Dmitriy M. Chudakov
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Author Swipe
Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs Open
Single-cell RNA sequencing (scRNA-Seq) provides valuable insights into cell biology. However, current scRNA-Seq analytic approaches do not distinguish between spliced and unspliced mRNA at the level of dimensionality reduction. RNA velocit…
Discovery of rare antigen-specific TCRs via replicate profiling Open
Development of effective vaccines and targeted immunotherapies for cancer, autoimmunity, allergy, and infectious diseases requires comprehensive understanding of functionality and antigenic specificity of involved T cell clones. A major te…
Modern Laboratory Test-Systems as Platforms for Validation of Clinically Promising T-Cell Receptors Open
The development of therapeutic antigen-specific T-cell receptors (TCRs) requires comprehensive preclinical validation of their functional activity. One of the approaches in the development of new drugs for cell therapy based on antigen-spe…
Comprehensive analysis of αβT-cell receptor repertoires reveals signatures of thymic selection Open
Thymic selection is crucial for forming a pool of T-cells that can efficiently discriminate self from non-self using their T-cell receptors (TCRs) to develop adaptive immunity. In the present study we analyzed how a diverse set of physicoc…
FCRLs and atypical transcriptional pattern in tumor infiltrating B cells from lung and renal cancer Open
Advances in high-dimensional flow cytometry and single-cell RNA sequencing (scRNA-seq) have enhanced our understanding of the heterogeneity of tumor-infiltrating B cells (TIBs). Subpopulations of TIBs exhibit diverse, sometimes opposing ro…
Neighborhood enrichment for the identification of antigen-specific T-cell receptors Open
Understanding T-cell receptor (TCR) specificity is not only essential for fundamental research, but could open up novel avenues for diagnostics, cancer immunotherapy, and the targeted treatment of autoimmune diseases. The immune system res…
Engaging T cells for cleanup Open
T-cell engagers represent a transformative approach to cancer immunotherapy leveraging bispecific and multispecific antibody constructs to redirect T-cell cytotoxicity toward malignant cells. These molecules bridge T cells and tumor cells …
Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq Open
Introduction The functional programs of CD4 + T helper (Th) cell clones play a central role in shaping immune responses to different challenges. While advances in single-cell RNA sequencing (scRNA-Seq) have significantly improved our under…
Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or may develop organized lymphoid structures, where somatic hypermutation and anti…
Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or may develop organized lymphoid structures, where somatic hypermutation and anti…
View article: Tracking antigen-specific T cell response to cancer immunotherapy
Tracking antigen-specific T cell response to cancer immunotherapy Open
In each human or model animal, T cell receptor (TCR) of each effector/memory T cell clone recognizes from one to several cognate peptide-MHC complexes (pMHC). Limited knowledge on TCR repertoire specificities restricts our capacity to rati…
FCRLs and atypical transcriptional pattern in tumor infiltrating B cells from lung and renal cancer Open
Advances in high-dimensional flow cytometry and single-cell RNA sequencing (scRNA-seq) have enhanced our understanding of the heterogeneity of tumor-infiltrating B cells (TIBs). Subpopulations of TIBs exhibit diverse, sometimes opposing ro…
Author response: Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or develop organized lymphoid structures, where somatic hypermutation and antigen-…
Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or develop organized lymphoid structures, where somatic hypermutation and antigen-…
Interferon signature in the development of SLE: molecular mechanisms, approaches to diagnosis and treatment Open
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by inflammation of connective tissue and damage to various organs, including joints, skin, kidneys and heart. The disease has a significant gender predisposit…
Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism Open
Suppressive function of regulatory T cells (Treg) is dependent on signaling of their antigen receptors triggered by cognate self, dietary, or microbial peptides presented on MHC II. However, it remains largely unknown whether distinct or s…
Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein Open
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 …
Splicing-aware resolution of scRNA-Seq data Open
Single-cell RNA sequencing (scRNA-Seq) provides invaluable insights in cell biology. Current scRNA-Seq analytic approaches do not distinguish between spliced and unspliced mRNA. RNA velocity paradigm suggests that the presence of unspliced…
Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism Open
Summary Suppressive function of regulatory T cells (Treg) is dependent on signaling of their antigen receptors triggered by cognate self, dietary or microbial antigens in the form of peptide-MHC class II complexes. However, it remains larg…
Author Response: Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism Open
Suppressive function of regulatory T cells (Treg) is dependent on signaling of their antigen receptors triggered by cognate self, dietary or microbial antigens in the form of peptide-MHC class II complexes. However, it remains largely unkn…
Autologous T-Cell-Free Antigen Presentation System Unveils hCMV-Specific NK Cell Response Open
NK cells play a decisive role in controlling hCMV infection by combining innate and adaptive-like immune reactions. The hCMV-derived VMAPRTLFL (LFL) peptide is a potent activator of NKG2C+ NK cells. Proposed here is an autologous system of…
View article: Effectiveness and safety of BCD180, anti-TRBV9<sup>+</sup> T-lymphocytes monoclonal antibody in patients with active radiographic axial spondyloarthritis: 36-week results of double-blind randomized placebo-controlled phase II clinical study ELEFTA
Effectiveness and safety of BCD180, anti-TRBV9<sup>+</sup> T-lymphocytes monoclonal antibody in patients with active radiographic axial spondyloarthritis: 36-week results of double-blind randomized placebo-controlled phase II clinical study ELEFTA Open
The aim – to evaluate the clinical effectiveness, safety, pharmacokinetics, pharmacodynamics, and immunogenicity of seniprutug (BCD-180) in patients with radiographic active axial spondyloarthritis (r-axSpA, or ankylosing spondylitis). Sub…
Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or may develop organized lymphoid structures, where somatic hypermutation and anti…
Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers Open
The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or develop organized lymphoid structures, where somatic hypermutation and antigen-…
View article: Robust detection of SARS-CoV-2 exposure in the population using T-cell repertoire profiling
Robust detection of SARS-CoV-2 exposure in the population using T-cell repertoire profiling Open
The COVID-19 pandemic offers a powerful opportunity to develop methods for monitoring the spread of infectious diseases based on their signatures in population immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become …
View article: Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis
Targeted depletion of TRBV9+ T cells as immunotherapy in a patient with ankylosing spondylitis Open
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 …
Reviewer #3 (Public Review): Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism Open
Suppressive function of regulatory T (Treg) cells is dependent on signaling of their antigen receptors triggered by cognate self, dietary or microbial antigens in the form of peptide-MHC class II complexes. However, it remains largely unkn…