Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.

• MeSH
• alely * MeSH
• algoritmy * MeSH
• genetická variace MeSH
• lidé MeSH
• receptory antigenů B-buněk genetika   imunologie   MeSH
• receptory antigenů T-buněk genetika   imunologie   MeSH
• sekvenční analýza DNA metody   MeSH
• software * MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

B-cell precursors (BCP) arise from hematopoietic stem cells in bone marrow (BM). Identification and characterization of the different BCP subsets has contributed to the understanding of normal B-cell development. BCP first rearrange their immunoglobulin (Ig) heavy chain (IGH) genes to form the pre-B-cell receptor (pre-BCR) complex together with surrogate light chains. Appropriate signaling via this pre-BCR complex is followed by rearrangement of the Ig light chain genes, resulting in the formation, and selection of functional BCR molecules. Consecutive production, expression, and functional selection of the pre-BCR and BCR complexes guide the BCP differentiation process that coincides with corresponding immunophenotypic changes. We studied BCP differentiation in human BM samples from healthy controls and patients with a known genetic defect in V(D)J recombination or pre-BCR signaling to unravel normal immunophenotypic changes and to determine the effect of differentiation blocks caused by the specific genetic defects. Accordingly, we designed a 10-color antibody panel to study human BCP development in BM by flow cytometry, which allows identification of classical preB-I, preB-II, and mature B-cells as defined via BCR-related markers with further characterization by additional markers. We observed heterogeneous phenotypes associated with more than one B-cell maturation pathway, particularly for the preB-I and preB-II stages in which V(D)J recombination takes place, with asynchronous marker expression patterns. Next Generation Sequencing of complete IGH gene rearrangements in sorted BCP subsets unraveled their rearrangement status, indicating that BCP differentiation does not follow a single linear pathway. In conclusion, B-cell development in human BM is not a linear process, but a rather complex network of parallel pathways dictated by V(D)J-recombination-driven checkpoints and pre-BCR/BCR mediated-signaling occurring during B-cell production and selection. It can also be described as asynchronous, because precursor B-cells do not differentiate as full population between the different stages, but rather transit as a continuum, which seems influenced (in part) by V-D-J recombination-driven checkpoints.

• MeSH
• buněčná diferenciace genetika   imunologie   MeSH
• dítě MeSH
• lidé MeSH
• prekurzorové B-lymfoidní buňky imunologie   MeSH
• průtoková cytometrie metody   MeSH
• receptory antigenů B-buněk genetika   imunologie   MeSH
• syndromy imunologické nedostatečnosti genetika   imunologie   MeSH
• těžké řetězce imunoglobulinů genetika   MeSH
• V(D)J rekombinace genetika   imunologie   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem 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.

• 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

The current mammalian paradigm states that 1) rearrangements in the IgH locus precede those in IgL loci, 2) IgLλ genes rearrange only when IgLκ genes are consumed, and 3) the surrogate L chain is necessary for selection of productive IgH gene rearrangements. We show in swine that IgL rearrangements precede IgH gene rearrangements, resulting in the expression of naked IgL on a surface of precursor B cells. Findings also suggest that there is no dependency on the surrogate L chain, and thus the authentic IgL proteins may be used for selection of the IgH repertoire. Although rearrangement starts with IgLκ genes, it is rapidly replaced by IgLλ rearrangement. Fast replacement is characterized by occurrence of IgLλ(lo)IgLκ(lo) dual-expressing precursors in which IgLκ expression is a remnant of a previous translation. Most IgLκ(+) B cells are then generated later, indicating that there are two waves of IgLκ synthesis in different developmental stages with IgLλ gene rearrangements in between. In the absence of stromal cells, the stepwise order of rearrangements is blocked so that IgLλ gene rearrangements predominate in early B cell development. To our knowledge, this is the first evidence that some mammals can use an inverted order of Ig loci rearrangement. Moreover, a situation in which the generation of BCR-bearing IgLκ is delayed until after IgLλ becomes the dominant isotype may help explain the extreme deviations in the IgLκ/IgLλ ratios among mammals.

• MeSH
• B-lymfocyty imunologie   fyziologie   MeSH
• geny pro imunoglobuliny MeSH
• imunoglobuliny - kappa-řetězce genetika   MeSH
• lehké řetězce imunoglobulinů genetika   imunologie   MeSH
• prasata MeSH
• přestavba genů pro lehké řetězce B-lymfocytů * MeSH
• přestavba genů pro těžké řetězce B-lymfocytů MeSH
• receptory antigenů B-buněk genetika   imunologie   MeSH
• těžké řetězce imunoglobulinů genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

The relationship between Epstein-Barr virus (EBV) and the germinal centre (GC) of the asymptomatic host remains an enigma. The occasional appearance of EBV-positive germinal centres in some patients, particularly those with a history of immunosuppression, suggests that EBV numbers in the GC are subject to immune control. The relationship, if any, between lymphoid hyperplasia with EBV-positive germinal centres and subsequent or concurrent lymphomagenesis remains to be clarified. As far as the development of EBV-associated Hodgkin's lymphoma is concerned, the suppression of virus replication, mediated by LMP1 on the one hand, and the loss of B-cell receptor signalling on the other, appears to be an important pathogenic mechanism. A further important emerging concept is that alterations in the microenvironment of the EBV-infected B-cell may be important for lymphomagenesis.

• MeSH
• B-lymfocyty imunologie   virologie   MeSH
• buněčná diferenciace imunologie   MeSH
• dospělí MeSH
• Hodgkinova nemoc imunologie   virologie   MeSH
• infekce virem Epsteina-Barrové virologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• proteiny virové matrix MeSH
• pseudolymfom virologie   MeSH
• receptory antigenů B-buněk imunologie   MeSH
• replikace viru imunologie   MeSH
• virus Epsteinův-Barrové imunologie   MeSH
• zárodečné centrum lymfatické uzliny imunologie   virologie   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Roughly 30% of patients with chronic lymphocytic leukemia (CLL) carry immunoglobulin receptors with highly similar primary sequences. Highly similar, quasi-identical immunoglobulins are termed stereotyped. Patients with CLL can be assigned to different subsets expressing different types of stereotyped immunoglobulin receptors. Reliable identification of stereotypy may assist in the molecular classification of CLL and thus better-guided, compartmentalized research. In several major subsets, stereotypy extends from shared primary sequences to shared clinicobiological features and outcome. Reliable identification of stereotypy in CLL may pave the way for tailored treatment strategies applicable to each major stereotyped subset.

• MeSH
• chronická lymfatická leukemie klasifikace   genetika   imunologie   MeSH
• imunoglobuliny klasifikace   imunologie   metabolismus   MeSH
• lidé MeSH
• receptory antigenů B-buněk genetika   imunologie   metabolismus   MeSH
• rozmanitost protilátek imunologie   MeSH
• somatická hypermutace imunoglobulinových genů MeSH
• těžké řetězce imunoglobulinů genetika   imunologie   MeSH
• variabilní oblast imunoglobulinu genetika   imunologie   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Recent research has revealed the existence of subsets (clusters) of patients with different types of B-cell lymphomas and leukemias with restricted, "stereotyped" immunoglobulin (IG) variable heavy complementarity-determining region 3 (VH CDR3) sequences within their B cell receptors (BcR), suggesting selection by common epitopes or classes of structurally similar epitopes. BcR stereotypy was initially described in chronic lymphocytic leukemia (CLL), where it constitutes a remarkably frequent feature of the IG repertoire, and subsequently identified in other malignancies, including mantle cell lymphoma and splenic marginal-zone lymphoma. Of note, at least in CLL, emerging evidence indicates that the grouping of cases into distinct clusters with stereotyped BcR is functionally and prognostically relevant. Hence, the reliable identification of BcR stereotypy may assist in the investigation of the nature of the selecting antigens and immune pathways leading to lymphoma development, and also potentially pave the way for tailored treatment strategies applicable to each major stereotyped subset. In this chapter, we provide an overview of BcR stereotypy in human B-cell malignancies, and outline previous and current methodological approaches used for its identification.

• MeSH
• B-buněčný lymfom metabolismus   MeSH
• leukemie B-buněčná metabolismus   MeSH
• lidé MeSH
• receptory antigenů B-buněk chemie   imunologie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Chronická lymfocytární leukemie (CLL) je nejčastější a stále konvenčními metodami nevyléčitelnou leukemií dospělé populace v západním světě. Hromadící se poznatky o úloze signalizace zprostředkované B buněčným receptorem (BCR) v bio­logii maligních CLL B lymfocytů vedly k úvahám o možnosti klinického využití „BCR inhibitorů“. V nedávné době byly publikovány výsledky klinických studií tří různých molekul (fostamatinib, ibrutinib a GS‑1101) inhibujících kinázy zapojené v BCR dráze (Syk, Btk, PI3K), které vedly k impresivní klinické odpovědi u CLL. Domníváme se, že výsledky těchto klinických studií mohou výrazně změnit léčbu chronické lymfocytární leukemie a ně­kte­rých dalších B buněčných lymfomů v několika následujících letech a „BCR inhibitory“ možná představují tolik hledanou „cílenou léčbu“. V následujícím textu shrneme poznatky o molekulární podstatě deregulace BCR signalizace u CLL lymfocytů a výsledky klinických studií využívajících jejích inhibitorů.

Chronic lymphocytic leukemia (CLL) is the most frequent, yet by conventional therapy still incurable, leukemia in the Western world. Accumulating evidence of the role of B cell receptor (BCR) pathway in CLL B cell bio­logy suggests the possible use of 'BCR inhibitors' for targeted therapy. Recently published results of clinical trials of three different molecules (fosfamatinib, ibrutinib and GS‑1101) targeting BCR‑associated kinases (Syk, Btk, PI3K) showed impressive clinical activity in CLL. These findings will likely modify treatment approaches for chronic lymphocytic leukemia and some other B cell lymphomas in the near future. Herein, we review the data on BCR pathway deregulation in malignant CLL B cells, and the results of clinical trials utilizing fosfamatinib, ibrutinib and GS‑1101.

• MeSH
• B-buněčný lymfom * metabolismus   terapie   MeSH
• chronická lymfatická leukemie terapie   MeSH
• cílená molekulární terapie MeSH
• fixní kombinace léků MeSH
• fosfatidylinositol-3-kinasy * imunologie   metabolismus   MeSH
• genom lidský MeSH
• inhibitory fosfoinositid-3-kinasy MeSH
• inhibitory proteinkinas * terapeutické užití   MeSH
• klinické zkoušky jako téma MeSH
• lidé středního věku MeSH
• lidé MeSH
• oxaziny MeSH
• pyridiny MeSH
• pyrimidiny MeSH
• receptory antigenů B-buněk * antagonisté a inhibitory   imunologie   metabolismus   MeSH
• sekvenční analýza DNA MeSH
• senioři MeSH
• signální transdukce MeSH
• thiazoly MeSH
• tyrosinkinasy * antagonisté a inhibitory   MeSH
• výsledek terapie MeSH
• výzkum MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• senioři MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH

Cross-linking the B cell Ag receptor (BCR) to surface Fc receptors for IgG (Fc gamma R) inhibits G1-to-S progression; the mechanism by which this occurs is not completely known. We investigated the regulation of three key cell cycle regulatory components by BCR-Fc gamma R co-cross-linking: G1-cyclins, cyclin-dependent kinases (Cdks), and the retinoblastoma gene product (Rb). Rb functions to suppress G1-to-S progression in mammalian cells. Rb undergoes cell-cycle-dependent phosphorylation, leading to its inactivation and thereby promoting S phase entry. We demonstrate in this paper for the first time that BCR-induced Rb phosphorylation is abrogated by co-cross-linking with Fc gamma R. The activation of Cdk4/6- and Cdk2-dependent Rb protein kinases is concomitantly blocked. Fc gamma R-mediated inhibition of Cdk2 activity results in part from an apparent failure to express Cdk2 protein. By contrast, inhibition of Cdk4/6 activities is not due to suppression of Cdk4/6 or cyclins D2/D3 expression or inhibition of Cdk-activating kinase activity. Cdk4- and Cdk6-immune complexes recovered from B cells following BCR-Fc gamma R co-cross-linking are devoid of coprecipitated D-type cyclins, indicating that inhibition of their Rb protein kinase activities is due in part to the absence of bound D-type cyclin. Thus, BCR-derived activation signals that up-regulate D-type cyclin and Cdk4/6 protein expression remain intact; however, Fc gamma R-mediated signals block cyclin D-Cdk4/6 assembly or stabilization. These results suggest that assembly or stabilization of D-type cyclin holoenzyme complexes 1) is an important step in the activation of Cdk4/6 by BCR signals, and 2) suffice in providing a mechanism to account for inhibition of BCR-stimulated Rb protein phosphorylation by Fc gamma R.

• MeSH
• aktivace enzymů imunologie   MeSH
• B-lymfocyty enzymologie   imunologie   metabolismus   MeSH
• buněčná diferenciace imunologie   MeSH
• cyklin D MeSH
• cyklin E antagonisté a inhibitory   biosyntéza   MeSH
• cyklin-dependentní kinasa 2 MeSH
• cyklin-dependentní kinasa 4 MeSH
• cyklin-dependentní kinasa 6 MeSH
• cyklin-dependentní kinasa 9 MeSH
• cyklin-dependentní kinasy antagonisté a inhibitory   biosyntéza   metabolismus   MeSH
• cykliny antagonisté a inhibitory   biosyntéza   MeSH
• DNA antagonisté a inhibitory   biosyntéza   MeSH
• fosforylace MeSH
• G1 fáze imunologie   MeSH
• holoenzymy biosyntéza   MeSH
• imunoglobuliny - Fab fragmenty farmakologie   MeSH
• inhibitor p27 cyklin-dependentní kinasy MeSH
• kinasy CDC2-CDC28 * MeSH
• myši inbrední BALB C MeSH
• myši MeSH
• nádorové supresorové proteiny * MeSH
• protein-serin-threoninkinasy antagonisté a inhibitory   biosyntéza   metabolismus   MeSH
• proteiny asociované s mikrotubuly biosyntéza   MeSH
• proteiny buněčného cyklu * MeSH
• protilátky anti-idiotypické farmakologie   MeSH
• protoonkogenní proteiny * MeSH
• receptory antigenů B-buněk antagonisté a inhibitory   imunologie   metabolismus   fyziologie   MeSH
• receptory IgG metabolismus   MeSH
• retinoblastomový protein antagonisté a inhibitory   metabolismus   MeSH
• RNA antagonisté a inhibitory   biosyntéza   MeSH
• upregulace imunologie   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH

• MeSH
• imunitní systém fyziologie   MeSH
• receptory antigenů B-buněk fyziologie   imunologie   MeSH
• receptory antigenů T-buněk fyziologie   imunologie   MeSH
• receptory antigenů fyziologie   imunologie   MeSH