Период обученияСтрана, городУчебное заведениеДополнительная информация
2009–2014 Россия, Москва МГУ им. М.В. Ломоносова

Научные интересы


Гранты и проекты

ПериодДополнительная информация
2018–2018 Программа президиума РАН «Молекулярная и клеточная биология», 2014-2015. "Исследование адаптивного иммунитета человека и модельных животных с применением методов секвенирования нового поколения".
2018–2018 РНФ, 14-14-00533, 2014-2016. "Возрастные изменения в структуре гуморального иммунитета".
2018–2018 РНФ, 14-35-00105, 2014-2016. "Комплексное исследование молекулярной эволюции злокачественных опухолей для разработки персонифицированных подходов к ведению онкологических больных ".
2018–2018 РФФИ, 2015-2016, 15-34-21052 мол_а_вед. "Исследование новых подходов к анализу данных массированного секвенирования с применением молекулярного баркодирования".
2018–2018 РФФИ, 16-34-00753 мол_а. "Анализ популяционной гетерогенности CMV-специфичных вариантов Т-клеточных рецепторов".

Избранные публикации

  1. Komech E.A., Pogorelyy M.V., Egorov E.S., Britanova O.V., Rebrikov D.V., Bochkova A.G., Shmidt E.I., Shostak N.A., Shugay M., Lukyanov S., Mamedov I.Z., Lebedev Y.B., Chudakov D.M., Zvyagin I.V. (2018). CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Rheumatology (Oxford) , [+]

    The risk of AS is associated with genomic variants related to antigen presentation and specific cytokine signalling pathways, suggesting the involvement of cellular immunity in disease initiation/progression. The aim of the present study was to explore the repertoire of TCR sequences in healthy donors and AS patients to uncover AS-linked TCR variants.

  2. Izraelson M., Nakonechnaya T.O., Moltedo B., Egorov E.S., Kasatskaya S.A., Putintseva E.V., Mamedov I.Z., Staroverov D.B., Shemiakina I.I., Zakharova M.Y., Davydov A.N., Bolotin D.A., Shugay M., Chudakov D.M., Rudensky A.Y., Britanova O.V. (2018). Comparative analysis of murine T-cell receptor repertoires. Immunology 153 (2), 133–144 [+]

    For understanding the rules and laws of adaptive immunity, high-throughput profiling of T-cell receptor (TCR) repertoires becomes a powerful tool. The structure of TCR repertoires is instructive even before the antigen specificity of each particular receptor becomes available. It embodies information about the thymic and peripheral selection of T cells; the readiness of an adaptive immunity to withstand new challenges; the character, magnitude and memory of immune responses; and the aetiological and functional proximity of T-cell subsets. Here, we describe our current analytical approaches for the comparative analysis of murine TCR repertoires, and show several examples of how these approaches can be applied for particular experimental settings. We analyse the efficiency of different metrics used for estimation of repertoire diversity, repertoire overlap, V-gene and J-gene segments usage similarity, and amino acid composition of CDR3. We discuss basic differences of these metrics and their advantages and limitations in different experimental models, and we provide guidelines for choosing an efficient way to lead a comparative analysis of TCR repertoires. Applied to the various known and newly developed mouse models, such analysis should allow us to disentangle multiple sophisticated puzzles in adaptive immunity.

  3. Egorov E.S., Kasatskaya S.A., Zubov V.N., Izraelson M., Nakonechnaya T.O., Staroverov D.B., Angius A., Cucca F., Mamedov I.Z., Rosati E., Franke A., Shugay M., Pogorelyy M.V., Chudakov D.M., Britanova O.V. (2018). The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging. Front Immunol 9, 1618 [+]

    Human aging is associated with a profound loss of thymus productivity, yet naïve T lymphocytes still maintain their numbers by division in the periphery for many years. The extent of such proliferation may depend on the cytokine environment, including IL-7 and T-cell receptor (TCR) "tonic" signaling mediated by self pMHCs recognition. Additionally, intrinsic properties of distinct subpopulations of naïve T cells could influence the overall dynamics of aging-related changes within the naïve T cell compartment. Here, we investigated the differences in the architecture of TCR beta repertoires for naïve CD4, naïve CD8, naïve CD4CD25CD31 (enriched with recent thymic emigrants, RTE), and mature naïve CD4CD25CD31 peripheral blood subsets between young and middle-age/old healthy individuals. In addition to observing the accumulation of clonal expansions (as was shown previously), we reveal several notable changes in the characteristics of T cell repertoire. We observed significant decrease of CDR3 length, NDN insert, and number of non-template added N nucleotides within TCR beta CDR3 with aging, together with a prominent change of physicochemical properties of the central part of CDR3 loop. These changes were similar across CD4, CD8, RTE-enriched, and mature CD4 subsets of naïve T cells, with minimal or no difference observed between the latter two subsets for individuals of the same age group. We also observed an increase in "publicity" (fraction of shared clonotypes) of CD4, but not CD8 naïve T cell repertoires. We propose several explanations for these phenomena built upon previous studies of naïve T-cell homeostasis, and call for further studies of the mechanisms causing the observed changes and of consequences of these changes in respect of the possible holes formed in the landscape of naïve T cell TCR repertoire.

  4. Shugay M., Bagaev D.V., Zvyagin I.V., Vroomans R.M., Crawford J.C., Dolton G., Komech E.A., Sycheva A.L., Koneva A.E., Egorov E.S., Eliseev A.V., VanDyk E., Dash P., Attaf M., Rius C., Ladell K., McLaren J.E., Matthews K.K., Clemens E.B., Douek D.C., Luciani F., vanBaarle D., Kedzierska K., Kesmir C., Thomas P.G., Price D.A., Sewell A.K., Chudakov D.M. (2017). VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Res. , [+]

    The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3.net and https://github.com/antigenomics/vdjdb-db.

  5. Vdovin A.S., Filkin S.Y., Yefimova P.R., Sheetikov S.A., Kapranov N.M., Davydova Y.O., Egorov E.S., Khamaganova E.G., Drokov M.Y., Kuzmina L.A., Parovichnikova E.N., Efimov G.A., Savchenko V.G. (2016). Recombinant MHC Tetramers for Isolation of Virus-Specific CD8(+) Cells from Healthy Donors: Potential Approach for Cell Therapy of Posttransplant Cytomegalovirus Infection. Biochemistry Mosc. 81 (11), 1371–1383 [+]

    Patients undergoing allogeneic hematopoietic stem cell transplantation have a high risk of cytomegalovirus reactivation, which in the absence of T-cell immunity can result in the development of an acute inflammatory reaction and damage of internal organs. Transfusion of the virus-specific donor T-lymphocytes represents an alternative to a highly toxic and often ineffective antiviral therapy. Potentially promising cell therapy approach comprises transfusion of cytotoxic T-lymphocytes, specific to the viral antigens, immediately after their isolation from the donor's blood circulation without any in vitro expansion. Specific T-cells could be separated from potentially alloreactive lymphocytes using recombinant major histocompatibility complex (MHC) multimers, carrying synthetic viral peptides. Rapid transfusion of virus-specific T-cells to patients has several crucial advantages in comparison with methods based on the in vitro expansion of the cells. About 30% of hematopoietic stem cell donors and 46% of transplant recipients at the National Research Center for Hematology were carriers of the HLA-A*02 allele. Moreover, 94% of Russian donors have an immune response against the cytomegalovirus (CMV). Using recombinant HLA-A*02 multimers carrying an immunodominant cytomegalovirus peptide (NLV), we have shown that the majority of healthy donors have pronounced T-cell immunity against this antigen, whereas shortly after the transplantation the patients do not have specific T-lymphocytes. The donor cells have the immune phenotype of memory cells and can be activated and proliferate after stimulation with the specific antigen. Donor lymphocytes can be substantially enriched to significant purity by magnetic separation with recombinant MHC multimers and are not activated upon cocultivation with the antigen-presenting cells from HLA-incompatible donors without addition of the specific antigen. This study demonstrated that strong immune response to CMV of healthy donors and prevalence of HLA-A*02 allele in the Russian population make it possible to isolate a significant number of virus-specific cells using HLA-A*02-NLV multimers. After the transfusion, these cells should protect patients from CMV without development of allogeneic immune response.

  6. Turchaninova M.A., Davydov A., Britanova O.V., Shugay M., Bikos V., Egorov E.S., Kirgizova V.I., Merzlyak E.M., Staroverov D.B., Bolotin D.A., Mamedov I.Z., Izraelson M., Logacheva M.D., Kladova O., Plevova K., Pospisilova S., Chudakov D.M. (2016). High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 11 (9), 1599–616 [+]

    High-throughput sequencing analysis of hypermutating immunoglobulin (IG) repertoires remains a challenging task. Here we present a robust protocol for the full-length profiling of human and mouse IG repertoires. This protocol uses unique molecular identifiers (UMIs) introduced in the course of cDNA synthesis to control bottlenecks and to eliminate PCR and sequencing errors. Using asymmetric 400+100-nt paired-end Illumina sequencing and UMI-based assembly with the new version of the MIGEC software, the protocol allows up to 750-nt lengths to be sequenced in an almost error-free manner. This sequencing approach should also be applicable to various tasks beyond immune repertoire studies. In IG profiling, the achieved length of high-quality sequence covers the variable region of even the longest chains, along with the fragment of a constant region carrying information on the antibody isotype. The whole protocol, including preparation of cells and libraries, sequencing and data analysis, takes 5 to 6 d.

  7. Britanova O.V., Shugay M., Merzlyak E.M., Staroverov D.B., Putintseva E.V., Turchaninova M.A., Mamedov I.Z., Pogorelyy M.V., Bolotin D.A., Izraelson M., Davydov A.N., Egorov E.S., Kasatskaya S.A., Rebrikov D.V., Lukyanov S., Chudakov D.M. (2016). Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J. Immunol. 196 (12), 5005–13 [+]

    The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.

  8. Sarkisyan K.S., Bolotin D.A., Meer M.V., Usmanova D.R., Mishin A.S., Sharonov G.V., Ivankov D.N., Bozhanova N.G., Baranov M.S., Soylemez O., Bogatyreva N.S., Vlasov P.K., Egorov E.S., Logacheva M.D., Kondrashov A.S., Chudakov D.M., Putintseva E.V., Mamedov I.Z., Tawfik D.S., Lukyanov K.A., Kondrashov F.A. (2016). Local fitness landscape of the green fluorescent protein. Nature 533 (7603), 397–401 [+]

    Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.

  9. Egorov E.S., Merzlyak E.M., Shelenkov A.A., Britanova O.V., Sharonov G.V., Staroverov D.B., Bolotin D.A., Davydov A.N., Barsova E., Lebedev Y.B., Shugay M., Chudakov D.M. (2015). Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers. J. Immunol. 194 (12), 6155–63 [+]

    Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications.

  10. Sarkisyan K.S., Zlobovskaya O.A., Gorbachev D.A., Bozhanova N.G., Sharonov G.V., Staroverov D.B., Egorov E.S., Ryabova A.V., Solntsev K.M., Mishin A.S., Lukyanov K.A. (2015). KillerOrange, a Genetically Encoded Photosensitizer Activated by Blue and Green Light. PLoS ONE 10 (12), e0145287 [+]

    Genetically encoded photosensitizers, proteins that produce reactive oxygen species when illuminated with visible light, are increasingly used as optogenetic tools. Their applications range from ablation of specific cell populations to precise optical inactivation of cellular proteins. Here, we report an orange mutant of red fluorescent protein KillerRed that becomes toxic when illuminated with blue or green light. This new protein, KillerOrange, carries a tryptophan-based chromophore that is novel for photosensitizers. We show that KillerOrange can be used simultaneously and independently from KillerRed in both bacterial and mammalian cells offering chromatic orthogonality for light-activated toxicity.

  11. Pletneva N.V., Pletnev V.Z., Sarkisyan K.S., Gorbachev D.A., Egorov E.S., Mishin A.S., Lukyanov K.A., Dauter Z., Pletnev S. (2015). Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore. PLoS ONE 10 (12), e0145740 [+]

    Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.81 and 1.57 Å resolution, respectively. They are the first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). Same as their red progenitors, both orange photosensitizers have a water-filled channel connecting the chromophore to the β-barrel exterior and enabling transport of ROS. In both proteins, Trp66 of the chromophore adopts an unusual trans-cis conformation stabilized by H-bond with the nearby Gln159. This trans-cis conformation along with the water channel was shown to be a key structural feature providing bright orange emission and phototoxicity of both examined orange photosensitizers.