Ivan V Zvyagin

Ivan V Zvyagin
Shemyakin-Ovchinnikov institute of bioorganic chemistry

PhD

About

45
Publications
16,513
Reads
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1,808
Citations
Additional affiliations
February 2013 - February 2015
Masaryk University
Position
  • PostDoc Position
September 2010 - December 2011
JSC Evrogen IP
Position
  • Design of PCR-system for detection of oncogenic somatic SNPs
March 2010 - May 2011
JSC Novtechmat
Position
  • Design of expression vectors for stable expression in mammalian cells
Education
October 2007 - September 2011
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
Field of study
  • Molecular biology
September 2005 - June 2007
Pushchino State University
Field of study
  • Physical-Chemistry Biology and Biotechnology
September 2001 - July 2005

Publications

Publications (45)
Preprint
Spondyloarthritis (SpA) comprises a number of inflammatory rheumatic diseases with overlapping clinical manifestations. Strong association with several HLA-I alleles and T cell infiltration into an inflamed joint suggest involvement of T cells in SpA pathogenesis. In this study, we performed high-throughput T cell repertoire profiling of synovial f...
Preprint
T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility complex (MHC) proteins is a crucial step in triggering the adaptive immune response. Prediction of TCR:peptide recognition is important for many clinically relevant problems: prediction of cross-reactivity of TCRs used in adoptive T-cell-based therapies, ide...
Preprint
Full-text available
B-cell mediated immune memory holds both plasticity and conservatism to respond to new challenges and repeated infections. Here, we analyze the dynamics of immunoglobulin heavy chain (IGH) repertoires of memory B cells, plasmablasts and plasma cells sampled several times during one year from peripheral blood of volunteers without severe inflammator...
Article
Full-text available
Background Different studies show involvement of T-cells in pathogenesis of spondyloarthropathies (SpAs) - a group of rheumatic diseases strongly associated with presence of several MHC-I alleles (HLA-B*27, -B*38, -B*39, etc). Recently we and others identified a specific T-cell receptor motif in blood and synovial fluid of HLA-B*27+ AS patients tha...
Article
Full-text available
Background Recently a group of T-cell clones with characteristic T-cell receptor (TCR) motif was identified in peripheral blood and synovial fluid of HLA-B*27+ patients with ankylosing spondylitis (AS) [1-2] - a prototypic disease from a wider group of spondyloarthropathies (SpAs). Extraarticular manifestations of AS could involve skin, intestine o...
Article
Full-text available
The delayed recovery of adaptive immunity underlies transplant-related mortality (TRM) after αβ T cell-depleted hematopoietic stem cell transplantation (HSCT). We tested the use of low-dose memory donor lymphocyte infusions (mDLIs) after engraftment of αβ T cell-depleted grafts. A cohort of 131 pediatric patients (median age 9 years) were grafted w...
Preprint
Full-text available
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 landsc...
Article
Full-text available
T cells that express CD56 in peripheral blood of healthy humans represent a heterogeneous and poorly studied subset. In this work, we analyzed this subset for NKG2C expression. In both CD56 ⁺ and CD56 ⁻ subsets most of the NKG2C ⁺ T cells had a phenotype of highly differentiated CD8 ⁺ TEMRA cells. The CD56 ⁺ NKG2C ⁺ T cells also expressed a number...
Article
Full-text available
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...
Article
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...
Article
Механизмы поддержания иммунологической памяти, обусловливающей хроническое течение сезонного аллергического ринита у человека, слабо изучены. Рациональный дизайн новых подходов к терапии аллергических заболеваний требует детального понимания этих механизмов. Известно, что уровень аллергенспецифичных антител класса IgE (sIgE), являющихся ключевым аг...
Article
Full-text available
Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specific...
Article
Phosphorus (P) is central to storing and transferring energy and information in living cells, including those of microalgae. Many microalgal species dwelling in low P environments are naturally equipped to take up and store P whenever it becomes available through a complex phenomenon known as "luxury P uptake." Its research is required for better u...
Conference Paper
Full-text available
Background Diagnosis of psoriatic arthritis (PsA) is primarily based on clinical phenotype because of the diversity of the associated features [1]. The heterogeneity likely implies different mechanisms of the disease progression or initiation. Certain HLA alleles have been shown as risk factors for different spondyloarthropathies (SpAs), implying r...
Article
Full-text available
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) sequence...
Conference Paper
Spondyloarthropathies (SpA) are a group of autoimmune diseases with similar clinical and genetic features, which includes ankylos- ing spondylitis (AS), psoriatic arthritis (PsA), enteropathic arthri- tis, undifferentiated SpA and reactive arthritis (ReA). Recently a characteristic TCRbeta motif represented by highly homologous CD8+ TRBV9+ clonotyp...
Article
Full-text available
Recent studies of T-cell clonal repertoires of patients with ankylosing spondylitis (AS) have led to the discovery of AS-associated T-cell clones with a highly homologous T-cell receptor structure. The role of T-lymphocytes in the disease progression cannot be elucidated without analyzing the diversity and abundance of functionally different T-cell...
Article
Full-text available
Autologous hematopoietic stem cell transplantation (HSCT), a safer type of HSCT than allogeneic HSCT, is a promising therapy for patients with severe autoimmune diseases (ADs). Despite the long history of medical practice, structural changes in the adaptive immune system as a result of autologous HSCT in patients with various types of ADs remain po...
Article
Objective: 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-linke...
Article
Vaccination against influenza is widely used to protect against seasonal flu epidemic although its effectiveness is debated. Here we performed deep quantitative T cell receptor repertoire profiling in peripheral blood of a healthy volunteer in response to trivalent subunit influenza vaccine. We did not observe significant rebuilding of peripheral b...
Article
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 technolo...
Presentation
Full-text available
Taking up nutrients such as phosphorus (P) in amounts exceeding the demand for supporting cell division in the absence of limitation is termed luxury uptake (LU). Although LU is long known in microalgae and regarded as a promising vehicle for recycling of P from waste streams [1], it remains poorly elucidated. We studied the relationships between c...
Article
Allogeneic transplantation of hematopoietic cells (HSCT) is an established method to treat different hematologic malignancies and disorders of hematopoietic and lymphoid system. Graft-versus-host-disease is one of the main risk factor for success of the procedure. Simultaneous depletion of alpha-beta T-cells and CD19+ cells in graft is the promisin...
Article
αβT-cell depleted allogeneic hematopoietic cells transplantation holds promise for the safe and accessible therapy of both malignant and non-malignant blood disorders. Here we employed molecular barcoding-normalized T-cell receptor (TCR) profiling to quantitatively track T-cell immune reconstitution after TCRαβ/CD19-depleted transplantation in chil...
Article
Full-text available
Background The repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile...
Article
Bone Marrow Transplantation is a high quality, peer-reviewed journal covering all aspects of clinical and basic haemopoietic stem cell transplantation.
Article
Full-text available
Author Summary High-throughput profiling of T- and B-cell antigen receptor repertoires promises great advances in our understanding of the mechanisms underlying adaptive immune system function, treatment of autoimmune and infectious diseases, and development of novel approaches in cancer immunotherapy. A number of recently developed software tools...
Article
Full-text available
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 analysi...
Article
Full-text available
Adaptive immunity in humans is provided by hypervariable Ig-like molecules on the surface of B and T cells. The final set of these molecules in each organism is formed under the influence of two forces: individual genetic traits and the environment, which includes the diverse spectra of alien and self-antigens. Here we assess the impact of individu...
Article
Full-text available
High-throughput sequencing has the power to reveal the nature of adaptive immunity as represented by the full complexity of T-cell receptor (TCR) and antibody (IG) repertoires, but is at present severely compromised by the quantitative bias, bottlenecks, and accumulated errors that inevitably occur in the course of library preparation and sequencin...
Article
Our ability to analyze adaptive immunity and engineer its activity has long been constrained by our limited ability to identify native pairs of heavy-light antibody chains and alpha-beta T-cell receptor (TCR) chains - both of which comprise coupled "halves of a key", collectively capable of recognizing specific antigens. Here we report a cell-based...
Article
The TCR repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next generation sequencing (NGS) is becoming a powerful tool for deep TCR profiling; yet, questions abound regarding the methodological approaches for sample preparation and correct data interpretation. Accumulate...
Article
Full-text available
Autologous haematopoietic stem cell transplantation is highly efficient for the treatment of systemic autoimmune diseases, but its consequences for the immune system remain poorly understood. Here, we describe an optimized RNA-based technology for unbiased amplification of T cell receptor beta-chain libraries and use it to perform the first detaile...
Article
Full-text available
Increasing evidence points to a role for killer immunoglobulin-like receptors (KIRs) in the development of autoimmune diseases. In particular, a positive association of KIR3DS1 (activating receptor) and a negative association of KIR3DL1 (inhibitory receptor) alleles with ankylosing spondylitis (AS) have been reported by several groups. However, non...
Article
Full-text available
Ankylosing spondylitis (AS) belongs to a group of autoimmune diseases affecting the axial skeleton. Beside thehla-b*27allele, several other human genes that control the variety processes of immune homeostasis are considered to be associated with AS manifestation in different human populations. Among strong associated non-MHC geneserap1 encodingthe...
Article
Full-text available
Increasing evidence points to a role for killer immunoglobulin-like receptors (KIRs) in the development of autoimmune diseases. In particular, a positive association of KIR3DS1 (activating receptor) and a negative association of KIR3DL1 (inhibitory receptor) alleles with ankylosing spondylitis (AS) have been reported by several groups. However, non...
Article
Full-text available
A novel experimental approach to the investigation of the repertoire of peripheral T lymphocytes of patients suffering from ankylosing spondylitis (AS) is proposed. This approach is based on the wide-range sequencing of cDNA of the β-chain of the T-cellular receptor (TcR). The results of the analysis of the diversity of sequences of the TcR antigen...
Article
Full-text available
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...
Article
Full-text available
GFP-like fluorescent proteins (FPs) are crucial in biological and biomedical studies. The majority of FP purification techniques either include multiple time-consuming chromatography steps with a low yield of the desired product or require prior protein modification (addition of special tags). In the present work, we propose an alternative ethanol...

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