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Sheetikov SA, Khmelevskaya AA, Zornikova KV, Zvyagin IV, Shomuradova AS, Serdyuk YV, Shakirova NT, Peshkova IO, Titov A, Romaniuk DS, Shagina IA, Chudakov DM, Kiryukhin DO, Shcherbakova OV, Khamaganova EG, Dzutseva V, Afanasiev A, Bogolyubova AV, Efimov GA. Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein. Front Immunol 2024; 15:1369436. [PMID: 38629062 PMCID: PMC11018901 DOI: 10.3389/fimmu.2024.1369436] [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: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Adenovirus vaccines, particularly the COVID-19 Ad5-nCoV adenovirus vaccine, have emerged as promising tools in the fight against infectious diseases. In this study, we investigated the structure of the T cell response to the Spike protein of the SARS-CoV-2 virus used in the COVID-19 Ad5-nCoV adenoviral vaccine in a phase 3 clinical trial (NCT04540419). In 69 participants, we collected peripheral blood samples at four time points after vaccination or placebo injection. Sequencing of T cell receptor repertoires from Spike-stimulated T cell cultures at day 14 from 17 vaccinated revealed a more diverse CD4+ T cell repertoire compared to CD8+. Nevertheless, CD8+ clonotypes accounted for more than half of the Spike-specific repertoire. Our longitudinal analysis showed a peak T cell response at day 14, followed by a decline until month 6. Remarkably, multiple T cell clonotypes persisted for at least 6 months after vaccination, as demonstrated by ex vivo stimulation. Examination of CDR3 regions revealed homologous sequences in both CD4+ and CD8+ clonotypes, with major CD8+ clonotypes sharing high similarity with annotated sequences specific for the NYNYLYRLF peptide, suggesting potential immunodominance. In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases.
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Affiliation(s)
- Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra A. Khmelevskaya
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan V. Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alina S. Shomuradova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana V. Serdyuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Naina T. Shakirova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Iuliia O. Peshkova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Aleksei Titov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Dmitrii S. Romaniuk
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Irina A. Shagina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M. Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Dmitry O. Kiryukhin
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Olga V. Shcherbakova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Ekaterina G. Khamaganova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Vitalina Dzutseva
- Novosibirsk State University, Medical School, Novosibirsk, Russia
- NPO Petrovax Pharm LLC, Moscow, Russia
| | | | | | - Grigory A. Efimov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
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Bryushkova EA, Mushenkova NV, Turchaninova MA, Lukyanov DK, Chudakov DM, Serebrovskaya EO. B cell clonality in cancer. Semin Immunol 2024; 72:101874. [PMID: 38508089 DOI: 10.1016/j.smim.2024.101874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 03/22/2024]
Abstract
Carcinogenesis in the process of long-term co-evolution of tumor cells and immune environment essentially becomes possible due to incorrect decisions made, remembered, and reproduced by the immune system at the level of clonal populations of antigen-specific T- and B-lymphocytes. Tumor-immunity interaction determines the nature of such errors and, consequently, delineates the possible ways of successful immunotherapeutic intervention. It is generally recognized that tumor-infiltrating B cells (TIL-B) can play both pro-tumor and anti-tumor roles. However, the exact mechanisms that determine the contribution of clonal B cell lineages with different specificities and functions remain largely unclear. This is due to the variability of cancer types, the molecular heterogeneity of tumor cells, and, to a large extent, the individual pattern of each immune response. Further progress requires detailed investigation of the functional properties and phenotypes of clonally heterogeneous B cells in relation to their antigenic specificities, which determine the functionality of both effector B lymphocytes and immunoglobulins produced in the tumor environment. Based on a real understanding of the role of clonal antigen-specific populations of B lymphocytes in the tumor microenvironment, we need to learn how to develop new methods of targeted immunotherapy, as well as adapt existing treatment options to the specific needs of different patients and patient subgroups. In this review, we will cover B cells functional diversity and their multifaceted roles in the tumor environment.
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Affiliation(s)
- E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, Moscow, Russia
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
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3
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Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
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Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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Britanova OV, Lupyr KR, Staroverov DB, Shagina IA, Aleksandrov AA, Ustyugov YY, Somov DV, Klimenko A, Shostak NA, Zvyagin IV, Stepanov AV, Merzlyak EM, Davydov AN, Izraelson M, Egorov ES, Bogdanova EA, Vladimirova AK, Iakovlev PA, Fedorenko DA, Ivanov RA, Skvortsova VI, Lukyanov S, Chudakov DM. Targeted depletion of TRBV9 + T cells as immunotherapy in a patient with ankylosing spondylitis. Nat Med 2023; 29:2731-2736. [PMID: 37872223 PMCID: PMC10667094 DOI: 10.1038/s41591-023-02613-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023]
Abstract
Autoimmunity is intrinsically driven by memory T and B cell clones inappropriately targeted at self-antigens. Selective depletion or suppression of self-reactive T cells remains a holy grail of autoimmune therapy, but disease-associated T cell receptors (TCRs) and cognate antigenic epitopes remained elusive. A TRBV9-containing CD8+ TCR motif was recently associated with the pathogenesis of ankylosing spondylitis, psoriatic arthritis and acute anterior uveitis, and cognate HLA-B*27-presented epitopes were identified. Following successful testing in nonhuman primate models, here we report human TRBV9+ T cell elimination in ankylosing spondylitis. The patient achieved remission within 3 months and ceased anti-TNF therapy after 5 years of continuous use. Complete remission has now persisted for 4 years, with three doses of anti-TRBV9 administered per year. We also observed a profound improvement in spinal mobility metrics and the Bath Ankylosing Spondylitis Metrology Index (BASMI). This represents a possibly curative therapy of an autoimmune disease via selective depletion of a TRBV-defined group of T cells. The anti-TRBV9 therapy could potentially be applicable to other HLA-B*27-associated spondyloarthropathies. Such targeted elimination of the underlying cause of the disease without systemic immunosuppression could offer a new generation of safe and efficient therapies for autoimmunity.
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Affiliation(s)
- Olga V Britanova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Kseniia R Lupyr
- Pirogov Russian National Research Medical University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitry B Staroverov
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Dmitry V Somov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alesia Klimenko
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadejda A Shostak
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V Zvyagin
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey V Stepanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina M Merzlyak
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- MiLaboratories Inc., Sunnyvale, CA, USA
| | | | - Evgeniy S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | | | | | | | - Denis A Fedorenko
- Department of Hematology and Chemotherapy, Pirogov National Medical and Surgical Center, Moscow, Russia
| | | | - Veronika I Skvortsova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Medical Biological Agency, Moscow, Russia
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
- Abu Dhabi Stem Cell Center, Al Muntazah, United Arab Emirates.
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Davydov AN, Bolotin DA, Poslavsky SV, Chudakov DM. Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'. Brief Bioinform 2023; 24:bbad354. [PMID: 37824737 PMCID: PMC10569745 DOI: 10.1093/bib/bbad354] [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: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/14/2023] Open
Abstract
Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell/B-cell receptors sequencing (TCR-Seq/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis.
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Affiliation(s)
- Alexey N Davydov
- MiLaboratories Inc, San Francisco, CA, USA
- Central European Institute of Technology, Brno, Czech Republic
| | | | | | - Dmitry M Chudakov
- MiLaboratories Inc, San Francisco, CA, USA
- Central European Institute of Technology, Brno, Czech Republic
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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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Bryushkova EA, Skatova VD, Mutovina ZY, Zagrebneva AI, Fomina DS, Kruglova TS, Akopyan AA, Strazhesko ID, Lukyanov SA, Tkacheva ON, Lysenko MA, Chudakov DM. Tocilizumab, netakimab, and baricitinib in patients with mild-to-moderate COVID-19: An observational study. PLoS One 2022; 17:e0273340. [PMID: 36001576 PMCID: PMC9401152 DOI: 10.1371/journal.pone.0273340] [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: 03/01/2022] [Accepted: 08/06/2022] [Indexed: 12/15/2022] Open
Abstract
Objective The aim of the study was to assess inflammatory markers and clinical outcomes in adult patients admitted to hospital with mild-to-moderate COVID-19 and treated with a combination of standard-of-care (SOC) and targeted immunosuppressive therapy including anti-IL-17A (netakimab), anti-IL-6R (tocilizumab), or JAK1/JAK2 inhibitor (baricitinib) or with a standard-of-care therapy alone. Methods The observational cohort study included 154 adults hospitalized between February and August, 2020 with RT-PCR-confirmed SARS-CoV-2 with National Early Warning Score2 (NEWS2) < 7 and C-reactive protein (CRP) levels ≤ 140 mg/L on the day of the start of the therapy or observation. Patients were divided into the following groups: I) 4 mg baricitinib, 1 or 2 times a day for an average of 5 days (n = 38); II) 120 mg netakimab, one dose (n = 48); III) 400 mg tocilizumab, one dose (n = 34), IV) SOC only: hydroxychloroquine, antiviral, antibacterial, anticoagulant, and dexamethasone (n = 34). Results CRP levels significantly decreased after 72 h in the tocilizumab (p = 1 x 10-5) and netakimab (p = 8 x 10-4) groups and remained low after 120 h. The effect was stronger with tocilizumab compared to other groups (p = 0.028). A significant decrease in lactate dehydrogenase (LDH) levels was observed 72 h after netakimab therapy (p = 0.029). NEWS2 scores significantly improved 72 h after tocilizumab (p = 6.8 x 10-5) and netakimab (p = 0.01) therapy, and 120 h after the start of tocilizumab (p = 8.6 x 10-5), netakimab (p = 0.001), or baricitinib (p = 4.6 x 10-4) therapy, but not in the SOC group. Blood neutrophil counts (p = 6.4 x 10-4) and neutrophil-to-lymphocyte ratios (p = 0.006) significantly increased 72 h after netakimab therapy and remained high after 120 h. The percentage of patients discharged 5-7 days after the start of therapy was higher in the tocilizumab (44.1%) and netakimab (41.7%) groups than in the baricitinib (31.6%) and SOC (23.5%) groups. Compared to SOC (3 of the 34; 8.8%), mortality was lower in netakimab (0 of the 48; 0%, RR = 0.1 (95% CI: 0.0054 to 1.91)), tocilizumab (0 of the 34; 0%, RR = 0.14 (95% CI: 0.0077 to 2.67)), and baricitinib (1 of the 38; 2.6%, RR = 0.3 (95% CI: 0.033 to 2.73)) groups. Conclusion In hospitalized patients with mild-to-moderate COVID-19, the combination of SOC with anti-IL-17A or anti-IL-6R therapy were superior or comparable to the combination with JAK1/JAK2 inhibitor, and all three were superior to SOC alone. Whereas previous studies did not demonstrate significant benefit of anti-IL-17A therapy for severe COVID-19, our data suggest that such therapy could be a rational choice for mild-to-moderate disease, considering the generally high safety profile of IL-17A blockers. The significant increase in blood neutrophil count in the netakimab group may reflect efflux of neutrophils from inflamed tissues. We therefore hypothesize that neutrophil count and neutrophil-to-lymphocyte ratio could serve as markers of therapeutic efficiency for IL-17A-blocking antibodies in the context of active inflammation.
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Affiliation(s)
- Ekaterina A. Bryushkova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Valeria D. Skatova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Zinaida Y. Mutovina
- City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Alena I. Zagrebneva
- City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Daria S. Fomina
- City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Tatyana S. Kruglova
- City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Anna A. Akopyan
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Olga N. Tkacheva
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maryana A. Lysenko
- Pirogov Russian National Research Medical University, Moscow, Russia
- City Clinical Hospital No.52 of Moscow Healthcare Department, Moscow, Russia
| | - Dmitry M. Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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8
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Izosimova AV, Yuzhakova DV, Skatova VD, Volchkova LN, Zagainova EV, Chudakov DM, Sharonov GV. Deciphering Repertoire of B16 Melanoma Reactive TCRs by Immunization, In Vitro Restimulation and Sequencing of IFNγ-Secreting T Cells. Int J Mol Sci 2021; 22:ijms22189859. [PMID: 34576023 PMCID: PMC8469664 DOI: 10.3390/ijms22189859] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Recent advances in cancer immunotherapy have great promise for the treatment of solid tumors. One of the key limiting factors that hamper the decoding of physiological responses to these therapies is the inability to distinguish between specific and nonspecific responses. The identification of tumor-specific lymphocytes is also the most challenging step in cancer cell therapies such as adoptive cell transfer and T cell receptor (TCR) cloning. Here, we have elaborated a protocol for the identification of tumor-specific T lymphocytes and the deciphering of their repertoires. B16 melanoma engraftment following anti-PD1 checkpoint therapy provides better antitumor immunity compared to repetitive immunization with heat-shocked tumor cells. We have also revealed that the most error-prone part of dendritic cell (DC) generation, i.e., their maturation step, can be omitted if DCs are cultured at a sufficiently high density. Using this optimized protocol, we have achieved a robust IFNγ response to B16F0 antigens, but only within CD4+ T helper cells. A comparison of the repertoires of IFNγ-positive and -negative cells shows a prominent enrichment of certain clones with putative tumor specificity among the IFNγ+ fraction. In summary, our optimized protocol and the data provided here will aid in the acquisition of broad statistical data and the creation of a meaningful database of B16-specific TCRs.
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Affiliation(s)
- Anna V. Izosimova
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
- Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia
| | - Diana V. Yuzhakova
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
| | - Valeria D. Skatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia;
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 1 Ostrovityanova, 117997 Moscow, Russia
| | - Lilia N. Volchkova
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
| | - Elena V. Zagainova
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
- Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603950 Nizhny Novgorod, Russia
| | - Dmitry M. Chudakov
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia;
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 1 Ostrovityanova, 117997 Moscow, Russia
| | - George V. Sharonov
- Institute of Experimental Oncology and Biomedicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603950 Nizhny Novgorod, Russia; (A.V.I.); (D.V.Y.); (L.N.V.); (E.V.Z.); (D.M.C.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya, 117997 Moscow, Russia;
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, 1 Ostrovityanova, 117997 Moscow, Russia
- Correspondence:
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9
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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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10
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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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11
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Muslinkina L, Pletnev VZ, Pletneva NV, Ruchkin DA, Kolesov DV, Bogdanov AM, Kost LA, Rakitina TV, Agapova YK, Shemyakina II, Chudakov DM, Pletnev S. Two independent routes of post-translational chemistry in fluorescent protein FusionRed. Int J Biol Macromol 2020; 155:551-559. [PMID: 32243936 DOI: 10.1016/j.ijbiomac.2020.03.244] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 10/24/2022]
Abstract
The crystal structure of monomeric red fluorescent protein FusionRed (λex/λem 580/608 mn) has been determined at 1.09 Å resolution and revealed two alternative routes of post-translational chemistry, resulting in distinctly different products. The refinement occupancies suggest the 60:40 ratio of the mature Met63-Tyr64-Gly65 chromophore and uncyclized chromophore-forming tripeptide with the protein backbone cleaved between Met63 and the preceding Phe62 and oxidized Cα-Cβ bond of Tyr64. We analyzed the structures of FusionRed and several related red fluorescent proteins, identified structural elements causing hydrolysis of the peptide bond, and verified their impact by single point mutagenesis. These findings advance the understanding of the post-translational chemistry of GFP-like fluorescent proteins beyond the canonical cyclization-dehydration-oxidation mechanism. They also show that impaired cyclization does not prevent chromophore-forming tripeptide from further transformations enabled by the same set of catalytic residues. Our mutagenesis efforts resulted in inhibition of the peptide backbone cleavage, and a FusionRed variant with ~30% improved effective brightness.
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Affiliation(s)
- Liya Muslinkina
- Basic Science Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA
| | - Vladimir Z Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadya V Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Ruchkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Danila V Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Lubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Rakitina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yulia K Agapova
- National Research Center "Kurchatov Institute," Moscow, Russia
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergei Pletnev
- Basic Science Program, Frederick National Laboratory for Cancer Research, Argonne, IL 60439, USA.
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12
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Janssen A, Villacorta Hidalgo J, Beringer DX, van Dooremalen S, Fernando F, van Diest E, Terrizi AR, Bronsert P, Kock S, Schmitt-Gräff A, Werner M, Heise K, Follo M, Straetemans T, Sebestyen Z, Chudakov DM, Kasatskaya SA, Frenkel FE, Ravens S, Spierings E, Prinz I, Küppers R, Malkovsky M, Fisch P, Kuball J. γδ T-cell Receptors Derived from Breast Cancer-Infiltrating T Lymphocytes Mediate Antitumor Reactivity. Cancer Immunol Res 2020; 8:530-543. [PMID: 32019779 DOI: 10.1158/2326-6066.cir-19-0513] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/25/2019] [Accepted: 01/31/2020] [Indexed: 11/16/2022]
Abstract
γδ T cells in human solid tumors remain poorly defined. Here, we describe molecular and functional analyses of T-cell receptors (TCR) from tumor-infiltrating γδ T lymphocytes (γδ TIL) that were in direct contact with tumor cells in breast cancer lesions from archival material. We observed that the majority of γδ TILs harbored a proinflammatory phenotype and only a minority associated with the expression of IL17. We characterized TCRγ or TCRδ chains of γδ TILs and observed a higher proportion of Vδ2+ T cells compared with other tumor types. By reconstructing matched Vδ2- TCRγ and TCRδ pairs derived from single-cell sequencing, our data suggest that γδ TILs could be active against breast cancer and other tumor types. The reactivity pattern against tumor cells depended on both the TCRγ and TCRδ chains and was independent of additional costimulation through other innate immune receptors. We conclude that γδ TILs can mediate tumor reactivity through their individual γδ TCR pairs and that engineered T cells expressing TCRγ and δ chains derived from γδ TILs display potent antitumor reactivity against different cancer cell types and, thus, may be a valuable tool for engineering immune cells for adoptive cell therapies.
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Affiliation(s)
- Anke Janssen
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jose Villacorta Hidalgo
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis X Beringer
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sanne van Dooremalen
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Febilla Fernando
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Eline van Diest
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Antonela R Terrizi
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annette Schmitt-Gräff
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany
| | - Kerstin Heise
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | - Marie Follo
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Trudy Straetemans
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyen
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dmitry M Chudakov
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Sofya A Kasatskaya
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Sarina Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Eric Spierings
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
| | | | - Paul Fisch
- Institute for Surgical Pathology, University Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Kuball
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands. .,Department of Hematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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13
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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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14
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Mikelov AI, Staroverov DB, Komech EA, Lebedev Y, Chudakov DM, Zvyagin IV. Correlated dynamics of serum IGE and IGE+ clonotype count with allergen air level in seasonal allergic rhinitis. BRSMU 2019. [DOI: 10.24075/brsmu.2019.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanisms of maintenance of immunological memory in the chronic course of seasonal allergic rhinitis remain poorly understood. The detailed understanding of these mechanisms is required for design of new approaches for allergy treatment. It is known that the level of allergen-specific IgE antibodies (sIgE), which play a key role in the development of the disease, is increased in patients with seasonal allergic rhinitis during pollination season. This study aimed to investigate the dynamics of serum IgE levels and characteristics of the clonal repertoire of IgE-secreting lymphocytes depending on the intensity of the patient's contact with the allergen. For three patients, allergic to birch pollen (22, 22, and 28 y.o.), we measured total IgE and birch pollen specific IgE levels at 6 time points with 2 week interval during the birch pollination season. Immunoglobulin heavy chain gene (IGH) clonal repertoire data for several B-cell subpopulations at different time points were obtained for one patient. We observe growth of the sIgE level (91%, 37%, and 64% compared to the baseline) at the peak of pollination season in all three donors. Initial increase in sIgE and IgE levels coincides with the birch pollination initiation; sIgE and total IgE levels correlate with the birch pollen air level (sIgE: R2 = 0.98 at p < 0.05; total IgE: R2 = 0.95 at p < 0.05). We detected IgE clonotypes only in samples obtained during the birch pollination, which indicates an increase of IGE-expressing cells concentration during this period. The frequency of IgE clonotypes was extremely low compared to that of the clonotypes of other isotypes (IgE — 0.01%, IgM — 48.4%, IgD — 14%, IgG — 17.4%, IgA — 19.8%). Hypermutation and phylogenetic analysis of the sequences from the 13 detected IgE-containing clonal groups showed that these IgE clonotypes could originate from IgG as a result of sequential isotype-switching.
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Affiliation(s)
- AI Mikelov
- Skoltech, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - EA Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - YuB Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - DM Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - IV Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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15
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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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16
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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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17
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Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 2018; 15:601-604. [PMID: 29988095 DOI: 10.1038/s41592-018-0052-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Aline R Faro
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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18
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Kost LA, Nikitin ES, Ivanova VO, Sung U, Putintseva EV, Chudakov DM, Balaban PM, Lukyanov KA, Bogdanov AM. Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor. PLoS One 2017; 12:e0184225. [PMID: 28863184 PMCID: PMC5580962 DOI: 10.1371/journal.pone.0184225] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 03/13/2017] [Accepted: 08/21/2017] [Indexed: 11/19/2022] Open
Abstract
Visualization of electrical activity in living cells represents an important challenge in context of basic neurophysiological studies. Here we report a new voltage sensitive fluorescent indicator which response could be detected by fluorescence monitoring in a single red channel. To the best of our knowledge, this is the first fluorescent protein-based voltage sensor which uses insertion-into-circular permutant topology to provide an efficient interaction between sensitive and reporter domains. Its fluorescent core originates from red fluorescent protein (FP) FusionRed, which has optimal spectral characteristics to be used in whole body imaging techniques. Indicators using the same domain topology could become a new perspective for the FP-based voltage sensors that are traditionally based on Förster resonance energy transfer (FRET).
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Affiliation(s)
- Liubov A. Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Evgeny S. Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Violetta O. Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Uhna Sung
- Center for Functional Connectomics, Korea Institute of Science & Technology, Seoul, Korea
| | | | - Dmitry M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel M. Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
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19
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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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20
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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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21
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Drutskaya MS, Efimov GA, Zvartsev RV, Chashchina AA, Chudakov DM, Tillib SV, Kruglov AA, Nedospasov SA. Experimental models of arthritis in which pathogenesis is dependent on TNF expression. Biochemistry (Mosc) 2015; 79:1349-57. [PMID: 25716728 DOI: 10.1134/s0006297914120086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rheumatoid arthritis (RA) is an autoimmune inflammatory disease characterized by joint damage as well as systemic manifestations. The exact cause of RA is not known. Both genetic and environmental factors are believed to contribute to the development of this disease. Increased expression of tumor necrosis factor (TNF) has been implicated in the pathogenesis of RA. Currently, the use of anti-TNF drugs is one of the most effective strategies for the treatment of RA, although therapeutic response is not observed in all patients. Furthermore, due to non-redundant protective functions of TNF, systemic anti-TNF therapy is often associated with unwanted side effects such as increased frequency of infectious diseases. Development of experimental models of arthritis in mice is necessary for studies on the mechanisms of pathogenesis of this disease and can be useful for comparative evaluation of various anti-TNF drugs. Here we provide an overview of the field and present our own data with two experimental models of autoimmune arthritis - collagen-induced arthritis and antibody-induced arthritis in C57Bl/6 and BALB/c mice, as well as in tnf-humanized mice generated on C57Bl/6 background. We show that TNF-deficient mice are resistant to the development of collagen-induced arthritis, and the use of anti-TNF therapy significantly reduces the disease symptoms. We also generated and evaluated a fluorescent detector of TNF overexpression in vivo. Overall, we have developed an experimental platform for studying the mechanisms of action of existing and newly developed anti-TNF drugs for the treatment of rheumatoid arthritis.
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Affiliation(s)
- M S Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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22
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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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23
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Pletnev VZ, Pletneva NV, Lukyanov KA, Souslova EA, Fradkov AF, Chudakov DM, Chepurnykh T, Yampolsky IV, Wlodawer A, Dauter Z, Pletnev S. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr D Biol Crystallogr 2013; 69:1850-60. [PMID: 23999308 PMCID: PMC3760133 DOI: 10.1107/s0907444913015424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022]
Abstract
A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λex/λem = 502/511 nm) and red laRFP (λex/λem ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(β) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.
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Affiliation(s)
- Vladimir Z. Pletnev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina A. Souslova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Arkady F. Fradkov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry M. Chudakov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatyana Chepurnykh
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilia V. Yampolsky
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
- Basic Research Program, SAIC-Frederick, Argonne, IL 60439, USA
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24
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Pletneva NV, Pletnev VZ, Souslova E, Chudakov DM, Lukyanov S, Martynov VI, Arhipova S, Artemyev I, Wlodawer A, Dauter Z, Pletnev S. Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis. Acta Crystallogr D Biol Crystallogr 2013; 69:1005-12. [PMID: 23695245 PMCID: PMC3663121 DOI: 10.1107/s0907444913004034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/09/2013] [Indexed: 11/10/2022]
Abstract
The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow-orange range (535-555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The `yellow' chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina Souslova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry M. Chudakov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sergey Lukyanov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russian Federation
| | - Vladimir I. Martynov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Svetlena Arhipova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Igor Artemyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
- Basic Research Program, SAIC-Frederick, 9700 South Cass Avenue, Argonne, IL 60439, USA
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25
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Pletnev S, Pletneva NV, Souslova EA, Chudakov DM, Lukyanov S, Wlodawer A, Dauter Z, Pletnev V. Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670. Acta Crystallogr D Biol Crystallogr 2012; 68:1088-97. [PMID: 22948909 PMCID: PMC3489099 DOI: 10.1107/s0907444912020598] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/07/2012] [Indexed: 11/10/2022]
Abstract
The crystal structures of the far-red fluorescent proteins (FPs) eqFP650 (λ(ex)(max)/λ(em)(max) 592/650 nm) and eqFP670 (λ(ex)(max)/λ(em)(max) 605/670 nm), the successors of the far-red FP Katushka (λ(ex)(max)/λ(em)(max) 588/635 nm), have been determined at 1.8 and 1.6 Å resolution, respectively. An examination of the structures demonstrated that there are two groups of changes responsible for the bathochromic shift of excitation/emission bands of these proteins relative to their predecessor. The first group of changes resulted in an increase of hydrophilicity at the acylimine site of the chromophore due to the presence of one and three water molecules in eqFP650 and eqFP670, respectively. These water molecules provide connection of the chromophore with the protein scaffold via hydrogen bonds causing an ~15 nm bathochromic shift of the eqFP650 and eqFP670 emission bands. The second group of changes observed in eqFP670 arises from substitution of both Ser143 and Ser158 by asparagines. Asn143 and Asn158 of eqFP670 are hydrogen bonded with each other, as well as with the protein scaffold and with the p-hydroxyphenyl group of the chromophore, resulting in an additional ~20 nm bathochromic shift of the eqFP670 emission band as compared to eqFP650. The role of the observed structural changes was verified by mutagenesis.
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Affiliation(s)
- Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA.
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26
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Shemiakina II, Ermakova GV, Cranfill PJ, Baird MA, Evans RA, Souslova EA, Staroverov DB, Gorokhovatsky AY, Putintseva EV, Gorodnicheva TV, Chepurnykh TV, Strukova L, Lukyanov S, Zaraisky AG, Davidson MW, Chudakov DM, Shcherbo D. A monomeric red fluorescent protein with low cytotoxicity. Nat Commun 2012; 3:1204. [PMID: 23149748 DOI: 10.1038/ncomms2208] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 10/16/2012] [Indexed: 11/09/2022] Open
Abstract
Multicolour labelling with fluorescent proteins is frequently used to differentially highlight specific structures in living systems. Labelling with fusion proteins is particularly demanding and is still problematic with the currently available palette of fluorescent proteins that emit in the red range due to unsuitable subcellular localization, protein-induced toxicity and low levels of labelling efficiency. Here we report a new monomeric red fluorescent protein, called FusionRed, which demonstrates both high efficiency in fusions and low toxicity in living cells and tissues.
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Affiliation(s)
- I I Shemiakina
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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27
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Shui B, Wang Q, Lee F, Byrnes LJ, Chudakov DM, Lukyanov SA, Sondermann H, Kotlikoff MI. Circular permutation of red fluorescent proteins. PLoS One 2011; 6:e20505. [PMID: 21647365 PMCID: PMC3103546 DOI: 10.1371/journal.pone.0020505] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [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: 12/29/2010] [Accepted: 05/03/2011] [Indexed: 11/18/2022] Open
Abstract
Circular permutation of fluorescent proteins provides a substrate for the design of molecular sensors. Here we describe a systematic exploration of permutation sites for mCherry and mKate using a tandem fusion template approach. Circular permutants retaining more than 60% (mCherry) and 90% (mKate) brightness of the parent molecules are reported, as well as a quantitative evaluation of the fluorescence from neighboring mutations. Truncations of circular permutants indicated essential N- and C-terminal segments and substantial flexibility in the use of these molecules. Structural evaluation of two cp-mKate variants indicated no major conformational changes from the previously reported wild-type structure, and cis conformation of the chromophores. Four cp-mKates were identified with over 80% of native fluorescence, providing important new building blocks for sensor and complementation experiments.
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Affiliation(s)
- Bo Shui
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Qi Wang
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Frank Lee
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Laura J. Byrnes
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Dmitry M. Chudakov
- Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russian Federation
| | - Sergey A. Lukyanov
- Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russian Federation
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Michael I. Kotlikoff
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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Korzh V, Teh C, Kondrychyn I, Chudakov DM, Lukyanov S. Visualizing Compound Transgenic Zebrafish in Development: A Tale of Green Fluorescent Protein and KillerRed. Zebrafish 2011; 8:23-9. [DOI: 10.1089/zeb.2011.0689] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Vladimir Korzh
- Genomics and Development Division, Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cathleen Teh
- Genomics and Development Division, Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - Igor Kondrychyn
- Genomics and Development Division, Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - Dmitry M. Chudakov
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Sergey Lukyanov
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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29
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Figueiredo M, Lane S, Tang F, Liu BH, Hewinson J, Marina N, Kasymov V, Souslova EA, Chudakov DM, Gourine AV, Teschemacher AG, Kasparov S. Optogenetic experimentation on astrocytes. Exp Physiol 2010; 96:40-50. [PMID: 21041318 DOI: 10.1113/expphysiol.2010.052597] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [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: 12/29/2022]
Affiliation(s)
- M Figueiredo
- School of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
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30
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Teh C, Chudakov DM, Poon KL, Mamedov IZ, Sek JY, Shidlovsky K, Lukyanov S, Korzh V. Optogenetic in vivo cell manipulation in KillerRed-expressing zebrafish transgenics. BMC Dev Biol 2010; 10:110. [PMID: 21040591 PMCID: PMC2989954 DOI: 10.1186/1471-213x-10-110] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 11/02/2010] [Indexed: 11/10/2022]
Abstract
Background KillerRed (KR) is a novel photosensitizer that efficiently generates reactive oxygen species (ROS) in KR-expressing cells upon intense green or white light illumination in vitro, resulting in damage to their plasma membrane and cell death. Results We report an in vivo modification of this technique using a fluorescent microscope and membrane-tagged KR (mem-KR)-expressing transgenic zebrafish. We generated several stable zebrafish Tol2 transposon-mediated enhancer-trap (ET) transgenic lines expressing mem-KR (SqKR series), and mapped the transposon insertion sites. As mem-KR accumulates on the cell membrane and/or Golgi, it highlights cell bodies and extensions, and reveals details of cellular morphology. The photodynamic property of KR made it possible to damage cells expressing this protein in a dose-dependent manner. As a proof-of-principle, two zebrafish transgenic lines were used to affect cell viability and function: SqKR2 expresses mem-KR in the hindbrain rhombomeres 3 and 5, and elsewhere; SqKR15 expresses mem-KR in the heart and elsewhere. Photobleaching of KR by intense light in the heart of SqKR15 embryos at lower levels caused a reduction in pumping efficiency of the heart and pericardial edema and at higher levels - in cell death in the hindbrain of SqKR2 and in the heart of SqKR15 embryos. Conclusions An intense illumination of tissues expressing mem-KR affects cell viability and function in living zebrafish embryos. Hence, the zebrafish transgenics expressing mem-KR in a tissue-specific manner are useful tools for studying the biological effects of ROS.
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Affiliation(s)
- Cathleen Teh
- Institute of Molecular and Cell Biology, A-STAR, Singapore
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31
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Zhang L, Gurskaia NG, Kopantseva EE, Mudrik NN, Vagner LL, Luk'ianov KA, Chudakov DM. [Identification of the amino acid residues responsible for the reversible photoconversion of the monomeric red fluorescent protein TagRFP protein]. Bioorg Khim 2010; 36:187-92. [PMID: 20531476 DOI: 10.1134/s1068162010020068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The site-directed mutagenesis of the monomeric red fluorescent protein TagRFP and its variants was performed with the goal of generating reversibly photoactivatable fluorescent proteins. Amino acids at positions 69, 148, 165, 179, and 181 (enumeration according to the green fluorescent protein GFP) were shown to play a key role in the manifestation of the photoactivatable properties. A reversibly photoactivatable red fluorescent protein KFP-HC with excitation and emission maxima at 585 and 615 nm, respectively, was generated. The KFP-HC fluorescent intensity was decreased by 5-10 times under green light (530-560 nm) irradiation (due to the fall of the fluorescence quantum yield) and restored under irradiation with blue light (450-490 nm) or after incubation in the dark (time of half reconstruction of 30 min).
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Affiliation(s)
- L Zhang
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997 Russia
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32
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Mamedov IZ, Britanova OV, Chkalina AV, Staroverov DB, Amosova AL, Mishin AS, Kurnikova MA, Zvyagin IV, Mutovina ZY, Gordeev AV, Khaidukov SV, Sharonov GV, Shagin DA, Chudakov DM, Lebedev YB. Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients. Autoimmunity 2009; 42:525-36. [PMID: 19657773 DOI: 10.1080/08916930902960362] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Ankylosing spondylitis (AS) is commonly characterized by clonal expansions of T cells. However, these clonal populations are poorly studied and their role in disease initiation and progression remains unclear. Here, we performed mass sequencing of TCR V beta libraries to search for the expanded T cell clones for two AS patients. A number of clones comprising more than 5% of the corresponding TCR V beta family were identified in both patients. For the first time, expanded clones were shown to be stably abundant in blood samples of AS patients for the prolonged period (1.5 and 2.5 years for two patients, correspondingly). These clones were individually characterized in respect to their differentiation status using fluorescent cell sorting with CD27, CD28, and CD45RA markers followed by quantitative identification of each clone within corresponding fraction using real time PCR analysis. Stable clones differed in phenotype and several were shown to belong to the proinflammatory CD27 - /CD28 - population. Their potentially cytotoxic status was confirmed by staining with perforin-specific antibodies. Search for the TCR V beta CRD3 sequences homologous to the identified clones revealed close matches with the previously reported T cell clones from AS and reactive arthritis patients, thus supporting their role in the disease and proposing consensus TCR V beta CDR3 motifs for AS. Interestingly, these motifs were also found to have homology with earlier reported virus-specific CDR3 variants, indicating that viral infections could play role in development of AS.
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Affiliation(s)
- I Z Mamedov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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33
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Zakharova MY, Kuznetsov NA, Dubiley SA, Kozyr AV, Fedorova OS, Chudakov DM, Knorre DG, Shemyakin IG, Gabibov AG, Kolesnikov AV. Substrate recognition of anthrax lethal factor examined by combinatorial and pre-steady-state kinetic approaches. J Biol Chem 2009; 284:17902-13. [PMID: 19359249 DOI: 10.1074/jbc.m807510200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lethal factor (LF), a zinc-dependent protease of high specificity produced by Bacillus anthracis, is the effector component of the binary toxin that causes death in anthrax. New therapeutics targeting the toxin are required to reduce systemic anthrax-related fatalities. In particular, new insights into the LF catalytic mechanism will be useful for the development of LF inhibitors. We evaluated the minimal length required for formation of bona fide LF substrates using substrate phage display. Phage-based selection yielded a substrate that is cleaved seven times more efficiently by LF than the peptide targeted in the protein kinase MKK6. Site-directed mutagenesis within the metal-binding site in the LF active center and within phage-selected substrates revealed a complex pattern of LF-substrate interactions. The elementary steps of LF-mediated proteolysis were resolved by the stopped-flow technique. Pre-steady-state kinetics of LF proteolysis followed a four-step mechanism as follows: initial substrate binding, rearrangement of the enzyme-substrate complex, a rate-limiting cleavage step, and product release. Examination of LF interactions with metal ions revealed an unexpected activation of the protease by Ca(2+) and Mn(2+). Based on the available structural and kinetic data, we propose a model for LF-substrate interaction. Resolution of the kinetic and structural parameters governing LF activity may be exploited to design new LF inhibitors.
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Affiliation(s)
- Maria Yu Zakharova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997
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34
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Shkrob MA, Mishin AS, Chudakov DM, Labas IA, Luk'ianov KA. [Chromoproteins of the green fluorescent protein family: properties and applications]. Bioorg Khim 2008; 34:581-90. [PMID: 19060933 DOI: 10.1134/s1068162008050014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The distribution in nature and the spectral and structural properties of chromoproteins of the green fluorescent protein (GFP) family and their differences from one another and other fluorescent proteins of this family are considered. Discussed in detail are practical applications of the chromoproteins and their mutant variants that have unique characteristics not found among natural proteins of the GFP family, such as far-red or photoconvertible fluorescence, a large Stokes shift, enhanced phototoxicity, etc.
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35
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Pletnev S, Shcherbo D, Chudakov DM, Pletneva N, Merzlyak EM, Wlodawer A, Dauter Z, Pletnev V. A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore. J Biol Chem 2008; 283:28980-7. [PMID: 18682399 PMCID: PMC2570900 DOI: 10.1074/jbc.m800599200] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [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: 01/23/2008] [Revised: 06/17/2008] [Indexed: 11/06/2022] Open
Abstract
The far-red fluorescent protein mKate (lambda(ex), 588 nm; lambda(em), 635 nm; chromophore-forming triad Met(63)-Tyr(64)-Gly(65)), originating from wild-type red fluorescent progenitor eqFP578 (sea anemone Entacmaea quadricolor), is monomeric and characterized by the pronounced pH dependence of fluorescence, relatively high brightness, and high photostability. The protein has been crystallized at a pH ranging from 2 to 9 in three space groups, and four structures have been determined by x-ray crystallography at the resolution of 1.75-2.6 A. The pH-dependent fluorescence of mKate has been shown to be due to reversible cis-trans isomerization of the chromophore phenolic ring. In the non-fluorescent state at pH 2.0, the chromophore of mKate is in the trans-isomeric form. The weakly fluorescent state of the protein at pH 4.2 is characterized by a mixture of trans and cis isomers. The chromophore in a highly fluorescent state at pH 7.0/9.0 adopts the cis form. Three key residues, Ser(143), Leu(174), and Arg(197) residing in the vicinity of the chromophore, have been identified as being primarily responsible for the far-red shift in the spectra. A group of residues consisting of Val(93), Arg(122), Glu(155), Arg(157), Asp(159), His(169), Ile(171), Asn(173), Val(192), Tyr(194), and Val(216), are most likely responsible for the observed monomeric state of the protein in solution.
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Affiliation(s)
- Sergei Pletnev
- Macromolecular Crystallography Laboratory, NCI, National Institutes of Health, Argonne, Illinois 60439, USA.
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Abstract
Green fluorescent protein from Aequorea victoria and its many homologs are now widely used in basic and applied research. These genetically encoded fluorescent markers can detect localization of cell proteins and organelles in living cells and also cells and tissues in living organisms. Unique instruments and methods for studies of molecular biology of a cell and high throughput drug screenings are based on fluorescent proteins. This review deals with the most intensively evolving directions in this field, the development of genetically encoded sensors. Changes in their spectral properties are used for monitoring of cell enzyme activities or changes in concentrations of particular molecules.
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Affiliation(s)
- E A Souslova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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37
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Pletneva NV, Pletnev SV, Chudakov DM, Tikhonova TV, Popov VO, Martynov VI, Wlodawer A, Dauter Z, Pletnev VZ. [Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom]. Bioorg Khim 2007; 33:421-30. [PMID: 17886433 DOI: 10.1134/s1068162007040048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The three-dimensional structure of yellow fluorescent proteins zYFP538 (zFP538) from the button polyp Zoanthus sp. was determined at a resolution of 1.8 angstrom by X-ray analysis. The monomer of zYFP538 adopts a structure characteristic of the green fluorescent protein (GFP) family, a beta-barrel formed from 11 antiparallel beta segments and one internal alpha helix with a chromophore embedded into it. Like the TurboGFP, the beta-barrel of zYFP538 contains a water-filled pore leading to the chromophore Tyr67 residue, which presumably provides access of molecular oxygen necessary for the maturation process. The post-translational modification of the chromophore-forming triad Lys66-Tyr67-Gly68 results in a tricyclic structure consisting of a five-membered imidazolinone ring, a phenol ring of the Tyr67 residue, and an additional six-membered tetrahydropyridine ring. The chromophore formation is completed by cleavage of the protein backbone at the Calpha-N bond of Lys66. It was suggested that the energy conflict between the buried positive charge of the intact Lys66 side chain in the hydrophobic pocket formed by the Ile44, Leu46, Phe65, Leu204 and Leu219 side chains is the most probable trigger that induces the transformation of the bicyclic green form to the tricyclic yellow form. A stereochemical analysis of the contacting surfaces at the intratetramer interfaces helped reveal a group of conserved key residues responsible for the oligomerization. Along with others, these residues should be taken into account in designing monomeric forms suitable for practical application as markers of proteins and cell organelles.
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38
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Lukyanov KA, Chudakov DM, Fradkov AF, Labas YA, Matz MV, Lukyanov S. Discovery and properties of GFP-like proteins from nonbioluminescent anthozoa. Methods Biochem Anal 2006; 47:121-38. [PMID: 16335712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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Abstract
The fluorescence characteristics of photoactivatable proteins can be controlled by irradiating them with light of a specific wavelength, intensity and duration. This provides unique possibilities for the optical labelling and tracking of living cells, organelles and intracellular molecules in a spatio-temporal manner. Here, we discuss the properties of the available photoactivatable fluorescent proteins and their potential applications.
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Affiliation(s)
- Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia.
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40
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Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ. Kindling Fluorescent Protein fromAnemonia sulcata: Dark-State Structure at 1.38 Å Resolution†,‡. Biochemistry 2005; 44:5774-87. [PMID: 15823036 DOI: 10.1021/bi047644u] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [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] [Indexed: 11/29/2022]
Abstract
When the nonfluorescent chromoprotein asFP595 from Anemonia sulcata is subjected to sufficiently intense illumination near the absorbance maximum (lambda(abs)(max) = 568 nm), it undergoes a remarkable transition, termed "kindling", to a long-lived fluorescent state (lambda(em)(max) = 595 nm). In the dark recovery phase, the kindled state relaxes thermally on a time scale of seconds or can instantly be reverted upon illumination at 450 nm. The kindling phenomenon is enhanced by the Ala143 --> Gly point mutation, which slows the dark recovery time constant to 100 s at room temperature and increases the fluorescence quantum yield. To investigate the chemical nature of the chromophore and the possible role of chromophore isomerization in the kindling phenomenon, we determined the crystal structure of the "kindling fluorescent protein" asFP595-A143G (KFP) in the dark-adapted state at 1.38 A resolution and 100 K. The chromophore, derived from the Met63-Tyr64-Gly65 tripeptide, closely resembles that of the nonfluorescent chromoprotein Rtms5 in that the configuration is trans about the methylene bridge and there is substantial distortion from planarity. Unlike in Rtms5, in the native protein the polypeptide backbone is cleaved between Cys62 and Met63. The size and shape of the chromophore pocket suggest that the cis isomer of the chromophore could also be accommodated. Within the pocket, partially disordered His197 displays two conformations, which may constitute a binary switch that stabilizes different chromophore configurations. The energy barrier for thermal relaxation was found by Arrhenius plot analysis to be approximately 71 kJ/mol, somewhat higher than the value of approximately 55 kJ/mol observed for cis-trans isomerization of a model chromophore in solution.
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Affiliation(s)
- Michael L Quillin
- Department of Physics, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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41
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Bulina ME, Lukyanov KA, Yampolsky IV, Chudakov DM, Staroverov DB, Shcheglov AS, Gurskaya NG, Lukyanov S. New Class of Blue Animal Pigments Based on Frizzled and Kringle Protein Domains. J Biol Chem 2004; 279:43367-70. [PMID: 15297465 DOI: 10.1074/jbc.c400337200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nature of coloration in many marine animals remains poorly investigated. Here we studied the blue pigment of a scyfoid jellyfish Rhizostoma pulmo and determined it to be a soluble extracellular 30-kDa chromoprotein with a complex absorption spectrum peaking at 420, 588, and 624 nm. Furthermore, we cloned the corresponding cDNA and confirmed its identity by immunoblotting and mass spectrometry experiments. The chromoprotein, named rpulFKz1, consists of two domains, a Frizzled cysteine-rich domain and a Kringle domain, inserted into one another. Generally, Frizzleds are members of a basic Wnt signal transduction pathway investigated intensely with regard to development and cancerogenesis. Kringles are autonomous structural domains found throughout the blood clotting and fibrinolytic proteins. Neither Frizzled and Kringle domains association with any type of coloration nor Kringle intrusion into Frizzled sequence was ever observed. Thus, rpulFKz1 represents a new class of animal pigments, whose chromogenic group remains undetermined. The striking homology between a chromoprotein and members of the signal transduction pathway provides a novel node in the evolution track of growth factor-mediated morphogenesis compounds.
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Affiliation(s)
- Maria E Bulina
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow
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42
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Abstract
Green fluorescent protein (GFP) and its homologs are widely used as fluorescent markers of gene expression and for determination of protein localization and motility in living cells. In particular, based on GFP and GFP-like proteins a number of techniques have been developed that can be used either to estimate protein mobility in living cells, or to introduce a distinctive fluorescent signal in order to track the movement of labeled molecules directly. Considerable progress in the development of such technologies in the last two or three years motivates us to reevaluate the present scope of biotechnological instruments in studies of protein movement in cells.
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Affiliation(s)
- D M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.
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Verkhusha VV, Chudakov DM, Gurskaya NG, Lukyanov S, Lukyanov KA. Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins. Chem Biol 2004; 11:845-54. [PMID: 15217617 DOI: 10.1016/j.chembiol.2004.04.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Revised: 04/06/2004] [Accepted: 04/07/2004] [Indexed: 11/26/2022]
Abstract
The mechanism of the chromophore maturation in members of the green fluorescent protein (GFP) family such as DsRed and other red fluorescent and chromoproteins was analyzed. The analysis indicates that the red chromophore results from a chemical transformation of the protonated form of the GFP-like chromophore, not from the anionic form, which appears to be a dead-end product. The data suggest a rational strategy to achieve the complete red chromophore maturation utilizing substitutions to favor the formation of the neutral phenol in GFP-like chromophore. Our approach to detect the neutral chromophore form expands the application of fluorescent timer proteins to faster promoter activities and more spectrally distinguishable fluorescent colors. Light sensitivity found in the DsRed neutral form, resulting in its instant transformation to the mature red chromophore, could be exploited to accelerate the fluorescence acquisition.
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Affiliation(s)
- Vladislav V Verkhusha
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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Bulina ME, Verkhusha VV, Staroverov DB, Chudakov DM, Lukyanov KA. Hetero-oligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteins. Biochem J 2003; 371:109-14. [PMID: 12472468 PMCID: PMC1223255 DOI: 10.1042/bj20021796] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2002] [Accepted: 12/10/2002] [Indexed: 11/17/2022]
Abstract
The tendency for tetramerization is the main disadvantage in the green fluorescent protein homologues from Anthozoa species. We report a universal method called hetero-oligomeric tagging, which diminishes troublesome consequences of tetramerization of Anthozoa-derived fluorescent proteins (FP) in intracellular protein labelling. This approach is based on the co-expression of the FP-tagged protein of interest together with an excess of free non-fluorescent FP mutant. The resulting FP heterotetramers contain only a single target polypeptide and, therefore, can be considered pseudo-monomeric. Feasibility of the method has been demonstrated with a red FP fused with cytoplasmic beta-actin or tubulin-binding protein Tau34. In addition, heterotetramers appeared to be a unique model for biophysical characterization of Anthozoa FPs in pseudo-monomeric state.
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Affiliation(s)
- Maria E Bulina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russia
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Bulina ME, Chudakov DM, Mudrik NN, Lukyanov KA. Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis. BMC Biochem 2002; 3:7. [PMID: 11972899 PMCID: PMC113743 DOI: 10.1186/1471-2091-3-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2001] [Accepted: 04/24/2002] [Indexed: 11/21/2022]
Abstract
BACKGROUND Within the family of green fluorescent protein (GFP) homologs, one can mark two main groups, specifically, fluorescent proteins (FPs) and non-fluorescent or chromoproteins (CPs). Structural background of differences between FPs and CPs are poorly understood to date. RESULTS Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595) from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP) were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield (< 0.001). These spectral characteristics allow one to regard DsRed-NF as a true chromoprotein. CONCLUSIONS We located a novel point in asCP sequence (position 165) mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed.
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Affiliation(s)
- Maria E Bulina
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Dmitry M Chudakov
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Nikolay N Mudrik
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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