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.

• Klíčová slova
• Antigen, Immune repertoire, Immunogenicity, T cell receptor,
• MeSH
• epitopy imunologie   MeSH
• histokompatibilita - antigeny třídy I imunologie   MeSH
• lidé MeSH
• peptidy imunologie   MeSH
• receptory antigenů T-buněk imunologie   MeSH
• statistické modely MeSH
• T-lymfocyty imunologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• epitopy MeSH
• histokompatibilita - antigeny třídy I MeSH
• peptidy MeSH
• receptory antigenů T-buněk MeSH

Vδ2+ T cells form the predominant human γδ T-cell population in peripheral blood and mediate T-cell receptor (TCR)-dependent anti-microbial and anti-tumour immunity. Here we show that the Vδ2+ compartment comprises both innate-like and adaptive subsets. Vγ9+ Vδ2+ T cells display semi-invariant TCR repertoires, featuring public Vγ9 TCR sequences equivalent in cord and adult blood. By contrast, we also identify a separate, Vγ9- Vδ2+ T-cell subset that typically has a CD27hiCCR7+CD28+IL-7Rα+ naive-like phenotype and a diverse TCR repertoire, however in response to viral infection, undergoes clonal expansion and differentiation to a CD27loCD45RA+CX3CR1+granzymeA/B+ effector phenotype. Consistent with a function in solid tissue immunosurveillance, we detect human intrahepatic Vγ9- Vδ2+ T cells featuring dominant clonal expansions and an effector phenotype. These findings redefine human γδ T-cell subsets by delineating the Vδ2+ T-cell compartment into innate-like (Vγ9+) and adaptive (Vγ9-) subsets, which have distinct functions in microbial immunosurveillance.

• MeSH
• buněčná diferenciace genetika   imunologie   MeSH
• buněčné klony imunologie   metabolismus   MeSH
• Cytomegalovirus imunologie   fyziologie   MeSH
• dospělí MeSH
• imunofenotypizace MeSH
• kultivované buňky MeSH
• lidé MeSH
• novorozenec MeSH
• proliferace buněk * MeSH
• průtoková cytometrie MeSH
• receptory antigenů T-buněk gama-delta genetika   imunologie   metabolismus   MeSH
• T-lymfocyty - podskupiny imunologie   metabolismus   virologie   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• novorozenec MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• receptory antigenů T-buněk gama-delta MeSH

The ontogeny of the natural, public IgM repertoire remains incompletely explored. Here, high-resolution immunogenetic analysis of B cells from (unrelated) fetal, child, and adult samples, shows that although fetal liver (FL) and bone marrow (FBM) IgM repertoires are equally diversified, FL is the main source of IgM natural immunity during the 2nd trimester. Strikingly, 0.25% of all prenatal clonotypes, comprising 18.7% of the expressed repertoire, are shared with the postnatal samples, consistent with persisting fetal IgM+ B cells being a source of natural IgM repertoire in adult life. Further, the origins of specific stereotypic IgM+ B cell receptors associated with chronic lymphocytic leukemia, can be traced back to fetal B cell lymphopoiesis, suggesting that persisting fetal B cells can be subject to malignant transformation late in life. Overall, these novel data provide unique insights into the ontogeny of physiological and malignant B lymphopoiesis that spans the human lifetime.

• Klíčová slova
• Fetal, Human, IgH repertoire,
• MeSH
• B-lymfocyty imunologie   MeSH
• chronická lymfatická leukemie genetika   imunologie   MeSH
• imunoglobulin M genetika   imunologie   MeSH
• játra imunologie   MeSH
• kostní dřeň imunologie   MeSH
• lidé MeSH
• lymfopoéza genetika   imunologie   MeSH
• plod imunologie   MeSH
• receptory antigenů B-buněk genetika   imunologie   MeSH
• sekvenční analýza DNA MeSH
• těžké řetězce imunoglobulinů genetika   imunologie   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• imunoglobulin M MeSH
• receptory antigenů B-buněk MeSH
• těžké řetězce imunoglobulinů MeSH

γδ T cells are considered to be innate-like lymphocytes that respond rapidly to stress without clonal selection and differentiation. Here we use next-generation sequencing to probe how this paradigm relates to human Vδ2neg T cells, implicated in responses to viral infection and cancer. The prevalent Vδ1 T cell receptor (TCR) repertoire is private and initially unfocused in cord blood, typically becoming strongly focused on a few high-frequency clonotypes by adulthood. Clonal expansions have differentiated from a naive to effector phenotype associated with CD27 downregulation, retaining proliferative capacity and TCR sensitivity, displaying increased cytotoxic markers and altered homing capabilities, and remaining relatively stable over time. Contrastingly, Vδ2+ T cells express semi-invariant TCRs, which are present at birth and shared between individuals. Human Vδ1+ T cells have therefore evolved a distinct biology from the Vδ2+ subset, involving a central, personalized role for the γδ TCR in directing a highly adaptive yet unconventional form of immune surveillance.

• MeSH
• antigeny CD27 metabolismus   MeSH
• biologické markery metabolismus   MeSH
• buněčná diferenciace MeSH
• buněčné klony cytologie   MeSH
• CX3C chemokinový receptor 1 metabolismus   MeSH
• cytotoxicita imunologická MeSH
• dárci tkání MeSH
• dospělí MeSH
• fenotyp MeSH
• genetická variace MeSH
• hypervariabilní oblasti genetika   MeSH
• imunitní dozor * MeSH
• interleukin-15 farmakologie   MeSH
• lidé MeSH
• proliferace buněk MeSH
• receptory antigenů T-buněk gama-delta metabolismus   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny CD27 MeSH
• biologické markery MeSH
• CX3C chemokinový receptor 1 MeSH
• CX3CR1 protein, human MeSH Prohlížeč
• hypervariabilní oblasti MeSH
• interleukin-15 MeSH
• receptory antigenů T-buněk gama-delta MeSH

BACKGROUND: The repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles. RESULTS: Here we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination. CONCLUSIONS: VDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz .

• Klíčová slova
• B-cell, Browser, High-throughput sequencing, Immunology, Repertoire sequencing, T-cell,
• MeSH
• B-lymfocyty imunologie   metabolismus   MeSH
• genomika metody   normy   MeSH
• hypervariabilní oblasti genetika   MeSH
• internetový prohlížeč MeSH
• klonální evoluce genetika   MeSH
• lidé MeSH
• shluková analýza MeSH
• software * MeSH
• T-lymfocyty imunologie   metabolismus   MeSH
• V(D)J rekombinace * MeSH
• výpočetní biologie metody   normy   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hypervariabilní oblasti MeSH

Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

• MeSH
• dítě MeSH
• dospělí MeSH
• dvojčata genetika   MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• receptory antigenů T-buněk chemie   genetika   metabolismus   MeSH
• roztroušená skleróza genetika   MeSH
• sekvenční analýza DNA metody   MeSH
• shluková analýza MeSH
• software * MeSH
• transplantace hematopoetických kmenových buněk MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• receptory antigenů T-buněk MeSH

• Klíčová slova
• NGS data analysis, TCR beta, TCR repertoire, adaptive immunity, overlap,
• Publikační typ
• časopisecké články MeSH

The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T cell receptor (TCR) repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5 × 10(5) to 2 × 10(6) TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TCR beta variable segment usage frequency and relative overlap of TCR beta complementarity-determining region 3 (CDR3) repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.

• Klíčová slova
• NGS, T cell receptor, TCR repertoires, autoimmune diseases, haploidentical transplantation, maternal-fetal exchange, microchimerism, public clonotypes,
• Publikační typ
• časopisecké články MeSH