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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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Pavlova AV, Zvyagin IV, Shugay M. Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires. Front Immunol 2024; 15:1321603. [PMID: 38633256 PMCID: PMC11021634 DOI: 10.3389/fimmu.2024.1321603] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
An individual's T-cell repertoire constantly changes under the influence of external and internal factors. Cells that do not receive a stimulatory signal die, while those that encounter and recognize a pathogen or receive a co-stimulatory signal divide, resulting in clonal expansions. T-cell clones can be traced by monitoring the presence of their unique T-cell receptor (TCR) sequence, which is assembled de novo through a process known as V(D)J rearrangement. Tracking T cells can provide valuable insights into the survival of cells after hematopoietic stem cell transplantation (HSCT) or cancer treatment response and can indicate the induction of protective immunity by vaccination. In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals.
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Affiliation(s)
- Anastasia V. Pavlova
- 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
| | - Ivan V. Zvyagin
- 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
- Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - 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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3
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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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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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5
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Quiniou V, Barennes P, Mhanna V, Stys P, Vantomme H, Zhou Z, Martina F, Coatnoan N, Barbie M, Pham HP, Clémenceau B, Vie H, Shugay M, Six A, Brandao B, Mallone R, Mariotti-Ferrandiz E, Klatzmann D. Human thymopoiesis produces polyspecific CD8 + α/β T cells responding to multiple viral antigens. eLife 2023; 12:81274. [PMID: 36995951 PMCID: PMC10063231 DOI: 10.7554/elife.81274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/12/2023] [Indexed: 03/31/2023] Open
Abstract
T-cell receptors (TCRs) are formed by stochastic gene rearrangements, theoretically generating >1019 sequences. They are selected during thymopoiesis, which releases a repertoire of about 108 unique TCRs per individual. How evolution shaped a process that produces TCRs that can effectively handle a countless and evolving set of infectious agents is a central question of immunology. The paradigm is that a diverse enough repertoire of TCRs should always provide a proper, though rare, specificity for any given need. Expansion of such rare T cells would provide enough fighters for an effective immune response and enough antigen-experienced cells for memory. We show here that human thymopoiesis releases a large population of clustered CD8+ T cells harboring α/β paired TCRs that (i) have high generation probabilities and (ii) a preferential usage of some V and J genes, (iii) which CDR3 are shared between individuals, and (iv) can each bind and be activated by multiple unrelated viral peptides, notably from EBV, CMV, and influenza. These polyspecific T cells may represent a first line of defense that is mobilized in response to infections before a more specific response subsequently ensures viral elimination. Our results support an evolutionary selection of polyspecific α/β TCRs for broad antiviral responses and heterologous immunity.
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Affiliation(s)
- Valentin Quiniou
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Pierre Barennes
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Vanessa Mhanna
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Paul Stys
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
| | - Helene Vantomme
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Federica Martina
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Nicolas Coatnoan
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | - Michele Barbie
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
| | | | - Béatrice Clémenceau
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Henri Vie
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mikhail Shugay
- Center of Life Sciences, Skoltech, Moscow, Russian Federation
| | - Adrien Six
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
| | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
| | | | - David Klatzmann
- Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center for Biotherapies (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), Paris, France
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6
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Shcherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes. Front Immunol 2022; 13:1067463. [PMID: 36605212 PMCID: PMC9808399 DOI: 10.3389/fimmu.2022.1067463] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are the most polymorphic loci in the human genome and code for proteins that play a key role in guiding adaptive immune responses by presenting foreign and self peptides (ligands) to T cells. Each person carries up to 6 HLA class I variants (maternal and paternal copies of HLA-A, HLA-B and HLA-C genes) and also multiple HLA class II variants, which cumulatively define the landscape of peptides presented to T cells. Each HLA variant has its own repertoire of presented peptides with a certain sequence motif which is mainly defined by peptide anchor residues (typically the second and the last positions for HLA class I ligands) forming key interactions with the peptide-binding groove of HLA. In this study, we aimed to characterize HLA binding preferences in terms of molecular functions of presented proteins. To focus on the ligand presentation bias introduced specifically by HLA-peptide interaction we performed large-scale in silico predictions of binding of all peptides from human proteome for a wide range of HLA variants and established which functions are characteristic for proteins that are more or less preferentially presented by different HLA variants using statistical calculations and gene ontology (GO) analysis. We demonstrated marked distinctions between HLA variants in molecular functions of preferentially presented proteins (e.g. some HLA variants preferentially present membrane and receptor proteins, while others - ribosomal and DNA-binding proteins) and reduced presentation of extracellular matrix and collagen proteins by the majority of HLA variants. To explain these observations we demonstrated that HLA preferentially presents proteins enriched in amino acids which are required as anchor residues for the particular HLA variant. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Taking into consideration that HLA alleles are inherited in haplotypes, we hypothesized that haplotypes composed of a combination of HLA variants with different presentation preferences should be more advantageous as they allow presenting a larger repertoire of peptides and avoiding holes in immunopeptidome. Indeed, we demonstrated that HLA-A/HLA-B and HLA-A/HLA-C haplotypes which have a high frequency in the human population are comprised of HLA variants that are more distinct in terms of functions of preferentially presented proteins than the control pairs.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Dmitrii Shcherbinin
- 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
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia,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
| | - Ivan V. Zvyagin
- 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
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM) Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mikhail Shugay
- 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,*Correspondence: Mikhail Shugay,
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7
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Komech EA, Koltakova AD, Barinova AA, Minervina AA, Salnikova MA, Shmidt EI, Korotaeva TV, Loginova EY, Erdes SF, Bogdanova EA, Shugay M, Lukyanov S, Lebedev YB, Zvyagin IV. TCR repertoire profiling revealed antigen-driven CD8+ T cell clonal groups shared in synovial fluid of patients with spondyloarthritis. Front Immunol 2022; 13:973243. [PMID: 36325356 PMCID: PMC9618624 DOI: 10.3389/fimmu.2022.973243] [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: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Spondyloarthritis (SpA) comprises a number of inflammatory rheumatic diseases with overlapping clinical manifestations. Strong association with several HLA-I alleles and T cell infiltration into an inflamed joint suggest involvement of T cells in SpA pathogenesis. In this study, we performed high-throughput T cell repertoire profiling of synovial fluid (SF) and peripheral blood (PB) samples collected from a large cohort of SpA patients. We showed that synovial fluid is enriched with expanded T cell clones that are shared between patients with similar HLA genotypes and persist during recurrent synovitis. Using an algorithm for identification of TCRs involved in immune response we discovered several antigen-driven CD8+ clonal groups associated with risk HLA-B*27 or HLA-B*38 alleles. We further show that these clonal groups were enriched in SF and had higher frequency in PB of SpA patients vs healthy donors, implying their relevance to SpA pathogenesis. Several of the groups were shared among patients with different SpAs that suggests a common immunopathological mechanism of the diseases. In summary, our results provide evidence for the role of specific CD8+ T cell clones in pathogenesis of SpA.
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Affiliation(s)
- Ekaterina A. Komech
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia D. Koltakova
- Department of Systemic Sclerosis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Anna A. Barinova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia A. Minervina
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Maria A. Salnikova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Evgeniya I. Shmidt
- Department of Rheumatology, Pirogov City Clinical Hospital #1, Moscow, Russia
| | - Tatiana V. Korotaeva
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Elena Y. Loginova
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Shandor F. Erdes
- Department of Spondyloarthritis, Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Ekaterina A. Bogdanova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mikhail Shugay
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sergey Lukyanov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Yury B. Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V. Zvyagin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Ivan V. Zvyagin,
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8
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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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9
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Liu G, Qin L, Li Y, Zhao S, Shugay M, Yan Y, Ye Y, Chen Y, Huang C, Bayaer N, Adah D, Zhang H, Su Z, Chen X. Subsequent malaria enhances virus-specific T cell immunity in SIV-infected Chinese rhesus macaques. Cell Commun Signal 2022; 20:101. [PMID: 35778766 PMCID: PMC9248186 DOI: 10.1186/s12964-022-00910-7] [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: 03/14/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background Coinfection with HIV and Plasmodium parasites is fairly common, but the sequence of infection with these two pathogens and their impact on disease progression are poorly understood. Methods A Chinese rhesus macaque HIV and Plasmodium coinfection model was established to compare the impact of pre-existing and subsequent malaria on the progression of SIV infection. Results We found that a pre-existing malaria caused animals to produce a greater number of CD4+CCR5+ T cells for SIV replication, resulting in higher viral loads. Conversely, subsequent malaria induced a substantially larger proportion of CD4+CD28highCD95high central memory T cells and a stronger SIV-specific T cell response, maintained the repertoire diversity of SIV-specific T cell receptors, and generated new SIV-specific T cell clonotypes to trace SIV antigenic variation, resulting in improved survival of SIV-infected animals. Conclusion The complex outcomes of this study may have important implications for research on human HIV and malaria coinfection. The infection order of the two pathogens (HIV and malaria parasites) should be emphasized. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00910-7.
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Affiliation(s)
- Guangjie Liu
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Graduate School, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,The Fist Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Li Qin
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,CAS Lamvac Biotech Co., Ltd, Guangzhou, China
| | - Youjia Li
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,The Fist Affiliated Hospital of Shenzhen University, Shenzhen, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China.,Shenzhen Institute of Geriatrics, Shenzhen, China
| | - Siting Zhao
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,CAS Lamvac Biotech Co., Ltd, Guangzhou, China
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Laboratory, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Yongxiang Yan
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yijian Ye
- Laboratory of Immunobiology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Chen
- Laboratory of Immunobiology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Cuizhu Huang
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Nashun Bayaer
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Dickson Adah
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Zhong Su
- Laboratory of Immunobiology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoping Chen
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. .,CAS Lamvac Biotech Co., Ltd, Guangzhou, China.
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10
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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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11
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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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12
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Karnaukhov V, Paes W, Woodhouse IB, Partridge T, Nicastri A, Brackenridge S, Scherbinin D, Chudakov DM, Zvyagin IV, Ternette N, Koohy H, Borrow P, Shugay M. HLA binding of self-peptides is biased towards proteins with specific molecular functions. bioRxiv 2021:2021.02.16.431395. [PMID: 33619495 PMCID: PMC7899460 DOI: 10.1101/2021.02.16.431395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.
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Affiliation(s)
- Vadim Karnaukhov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Isaac B. Woodhouse
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dmitrii Scherbinin
- 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
| | - Dmitry M. Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- 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
| | - Ivan V. Zvyagin
- 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
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hashem Koohy
- Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mikhail Shugay
- 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
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13
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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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14
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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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15
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Philip H, Snir T, Gordin M, Shugay M, Zilberberg A, Efroni S. A T cell repertoire timestamp is at the core of responsiveness to CTLA-4 blockade. iScience 2021; 24:102100. [PMID: 33604527 PMCID: PMC7876555 DOI: 10.1016/j.isci.2021.102100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/10/2020] [Revised: 11/02/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Biology of the response to anti-CTLA-4 involves the dynamics of specific T cell clones. Reasons for clinical success and failure of this treatment are still largely unknown. Here, we quantified the dynamics of the T cell receptor (TCR) repertoire, throughout 4 weeks involving treatment with anti-CTLA-4, in a syngeneic mouse model for colorectal cancer. These dynamics show an initial increase in clonality in tandem with a decrease in diversity, effects which gradually subside. Furthermore, response to treatment is tightly connected to the shared and public parts of the T cell repertoire. We were able to recognize time-dependent behaviors of specific TCR sequences and cell types and to show the response is dominated by specific motifs. We see that a single, specific time point might be useful to inform a physician of the true response to treatmentThe research further highlights the importance of temporal analyses of the immune response. Response to ICI is associated with pre-treatment TCR repertoire in mice TCR repertoire goes through distinct, ICI-dependent changes with time Tumor size and its response to ICI can be tracked by TCR repertoire metrics A single time point is found to be a focal point of the immune response
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Affiliation(s)
- Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tom Snir
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Miri Gordin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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16
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Anoshkin K, Vasilyev I, Karandasheva K, Shugay M, Kudryavtseva V, Egorov A, Gurevich L, Mironova A, Serikov A, Kutsev S, Strelnikov V. New Regions With Molecular Alterations in a Rare Case of Insulinomatosis: Case Report With Literature Review. Front Endocrinol (Lausanne) 2021; 12:760154. [PMID: 34737724 PMCID: PMC8563021 DOI: 10.3389/fendo.2021.760154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Insulinomatosis is characterized by monohormonality of multiple macro-tumors and micro-tumors that arise synchronously and metachronously in all regions of the pancreas, and often recurring hypoglycemia. One of the main characteristics of insulinomatosis is the presence of insulin-expressing monohormonal endocrine cell clusters that are exclusively composed of proliferating insulin-positive cells, are less than 1 mm in size, and show solid islet-like structure. It is presumed that insulinomatosis affects the entire population of β-cells. With regards to molecular genetics, this phenomenon is not related to mutation in MEN1 gene and is more similar to sporadic benign insulinomas, however, at the moment molecular genetics of this disease remains poorly investigated. NGS sequencing was performed with a panel of 409 cancer-related genes. Results of sequencing were analyzed by bioinformatic algorithms for detecting point mutations and copy number variations. DNA copy number variations were detected that harbor a large number of genes in insulinoma and fewer genes in micro-tumors. qPCR was used to confirm copy number variations at ATRX, FOXL2, IRS2 and CEBPA genes. Copy number alterations involving FOXL2, IRS2, CEBPA and ATRX genes were observed in insulinoma as well as in micro-tumors samples, suggesting that alterations of these genes may promote malignization in the β-cells population.
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Affiliation(s)
- Kirill Anoshkin
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ivan Vasilyev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Valeriya Kudryavtseva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Egorov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Larisa Gurevich
- Morphological Department of Oncology, M.F. Vladimirsky Moscow Regional Research and Clinical Institute, Moscow, Russia
| | - Anna Mironova
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey Serikov
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Sergei Kutsev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Vladimir Strelnikov
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
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17
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Shomuradova AS, Vagida MS, Sheetikov SA, Zornikova KV, Kiryukhin D, Titov A, Peshkova IO, Khmelevskaya A, Dianov DV, Malasheva M, Shmelev A, Serdyuk Y, Bagaev DV, Pivnyuk A, Shcherbinin DS, Maleeva AV, Shakirova NT, Pilunov A, Malko DB, Khamaganova EG, Biderman B, Ivanov A, Shugay M, Efimov GA. SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors. Immunity 2020; 53:1245-1257.e5. [PMID: 33326767 PMCID: PMC7664363 DOI: 10.1016/j.immuni.2020.11.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/02/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion or activation of preexisting immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike protein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity.
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Affiliation(s)
- Alina S Shomuradova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Savely A Sheetikov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ksenia V Zornikova
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Aleksei Titov
- National Research Center for Hematology, Moscow, Russia
| | | | - Alexandra Khmelevskaya
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Dianov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Malasheva
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anton Shmelev
- National Research Center for Hematology, Moscow, Russia
| | - Yana Serdyuk
- National Research Center for Hematology, Moscow, Russia
| | - Dmitry V Bagaev
- Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anastasia Pivnyuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitrii S Shcherbinin
- Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Artem Pilunov
- National Research Center for Hematology, Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Alexander Ivanov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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18
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Blagov S, Zvyagin IV, Shelikhova L, Khismatullina R, Balashov D, Komech E, Fomchenkova V, Shugay M, Starichkova J, Kurnikova E, Pershin D, Fadeeva M, Glushkova S, Muzalevskii Y, Kazachenok A, Efimenko M, Osipova E, Novichkova G, Chudakov D, Maschan A, Maschan M. T-cell tracking, safety, and effect of low-dose donor memory T-cell infusions after αβ T cell-depleted hematopoietic stem cell transplantation. Bone Marrow Transplant 2020; 56:900-908. [PMID: 33203952 DOI: 10.1038/s41409-020-01128-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022]
Abstract
The delayed recovery of adaptive immunity underlies transplant-related mortality (TRM) after αβ T cell-depleted hematopoietic stem cell transplantation (HSCT). We tested the use of low-dose memory donor lymphocyte infusions (mDLIs) after engraftment of αβ T cell-depleted grafts.A cohort of 131 pediatric patients (median age 9 years) were grafted with αβ T cell-depleted products from either haplo (n = 79) or unrelated donors (n = 52). After engraftment, patients received mDLIs prepared by CD45RA depletion. Cell dose was escalated monthly from 25 × 103 to 100 × 103/kg (haplo) and from 100 × 103 to 300 × 103 /kg (MUD). In a subcohort of 16 patients, T-cell receptor (TCR) repertoire profiling with deep sequencing was used to track T-cell clones and to evaluate the contribution of mDLI to the immune repertoire.In total, 343 mDLIs were administered. The cumulative incidence (CI) of grades II and III de novo acute graft-versus-host disease (aGVHD) was 5% and 2%, respectively, and the CI of chronic graft-versus-host disease was 7%. Half of the patients with undetectable CMV-specific T cells before mDLI recovered CMV-specific T cells. TCR repertoire profiling confirmed that mDLI-derived T cells significantly contribute to the TCR repertoire up to 1 year after HSCT and include persistent, CMV-specific T-cell clones.
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Affiliation(s)
- Sergey Blagov
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ivan V Zvyagin
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Larisa Shelikhova
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Rimma Khismatullina
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitriy Balashov
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Komech
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Viktoria Fomchenkova
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Julia Starichkova
- Department of Statistics, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Elena Kurnikova
- Transfusion Medicine Service, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitriy Pershin
- Transplantation Immunology and Immunotherapy Laboratory, Dmitriy Rogachev National Center of pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Maria Fadeeva
- Transplantation Immunology and Immunotherapy Laboratory, Dmitriy Rogachev National Center of pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Svetlana Glushkova
- Transplantation Immunology and Immunotherapy Laboratory, Dmitriy Rogachev National Center of pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Yakov Muzalevskii
- Transfusion Medicine Service, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexei Kazachenok
- Transfusion Medicine Service, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Maria Efimenko
- Stem Cell Physiology Laboratory, Dmitriy Rogachev National center of pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Elena Osipova
- Stem Cell Physiology Laboratory, Dmitriy Rogachev National center of pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitriy Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 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
| | - Alexei Maschan
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Michael Maschan
- Department of Hematopoietic Stem Cell Transplantation, Dmitriy Rogachev National Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
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19
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Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D'Angelo I, Olson B, Reddy S, Greiff V, Trück J, Marquez S, Lees W, Miho E. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics 2020; 36:1731-1739. [PMID: 31873728 PMCID: PMC7075533 DOI: 10.1093/bioinformatics/btz845] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 06/21/2019] [Revised: 10/21/2019] [Accepted: 12/19/2019] [Indexed: 01/01/2023] Open
Abstract
Summary Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets. We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. Availability and implementation All tools utilized in the paper are free for academic use. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erand Smakaj
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund 223, Sweden
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deniz Tosoni
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Christopher Galli
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Vendi Grobelsek
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Igor D'Angelo
- One Amgen Center Drive, Amgen, Inc., Therapeutic Discovery/Molecular Engineering, Thousand Oaks, CA 91320, USA
| | - Branden Olson
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Sai Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo 0372, Norway
| | - Johannes Trück
- Paediatric Immunology, Children's Research Center, University Children's Hospital, University of Zurich, Zurich 8032, Switzerland
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA
| | - William Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland.,aiNET GmbH, Switzerland Innovation Park Basel Area AG, Basel 4057, Switzerland
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20
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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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21
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Zvyagin IV, Tsvetkov VO, Chudakov DM, Shugay M. An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity. Immunogenetics 2019; 72:77-84. [PMID: 31741011 DOI: 10.1007/s00251-019-01139-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/16/2019] [Indexed: 11/26/2022]
Abstract
Recent advances in molecular and bioinformatic methods have greatly improved our ability to study the formation of an adaptive immune response towards foreign pathogens, self-antigens, and cancer neoantigens. T cell receptors (TCR) are the key players in this process that recognize peptides presented by major histocompatibility complex (MHC). Owing to the huge diversity of both TCR sequence variants and peptides they recognize, accumulation and complex analysis of large amounts of TCR-antigen specificity data is required for understanding the structure and features of adaptive immune responses towards pathogens, vaccines, cancer, as well as autoimmune responses. In the present review, we summarize recent efforts on gathering and interpreting TCR-antigen specificity data and outline the critical role of tighter integration with other immunoinformatics data sources that include epitope MHC restriction, TCR repertoire structure models, and TCR/peptide/MHC structural data. We suggest that such integration can lead to the ability to accurately annotate individual TCR repertoires, efficiently estimate epitope and neoantigen immunogenicity, and ultimately, in silico identify TCRs specific to yet unstudied antigens and predict self-peptides related to autoimmunity.
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Affiliation(s)
- Ivan V Zvyagin
- Pirogov Russian Medical State University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Vasily O Tsvetkov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry 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
| | - 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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22
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Olson BJ, Moghimi P, Schramm CA, Obraztsova A, Ralph D, Vander Heiden JA, Shugay M, Shepherd AJ, Lees W, Matsen FA. sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation. Front Immunol 2019; 10:2533. [PMID: 31736960 PMCID: PMC6838214 DOI: 10.3389/fimmu.2019.02533] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introduce sumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show how sumrep can be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.
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Affiliation(s)
- Branden J Olson
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Statistics, University of Washington, Seattle, WA, United States
| | - Pejvak Moghimi
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Anna Obraztsova
- 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
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jason A Vander Heiden
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, United States
| | - 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
| | - Adrian J Shepherd
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - William Lees
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
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23
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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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24
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Pogorelyy MV, Shugay M. A Framework for Annotation of Antigen Specificities in High-Throughput T-Cell Repertoire Sequencing Studies. Front Immunol 2019; 10:2159. [PMID: 31616409 PMCID: PMC6775185 DOI: 10.3389/fimmu.2019.02159] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 06/23/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
Recently developed molecular methods allow large-scale profiling of T-cell receptor (TCR) sequences that encode for antigen specificity and immunological memory of these cells. However, it is well-known that the even unperturbed TCR repertoire structure is extremely complex due to the high diversity of TCR rearrangements and multiple biases imprinted by VDJ rearrangement process. The latter gives rise to the phenomenon of "public" TCR clonotypes that can be shared across multiple individuals and non-trivial structure of the TCR similarity network. Here, we outline a framework for TCR sequencing data analysis that can control for these biases in order to infer TCRs that are involved in response to antigens of interest. We apply two previously published methods, ALICE and TCRNET, to detect groups of homologous TCRs that are enriched in samples of interest. Using an example dataset of donors with known HLA haplotype and CMV status, we demonstrate that by applying HLA restriction rules and matching against a database of TCRs with known antigen specificity, it is possible to robustly detect motifs of epitope-specific responses in individual repertoires. We also highlight potential shortcomings of TCR clustering methods and demonstrate that highly expanded TCRs should be individually assessed to get the full picture of antigen-specific response.
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Affiliation(s)
- Mikhail V Pogorelyy
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian Medical State University, Moscow, Russia
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Department, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian Medical State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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25
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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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26
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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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27
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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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28
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Pogorelyy MV, Fedorova AD, McLaren JE, Ladell K, Bagaev DV, Eliseev AV, Mikelov AI, Koneva AE, Zvyagin IV, Price DA, Chudakov DM, Shugay M. Exploring the pre-immune landscape of antigen-specific T cells. Genome Med 2018; 10:68. [PMID: 30144804 PMCID: PMC6109350 DOI: 10.1186/s13073-018-0577-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 05/30/2018] [Accepted: 08/06/2018] [Indexed: 12/26/2022] Open
Abstract
Background Adaptive immune responses to newly encountered pathogens depend on the mobilization of antigen-specific clonotypes from a vastly diverse pool of naive T cells. Using recent advances in immune repertoire sequencing technologies, models of the immune receptor rearrangement process, and a database of annotated T cell receptor (TCR) sequences with known specificities, we explored the baseline frequencies of T cells specific for defined human leukocyte antigen (HLA) class I-restricted epitopes in healthy individuals. Methods We used a database of TCR sequences with known antigen specificities and a probabilistic TCR rearrangement model to estimate the baseline frequencies of TCRs specific to distinct antigens epitopespecificT-cells. We verified our estimates using a publicly available collection of TCR repertoires from healthy individuals. We also interrogated a database of immunogenic and non-immunogenic peptides is used to link baseline T-cell frequencies with epitope immunogenicity. Results Our findings revealed a high degree of variability in the prevalence of T cells specific for different antigens that could be explained by the physicochemical properties of the corresponding HLA class I-bound peptides. The occurrence of certain rearrangements was influenced by ancestry and HLA class I restriction, and umbilical cord blood samples contained higher frequencies of common pathogen-specific TCRs. We also identified a quantitative link between specific T cell frequencies and the immunogenicity of cognate epitopes presented by defined HLA class I molecules. Conclusions Our results suggest that the population frequencies of specific T cells are strikingly non-uniform across epitopes that are known to elicit immune responses. This inference leads to a new definition of epitope immunogenicity based on specific TCR frequencies, which can be estimated with a high degree of accuracy in silico, thereby providing a novel framework to integrate computational and experimental genomics with basic and translational research efforts in the field of T cell immunology. Electronic supplementary material The online version of this article (10.1186/s13073-018-0577-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alla D Fedorova
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - James E McLaren
- 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
| | - Dmitri V Bagaev
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - Alexey V Eliseev
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Artem I Mikelov
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia
| | - Anna E Koneva
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia
| | - Ivan V Zvyagin
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, 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
| | - Dmitry M Chudakov
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia.,Central European Institute of Technology, CEITEC, Brno, Czech Republic
| | - Mikhail Shugay
- Department of Genomics of Adaptive Immunity, IBCH RAS, Moscow, Russia. .,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia. .,Center for Data-Intensive Biomedicine and Biotechnology, Skoltech, Moscow, Russia.
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29
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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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30
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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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31
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Izraelson M, Nakonechnaya TO, Moltedo B, Egorov ES, Kasatskaya SA, Putintseva EV, Mamedov IZ, Staroverov DB, Shemiakina II, Zakharova MY, Davydov AN, Bolotin DA, Shugay M, Chudakov DM, Rudensky AY, Britanova OV. Comparative analysis of murine T-cell receptor repertoires. Immunology 2017; 153:133-144. [PMID: 29080364 DOI: 10.1111/imm.12857] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
For understanding the rules and laws of adaptive immunity, high-throughput profiling of T-cell receptor (TCR) repertoires becomes a powerful tool. The structure of TCR repertoires is instructive even before the antigen specificity of each particular receptor becomes available. It embodies information about the thymic and peripheral selection of T cells; the readiness of an adaptive immunity to withstand new challenges; the character, magnitude and memory of immune responses; and the aetiological and functional proximity of T-cell subsets. Here, we describe our current analytical approaches for the comparative analysis of murine TCR repertoires, and show several examples of how these approaches can be applied for particular experimental settings. We analyse the efficiency of different metrics used for estimation of repertoire diversity, repertoire overlap, V-gene and J-gene segments usage similarity, and amino acid composition of CDR3. We discuss basic differences of these metrics and their advantages and limitations in different experimental models, and we provide guidelines for choosing an efficient way to lead a comparative analysis of TCR repertoires. Applied to the various known and newly developed mouse models, such analysis should allow us to disentangle multiple sophisticated puzzles in adaptive immunity.
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Affiliation(s)
- Mark Izraelson
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evgeniy S Egorov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Ilgar Z Mamedov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy B Staroverov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina I Shemiakina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria Y Zakharova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Dmitriy A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Mikhail Shugay
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Dmitriy M Chudakov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olga V Britanova
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
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32
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Bolotin DA, Poslavsky S, Davydov AN, Frenkel FE, Fanchi L, Zolotareva OI, Hemmers S, Putintseva EV, Obraztsova AS, Shugay M, Ataullakhanov RI, Rudensky AY, Schumacher TN, Chudakov DM. Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol 2017; 35:908-911. [PMID: 29020005 PMCID: PMC6169298 DOI: 10.1038/nbt.3979] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dmitriy A Bolotin
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Stanislav Poslavsky
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Lorenzo Fanchi
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Saskia Hemmers
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Ekaterina V Putintseva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Anna S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Shugay
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ravshan I Ataullakhanov
- BostonGene LLC, Lincoln, Massachusetts, USA
- Institute of Immunology FMBA, Moscow, Russia
- Faculties for Physics and Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
- Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
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33
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Shagin DA, Turchaninova MA, Shagina IA, Shugay M, Zaretsky AR, Zueva OI, Bolotin DA, Lukyanov S, Chudakov DM. Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. BMC Genomics 2017; 18:440. [PMID: 28583065 PMCID: PMC5460480 DOI: 10.1186/s12864-017-3815-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 08/01/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
Background Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleotide overlapping with the 3′-end of unwanted amplification primer (NOPE oligo) simultaneously provides a template for its elongation. This elongation disrupts specificity of unwanted primer, preventing its further participation in PCR. The suggested approach allows to rationally manage the course of PCR reactions in order to facilitate analysis of complex DNA mixtures as well as to perform multistage PCR bypassing intermediate purification steps. Results Here we apply NOPE method to DNA library preparation for the high-throughput sequencing (HTS) with the PCR-based introduction of unique molecular identifiers (UMI). We show that NOPE oligo efficiently neutralizes UMI-containing oligonucleotides after introduction of UMI into sample DNA molecules, thus allowing to proceed with further amplification steps without purification and associated loss of starting material. At the same time, NOPE oligo does not affect the efficiency of target PCR amplification. Conclusion We describe a simple, robust and cheap modification of UMI-labeled HTS libraries preparation procedure, that allows to bypass purification step and thus to preserve starting material which may be limited, e.g. circulating tumor DNA, circulating fetal DNA, or small amounts of isolated cells of interest. Furthermore, demonstrated simplicity and robustness of NOPE method should make it popular in various PCR protocols.
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Affiliation(s)
- Dmitriy A Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Maria A Turchaninova
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Olga I Zueva
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy A Bolotin
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia. .,Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic. .,Skolkovo Institute of Science and Technology, Moscow, Russia.
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34
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Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M. A high-throughput assay for quantitative measurement of PCR errors. Sci Rep 2017; 7:2718. [PMID: 28578414 PMCID: PMC5457411 DOI: 10.1038/s41598-017-02727-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 01/01/2023] Open
Abstract
The accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.
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Affiliation(s)
- Dmitriy A Shagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ilya V Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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35
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Eliseev AV, Fedorova AD, Lebedin MY, Chudakov DM, Shugay M. Estimating the number of HIV-specific T-cells in healthy donors using high-throughput sequencing profiles of T-cell receptor repertoires. Bulletin of RSMU 2017. [DOI: 10.24075/brsmu.2017-05-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Zvyagin IV, Mamedov IZ, Tatarinova OV, Komech EA, Kurnikova EE, Boyakova EV, Brilliantova V, Shelikhova LN, Balashov DN, Shugay M, Sycheva AL, Kasatskaya SA, Lebedev YB, Maschan AA, Maschan MA, Chudakov DM. Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children. Leukemia 2016; 31:1145-1153. [DOI: 10.1038/leu.2016.321] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/14/2016] [Accepted: 10/13/2016] [Indexed: 12/15/2022]
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37
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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38
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Bagaev DV, Zvyagin IV, Putintseva EV, Izraelson M, Britanova OV, Chudakov DM, Shugay M. VDJviz: a versatile browser for immunogenomics data. BMC Genomics 2016; 17:453. [PMID: 27297497 PMCID: PMC4907000 DOI: 10.1186/s12864-016-2799-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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] [Received: 12/01/2015] [Accepted: 05/25/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles. RESULTS Here we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination. CONCLUSIONS VDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz .
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Affiliation(s)
- Dmitriy V. Bagaev
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan V. Zvyagin
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Ekaterina V. Putintseva
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Mark Izraelson
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Olga V. Britanova
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Dmitriy M. Chudakov
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Mikhail Shugay
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
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39
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Joachims ML, Leehan KM, Lawrence C, Pelikan RC, Moore JS, Pan Z, Rasmussen A, Radfar L, Lewis DM, Grundahl KM, Kelly JA, Wiley GB, Shugay M, Chudakov DM, Lessard CJ, Stone DU, Scofield RH, Montgomery CG, Sivils KL, Thompson LF, Farris AD. Single-cell analysis of glandular T cell receptors in Sjögren's syndrome. JCI Insight 2016; 1. [PMID: 27358913 DOI: 10.1172/jci.insight.85609] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
CD4+ T cells predominate in salivary gland (SG) inflammatory lesions in Sjögren's syndrome (SS). However, their antigen specificity, degree of clonal expansion, and relationship to clinical disease features remain unknown. We used multiplex reverse-transcriptase PCR to amplify paired T cell receptor α (TCRα) and β transcripts of single CD4+CD45RA- T cells from SG and peripheral blood (PB) of 10 individuals with primary SS, 9 of whom shared the HLA DR3/DQ2 risk haplotype. TCRα and β sequences were obtained from a median of 91 SG and 107 PB cells per subject. The degree of clonal expansion and frequency of cells expressing two productively rearranged α genes were increased in SG versus PB. Expanded clones from SG exhibited complementary-determining region 3 (CDR3) sequence similarity both within and among subjects, suggesting antigenic selection and shared antigen recognition. CDR3 similarities were shared among expanded clones from individuals discordant for canonical Ro and La autoantibodies, suggesting recognition of alternative SG antigen(s). The extent of SG clonal expansion correlated with reduced saliva production and increased SG fibrosis, linking expanded SG T cells with glandular dysfunction. Knowledge of paired TCRα and β sequences enables further work toward identification of target antigens and development of novel therapies.
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Affiliation(s)
- Michelle L Joachims
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Kerry M Leehan
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Christina Lawrence
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Richard C Pelikan
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Jacen S Moore
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Zijian Pan
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Lida Radfar
- Department of Oral Diagnosis and Radiology, College of Dentistry, OUHSC, Oklahoma City, Oklahoma, USA
| | - David M Lewis
- Department of Oral and Maxillofacial Pathology, College of Dentistry, OUHSC, Oklahoma City, Oklahoma, USA
| | - Kiely M Grundahl
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Graham B Wiley
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Christopher J Lessard
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Donald U Stone
- Department of Ophthalmology, College of Medicine, OUHSC, Oklahoma City, Oklahoma, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA; Section of Endocrinology and Diabetes, College of Medicine, OUHSC, Oklahoma City, Oklahoma, USA
| | - Courtney G Montgomery
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Linda F Thompson
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA
| | - A Darise Farris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation (OMRF), Oklahoma City, Oklahoma, USA; Department of Pathology, University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
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40
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Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J Immunol 2016; 196:5005-13. [PMID: 27183615 DOI: 10.4049/jimmunol.1600005] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/16/2016] [Indexed: 01/29/2023]
Abstract
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.
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Affiliation(s)
- Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Denis V Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; Vavilov Institute of General Genetics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
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41
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Affiliation(s)
- Mikhail Shugay
- Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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42
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Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, Hoyos BE, Moltedo B, Hemmers S, Treuting P, Leslie CS, Chudakov DM, Rudensky AY. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature 2015; 528:132-136. [PMID: 26605529 PMCID: PMC4862833 DOI: 10.1038/nature16141] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [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: 06/01/2015] [Accepted: 10/12/2015] [Indexed: 12/26/2022]
Abstract
T-cell receptor (TCR) signalling has a key role in determining T-cell fate. Precursor cells expressing TCRs within a certain low-affinity range for complexes of self-peptide and major histocompatibility complex (MHC) undergo positive selection and differentiate into naive T cells expressing a highly diverse self-MHC-restricted TCR repertoire. In contrast, precursors displaying TCRs with a high affinity for 'self' are either eliminated through TCR-agonist-induced apoptosis (negative selection) or restrained by regulatory T (Treg) cells, whose differentiation and function are controlled by the X-chromosome-encoded transcription factor Foxp3 (reviewed in ref. 2). Foxp3 is expressed in a fraction of self-reactive T cells that escape negative selection in response to agonist-driven TCR signals combined with interleukin 2 (IL-2) receptor signalling. In addition to Treg cells, TCR-agonist-driven selection results in the generation of several other specialized T-cell lineages such as natural killer T cells and innate mucosal-associated invariant T cells. Although the latter exhibit a restricted TCR repertoire, Treg cells display a highly diverse collection of TCRs. Here we explore in mice whether a specialized mechanism enables agonist-driven selection of Treg cells with a diverse TCR repertoire, and the importance this holds for self-tolerance. We show that the intronic Foxp3 enhancer conserved noncoding sequence 3 (CNS3) acts as an epigenetic switch that confers a poised state to the Foxp3 promoter in precursor cells to make Treg cell lineage commitment responsive to a broad range of TCR stimuli, particularly to suboptimal ones. CNS3-dependent expansion of the TCR repertoire enables Treg cells to control self-reactive T cells effectively, especially when thymic negative selection is genetically impaired. Our findings highlight the complementary roles of these two main mechanisms of self-tolerance.
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MESH Headings
- Animals
- Cell Differentiation
- Cell Lineage
- Conserved Sequence/genetics
- Enhancer Elements, Genetic/genetics
- Epigenesis, Genetic
- Female
- Forkhead Transcription Factors/genetics
- Introns/genetics
- Male
- Mice
- Promoter Regions, Genetic/genetics
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Interleukin-2/immunology
- Receptors, Interleukin-2/metabolism
- Self Tolerance/immunology
- Signal Transduction
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Transcription Factors/deficiency
- AIRE Protein
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Affiliation(s)
- Yongqiang Feng
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Miklukho-Maklaya 16/10, Moscow, Russia
- Pirogov Russian National Research Medical University, 117997, Ostrovityanova 1, Moscow, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Miklukho-Maklaya 16/10, Moscow, Russia
| | - Hatice U Osmanbeyoglu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stanislav Dikiy
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Beatrice E Hoyos
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Saskia Hemmers
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Piper Treuting
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Miklukho-Maklaya 16/10, Moscow, Russia
- Pirogov Russian National Research Medical University, 117997, Ostrovityanova 1, Moscow, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan-Kettering Cancer Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput Biol 2015; 11:e1004503. [PMID: 26606115 PMCID: PMC4659587 DOI: 10.1371/journal.pcbi.1004503] [Citation(s) in RCA: 377] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/13/2015] [Indexed: 12/11/2022] Open
Abstract
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.
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Affiliation(s)
- Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy V. Bagaev
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
| | - Maria A. Turchaninova
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy A. Bolotin
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga V. Britanova
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ekaterina V. Putintseva
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Vadim I. Nazarov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | | | | | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail:
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44
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Ye L, Goodall JC, Zhang L, Putintseva EV, Lam B, Jiang L, Liu W, Yin J, Lin L, Li T, Wu X, Yeo G, Shugay M, Chudakov DM, Gaston H, Xu H. TCR usage, gene expression and function of two distinct FOXP3
+
Treg subsets within CD4
+
CD25
hi
T cells identified by expression of CD39 and CD45RO. Immunol Cell Biol 2015; 94:293-305. [PMID: 26467610 DOI: 10.1038/icb.2015.90] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/29/2015] [Accepted: 09/29/2015] [Indexed: 02/08/2023]
Affiliation(s)
- Lingying Ye
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Jane C Goodall
- Department of Medicine, School of Clinical Medicine, Addenbrookes Hospital, University of Cambridge Cambridge UK
| | - Libin Zhang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Ekaterina V Putintseva
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Moscow Russian Federation
| | - Brian Lam
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrookes Hospital Cambridge UK
| | - Lei Jiang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Wei Liu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Jian Yin
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
| | - Giles Yeo
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science, Addenbrookes Hospital Cambridge UK
| | - Mikhail Shugay
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Moscow Russian Federation
- Pirogov Russian National Research Medical University Moscow Russia
| | - Dmitriy M Chudakov
- Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Moscow Russian Federation
- Pirogov Russian National Research Medical University Moscow Russia
| | - Hill Gaston
- Department of Medicine, School of Clinical Medicine, Addenbrookes Hospital, University of Cambridge Cambridge UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Second Military Medical University Shanghai China
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Sinadinos A, Young CNJ, Al-Khalidi R, Teti A, Kalinski P, Mohamad S, Floriot L, Henry T, Tozzi G, Jiang T, Wurtz O, Lefebvre A, Shugay M, Tong J, Vaudry D, Arkle S, doRego JC, Górecki DC. P2RX7 purinoceptor: a therapeutic target for ameliorating the symptoms of duchenne muscular dystrophy. PLoS Med 2015; 12:e1001888. [PMID: 26461208 PMCID: PMC4604078 DOI: 10.1371/journal.pmed.1001888] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is the most common inherited muscle disease, leading to severe disability and death in young men. Death is caused by the progressive degeneration of striated muscles aggravated by sterile inflammation. The pleiotropic effects of the mutant gene also include cognitive and behavioral impairments and low bone density. Current interventions in DMD are palliative only as no treatment improves the long-term outcome. Therefore, approaches with a translational potential should be investigated, and key abnormalities downstream from the absence of the DMD product, dystrophin, appear to be strong therapeutic targets. We and others have demonstrated that DMD mutations alter ATP signaling and have identified P2RX7 purinoceptor up-regulation as being responsible for the death of muscles in the mdx mouse model of DMD and human DMD lymphoblasts. Moreover, the ATP-P2RX7 axis, being a crucial activator of innate immune responses, can contribute to DMD pathology by stimulating chronic inflammation. We investigated whether ablation of P2RX7 attenuates the DMD model mouse phenotype to assess receptor suitability as a therapeutic target. METHODS AND FINDINGS Using a combination of molecular, histological, and biochemical methods and behavioral analyses in vivo we demonstrate, to our knowledge for the first time, that genetic ablation of P2RX7 in the DMD model mouse produces a widespread functional attenuation of both muscle and non-muscle symptoms. In dystrophic muscles at 4 wk there was an evident recovery in key functional and molecular parameters such as improved muscle structure (minimum Feret diameter, p < 0.001), increased muscle strength in vitro (p < 0.001) and in vivo (p = 0.012), and pro-fibrotic molecular signatures. Serum creatine kinase (CK) levels were lower (p = 0.025), and reduced cognitive impairment (p = 0.006) and bone structure alterations (p < 0.001) were also apparent. Reduction of inflammation and fibrosis persisted at 20 mo in leg (p = 0.038), diaphragm (p = 0.042), and heart muscles (p < 0.001). We show that the amelioration of symptoms was proportional to the extent of receptor depletion and that improvements were observed following administration of two P2RX7 antagonists (CK, p = 0.030 and p = 0.050) without any detectable side effects. However, approaches successful in animal models still need to be proved effective in clinical practice. CONCLUSIONS These results are, to our knowledge, the first to establish that a single treatment can improve muscle function both short and long term and also correct cognitive impairment and bone loss in DMD model mice. The wide-ranging improvements reflect the convergence of P2RX7 ablation on multiple disease mechanisms affecting skeletal and cardiac muscles, inflammatory cells, brain, and bone. Given the impact of P2RX7 blockade in the DMD mouse model, this receptor is an attractive target for translational research: existing drugs with established safety records could potentially be repurposed for treatment of this lethal disease.
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Affiliation(s)
- Anthony Sinadinos
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Christopher N. J. Young
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Rasha Al-Khalidi
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Anna Teti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Paweł Kalinski
- Departments of Surgery, Immunology, and Bioengineering, School of Medicine, University of Pittsburgh, Pittsburg, Pennsylvania, United States of America
| | - Shafini Mohamad
- School of Engineering, University of Portsmouth, Portsmouth, United Kingdom
| | - Léonore Floriot
- Platform of Behavioural Analysis (SCAC), University of Rouen, Mont-Saint-Aignan,Rouen, France
| | - Tiphaine Henry
- Platform of Behavioural Analysis (SCAC), University of Rouen, Mont-Saint-Aignan,Rouen, France
| | - Gianluca Tozzi
- School of Engineering, University of Portsmouth, Portsmouth, United Kingdom
| | - Taiwen Jiang
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Olivier Wurtz
- INSERM U982, Plate-Forme d’Imagerie PRIMACEN, IRIB, University of Rouen, Mont-Saint-Aignan, France
| | - Alexis Lefebvre
- Platform of Behavioural Analysis (SCAC), University of Rouen, Mont-Saint-Aignan,Rouen, France
| | - Mikhail Shugay
- Genomics of Adaptive Immunity Lab, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry and Pirogov Russian National Research Medical University, Moscow, Russia
| | - Jie Tong
- School of Engineering, University of Portsmouth, Portsmouth, United Kingdom
| | - David Vaudry
- INSERM U982, Plate-Forme d’Imagerie PRIMACEN, IRIB, University of Rouen, Mont-Saint-Aignan, France
| | - Stephen Arkle
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Jean-Claude doRego
- Platform of Behavioural Analysis (SCAC), University of Rouen, Mont-Saint-Aignan,Rouen, France
- National Center of Scientific Research (CNRS), Caen, France
| | - Dariusz C. Górecki
- Molecular Medicine, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
- * E-mail:
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Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ. tcR: an R package for T cell receptor repertoire advanced data analysis. BMC Bioinformatics 2015; 16:175. [PMID: 26017500 PMCID: PMC4445501 DOI: 10.1186/s12859-015-0613-1] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [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: 03/20/2015] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. Results Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies. Conclusions tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples.
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Affiliation(s)
- Vadim I Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia.
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ekaterina A Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ivan V Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Dmitry A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Yury B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
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47
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Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, Bolotin DA, Davydov AN, Barsova E, Lebedev YB, Shugay M, Chudakov DM. Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers. J I 2015; 194:6155-63. [DOI: 10.4049/jimmunol.1500215] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
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48
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Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, Lebedev YB, Chudakov DM. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J Immunol 2014; 192:2689-98. [PMID: 24510963 DOI: 10.4049/jimmunol.1302064] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decrease of TCR diversity with aging has never been studied by direct methods. In this study, we combined high-throughput Illumina sequencing with unique cDNA molecular identifier technology to achieve deep and precisely normalized profiling of TCR β repertoires in 39 healthy donors aged 6-90 y. We demonstrate that TCR β diversity per 10(6) T cells decreases roughly linearly with age, with significant reduction already apparent by age 40. The percentage of naive T cells showed a strong correlation with measured TCR diversity and decreased linearly up to age 70. Remarkably, the oldest group (average age 82 y) was characterized by a higher percentage of naive CD4(+) T cells, lower abundance of expanded clones, and increased TCR diversity compared with the previous age group (average age 62 y), suggesting the influence of age selection and association of these three related parameters with longevity. Interestingly, cross-analysis of individual TCR β repertoires revealed a set >10,000 of the most representative public TCR β clonotypes, whose abundance among the top 100,000 clones correlated with TCR diversity and decreased with aging.
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Affiliation(s)
- Olga V Britanova
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia
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49
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Shugay M, Bolotin DA, Putintseva EV, Pogorelyy MV, Mamedov IZ, Chudakov DM. Huge Overlap of Individual TCR Beta Repertoires. Front Immunol 2013; 4:466. [PMID: 24400005 PMCID: PMC3872297 DOI: 10.3389/fimmu.2013.00466] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
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50
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Putintseva EV, Britanova OV, Staroverov DB, Merzlyak EM, Turchaninova MA, Shugay M, Bolotin DA, Pogorelyy MV, Mamedov IZ, Bobrynina V, Maschan M, Lebedev YB, Chudakov DM. Mother and child T cell receptor repertoires: deep profiling study. Front Immunol 2013; 4:463. [PMID: 24400004 PMCID: PMC3872299 DOI: 10.3389/fimmu.2013.00463] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 07/18/2013] [Accepted: 12/03/2013] [Indexed: 12/03/2022] Open
Abstract
The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T cell receptor (TCR) repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5 × 105 to 2 × 106 TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TCR beta variable segment usage frequency and relative overlap of TCR beta complementarity-determining region 3 (CDR3) repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.
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Affiliation(s)
- Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Vlasta Bobrynina
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Mikhail Maschan
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
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