Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens. Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations. We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders - patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine). We validate the method with independent assays. ALICE requires no longitudinal data collection nor large cohorts, and it is directly applicable to most RepSeq datasets. Its results facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.

• MeSH
• adaptivní imunita genetika   MeSH
• antigeny virové MeSH
• antigeny MeSH
• hypervariabilní oblasti genetika   fyziologie   MeSH
• imunoterapie MeSH
• lidé MeSH
• receptory antigenů T-buněk imunologie   metabolismus   fyziologie   MeSH
• sekvenční analýza DNA metody   MeSH
• shluková analýza MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny virové MeSH
• antigeny MeSH
• hypervariabilní oblasti MeSH
• receptory antigenů T-buněk MeSH

The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

• Klíčová slova
• antigen, immunoglobulin gene, marginal zone lymphoma, ontogeny,
• MeSH
• genová přestavba B-lymfocytů genetika   MeSH
• geny pro imunoglobuliny genetika   MeSH
• geny pro těžké řetězce imunoglobulinů genetika   MeSH
• hypervariabilní oblasti genetika   MeSH
• lidé MeSH
• lymfom z B-buněk marginální zóny genetika   MeSH
• mutace genetika   MeSH
• nádorové mikroprostředí MeSH
• receptory antigenů B-buněk genetika   MeSH
• variabilní oblast imunoglobulinu genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hypervariabilní oblasti MeSH
• receptory antigenů B-buněk MeSH
• variabilní oblast imunoglobulinu MeSH

Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform repertoire-wide disease association studies of antigen receptor sequences. We developed a statistical framework for associating receptors to disease from only a small cohort of patients, with no need for a control cohort. Our method successfully identifies previously validated Cytomegalovirus and type one diabetes responsive TCR[Formula: see text] sequences .

• Klíčová slova
• computational biology, condition associated receptors, human, immunology, inflammation, repertoire sequencing, statistical analysis, systems biology,
• MeSH
• adaptivní imunita genetika   MeSH
• Cytomegalovirus imunologie   MeSH
• diabetes mellitus genetika   imunologie   MeSH
• genetická variace imunologie   MeSH
• hypervariabilní oblasti genetika   MeSH
• lidé MeSH
• receptory antigenů B-buněk genetika   MeSH
• receptory antigenů T-buněk genetika   imunologie   MeSH
• receptory antigenů genetika   imunologie   MeSH
• receptory imunologické genetika   imunologie   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hypervariabilní oblasti MeSH
• receptory antigenů B-buněk MeSH
• receptory antigenů T-buněk MeSH
• receptory antigenů MeSH
• receptory imunologické MeSH

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.

• Klíčová slova
• T cell, T-cell receptor repertoires, aging, diversity, functional T-cell subsets,
• MeSH
• buněčná imunita fyziologie   MeSH
• hypervariabilní oblasti genetika   imunologie   MeSH
• myši MeSH
• T-lymfocyty - podskupiny cytologie   imunologie   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• hypervariabilní oblasti 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

We report on markedly different frequencies of genetic lesions within subsets of chronic lymphocytic leukemia patients carrying mutated or unmutated stereotyped B-cell receptor immunoglobulins in the largest cohort (n=565) studied for this purpose. By combining data on recurrent gene mutations (BIRC3, MYD88, NOTCH1, SF3B1 and TP53) and cytogenetic aberrations, we reveal a subset-biased acquisition of gene mutations. More specifically, the frequency of NOTCH1 mutations was found to be enriched in subsets expressing unmutated immunoglobulin genes, i.e. #1, #6, #8 and #59 (22-34%), often in association with trisomy 12, and was significantly different (P<0.001) to the frequency observed in subset #2 (4%, aggressive disease, variable somatic hypermutation status) and subset #4 (1%, indolent disease, mutated immunoglobulin genes). Interestingly, subsets harboring a high frequency of NOTCH1 mutations were found to carry few (if any) SF3B1 mutations. This starkly contrasts with subsets #2 and #3 where, despite their immunogenetic differences, SF3B1 mutations occurred in 45% and 46% of cases, respectively. In addition, mutations within TP53, whilst enriched in subset #1 (16%), were rare in subsets #2 and #8 (both 2%), despite all being clinically aggressive. All subsets were negative for MYD88 mutations, whereas BIRC3 mutations were infrequent. Collectively, this striking bias and skewed distribution of mutations and cytogenetic aberrations within specific chronic lymphocytic leukemia subsets implies that the mechanisms underlying clinical aggressiveness are not uniform, but rather support the existence of distinct genetic pathways of clonal evolution governed by a particular stereotyped B-cell receptor selecting a certain molecular lesion(s).

• MeSH
• chronická lymfatická leukemie genetika   metabolismus   mortalita   MeSH
• cytogenetické vyšetření MeSH
• frekvence genu MeSH
• genová přestavba B-lymfocytů MeSH
• geny pro imunoglobuliny MeSH
• hypervariabilní oblasti genetika   MeSH
• imunoglobuliny - vazebný region genetika   MeSH
• jednonukleotidový polymorfismus MeSH
• lidé MeSH
• mutace * MeSH
• nádorové biomarkery * MeSH
• prognóza MeSH
• receptory antigenů B-buněk genetika   metabolismus   MeSH
• těžké řetězce imunoglobulinů genetika   MeSH
• variabilní oblast imunoglobulinu genetika   MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hypervariabilní oblasti MeSH
• imunoglobuliny - vazebný region MeSH
• nádorové biomarkery * MeSH
• receptory antigenů B-buněk MeSH
• těžké řetězce imunoglobulinů MeSH
• variabilní oblast imunoglobulinu 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

PURPOSE: Prompted by the extensive biases in the immunoglobulin (IG) gene repertoire of splenic marginal-zone lymphoma (SMZL), supporting antigen selection in SMZL ontogeny, we sought to investigate whether antigen involvement is also relevant post-transformation. EXPERIMENTAL DESIGN: We conducted a large-scale subcloning study of the IG rearrangements of 40 SMZL cases aimed at assessing intraclonal diversification (ID) due to ongoing somatic hypermutation (SHM). RESULTS: ID was identified in 17 of 21 (81%) rearrangements using the immunoglobulin heavy variable (IGHV)1-2*04 gene versus 8 of 19 (40%) rearrangements utilizing other IGHV genes (P= 0.001). ID was also evident in most analyzed IG light chain gene rearrangements, albeit was more limited compared with IG heavy chains. Identical sequence changes were shared by subclones from different patients utilizing the IGHV1-2*04 gene, confirming restricted ongoing SHM profiles. Non-IGHV1-2*04 cases displayed both a lower number of ongoing SHMs and a lack of shared mutations (per group of cases utilizing the same IGHV gene). CONCLUSIONS: These findings support ongoing antigen involvement in a sizable portion of SMZL and further argue that IGHV1-2*04 SMZL may represent a distinct molecular subtype of the disease.

• MeSH
• alely * MeSH
• aminokyselinové motivy MeSH
• antigeny imunologie   MeSH
• biologické modely MeSH
• hypervariabilní oblasti chemie   genetika   MeSH
• lidé MeSH
• lymfom z B-buněk marginální zóny genetika   imunologie   patologie   MeSH
• mutace MeSH
• nádory sleziny genetika   imunologie   patologie   MeSH
• přestavba genů pro těžké řetězce B-lymfocytů MeSH
• receptory antigenů B-buněk genetika   MeSH
• sekvence aminokyselin MeSH
• stanovení celkové genové exprese MeSH
• substituce aminokyselin MeSH
• těžké řetězce imunoglobulinů chemie   genetika   MeSH
• transkriptom MeSH
• variabilní oblast imunoglobulinu chemie   genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny MeSH
• hypervariabilní oblasti MeSH
• receptory antigenů B-buněk MeSH
• těžké řetězce imunoglobulinů MeSH
• variabilní oblast imunoglobulinu MeSH

BACKGROUND: V(D)J recombination takes place during lymphocyte development to generate a large repertoire of T- and B-cell receptors. Mutations in recombination-activating gene 1 (RAG1) and RAG2 result in loss or reduction of V(D)J recombination. It is known that different mutations in RAG genes vary in residual recombinase activity and give rise to a broad spectrum of clinical phenotypes. OBJECTIVE: We sought to study the immunologic mechanisms causing the clinical spectrum of RAG deficiency. METHODS: We included 22 patients with similar RAG1 mutations (c.519delT or c.368_369delAA) resulting in N-terminal truncated RAG1 protein with residual recombination activity but presenting with different clinical phenotypes. We studied precursor B-cell development, immunoglobulin and T-cell receptor repertoire formation, receptor editing, and B- and T-cell numbers. RESULTS: Clinically, patients were divided into 3 main categories: T(-)B(-) severe combined immunodeficiency, Omenn syndrome, and combined immunodeficiency. All patients showed a block in the precursor B-cell development, low B- and T-cell numbers, normal immunoglobulin gene use, limited B- and T-cell repertoires, and slightly impaired receptor editing. CONCLUSION: This study demonstrates that similar RAG mutations can result in similar immunobiological effects but different clinical phenotypes, indicating that the level of residual recombinase activity is not the only determinant for clinical outcome. We postulate a model in which the type and moment of antigenic pressure affect the clinical phenotypes of these patients.

• Klíčová slova
• B- and T-cell receptor repertoire, RAG deficiency, V(D)J recombination, autoimmunity, immune repertoire analysis, next generation sequencing, receptor editing,
• MeSH
• B-lymfocyty imunologie   metabolismus   MeSH
• exprese genu MeSH
• fenotyp * MeSH
• genetické asociační studie * MeSH
• genotyp MeSH
• homeodoménové proteiny genetika   metabolismus   MeSH
• hypervariabilní oblasti genetika   MeSH
• kojenec MeSH
• lidé MeSH
• mutace * MeSH
• novorozenec MeSH
• počet lymfocytů MeSH
• předškolní dítě MeSH
• T-lymfocyty imunologie   metabolismus   MeSH
• těžká kombinovaná imunodeficience diagnóza   genetika   imunologie   metabolismus   MeSH
• těžké řetězce imunoglobulinů genetika   MeSH
• V(D)J rekombinace MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• novorozenec MeSH
• předškolní dítě MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• homeodoménové proteiny MeSH
• hypervariabilní oblasti MeSH
• RAG-1 protein MeSH Prohlížeč
• těžké řetězce imunoglobulinů MeSH

Despite novel treatment strategies, multiple myeloma (MM) remains an incurable disease with low immunogenicity and multiple immune defects. We developed an ex vivo strategy for inducing myeloma-specific cytotoxic T lymphocytes (CTLs) and demonstrate the possibility of identification and long-term in vivo monitoring of individual myeloma-specific T-cell clones using the most sensitive clonotypic assay that is able to detect low frequencies of T-cell clones (1 clonotypic cell in 10(6) cells). Ten patients with MM were examined for the presence of tumour-reactive T cells using dendritic cells loaded with autologous tumour cells. All patients had detectable myeloma-reactive T cells in vitro. Expanded myeloma-reactive T cells demonstrated specific cytotoxic effects against autologous tumour cells in vitro (median 39.6% at an effector:target ratio of 40:1). The clonality of myeloma-specific T cells was studied with a clonotypic assay, which demonstrated both oligoclonal and monoclonal populations of myeloma-specific T cells. CD8(+) CTLs were the most immunodominant myeloma-specific T-cell clones and clinical responses were closely associated with the in vivo expansion and long-term persistence of individual CD8(+) T-cell clones, usually at very low frequencies (10(-3)-10(-6)). We conclude that the clonotypic assay is the most sensitive tool for immunomonitoring of low-frequency T cells.

• MeSH
• aktivace lymfocytů imunologie   MeSH
• antigeny nádorové imunologie   MeSH
• buněčná diferenciace imunologie   MeSH
• buněčné klony imunologie   MeSH
• cytotoxicita imunologická imunologie   MeSH
• cytotoxické T-lymfocyty imunologie   MeSH
• dendritické buňky imunologie   MeSH
• hypervariabilní oblasti genetika   imunologie   MeSH
• imunodominantní epitopy imunologie   MeSH
• imunomagnetická separace metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mnohočetný myelom imunologie   terapie   MeSH
• molekulární sekvence - údaje MeSH
• monitorování imunologické metody   MeSH
• nádorové buňky kultivované MeSH
• následné studie MeSH
• prezentace antigenu imunologie   MeSH
• sekvence aminokyselin MeSH
• senioři MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antigeny nádorové MeSH
• hypervariabilní oblasti MeSH
• imunodominantní epitopy MeSH