiple sclerosis (MS), a severe neuroinflammatory disease with a yet unknown etiology. Here, we elucidate specific properties of B regulatory cells in MS.MethodsWe performed a prospective study of the transitional Breg (tBreg) subpopulations with the CD19+CD24highCD38high phenotype from MS patients and healthy donors by (i) measuring their content during two diverging courses of relapsing-remitting MS: benign multiple sclerosis (BMS) and highly active multiple sclerosis (HAMS); (ii) analyzing BCR repertoires of circulating B cells by high-throughput sequencing; and (iii) measuring the percentage of CD27+ cells in tBregs.ResultsThe tBregs from HAMS patients carry the heavy chain with a lower amount of hypermutations than tBregs from healthy donors. The percentage of transitional CD24highCD38high B cells is elevated, whereas the frequency of differentiated CD27+ cells in this transitional B cell subset was decreased in the MS patients as compared with healthy donors.ConclusionsImpaired maturation of regulatory B cells is associated with MS progression.
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Affiliation(s)
- Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Dmitriy B. Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Artem Mikelov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Maria Y. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadezda A. Bykova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
| | - Vera S. Mukhina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Alexander V. Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
- Quantitative Sciences Division, Department of Oncology, Johns Hopkins University, Baltimore, MD, United States
| | - Maria Ivanova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Taras Simaniv
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Yury P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria N. Zakharova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | | | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
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16
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Goncharov MM, Bryushkova EA, Sharaev NI, Skatova VD, Baryshnikova AM, Sharonov GV, Karnaukhov V, Vakhitova MT, Samoylenko IV, Demidov LV, Lukyanov S, Chudakov DM, Serebrovskaya EO. Pinpointing the tumor-specific T-cells via TCR clusters. eLife 2022; 11:77274. [PMID: 35377314 PMCID: PMC9023053 DOI: 10.7554/elife.77274] [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: 01/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Adoptive cell transfer (ACT) is a promising approach to cancer immunotherapy, but its efficiency fundamentally depends on the extent of tumor-specific T cell enrichment within the graft. This can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lysed tumor cells, but these approaches remain laborious, time-consuming, and functionally limited, hampering clinical development of ACT. Here, we demonstrate that homology cluster analysis of T cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs allowing to: (1) detect their presence within the pool of tumor-infiltrating lymphocytes (TILs); (2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; (3) investigate surface marker-based enrichment for tumor-targeting T cells in freshly isolated TILs (enrichment confirmed for CD4+ and CD8+ PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). We believe that this approach to the rapid assessment of tumor-specific TCR enrichment should accelerate T cell therapy development.
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Affiliation(s)
- Mikhail M Goncharov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | | | - Nikita I Sharaev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Valeria D Skatova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Anastasiya M Baryshnikova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - George V Sharonov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Maria T Vakhitova
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Igor V Samoylenko
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Lev V Demidov
- Oncodermatology Department, NN Blokhin Russian Cancer Research Center, Moscow, Russian Federation
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Dmitriy M Chudakov
- Department of genomics of adaptive immunity, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
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17
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Dyugay IA, Lukyanov DK, Turchaninova MA, Serebrovskaya EO, Bryushkova EA, Zaretsky AR, Khalmurzaev O, Matveev VB, Shugay M, Shelyakin PV, Chudakov DM. Accounting for B-cell Behavior and Sampling Bias Predicts Anti-PD-L1 Response in Bladder Cancer. Cancer Immunol Res 2022; 10:343-353. [PMID: 35013004 PMCID: PMC9381118 DOI: 10.1158/2326-6066.cir-21-0489] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Received: 06/21/2021] [Revised: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 01/07/2023]
Abstract
Cancer immunotherapy is predominantly based on T cell-centric approaches. At the same time, the adaptive immune response in the tumor environment also includes clonally produced immunoglobulins and clonal effector/memory B cells that participate in antigen-specific decisions through their interactions with T cells. Here, we investigated the role of infiltrating B cells in bladder cancer via patient dataset analysis of intratumoral immunoglobulin repertoires. We showed that the IgG1/IgA ratio is a prognostic indicator for several subtypes of bladder cancer and for the whole IMVigor210 anti-PD-L1 immunotherapy study cohort. A high IgG1/IgA ratio associated with the prominence of a cytotoxic gene signature, T-cell receptor signaling, and IL21-mediated signaling. Immunoglobulin repertoire analysis indicated that effector B-cell function, rather than clonally produced antibodies, was involved in antitumor responses. From the T-cell side, we normalized a cytotoxic signature against the extent of immune cell infiltration to neutralize the artificial sampling-based variability in immune gene expression. Resulting metrics reflected proportion of cytotoxic cells among tumor-infiltrating immune cells and improved prediction of anti-PD-L1 responses. At the same time, the IgG1/IgA ratio remained an independent prognostic factor. Integration of the B-cell, natural killer cell, and T-cell signatures allowed for the most accurate prediction of anti-PD-L1 therapy responses. On the basis of these findings, we developed a predictor called PRedIctive MolecUlar Signature (PRIMUS), which outperformed PD-L1 expression scores and known gene signatures. Overall, PRIMUS allows for reliable identification of responders among patients with muscle-invasive urothelial carcinoma, including the subcohort with the low-infiltrated "desert" tumor phenotype.
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Affiliation(s)
- Ilya A. Dyugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daniil K. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A. Turchaninova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O. Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A. Bryushkova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Molecular Biology Department, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew R. Zaretsky
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Oybek Khalmurzaev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vsevolod B. Matveev
- Department of Urology, Federal State Budgetary Institution “N.N. Blokhin National Medical Research Center of Oncology” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel V. Shelyakin
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Corresponding Author: Dmitriy M. Chudakov, Genomics of Adaptive Immunity, IBCH RAS, Miklukho-Maklaya, 16/10, Moscow 117997, Russia. Phone: 7 (495) 335-01-00; E-mail:
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18
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Zhitnyuk YV, Koval AP, Alferov AA, Shtykova YA, Mamedov IZ, Kushlinskii NE, Chudakov DM, Shcherbo DS. Deep cfDNA fragment end profiling enables cancer detection. Mol Cancer 2022; 21:26. [PMID: 35062943 PMCID: PMC8780681 DOI: 10.1186/s12943-021-01491-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/26/2021] [Indexed: 11/10/2022] Open
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19
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Maiorova V, Mollaev MD, Vikhreva P, Kulakovskaya E, Pershin D, Chudakov DM, Kibardin A, Maschan MA, Larin S. Natural Flt3Lg-Based Chimeric Antigen Receptor (Flt3-CAR) T Cells Successfully Target Flt3 on AML Cell Lines. Vaccines (Basel) 2021; 9:vaccines9111238. [PMID: 34835169 PMCID: PMC8621097 DOI: 10.3390/vaccines9111238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
Relapsed/refractory acute myeloid leukemia (AML) cannot be cured with chemotherapy alone, as the blasts survive the treatment. Chimeric antigen receptor (CAR) approaches for AML are being actively developed. CARs promote immune reactions through recognition of the target molecular epitopes at the surface of cancer cells. The recognition involves the extracellular portion of the CAR protein, which corresponds to either the antibody or the physiological binding partner of the targeted antigen. Here, we design a chimeric receptor with a full-length natural Flt3-ligand recognition module that targets Flt3 tyrosine kinase, known as an adverse marker in AML. We demonstrate specific killing of Flt3-positive THP-1 cells by Flt3-CAR T cells and the lack of cytotoxicity towards Flt3-negative U937 cells. We prove that the inherent cytolytic capacity of T cells is essential for the killing. Finally, we confirm the authenticity of targeting by its competitive dose-dependent inhibition with a soluble Flt3-ligand. The developed system can be viewed as a non-immunogenic functional equivalent of scFv-mediated targeting. The robust in vitro antitumor effects of Flt3-CAR T cells, combined with their low off-target cytotoxicity, hold promise for AML treatment.
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Affiliation(s)
- Varvara Maiorova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
- Correspondence:
| | - Murad D. Mollaev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Polina Vikhreva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Elena Kulakovskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Dmitry Pershin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Dmitriy M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Alexey Kibardin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Michael A. Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
| | - Sergey Larin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (M.D.M.); (P.V.); (E.K.); (D.P.); (A.K.); (M.A.M.); (S.L.)
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20
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Shelyakin PV, Lupyr KR, Egorov ES, Kofiadi IA, Staroverov DB, Kasatskaya SA, Kriukova VV, Shagina IA, Merzlyak EM, Nakonechnaya TO, Latysheva EA, Manto IA, Khaitov MR, Lukyanov SA, Chudakov DM, Britanova OV. Naïve Regulatory T Cell Subset Is Altered in X-Linked Agammaglobulinemia. Front Immunol 2021; 12:697307. [PMID: 34489944 PMCID: PMC8417104 DOI: 10.3389/fimmu.2021.697307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/19/2021] [Accepted: 07/29/2021] [Indexed: 11/14/2022] Open
Abstract
The interplay between T- and B-cell compartments during naïve, effector and memory T cell maturation is critical for a balanced immune response. Primary B-cell immunodeficiency arising from X-linked agammaglobulinemia (XLA) offers a model to explore B cell impact on T cell subsets, starting from the thymic selection. Here we investigated characteristics of naïve and effector T cell subsets in XLA patients, revealing prominent alterations in the corresponding T-cell receptor (TCR) repertoires. We observed immunosenescence in terms of decreased diversity of naïve CD4+ and CD8+ TCR repertoires in XLA donors. The most substantial alterations were found within naïve CD4+ subsets, and we have investigated these in greater detail. In particular, increased clonality and convergence, along with shorter CDR3 regions, suggested narrower focused antigen-specific maturation of thymus-derived naïve Treg (CD4+CD45RA+CD27+CD25+) in the absence of B cells - normally presenting diverse self and commensal antigens. The naïve Treg proportion among naïve CD4 T cells was decreased in XLA patients, supporting the concept of impaired thymic naïve Treg selection. Furthermore, the naïve Treg subset showed prominent differences at the transcriptome level, including increased expression of genes specific for antigen-presenting and myeloid cells. Altogether, our findings suggest active B cell involvement in CD4 T cell subsets maturation, including B cell-dependent expansion of the naïve Treg TCR repertoire that enables better control of self-reactive T cells.
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Affiliation(s)
- Pavel V Shelyakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia R Lupyr
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Kofiadi
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Valeriia V Kriukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Irina A Shagina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Irina A Manto
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Musa R Khaitov
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Sergey A Lukyanov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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21
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Grimsholm O, Piano Mortari E, Davydov AN, Shugay M, Obraztsova AS, Bocci C, Marasco E, Marcellini V, Aranburu A, Farroni C, Silvestris DA, Cristofoletti C, Giorda E, Scarsella M, Cascioli S, Barresi S, Lougaris V, Plebani A, Cancrini C, Finocchi A, Moschese V, Valentini D, Vallone C, Signore F, de Vincentiis G, Zaffina S, Russo G, Gallo A, Locatelli F, Tozzi AE, Tartaglia M, Chudakov DM, Carsetti R. The Interplay between CD27 dull and CD27 bright B Cells Ensures the Flexibility, Stability, and Resilience of Human B Cell Memory. Cell Rep 2021; 30:2963-2977.e6. [PMID: 32130900 DOI: 10.1016/j.celrep.2020.02.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/23/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
Memory B cells (MBCs) epitomize the adaptation of the immune system to the environment. We identify two MBC subsets in peripheral blood, CD27dull and CD27bright MBCs, whose frequency changes with age. Heavy chain variable region (VH) usage, somatic mutation frequency replacement-to-silent ratio, and CDR3 property changes, reflecting consecutive selection of highly antigen-specific, low cross-reactive antibody variants, all demonstrate that CD27dull and CD27bright MBCs represent sequential MBC developmental stages, and stringent antigen-driven pressure selects CD27dull into the CD27bright MBC pool. Dynamics of human MBCs are exploited in pregnancy, when 50% of maternal MBCs are lost and CD27dull MBCs transit to the more differentiated CD27bright stage. In the postpartum period, the maternal MBC pool is replenished by the expansion of persistent CD27dull clones. Thus, the stability and flexibility of human B cell memory is ensured by CD27dull MBCs that expand and differentiate in response to change.
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Affiliation(s)
- Ola Grimsholm
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Department of Rheumatology and Inflammation Research, University of Gothenburg, Box 480, 405 30 Gothenburg, Sweden
| | - Eva Piano Mortari
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Alexey N Davydov
- Central European Institute of Technology, 625 00 Brno, Czech Republic
| | - Mikhail Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Anna S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Chiara Bocci
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Emiliano Marasco
- Division of Rheumatology, Bambino Gesù Children's Hospital IRCCS, 00146 Roma, Italy
| | - Valentina Marcellini
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Alaitz Aranburu
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Box 480, 405 30 Gothenburg, Sweden
| | - Chiara Farroni
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | | | | | - Ezio Giorda
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Marco Scarsella
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Simona Cascioli
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Vassilios Lougaris
- Department of Experimental and Clinical Sciences, University of Brescia, 25121 Brescia, Italy
| | - Alessandro Plebani
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy
| | - Caterina Cancrini
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy; School of Medicine, University of Tor Vergata, 00133 Rome, Italy
| | - Andrea Finocchi
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy; School of Medicine, University of Tor Vergata, 00133 Rome, Italy
| | - Viviana Moschese
- Pediatric Immunology Unit, Policlinico Tor Vergata, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Diletta Valentini
- Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gynaecology, Misericordia Hospital Grosseto, Usl Toscana Sud-est, 58100 Grosseto, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gynaecology, Misericordia Hospital Grosseto, Usl Toscana Sud-est, 58100 Grosseto, Italy
| | | | - Salvatore Zaffina
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | | | - Angela Gallo
- Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Franco Locatelli
- Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Department of Pediatrics, Sapienza, University of Rome, 00161 Rome, Italy
| | - Alberto E Tozzi
- Multifactorial Disease and Complex Phenotype Research Area, Bambino Gesù Children's Hospital, IRCSS, 00146 Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Dmitriy M Chudakov
- Central European Institute of Technology, 625 00 Brno, Czech Republic; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Rita Carsetti
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Diagnostic Immunology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
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22
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Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, Miskevich DA, Mamedov IZ, Volchkova LN, Nakonechnaya TO, Shugay M, Bolotin DA, Staroverov DB, Sharonov GV, Kondratyuk EY, Zagaynova EV, Lukyanov S, Shams I, Britanova OV, Chudakov DM. Distinct organization of adaptive immunity in the long-lived rodent Spalax galili. Nat Aging 2021; 1:179-189. [PMID: 37118630 DOI: 10.1038/s43587-021-00029-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/08/2021] [Indexed: 04/30/2023]
Abstract
A balanced immune response is a cornerstone of healthy aging. Here, we uncover distinctive features of the long-lived blind mole-rat (Spalax spp.) adaptive immune system, relative to humans and mice. The T-cell repertoire remains diverse throughout the Spalax lifespan, suggesting a paucity of large long-lived clones of effector-memory T cells. Expression of master transcription factors of T-cell differentiation, as well as checkpoint and cytotoxicity genes, remains low as Spalax ages. The thymus shrinks as in mice and humans, while interleukin-7 and interleukin-7 receptor expression remains high, potentially reflecting the sustained homeostasis of naive T cells. With aging, immunoglobulin hypermutation level does not increase and the immunoglobulin-M repertoire remains diverse, suggesting shorter B-cell memory and sustained homeostasis of innate-like B cells. The Spalax adaptive immune system thus appears biased towards sustained functional and receptor diversity over specialized, long-lived effector-memory clones-a unique organizational strategy that potentially underlies this animal's extraordinary longevity and healthy aging.
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Affiliation(s)
- M Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Metsger
- Central European Institute of Technology, Brno, Czech Republic
| | - A N Davydov
- Central European Institute of Technology, Brno, Czech Republic
| | - I A Shagina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Dronina
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - A S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D A Miskevich
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - I Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
| | - L N Volchkova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - T O Nakonechnaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D B Staroverov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - G V Sharonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Y Kondratyuk
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | - E V Zagaynova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - S Lukyanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Shams
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - O V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - D M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia.
- Pirogov Russian National Research Medical University, Moscow, Russia.
- Central European Institute of Technology, Brno, Czech Republic.
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23
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Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 2021; 39:236-245. [PMID: 32895550 DOI: 10.1038/s41587-020-0656-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.
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Affiliation(s)
- Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skoltech, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, UK
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, UK
| | - Theres Oakes
- Division of Infection and Immunity, University College London, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK
| | - Anne Eugster
- DFG-Centre for Regenerative Therapies Dresden, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Klatzmann
- Sorbonne Université, INSERM, 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, 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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24
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Brenna E, Davydov AN, Ladell K, McLaren JE, Bonaiuti P, Metsger M, Ramsden JD, Gilbert SC, Lambe T, Price DA, Campion SL, Chudakov DM, Borrow P, McMichael AJ. CD4 + T Follicular Helper Cells in Human Tonsils and Blood Are Clonally Convergent but Divergent from Non-Tfh CD4 + Cells. Cell Rep 2021; 30:137-152.e5. [PMID: 31914381 PMCID: PMC7029615 DOI: 10.1016/j.celrep.2019.12.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 06/21/2019] [Revised: 09/16/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
T follicular helper (Tfh) cells are fundamental for B cell selection and antibody maturation in germinal centers. Circulating Tfh (cTfh) cells constitute a minor proportion of the CD4+ T cells in peripheral blood, but their clonotypic relationship to Tfh populations resident in lymph nodes and the extent to which they differ from non-Tfh CD4+ cells have been unclear. Using donor-matched blood and tonsil samples, we investigate T cell receptor (TCR) sharing between tonsillar Tfh cells and peripheral Tfh and non-Tfh cell populations. TCR transcript sequencing reveals considerable clonal overlap between peripheral and tonsillar Tfh cell subsets as well as a clear distinction between Tfh and non-Tfh cells. Furthermore, influenza-specific cTfh cell clones derived from blood can be found in the repertoire of tonsillar Tfh cells. Therefore, human blood samples can be used to gain insight into the specificity of Tfh responses occurring in lymphoid tissues, provided that cTfh subsets are studied.
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Affiliation(s)
- Elena Brenna
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Alexey N Davydov
- Central European Institute of Technology, Brno 601 77, Czech Republic
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Paolo Bonaiuti
- Istituto Firc di Oncologia Molecolare, Milano 20139, Italy
| | - Maria Metsger
- Central European Institute of Technology, Brno 601 77, Czech Republic
| | | | - Sarah C Gilbert
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Teresa Lambe
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Suzanne L Campion
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Dmitriy M Chudakov
- Central European Institute of Technology, Brno 601 77, Czech Republic; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russia
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK.
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25
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Minervina AA, Komech EA, Titov A, Bensouda Koraichi M, Rosati E, Mamedov IZ, Franke A, Efimov GA, Chudakov DM, Mora T, Walczak AM, Lebedev YB, Pogorelyy MV. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection. eLife 2021; 10:e63502. [PMID: 33399535 PMCID: PMC7806265 DOI: 10.7554/elife.63502] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is a global pandemic caused by the SARS-CoV-2 coronavirus. T cells play a key role in the adaptive antiviral immune response by killing infected cells and facilitating the selection of virus-specific antibodies. However, neither the dynamics and cross-reactivity of the SARS-CoV-2-specific T-cell response nor the diversity of resulting immune memory is well understood. In this study, we use longitudinal high-throughput T-cell receptor (TCR) sequencing to track changes in the T-cell repertoire following two mild cases of COVID-19. In both donors, we identified CD4+ and CD8+ T-cell clones with transient clonal expansion after infection. We describe characteristic motifs in TCR sequences of COVID-19-reactive clones and show preferential occurrence of these motifs in publicly available large dataset of repertoires from COVID-19 patients. We show that in both donors, the majority of infection-reactive clonotypes acquire memory phenotypes. Certain T-cell clones were detected in the memory fraction at the pre-infection time point, suggesting participation of pre-existing cross-reactive memory T cells in the immune response to SARS-CoV-2.
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Affiliation(s)
| | - Ekaterina A Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Aleksei Titov
- National Research Center for HematologyMoscowRussian Federation
| | - Meriem Bensouda Koraichi
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel UniversityKielGermany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Masaryk University, Central European Institute of TechnologyBrnoCzech Republic
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and PerinatologyMoscowRussian Federation
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel UniversityKielGermany
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Masaryk University, Central European Institute of TechnologyBrnoCzech Republic
| | - Thierry Mora
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École Normale Supérieure, ENS, PSL, Sorbonne Universite, Universite de Paris, and CNRSParisFrance
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Moscow State UniversityMoscowRussian Federation
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
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26
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Kasatskaya SA, Ladell K, Egorov ES, Miners KL, Davydov AN, Metsger M, Staroverov DB, Matveyshina EK, Shagina IA, Mamedov IZ, Izraelson M, Shelyakin PV, Britanova OV, Price DA, Chudakov DM. Functionally specialized human CD4 + T-cell subsets express physicochemically distinct TCRs. eLife 2020; 9:57063. [PMID: 33289628 PMCID: PMC7773335 DOI: 10.7554/elife.57063] [Citation(s) in RCA: 6] [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: 03/19/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.
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Affiliation(s)
- Sofya A Kasatskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Maria Metsger
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitry B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Elena K Matveyshina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Ilgar Z Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mark Izraelson
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Pavel V Shelyakin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
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27
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Galletti G, De Simone G, Mazza EMC, Puccio S, Mezzanotte C, Bi TM, Davydov AN, Metsger M, Scamardella E, Alvisi G, De Paoli F, Zanon V, Scarpa A, Camisa B, Colombo FS, Anselmo A, Peano C, Polletti S, Mavilio D, Gattinoni L, Boi SK, Youngblood BA, Jones RE, Baird DM, Gostick E, Llewellyn-Lacey S, Ladell K, Price DA, Chudakov DM, Newell EW, Casucci M, Lugli E. Two subsets of stem-like CD8 + memory T cell progenitors with distinct fate commitments in humans. Nat Immunol 2020; 21:1552-1562. [PMID: 33046887 PMCID: PMC7610790 DOI: 10.1038/s41590-020-0791-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [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: 04/21/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8+ memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8+ memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8+ memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.
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Affiliation(s)
- Giovanni Galletti
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Gabriele De Simone
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Emilia M C Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Simone Puccio
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Claudia Mezzanotte
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Maria Metsger
- Central European Institute of Technology, Brno, Czech Republic
| | - Eloise Scamardella
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Giorgia Alvisi
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Federica De Paoli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Veronica Zanon
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Alice Scarpa
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Barbara Camisa
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico S Colombo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Achille Anselmo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Clelia Peano
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano, Milan, Italy
- Genomic Unit, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
| | - Sara Polletti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Luca Gattinoni
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Regensburg Center for Interventional Immunology, Regensburg, Germany
- University of Regensburg, Regensburg, Germany
| | - Shannon K Boi
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Rhiannon E Jones
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Monica Casucci
- Innovative Immunotherapies Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center - IRCCS, Rozzano, Milan, Italy.
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28
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Kalinina AA, Nesterenko LN, Bruter AV, Balunets DV, Chudakov DM, Izraelson M, Britanova OV, Khromykh LM, Kazansky DB. Adoptive Immunotherapy Based on Chain-Centric TCRs in Treatment of Infectious Diseases. iScience 2020; 23:101854. [PMID: 33313494 PMCID: PMC7721641 DOI: 10.1016/j.isci.2020.101854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/27/2020] [Revised: 11/03/2020] [Accepted: 11/19/2020] [Indexed: 12/29/2022] Open
Abstract
Complications after vaccination, lack of vaccines against certain infections, and the emergence of antibiotic-resistant microorganisms point to the need for alternative ways of protection and treatment of infectious diseases. Here, we proposed a therapeutic approach to control salmonellosis based on adoptive cell therapy. We showed that the T cell receptor (TCR) repertoire of salmonella-specific memory cells contains 20% of TCR variants with the dominant-active α-chain. Transduction of intact T lymphocytes with the dominant salmonella-specific TCRα led to their enhanced in vitro proliferation in response to salmonella. Adoptive transfer of transduced T cells resulted in a significant decrease in bacterial loads in mice infected with salmonella before or after the adoptive transfer. We demonstrated that adoptive immunotherapy based on T cells, transduced with dominant-specific TCRα could be successfully applied for treatment and prevention of infectious diseases and represent a useful addition to vaccination and existing therapeutic strategies. A regular TCR repertoire of memory T cells contains alpha-chain-centric TCRs Dominant-active TCRα, paired with random TCRβ, recognizes specific microbial antigens Adoptive immunotherapy could be applied for treatment of infections
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Affiliation(s)
- Anastasiia A Kalinina
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" оf the Ministry of Health of the Russian Federation, 115478 Moscow, Russia
| | - Ludmila N Nesterenko
- "N. F. Gamaleya National Research Center of Epidemiology and Microbiology", the Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Alexandra V Bruter
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" оf the Ministry of Health of the Russian Federation, 115478 Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Denis V Balunets
- "N. F. Gamaleya National Research Center of Epidemiology and Microbiology", the Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ludmila M Khromykh
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" оf the Ministry of Health of the Russian Federation, 115478 Moscow, Russia
| | - Dmitry B Kazansky
- Federal State Budgetary Institution "N. N. Blokhin National Medical Research Center of Oncology" оf the Ministry of Health of the Russian Federation, 115478 Moscow, Russia
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29
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Aparicio‐Soto M, Riedel F, Leddermann M, Bacher P, Scheffold A, Kuhl H, Timmermann B, Chudakov DM, Molin S, Worm M, Heine G, Thierse H, Luch A, Siewert K. TCRs with segment TRAV9-2 or a CDR3 histidine are overrepresented among nickel-specific CD4+ T cells. Allergy 2020; 75:2574-2586. [PMID: 32298488 DOI: 10.1111/all.14322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Nickel is the most frequent cause of T cell-mediated allergic contact dermatitis worldwide. In vitro, CD4+ T cells from all donors respond to nickel but the involved αβ T cell receptor (TCR) repertoire has not been comprehensively analyzed. METHODS We introduce CD154 (CD40L) upregulation as a fast, unbiased, and quantitative method to detect nickel-specific CD4+ T cells ex vivo in blood of clinically characterized allergic and non allergic donors. Naïve (CCR7+ CD45RA+) and memory (not naïve) CD154+ CD4+ T cells were analyzed by flow cytometry after 5 hours of stimulation with 200 µmol/L NiSO4 ., TCR α- and β-chains of sorted nickel-specific and control cells were studied by high-throughput sequencing. RESULTS Stimulation of PBMCs with NiSO4 induced CD154 expression on ~0.1% (mean) of naïve and memory CD4+ T cells. In allergic donors with recent positive patch test, memory frequencies further increased ~13-fold and were associated with markers of in vivo activation. CD154 expression was TCR-mediated since single clones could be specifically restimulated. Among nickel-specific CD4+ T cells of allergic and non allergic donors, TCRs expressing the α-chain segment TRAV9-2 or a histidine in their α- or β-chain complementarity determining region 3 (CDR3) were highly overrepresented. CONCLUSIONS Induced CD154 expression represents a reliable method to study nickel-specific CD4+ T cells. TCRs with particular features respond in all donors, while strongly increased blood frequencies indicate nickel allergy for some donors. Our approach may be extended to other contact allergens for the further development of diagnostic and predictive in vitro tests.
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Affiliation(s)
- Marina Aparicio‐Soto
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Franziska Riedel
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Melanie Leddermann
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Petra Bacher
- Institute of Immunology Christian‐Albrechts Universität zu Kiel and Universitätsklinik Schleswig‐Holstein Kiel Germany
- Institute of Clinical Molecular Biology Christian‐Albrechts Universität zu Kiel Kiel Germany
| | - Alexander Scheffold
- Institute of Immunology Christian‐Albrechts Universität zu Kiel and Universitätsklinik Schleswig‐Holstein Kiel Germany
| | - Heiner Kuhl
- Sequencing Core Facility Max‐Planck‐Institute of Molecular Genetics Berlin Germany
| | - Bernd Timmermann
- Sequencing Core Facility Max‐Planck‐Institute of Molecular Genetics Berlin Germany
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Science Moscow Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine Pirogov Russian National Research Medical University Moscow Russia
- Center of Molecular Medicine CEITEC Masaryk University Brno Czech Republic
| | - Sonja Molin
- Division of Dermatology Queen's University Kingston ON Canada
- Department of Dermatology and Allergy Ludwig Maximilian University Munich Germany
| | - Margitta Worm
- Division of Allergy and Immunology Department of Dermatology, Venerology, and Allergy Charité – Universitätsmedizin Berlin Berlin Germany
| | - Guido Heine
- Division of Allergy and Immunology Department of Dermatology, Venerology, and Allergy Charité – Universitätsmedizin Berlin Berlin Germany
- Department of Dermatology and Allergy University Hospital Schleswig‐Holstein Kiel Germany
| | - Hermann‐Josef Thierse
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Andreas Luch
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Katherina Siewert
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
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30
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Bagaev DV, Vroomans RMA, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov ES, Zvyagin IV, Babel N, Cole DK, Godkin AJ, Sewell AK, Kesmir C, Chudakov DM, Luciani F, Shugay M. VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Nucleic Acids Res 2020; 48:D1057-D1062. [PMID: 31588507 PMCID: PMC6943061 DOI: 10.1093/nar/gkz874] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/17/2019] [Accepted: 09/29/2019] [Indexed: 01/11/2023] Open
Abstract
Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net.
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Affiliation(s)
- Dmitry V Bagaev
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Renske M A Vroomans
- Origins Center, Groningen, The Netherlands.,Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,School of Medical Sciences, UNSW Sydney, Sydney, Australia
| | - Ulrik Stervbo
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - Cristina Rius
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Garry Dolton
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Meriem Attaf
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Evgeny S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ivan V Zvyagin
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Nina Babel
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.,Immunocore Ltd., Abingdon, OX14 4RY, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Can Kesmir
- Theoretical Biology and Bioinformatics Department, Science Faculty, Utrecht University, Utrecht, Netherlands
| | - Dmitriy M Chudakov
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,School of Medical Sciences, UNSW Sydney, Sydney, Australia
| | - Mikhail Shugay
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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31
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Yuzhakova DV, Volchkova LN, Pogorelyy MV, Serebrovskaya EO, Shagina IA, Bryushkova EA, Nakonechnaya TO, Izosimova AV, Zavyalova DS, Karabut MM, Izraelson M, Samoylenko IV, Zagainov VE, Chudakov DM, Zagaynova EV, Sharonov GV. Measuring Intratumoral Heterogeneity of Immune Repertoires. Front Oncol 2020; 10:512. [PMID: 32457825 PMCID: PMC7227437 DOI: 10.3389/fonc.2020.00512] [Citation(s) in RCA: 6] [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: 12/04/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
There is considerable clinical and fundamental value in measuring the clonal heterogeneity of T and B cell expansions in tumors and tumor-associated lymphoid structures—along with the associated heterogeneity of the tumor neoantigen landscape—but such analyses remain challenging to perform. Here, we propose a straightforward approach to analyze the heterogeneity of immune repertoires between different tissue sections in a quantitative and controlled way, based on a beta-binomial noise model trained on control replicates obtained at the level of single-cell suspensions. This approach allows to identify local clonal expansions with high accuracy. We reveal in situ proliferation of clonal T cells in a mouse model of melanoma, and analyze heterogeneity of immunoglobulin repertoires between sections of a metastatically-infiltrated lymph node in human melanoma and primary human colon tumor. On the latter example, we demonstrate the importance of training the noise model on datasets with depth and content that is comparable to the samples being studied. Altogether, we describe here the crucial basic instrumentarium needed to facilitate proper experimental setup planning in the rapidly evolving field of intratumoral immune repertoires, from the wet lab to bioinformatics analysis.
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Affiliation(s)
- Diana Vladimirovna Yuzhakova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Lilia N Volchkova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mikhail Valerievich Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina A Bryushkova
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Department of Molecular Biology, Moscow State University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anna V Izosimova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Daria S Zavyalova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria M Karabut
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Mark Izraelson
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Igor V Samoylenko
- Oncodermatology Department, N. N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Vladimir E Zagainov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Volga District Medical Centre Under Federal Medical and Biological Agency, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Adaptive Immunity Group, Central European Institute of Technology, Masaryk University, Brno, Czechia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Elena V Zagaynova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - George Vladimirovich Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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32
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Zhigalova EA, Izosimova AI, Yuzhakova DV, Volchkova LN, Shagina IA, Turchaninova MA, Serebrovskaya EO, Zagaynova EV, Chudakov DM, Sharonov GV. RNA-Seq-Based TCR Profiling Reveals Persistently Increased Intratumoral Clonality in Responders to Anti-PD-1 Therapy. Front Oncol 2020; 10:385. [PMID: 32411589 PMCID: PMC7199218 DOI: 10.3389/fonc.2020.00385] [Citation(s) in RCA: 6] [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: 11/21/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
Substantial effort is being invested in the search for peripheral or intratumoral T cell receptor (TCR) repertoire features that could predict the response to immunotherapy. Here we demonstrate the utility of MiXCR software for TCR and immunoglobulin repertoire extraction from RNA-Seq data obtained from sorted tumor-infiltrating T and B cells. We use this approach to extract TCR repertoires from RNA-Seq data obtained from sorted tumor-infiltrating CD4+ and CD8+ T cells in an HKP1 (KrasG12Dp53-/-) syngeneic mouse model of lung cancer after anti-PD-1 treatment. For both subsets, we demonstrate decreased TCR diversity in response to therapy. At a later time point, repertoire diversity is restored in progressing disease but remains decreased in responders to therapy in both CD4+ and CD8+ subsets. These observations complement previous studies and suggest that stably increased intratumoral CD4+ and CD8+ T cell clonality after anti-PD-1/PD-L1 therapy could serve as a predictor of long-term response.
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Affiliation(s)
- Ekaterina A Zhigalova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna I Izosimova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Diana V Yuzhakova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Lilia N Volchkova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria A Turchaninova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Elena V Zagaynova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - George V Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Molecular Technologies Department, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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33
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Minervina AA, Pogorelyy MV, Komech EA, Karnaukhov VK, Bacher P, Rosati E, Franke A, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones. eLife 2020; 9:53704. [PMID: 32081129 PMCID: PMC7060039 DOI: 10.7554/elife.53704] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 11/18/2019] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The diverse repertoire of T-cell receptors (TCR) plays a key role in the adaptive immune response to infections. Using TCR alpha and beta repertoire sequencing for T-cell subsets, as well as single-cell RNAseq and TCRseq, we track the concentrations and phenotypes of individual T-cell clones in response to primary and secondary yellow fever immunization — the model for acute infection in humans — showing their large diversity. We confirm the secondary response is an order of magnitude weaker, albeit ∼10 days faster than the primary one. Estimating the fraction of the T-cell response directed against the single immunodominant epitope, we identify the sequence features of TCRs that define the high precursor frequency of the two major TCR motifs specific for this particular epitope. We also show the consistency of clonal expansion dynamics between bulk alpha and beta repertoires, using a new methodology to reconstruct alpha-beta pairings from clonal trajectories.
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Affiliation(s)
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Ekaterina A Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | | | - Petra Bacher
- Institute of Immunology, Kiel University, Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation.,Center of Life Sciences, Skoltech, Moscow, Russian Federation.,Masaryk University, Central European Institute of Technology, Brno, Czech Republic
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.,Masaryk University, Central European Institute of Technology, Brno, Czech Republic.,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russian Federation
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.,Moscow State University, Moscow, Russian Federation
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure, ENS, PSL, Sorbonne Université, Université de Paris, and CNRS, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École normale supérieure, ENS, PSL, Sorbonne Université, Université de Paris, and CNRS, Paris, France
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34
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Sharonov GV, Serebrovskaya EO, Yuzhakova DV, Britanova OV, Chudakov DM. B cells, plasma cells and antibody repertoires in the tumour microenvironment. Nat Rev Immunol 2020; 20:294-307. [DOI: 10.1038/s41577-019-0257-x] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2019] [Indexed: 02/07/2023]
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35
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De Simone G, Mazza EMC, Cassotta A, Davydov AN, Kuka M, Zanon V, De Paoli F, Scamardella E, Metsger M, Roberto A, Pilipow K, Colombo FS, Tenedini E, Tagliafico E, Gattinoni L, Mavilio D, Peano C, Price DA, Singh SP, Farber JM, Serra V, Cucca F, Ferrari F, Orrù V, Fiorillo E, Iannacone M, Chudakov DM, Sallusto F, Lugli E. CXCR3 Identifies Human Naive CD8 + T Cells with Enhanced Effector Differentiation Potential. J Immunol 2019; 203:3179-3189. [PMID: 31740485 PMCID: PMC6900484 DOI: 10.4049/jimmunol.1901072] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/16/2019] [Indexed: 01/19/2023]
Abstract
In mice, the ability of naive T (TN) cells to mount an effector response correlates with TCR sensitivity for self-derived Ags, which can be quantified indirectly by measuring surface expression levels of CD5. Equivalent findings have not been reported previously in humans. We identified two discrete subsets of human CD8+ TN cells, defined by the absence or presence of the chemokine receptor CXCR3. The more abundant CXCR3+ TN cell subset displayed an effector-like transcriptional profile and expressed TCRs with physicochemical characteristics indicative of enhanced interactions with peptide-HLA class I Ags. Moreover, CXCR3+ TN cells frequently produced IL-2 and TNF in response to nonspecific activation directly ex vivo and differentiated readily into Ag-specific effector cells in vitro. Comparative analyses further revealed that human CXCR3+ TN cells were transcriptionally equivalent to murine CXCR3+ TN cells, which expressed high levels of CD5. These findings provide support for the notion that effector differentiation is shaped by heterogeneity in the preimmune repertoire of human CD8+ T cells.
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Affiliation(s)
- Gabriele De Simone
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Emilia M C Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Alexey N Davydov
- Central European Institute of Technology, 621 00 Brno, Czech Republic
| | - Mirela Kuka
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Veronica Zanon
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Federica De Paoli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Eloise Scamardella
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Maria Metsger
- Central European Institute of Technology, 621 00 Brno, Czech Republic
| | - Alessandra Roberto
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Karolina Pilipow
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Federico S Colombo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Elena Tenedini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Enrico Tagliafico
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Luca Gattinoni
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Regensburg Center for Interventional Immunology, University Regensburg and University Hospital Regensburg, 93053 Regensburg, Germany
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Clelia Peano
- Division of Genetic and Biomedical Research, UoS Milan, National Research Council, 20089 Rozzano, Milan, Italy
- Genomic Unit, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Satya P Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joshua M Farber
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | - Valeria Orrù
- IRGB, National Research Council, 09042 Monserrato, Italy
| | | | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Dmitriy M Chudakov
- Central European Institute of Technology, 621 00 Brno, Czech Republic
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; and
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy;
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
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36
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Mikelov AI, Staroverov DB, Komech EA, Lebedev Y, Chudakov DM, Zvyagin IV. Correlated dynamics of serum IGE and IGE+ clonotype count with allergen air level in seasonal allergic rhinitis. BRSMU 2019. [DOI: 10.24075/brsmu.2019.072] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanisms of maintenance of immunological memory in the chronic course of seasonal allergic rhinitis remain poorly understood. The detailed understanding of these mechanisms is required for design of new approaches for allergy treatment. It is known that the level of allergen-specific IgE antibodies (sIgE), which play a key role in the development of the disease, is increased in patients with seasonal allergic rhinitis during pollination season. This study aimed to investigate the dynamics of serum IgE levels and characteristics of the clonal repertoire of IgE-secreting lymphocytes depending on the intensity of the patient's contact with the allergen. For three patients, allergic to birch pollen (22, 22, and 28 y.o.), we measured total IgE and birch pollen specific IgE levels at 6 time points with 2 week interval during the birch pollination season. Immunoglobulin heavy chain gene (IGH) clonal repertoire data for several B-cell subpopulations at different time points were obtained for one patient. We observe growth of the sIgE level (91%, 37%, and 64% compared to the baseline) at the peak of pollination season in all three donors. Initial increase in sIgE and IgE levels coincides with the birch pollination initiation; sIgE and total IgE levels correlate with the birch pollen air level (sIgE: R2 = 0.98 at p < 0.05; total IgE: R2 = 0.95 at p < 0.05). We detected IgE clonotypes only in samples obtained during the birch pollination, which indicates an increase of IGE-expressing cells concentration during this period. The frequency of IgE clonotypes was extremely low compared to that of the clonotypes of other isotypes (IgE — 0.01%, IgM — 48.4%, IgD — 14%, IgG — 17.4%, IgA — 19.8%). Hypermutation and phylogenetic analysis of the sequences from the 13 detected IgE-containing clonal groups showed that these IgE clonotypes could originate from IgG as a result of sequential isotype-switching.
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Affiliation(s)
- AI Mikelov
- Skoltech, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - EA Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - YuB Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - DM Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - IV Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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37
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Isaeva OI, Sharonov GV, Serebrovskaya EO, Turchaninova MA, Zaretsky AR, Shugay M, Chudakov DM. Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes. J Immunother Cancer 2019; 7:279. [PMID: 31665076 PMCID: PMC6819482 DOI: 10.1186/s40425-019-0747-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The role of tumor-infiltrating B-cells (TIBs) and intratumorally-produced antibodies in cancer-immunity interactions essentially remains terra incognita. In particular, it remains unexplored how driver mutations could be associated with distinct TIBs signatures and their role in tumor microenvironment. METHODS Here we analyzed associations of immunoglobulin isotypes and clonality with survival in TCGA RNA-Seq data for lung adenocarcinoma (LUAD), stratifying patients into 12 driver mutation and phenotypic tumor subgroups. RESULTS We revealed several unexpected associations between TIBs behavior and prognosis. Abundance and high proportion of IgG1 isotype, and low proportion of IgA among all intratumorally produced immunoglobulins were specifically associated with improved overall survival for KRASmut but not KRASwt LUAD, revealing the first link between a driver mutation and B-cell response. We found specific IgG1 signature associated with long survival, which suggests that particular specificities of IgG1+ TIBs could be beneficial in KRASmut LUAD. In contrast to our previous observations for melanoma, highly clonal IgG1 production by plasma cells had no meaningful effect on prognosis, suggesting that IgG1+ TIBs may exert a beneficial effect in KRASmut cases in an alternative way, such as efficient presentation of cognate antigens or direct B cell attack on tumor cells. Notably, a high proportion of the IgG1 isotype is positively correlated with the non-silent mutation burden both in the general LUAD cohort and in most patient subgroups, supporting a role for IgG1+ TIBs in antigen presentation. Complementing the recent finding that the presence of stromal IgG4-producing cells is associated with a favorable prognosis for patients with stage I squamous cell carcinoma, we show that the abundance of IgG4-producing TIBs likewise has a strong positive effect on overall survival in STK11mut and proximal proliferative subgroups of LUAD patients. We hypothesize that the positive role of IgG4 antibodies in some of the lung cancer subtypes could be associated with reported inability of IgG4 isotype to form immune complexes, thus preventing immunosuppression via activation of the myeloid-derived suppressor cell (MDSC) phenotype. CONCLUSIONS We discover prominent and distinct associations between TIBs antibody isotypes and survival in lung adenocarcinoma carrying specific driver mutations. These findings indicate that particular types of tumor-immunity relations could be beneficial in particular driver mutation context, which should be taken into account in developing strategies of cancer immunotherapy and combination therapies. Specificity of protective B cell populations in specific cancer subgroups could become a clue to efficient targeted immunotherapies for appropriate cohorts of patients.
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Affiliation(s)
- O I Isaeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,BostonGene LLC, Lincoln, MA, USA
| | - G V Sharonov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E O Serebrovskaya
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Turchaninova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - A R Zaretsky
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - M Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - D M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia. .,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia. .,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia.
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38
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Shugay M, Bagaev DV, Zvyagin IV, Vroomans RM, Crawford JC, Dolton G, Komech EA, Sycheva AL, Koneva AE, Egorov ES, Eliseev AV, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren JE, Matthews KK, Clemens EB, Douek DC, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas PG, Price DA, Sewell AK, Chudakov DM. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res 2019; 46:D419-D427. [PMID: 28977646 PMCID: PMC5753233 DOI: 10.1093/nar/gkx760] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [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] [Received: 06/23/2017] [Accepted: 08/17/2017] [Indexed: 01/02/2023] Open
Abstract
The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3.net and https://github.com/antigenomics/vdjdb-db.
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Affiliation(s)
- Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Central European Institute of Technology, Brno 60177, Czech Republic.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603950, Russia
| | - Dmitriy V Bagaev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Ivan V Zvyagin
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Renske M Vroomans
- Theoretical Biology and Bioinformatics, Science Faculty, Utrecht University, Utrecht 3512 JE, The Netherlands
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude's Children's Research Hospital, Memphis, TN 38105, USA
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Ekaterina A Komech
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anastasiya L Sycheva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Anna E Koneva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Evgeniy S Egorov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603950, Russia
| | - Alexey V Eliseev
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Ewald Van Dyk
- Theoretical Biology and Bioinformatics, Science Faculty, Utrecht University, Utrecht 3512 JE, The Netherlands
| | - Pradyot Dash
- Department of Immunology, St. Jude's Children's Research Hospital, Memphis, TN 38105, USA
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Katherine K Matthews
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville VIC 3010, Australia
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fabio Luciani
- Viral Immunology Systems Program, Kirby Institute, School of Medical Sciences, University of New South Wales, Kensington NSW 2052, Australia
| | - Debbie van Baarle
- Center for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven 3720 BA, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville VIC 3010, Australia
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Science Faculty, Utrecht University, Utrecht 3512 JE, The Netherlands
| | - Paul G Thomas
- Department of Immunology, St. Jude's Children's Research Hospital, Memphis, TN 38105, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.,Central European Institute of Technology, Brno 60177, Czech Republic.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603950, Russia
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39
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Pogorelyy MV, Minervina AA, Shugay M, Chudakov DM, Lebedev YB, Mora T, Walczak AM. Detecting T cell receptors involved in immune responses from single repertoire snapshots. PLoS Biol 2019; 17:e3000314. [PMID: 31194732 PMCID: PMC6592544 DOI: 10.1371/journal.pbio.3000314] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 03/05/2019] [Revised: 06/25/2019] [Accepted: 05/21/2019] [Indexed: 11/19/2022] Open
Abstract
Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens. Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations. We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders - patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine). We validate the method with independent assays. ALICE requires no longitudinal data collection nor large cohorts, and it is directly applicable to most RepSeq datasets. Its results facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.
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Affiliation(s)
- Mikhail V. Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Center of Life Sciences, Skoltech, Moscow, Russia
- Masaryk University, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Center of Life Sciences, Skoltech, Moscow, Russia
- Masaryk University, Central European Institute of Technology, Brno, Czech Republic
| | - Yuri B. Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Moscow State University, Moscow, Russia
| | - Thierry Mora
- Laboratoire de physique statistique, CNRS, Sorbonne Université, Université Paris-Diderot, and École normale supérieure (PSL University), Paris, France
- * E-mail: (TM); (AW)
| | - Aleksandra M. Walczak
- Laboratoire de physique théorique, CNRS, Sorbonne Université, Université Paris-Diderot, and École normale supérieure (PSL University), Paris, France
- * E-mail: (TM); (AW)
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40
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Weber J, de la Rosa J, Grove CS, Schick M, Rad L, Baranov O, Strong A, Pfaus A, Friedrich MJ, Engleitner T, Lersch R, Öllinger R, Grau M, Menendez IG, Martella M, Kohlhofer U, Banerjee R, Turchaninova MA, Scherger A, Hoffman GJ, Hess J, Kuhn LB, Ammon T, Kim J, Schneider G, Unger K, Zimber-Strobl U, Heikenwälder M, Schmidt-Supprian M, Yang F, Saur D, Liu P, Steiger K, Chudakov DM, Lenz G, Quintanilla-Martinez L, Keller U, Vassiliou GS, Cadiñanos J, Bradley A, Rad R. PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. Nat Commun 2019; 10:1415. [PMID: 30926791 PMCID: PMC6440946 DOI: 10.1038/s41467-019-09180-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 06/07/2018] [Accepted: 02/18/2019] [Indexed: 01/03/2023] Open
Abstract
B-cell lymphoma (BCL) is the most common hematologic malignancy. While sequencing studies gave insights into BCL genetics, identification of non-mutated cancer genes remains challenging. Here, we describe PiggyBac transposon tools and mouse models for recessive screening and show their application to study clonal B-cell lymphomagenesis. In a genome-wide screen, we discover BCL genes related to diverse molecular processes, including signaling, transcriptional regulation, chromatin regulation, or RNA metabolism. Cross-species analyses show the efficiency of the screen to pinpoint human cancer drivers altered by non-genetic mechanisms, including clinically relevant genes dysregulated epigenetically, transcriptionally, or post-transcriptionally in human BCL. We also describe a CRISPR/Cas9-based in vivo platform for BCL functional genomics, and validate discovered genes, such as Rfx7, a transcription factor, and Phip, a chromatin regulator, which suppress lymphomagenesis in mice. Our study gives comprehensive insights into the molecular landscapes of BCL and underlines the power of genome-scale screening to inform biology.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Jorge de la Rosa
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Carolyn S Grove
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- School of Medicine, University of Western Australia, Crawley, 6009, Australia
- Department of Haematology, PathWest and Sir Charles Gairdner Hospital, Queen Elizabeth II Medical Centre, Nedlands, 6009, Australia
| | - Markus Schick
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Lena Rad
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Olga Baranov
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anja Pfaus
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Mathias J Friedrich
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
| | - Michael Grau
- Department of Medicine A, University Hospital Münster, Münster, 48149, Germany
- Cluster of Excellence EXC 1003, Cells in Motion, Münster, 48149, Germany
| | - Irene Gonzalez Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Manuela Martella
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Ruby Banerjee
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Maria A Turchaninova
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, 603005, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Anna Scherger
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Gary J Hoffman
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- School of Medicine, University of Western Australia, Crawley, 6009, Australia
| | - Julia Hess
- Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Neuherberg, 85764, Germany
| | - Laura B Kuhn
- Helmholtz Zentrum München, Research Unit Gene Vectors, Munich, 81377, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, 61231, Germany
- German Center for Cardiovascular Research (DZHK), Rhine Main, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Kristian Unger
- Helmholtz Zentrum München, Research Unit Radiation Cytogenetics, Neuherberg, 85764, Germany
| | | | - Mathias Heikenwälder
- Divison of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Katja Steiger
- Comparative Experimental Pathology, Technische Universität München, Munich, 81675, Germany
| | - Dmitriy M Chudakov
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, 603005, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, 117997, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Center of Molecular Medicine, CEITEC, Masaryk University, Brno, 601 77, Czech Republic
| | - Georg Lenz
- Department of Medicine A, University Hospital Münster, Münster, 48149, Germany
- Cluster of Excellence EXC 1003, Cells in Motion, Münster, 48149, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Ulrich Keller
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
- Hematology and Oncology-Campus Benjamin Franklin (CBF), Charité-Universitätsmedizin Berlin, Berlin, 12203, Germany
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, CB2 0XY, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0PT, UK
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, 33193, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, 33006, Spain
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, 81675, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, 81675, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
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Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F. Memory CD4 + T cells are generated in the human fetal intestine. Nat Immunol 2019; 20:301-312. [PMID: 30664737 PMCID: PMC6420108 DOI: 10.1038/s41590-018-0294-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [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: 05/29/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022]
Abstract
The fetus is thought to be protected from exposure to foreign antigens,
yet CD45RO+ T cells reside in the fetal intestine. Here we combined
functional assays with mass cytometry, single-cell RNA-sequencing and
high-throughput T cell antigen receptor (TCR) sequencing to characterize the
CD4+ T cell compartment in the human fetal intestine. We
identified 22 CD4+ T cell clusters, including naive-like,
regulatory-like and memory-like subpopulations, which were confirmed and further
characterized at the transcriptional level. Memory-like CD4+ T cells
had high expression of Ki-67, indicative of cell division, and CD5, a surrogate
marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway
analysis revealed a differentiation trajectory associated with cellular
activation and proinflammatory effector functions, and TCR repertoire analysis
indicated clonal expansions, distinct repertoire characteristics and
interconnections between subpopulations of memory-like CD4+ T cells.
Imaging-mass cytometry indicated that memory-like CD4+ T cells
colocalized with antigen-presenting cells. Collectively, these results provide
evidence for the generation of memory-like CD4+ T cells in the human
fetal intestine that is consistent with exposure to foreign antigens.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands
| | - Nannan Guo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, Delft, the Netherlands
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia.,Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Boudewijn P F Lelieveldt
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
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42
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Pogorelyy MV, Minervina AA, Touzel MP, Sycheva AL, Komech EA, Kovalenko EI, Karganova GG, Egorov ES, Komkov AY, Chudakov DM, Mamedov IZ, Mora T, Walczak AM, Lebedev YB. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proc Natl Acad Sci U S A 2018; 115:12704-12709. [PMID: 30459272 PMCID: PMC6294963 DOI: 10.1073/pnas.1809642115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [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] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.
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Affiliation(s)
- Mikhail V Pogorelyy
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasia A Minervina
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Maximilian Puelma Touzel
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, École Normale Supérieure (PSL), 75005 Paris, France
| | - Anastasiia L Sycheva
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Ekaterina A Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Elena I Kovalenko
- Department of Immunology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Galina G Karganova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides, 142782 Moscow, Russia
- Department of Virology, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Evgeniy S Egorov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexander Yu Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117198 Moscow, Russia
| | - Dmitriy M Chudakov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, 121205 Moscow, Russia
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Ilgar Z Mamedov
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, Sorbonne Université, Université Paris-Diderot, École Normale Supérieure (PSL), 75005 Paris, France;
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, École Normale Supérieure (PSL), 75005 Paris, France;
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia;
- Biological Faculty, Moscow State University, 119991 Moscow, Russia
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43
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Bolotin DA, Poslavsky S, Davydov AN, Chudakov DM. Reply to "Evaluation of immune repertoire inference methods from RNA-seq data". Nat Biotechnol 2018; 36:1035-1036. [DOI: 10.1038/nbt.4296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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44
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Fan X, Moltedo B, Mendoza A, Davydov AN, Faire MB, Mazutis L, Sharma R, Pe'er D, Chudakov DM, Rudensky AY. CD49b defines functionally mature Treg cells that survey skin and vascular tissues. J Exp Med 2018; 215:2796-2814. [PMID: 30355617 PMCID: PMC6219731 DOI: 10.1084/jem.20181442] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 07/30/2018] [Revised: 09/22/2018] [Accepted: 09/25/2018] [Indexed: 12/12/2022] Open
Abstract
Fan et al. have identified a population of recirculating Treg cells with greater suppressive ability and a unique tissue distribution. Using single-cell RNA-seq, they place these Treg cells at the apex of the Treg developmental trajectory and show that similar cells may exist in humans. Regulatory T (Treg) cells prevent autoimmunity by limiting immune responses and inflammation in the secondary lymphoid organs and nonlymphoid tissues. While unique subsets of Treg cells have been described in some nonlymphoid tissues, their relationship to Treg cells in secondary lymphoid organs and circulation remains unclear. Furthermore, it is possible that Treg cells from similar tissue types share largely similar properties. We have identified a short-lived effector Treg cell subset that expresses the α2 integrin, CD49b, and exhibits a unique tissue distribution, being abundant in peripheral blood, vasculature, skin, and skin-draining lymph nodes, but uncommon in the intestines and in viscera-draining lymph nodes. CD49b+ Treg cells, which display superior functionality revealed by in vitro and in vivo assays, appear to develop after multiple rounds of cell division and TCR-dependent activation. Accordingly, single-cell RNA-seq analysis placed these cells at the apex of the Treg developmental trajectory. These results shed light on the identity and development of a functionally potent subset of mature effector Treg cells that recirculate through and survey peripheral tissues.
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Affiliation(s)
- Xiying Fan
- Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bruno Moltedo
- Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alejandra Mendoza
- Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mehlika B Faire
- Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Linas Mazutis
- Single Cell Research Initiative, Memorial Sloan Kettering Cancer Center, New York, NY.,Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Roshan Sharma
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY
| | - Dana Pe'er
- Single Cell Research Initiative, Memorial Sloan Kettering Cancer Center, New York, NY.,Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dmitriy M Chudakov
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Immunology Program, and Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY
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45
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Davydov AN, Obraztsova AS, Lebedin MY, Turchaninova MA, Staroverov DB, Merzlyak EM, Sharonov GV, Kladova O, Shugay M, Britanova OV, Chudakov DM. Comparative Analysis of B-Cell Receptor Repertoires Induced by Live Yellow Fever Vaccine in Young and Middle-Age Donors. Front Immunol 2018; 9:2309. [PMID: 30356675 PMCID: PMC6189279 DOI: 10.3389/fimmu.2018.02309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 04/26/2018] [Accepted: 09/17/2018] [Indexed: 12/25/2022] Open
Abstract
Age-related changes can significantly alter the state of adaptive immune system and often lead to attenuated response to novel pathogens and vaccination. In present study we employed 5′RACE UMI-based full length and nearly error-free immunoglobulin profiling to compare plasma cell antibody repertoires in young (19–26 years) and middle-age (45–58 years) individuals vaccinated with a live yellow fever vaccine, modeling a newly encountered pathogen. Our analysis has revealed age-related differences in the responding antibody repertoire ranging from distinct IGH CDR3 repertoire properties to differences in somatic hypermutation intensity and efficiency and antibody lineage tree structure. Overall, our findings suggest that younger individuals respond with a more diverse antibody repertoire and employ a more efficient somatic hypermutation process than elder individuals in response to a newly encountered pathogen.
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Affiliation(s)
- Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia
| | - Anna S Obraztsova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail Y Lebedin
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria A Turchaninova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina M Merzlyak
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - George V Sharonov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Olga Kladova
- Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Dmitriy M Chudakov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czechia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
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46
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Hunter S, Willcox CR, Davey MS, Kasatskaya SA, Jeffery HC, Chudakov DM, Oo YH, Willcox BE. Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations. J Hepatol 2018; 69:654-665. [PMID: 29758330 PMCID: PMC6089840 DOI: 10.1016/j.jhep.2018.05.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/27/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS γδ T cells comprise a substantial proportion of tissue-associated lymphocytes. However, our current understanding of human γδ T cells is primarily based on peripheral blood subsets, while the immunobiology of tissue-associated subsets remains largely unclear. Therefore, we aimed to elucidate the T cell receptor (TCR) diversity, immunophenotype and function of γδ T cells in the human liver. METHODS We characterised the TCR repertoire, immunophenotype and function of human liver infiltrating γδ T cells, by TCR sequencing analysis, flow cytometry, in situ hybridisation and immunohistochemistry. We focussed on the predominant tissue-associated Vδ2- γδ subset, which is implicated in liver immunopathology. RESULTS Intrahepatic Vδ2- γδ T cells were highly clonally focussed, with single expanded clonotypes featuring complex, private TCR rearrangements frequently dominating the compartment. Such T cells were predominantly CD27lo/- effector lymphocytes, whereas naïve CD27hi, TCR-diverse populations present in matched blood were generally absent in the liver. Furthermore, while a CD45RAhi Vδ2- γδ effector subset present in both liver and peripheral blood contained overlapping TCR clonotypes, the liver Vδ2- γδ T cell pool also included a phenotypically distinct CD45RAlo effector compartment that was enriched for expression of the tissue tropism marker CD69, the hepatic homing chemokine receptors CXCR3 and CXCR6, and liver-restricted TCR clonotypes, suggestive of intrahepatic tissue residency. Liver infiltrating Vδ2- γδ cells were capable of polyfunctional cytokine secretion, and unlike peripheral blood subsets, were responsive to both TCR and innate stimuli. CONCLUSION These findings suggest that the ability of Vδ2- γδ T cells to undergo clonotypic expansion and differentiation is crucial in permitting access to solid tissues, such as the liver, which results in functionally distinct peripheral and liver-resident memory γδ T cell subsets. They also highlight the inherent functional plasticity within the Vδ2- γδ T cell compartment and provide information that could be used for the design of cellular therapies that suppress liver inflammation or combat liver cancer. LAY SUMMARY γδ T cells are frequently enriched in many solid tissues, however the immunobiology of such tissue-associated subsets in humans has remained unclear. We show that intrahepatic γδ T cells are enriched for clonally expanded effector T cells, whereas naïve γδ T cells are largely excluded. Moreover, whereas a distinct proportion of circulating T cell clonotypes was present in both the liver tissue and peripheral blood, a functionally and clonotypically distinct population of liver-resident γδ T cells was also evident. Our findings suggest that factors triggering γδ T cell clonal selection and differentiation, such as infection, can drive enrichment of γδ T cells into liver tissue, allowing the development of functionally distinct tissue-restricted memory populations specialised in local hepatic immunosurveillance.
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Affiliation(s)
- Stuart Hunter
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom,Centre for Liver Research and National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Institute of Immunology & Immunotherapy, University of Birmingham, United Kingdom
| | - Carrie R. Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Martin S. Davey
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Sofya A. Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Hannah C. Jeffery
- Centre for Liver Research and National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Institute of Immunology & Immunotherapy, University of Birmingham, United Kingdom
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia,Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ye H. Oo
- Centre for Liver Research and National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Institute of Immunology & Immunotherapy, University of Birmingham, United Kingdom,University Hospital of Birmingham NHS Foundation Trust, United Kingdom,Corresponding authors. Addresses: Centre for Liver Research and NIHR Birmingham Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel.: +44 (0) 121 414 2246; fax: +44 (0) 121 415 8701 (Y. H. Oo), or Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel.: +44 0121 414 9533; fax: +44 0121 414 4486 (B. Willcox).
| | - Benjamin E. Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom,Corresponding authors. Addresses: Centre for Liver Research and NIHR Birmingham Biomedical Research Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel.: +44 (0) 121 414 2246; fax: +44 (0) 121 415 8701 (Y. H. Oo), or Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel.: +44 0121 414 9533; fax: +44 0121 414 4486 (B. Willcox).
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47
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Egorov ES, Kasatskaya SA, Zubov VN, Izraelson M, Nakonechnaya TO, Staroverov DB, Angius A, Cucca F, Mamedov IZ, Rosati E, Franke A, Shugay M, Pogorelyy MV, Chudakov DM, Britanova OV. The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging. Front Immunol 2018; 9:1618. [PMID: 30087674 PMCID: PMC6066563 DOI: 10.3389/fimmu.2018.01618] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022] Open
Abstract
Human aging is associated with a profound loss of thymus productivity, yet naïve T lymphocytes still maintain their numbers by division in the periphery for many years. The extent of such proliferation may depend on the cytokine environment, including IL-7 and T-cell receptor (TCR) “tonic” signaling mediated by self pMHCs recognition. Additionally, intrinsic properties of distinct subpopulations of naïve T cells could influence the overall dynamics of aging-related changes within the naïve T cell compartment. Here, we investigated the differences in the architecture of TCR beta repertoires for naïve CD4, naïve CD8, naïve CD4+CD25−CD31+ (enriched with recent thymic emigrants, RTE), and mature naïve CD4+CD25−CD31− peripheral blood subsets between young and middle-age/old healthy individuals. In addition to observing the accumulation of clonal expansions (as was shown previously), we reveal several notable changes in the characteristics of T cell repertoire. We observed significant decrease of CDR3 length, NDN insert, and number of non-template added N nucleotides within TCR beta CDR3 with aging, together with a prominent change of physicochemical properties of the central part of CDR3 loop. These changes were similar across CD4, CD8, RTE-enriched, and mature CD4 subsets of naïve T cells, with minimal or no difference observed between the latter two subsets for individuals of the same age group. We also observed an increase in “publicity” (fraction of shared clonotypes) of CD4, but not CD8 naïve T cell repertoires. We propose several explanations for these phenomena built upon previous studies of naïve T-cell homeostasis, and call for further studies of the mechanisms causing the observed changes and of consequences of these changes in respect of the possible holes formed in the landscape of naïve T cell TCR repertoire.
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Affiliation(s)
- Evgeny S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vasiliy N Zubov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mark Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Ilgar Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Mikhail Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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48
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Dolton G, Zervoudi E, Rius C, Wall A, Thomas HL, Fuller A, Yeo L, Legut M, Wheeler S, Attaf M, Chudakov DM, Choy E, Peakman M, Sewell AK. Optimized Peptide-MHC Multimer Protocols for Detection and Isolation of Autoimmune T-Cells. Front Immunol 2018; 9:1378. [PMID: 30008714 PMCID: PMC6034003 DOI: 10.3389/fimmu.2018.01378] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide–MHC (pMHC) multimers have become the “gold standard” for the detection and isolation of antigen-specific T-cells but recent evidence shows that normal use of these reagents can miss fully functional T-cells that bear T-cell receptors (TCRs) with low affinity for cognate antigen. This issue is particularly pronounced for anticancer and autoimmune T-cells as self-reactive T-cell populations are enriched for low-affinity TCRs due to the removal of cells with higher affinity receptors by immune tolerance mechanisms. Here, we stained a wide variety of self-reactive human T-cells using regular pMHC staining and an optimized technique that included: (i) protein kinase inhibitor (PKI), to prevent TCR triggering and internalization, and (ii) anti-fluorochrome antibody, to reduce reagent dissociation during washing steps. Lymphocytes derived from the peripheral blood of type 1 diabetes patients were stained with pMHC multimers made with epitopes from preproinsulin (PPI), insulin-β chain, glutamic acid decarboxylase 65 (GAD65), or glucose-6-phospate catalytic subunit-related protein (IGRP) presented by disease-risk allelles HLA A*02:01 or HLA*24:02. Samples from ankylosing spondylitis patients were stained with a multimerized epitope from vasoactive intestinal polypeptide receptor 1 (VIPR1) presented by HLA B*27:05. Optimized procedures stained an average of 40.5-fold (p = 0.01, range between 1.4 and 198) more cells than could be detected without the inclusion of PKI and cross-linking anti-fluorochrome antibody. Higher order pMHC dextramers recovered more cells than pMHC tetramers in parallel assays, and standard staining protocols with pMHC tetramers routinely recovered less cells than functional assays. HLA A*02:01-restricted PPI-specific and HLA B*27:05-restricted VIPR1-specific T-cell clones generated using the optimized procedure could not be stained by standard pMHC tetramer staining. However, these clones responded well to exogenously supplied peptide and endogenously processed and presented epitopes. We also showed that anti-fluorochrome antibody-conjugated magnetic beads enhanced staining of self-reactive T-cells that could not be stained using standard protocols, thus enabling rapid ex vivo isolation of autoimmune T-cells. We, therefore, conclude that regular pMHC tetramer staining is generally unsuitable for recovering self-reactive T-cells from clinical samples and recommend the use of the optimized protocols described herein.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Hannah L Thomas
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Lorraine Yeo
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Mateusz Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sophie Wheeler
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ernest Choy
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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49
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Pogorelyy MV, Minervina AA, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Method for identification of condition-associated public antigen receptor sequences. eLife 2018. [PMID: 29533178 PMCID: PMC5873893 DOI: 10.7554/elife.33050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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] [Indexed: 12/21/2022] Open
Abstract
Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform repertoire-wide disease association studies of antigen receptor sequences. We developed a statistical framework for associating receptors to disease from only a small cohort of patients, with no need for a control cohort. Our method successfully identifies previously validated Cytomegalovirus and type one diabetes responsive TCRβ sequences .
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Affiliation(s)
- Mikhail V Pogorelyy
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Anastasia A Minervina
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy M Chudakov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Central European Institute of Technology, Brno, Czech republic
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, Sorbonne University, Paris-Diderot University, École Normale Supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Theorique, CNRS, Sorbonne University, École Normale Supérieure, Paris, France
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50
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Komech EA, Pogorelyy MV, Egorov ES, Britanova OV, Rebrikov DV, Bochkova AG, Shmidt EI, Shostak NA, Shugay M, Lukyanov S, Mamedov IZ, Lebedev YB, Chudakov DM, Zvyagin IV. CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Rheumatology (Oxford) 2018; 57:1097-1104. [DOI: 10.1093/rheumatology/kex517] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- Ekaterina A Komech
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail V Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Evgeniy S Egorov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga V Britanova
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Denis V Rebrikov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Gynecology and Perinatology, Kulakov Research Center for Obstetrics, Moscow, Russia
| | - Anna G Bochkova
- V.A. Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Evgeniya I Shmidt
- City Clinical Hospital #1, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadejda A Shostak
- City Clinical Hospital #1, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sergey Lukyanov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z Mamedov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Gynecology and Perinatology, Kulakov Research Center for Obstetrics, Moscow, Russia
| | - Yuriy B Lebedev
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Biological Department, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy M Chudakov
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Ivan V Zvyagin
- Molecular Technologies Department, Translational Medicine Institute, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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