T-cell Receptor Beta Variable Gene Research Articles

T-cell receptor beta variable gene polymorphism predicts immune-related adverse events during checkpoint blockade immunotherapy

BackgroundImmune checkpoint inhibitors have revolutionized cancer treatment. However, they are associated with a unique spectrum of side effects, called immune-related adverse events (irAEs), which can cause significant morbidity and quickly...

EP08.01-009 TRBV Haplotype Profile Was Related to Immune-Induced Adverse Events in Chinese Patients With Advanced NSCLC

Immune-related adverse events (irAE) are inevitable following immunotherapy, which significantly impact the quality of life and possibly cause therapy discontinuation or interruption in cancer patients. Previous studies reported that T-cell receptor beta variable (TRBV) gene was related to irAE in Caucasian patients with non-small cell lung cancer (NSCLC). However, the relationship between TRBV gene and irAE remains to be revealed in Chinese NSCLC patients.

Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome

Abstract Multisystem Inflammatory Syndrome in Children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares many clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. The superantigen specificity for binding different Vβ-chains results in Vβ-skewing, whereby T cells with specific Vβ-chains and diverse antigen specificity are overrepresented in the TCR repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCR Beta Variable gene (TRBV)11-2. Furthermore, TRBV11-2 skewing was remarkably correlated with MIS-C severity and serum cytokine levels. Further analysis of TRBJ gene usage and CDR3 length distribution of MIS-C expanding TRBV11-2 clones revealed extensive junctional diversity, indicating a superantigen-mediated selection process for TRBV expansion. In silico modelling indicates that polyacidic residues in TCR Vβ11-2 engage in strong interactions with the superantigen-like motif of SARS-CoV-2 spike glycoprotein. Overall, our data indicate that the immune response in MIS-C is consistent with superantigenic activation.

The variations of TRBV genes usages in the peripheral blood of a healthy population are associated with their evolution and single nucleotide polymorphisms

T cell receptors (TCRs) are a class of T cell surface molecules that recognize the antigen-derived peptides presented by the major histocompatibility complex (MHC) and are able to trigger a series of immune responses. TCRs are important members of the adaptive immune system that arose in the jawed fish 500 million years ago. T cell receptor beta variable (TRBV) genes have been widely used to characterize TCR repertoires. Studying the evolution of TRBV may help us to better understand the adaptive immune system. To investigate TRBV evolution and its impacts on the usages of TRBV genes in human populations, we compared the TRBV genes and their homologous sequences among humans, mouse, rhesus and chimpanzee, analyzed the single-nucleotide polymorphisms (SNPs) located at TRBV loci, and sequenced TCR repertoires in the peripheral blood of 97 healthy donors. We found that functional TRBVs are more evolutionarily conserved but possess more SNPs in human populations than do nonfunctional (pseudo) TRBVs. Based on the conservation levels in the four species, we classified the functional TRBVs into 2 groups: old (conserved between mouse and humans) and new (conserved only in primates). The new TRBVs evolve faster and possess more SNPs than the old TRBVs. The variations in TRBV genes frequencies in the peripheral blood of healthy donors are negatively correlated with SNP density. These observations suggest that TRBV usages may be influenced by TCR-MHC co-evolution.

Molecular profile of the T cell receptor beta variable in peripheral blood lymphocytes from chronic asymptomatic HBV carriers.

T cell receptor beta variable (TCRBV) repertoire could imply the composition and function status of T cells in subjects with HBV infection. The gene melting spectral pattern (GMSP) can be used to determine the profile of TCRBV gene family. The molecular profile of TCRBV in peripheral lymphocytes from asymptomatic HBV carriers (AsC) remains ill-defined. Peripheral blood mononuclear cells (PBMCs) were separated and sorted, and the profiles of TCRBV complementarity-determining region 3 (CDR3) in CD4(+), CD8(+) T subsets and PBMCs were assayed using GMSP. The number of skewed TCRBV in the PBMCs was significantly lower than that in the CD4(+) or CD8(+) T subsets, and the number of monoclonal TCRBV families in the CD8(+) T subset was significantly higher than that in CD4(+) T subset. Compared to healthy donors, TCRBV11, BV13.1, BV20 and BV24 were used more frequently than other TCRBV members in PBMCs from AsC subjects. Furthermore, the relatively conserved CDR3 motifs were detected in these TCRBVs. The results indicate that the T cell response in AsC subjects involves several TCRBVs, and that the CD8(+) T subset maybe more relevant to pathogenesis of AsC. Moreover, the four relative conserved TCRBVs maybe a target for personalized treatments for persistent HBV infection.

Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses

The present study identifies the genomic structure and the gene content of the T cell receptor beta (TRB) locus in the Oryctolagus cuniculus whole genome assembly. The rabbit locus spans less than 600Kb and the general genomic organization is highly conserved with respect to other mammalian species. A pool of 74 TRB variable (TRBV) genes distributed in 24 subgroups are located upstream of two in tandem-aligned D-J-C gene clusters, each composed of one TRBD, six TRBJ genes, and one TRBC gene, followed by a single TRBV gene with an inverted transcriptional orientation. All TRB genes (functional, ORF, pseudogenes) of this paper have been approved by the IMGT/WHO-IUIS nomenclature committee. Additionally, five potentially functional protease serine (PRSS) trypsinogen or trypsinogen-like genes were identified: two in tandem PRSS-like genes, followed by two PRSS genes with unique traits, lie downstream of the TRBV1 gene and one PRSS gene is located about 400Kb away downstream of the TRBV genes. Comparative and phylogenetic analyses revealed that multiple duplication events within a few subgroups have generated the germline repertoire of the rabbit TRBV genes, which is substantially larger than those described in humans, mice, and dogs, suggesting that a strong evolutionary pressure has selected the development of a species-specific TRBV repertoire. Hence, the genomic organization of the TRB locus in the genomes appears to be the result of a balance between the maintenance of a core-number of genes essential for the immunological performances and the requirement of newly arisen genes.

Molecular characterization of T cell receptor beta variable in the peripheral blood T cell repertoire in subjects with active tuberculosis or latent tuberculosis infection

BackgroundT cells are closely linked to the clinical manifestations of subjects with Mycobacterium tuberculosis (MTB) infection. T cell receptor beta variable (TCRBV) is a signal and indicative molecule on the membrane of T lymphocytes, reflecting the composition and specificity of T cells. The molecular profiles of TCRBV in peripheral blood mononuclear cells (PBMCs) and their subpopulations (CD4+ and CD8+ T cells) from subjects with active tuberculosis (TB) or latent TB infection (LTBI) have not been well described.MethodsIn 42 subjects with active TB or LTBI, PMBCs and their subsets were separated and sorted. The molecular profiles of the TCRBV complementarity determining region 3 (CDR3) in the three cell populations were investigated using our recently developed gene melting spectral pattern (GMSP) assay. The TCRBV members were then cloned and sequenced when their GMSP image profiles showed a single-peak.ResultsThe average number of skewed TCRBV molecules in the CD4+ cell subset was significantly higher than that in PBMCs and CD8+ T cells. TCRBV12, BV13.1, BV13.2, and BV24 were expressed more prevalently than other TCRBV gene families in the three cell populations. In addition, relatively conserved amino acid motifs were identified in TCRBV5.1 and BV20 CDR3 in PBMCs and its subsets. The monoclonal TCRBV14 and BV23 expressed were different between active TB and LTBI subjects.ConclusionsThese results indicate that the T cell immune response is complex and multi-specific in active TB and LTBI subjects. Analysis of TCRBV expression in CD4+ T cells suggest that it could be useful in assessing the composition and status of circulating T cells. Furthermore, the expression of TCRBV14, BV23 and the sequencing of CDR3 amino acid motifs of TCRBV5.1, BV20 could be used in the differential diagnosis and treatment of subjects with active TB or LTBI.

Skewed T-cell receptor beta chain variable gene (TCRBV) usage among different clinical types of patients with chronic HBV infection

This study aimed to determine the degree of clonal expansion of T cells in peripheral blood mononuclear cells (PBMCs) isolated from patients suffering from different clinical types of hepatitis B (HB) infection and to analyse the clinical relevance of the skewed T-cell receptor beta variable (TCRBV). Sera and PBMCs were collected from 90 HB patients. Gene melting spectral pattern (GMSP) analysis was used to determine the distribution and expansion of populations expressing specific TCRBV complementary determined region 3 (CDR3) genes. TCRBV genes associated with monoclonal expansion were sequenced. TCRBV families from the majority of patients (80/90) displayed skewed T-cell expansion. Furthermore, TCRBV11, BV12 and BV13.1 were more frequent than other TCRBV genes; the sequence of TCRBV11 CDR3 was expressed as 'VYNEQ' in all patients and was accompanied by the BJ2.1 fragment. In patients with chronic HB, the frequency of skewed TCRBV was inversely correlated with hepatitis B virus (HBV) DNA levels. The persistently skewed TCRBV gene families in HB patients may be associated with the development and maintenance of hepatitis. GMSP analysis of TCRBV gene families may be helpful in estimating disease status, and BV11 may be associated with HBV replication in patients with chronic HBV infection.

Multiple myeloma patients at peripheral blood stem cell harvest: Restricted usage of TCR beta variable families

The immune systems of multiple myeloma patients are suppressed by the disease itself, and this immunosuppression is further enhanced by standard therapies. The aim of our study was to evaluate the effects of initial chemotherapy and a peripheral blood mobilisation regimen on T-cell population diversity. Reverse transcription-polymerase chain reaction (RT-PCR) with a new set of primers, in combination with capillary electrophoresis, was established. The methodology was used to analyse the relative expression of 27 T-cell receptor beta variable gene families (BV families) in multiple myeloma patients undergoing peripheral blood stem cell harvest. We found that the overall BV family usage in these patients was restricted; the relative expression of 10 BV families was significantly depressed in patients compared to healthy donors. These findings demonstrate that the preparative regimen for autologous stem cell transplantation affects the T-cell population in terms of the restriction of its T-cell receptor diversity.

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

T-cell receptor (TCR) genomic loci undergo somatic V(D)J recombination, plus the addition/subtraction of nontemplated bases at recombination junctions, in order to generate the repertoire of structurally diverse T cells necessary for antigen recognition. TCR beta subunits can be unambiguously identified by their hypervariable CDR3 (Complement Determining Region 3) sequence. This is the site of V(D)J recombination encoding the principal site of antigen contact. The complexity and dynamics of the T-cell repertoire remain unknown because the potential repertoire size has made conventional sequence analysis intractable. Here, we use 5'-RACE, Illumina sequencing, and a novel short read assembly strategy to sample CDR3(beta) diversity in human T lymphocytes from peripheral blood. Assembly of 40.5 million short reads identified 33,664 distinct TCR(beta) clonotypes and provides precise measurements of CDR3(beta) length diversity, usage of nontemplated bases, sequence convergence, and preferences for TRBV (T-cell receptor beta variable gene) and TRBJ (T-cell receptor beta joining gene) gene usage and pairing. CDR3 length between conserved residues of TRBV and TRBJ ranged from 21 to 81 nucleotides (nt). TRBV gene usage ranged from 0.01% for TRBV17 to 24.6% for TRBV20-1. TRBJ gene usage ranged from 1.6% for TRBJ2-6 to 17.2% for TRBJ2-1. We identified 1573 examples of convergence where the same amino acid translation was specified by distinct CDR3(beta) nucleotide sequences. Direct sequence-based immunoprofiling will likely prove to be a useful tool for understanding repertoire dynamics in response to immune challenge, without a priori knowledge of antigen.

ORIGINAL ARTICLE: Repertoire and Clonality of T‐Cell Receptor Beta Variable Genes Expressed in Endometrium and Blood T Cells of Patients with Recurrent Spontaneous Abortion

Recurrent spontaneous abortion (RSA) is a relatively common disorder, the underlying causes of which are thought to be immunological in most cases. Expression profile and clonality pattern of T-cell receptor beta variable (TCRBV) genes in endometrium and blood of patients with RSA were investigated by semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) using BV gene-specific primers. Relative expression of each BV family was determined and clonal expansion of the over-expressed genes was assessed by analysis of CDR3 length polymorphism. Compared to blood, relative expression of four TCRBV genes was significantly higher in the endometrium of RSA group. Over-expressed genes, except for TCRBV3, all had restricted and oligoclonal patterns of expression in the endometrium. Endometrial T cells have a skewed TCRBV repertoire with restricted transcript heterogeneity, which is shared by both groups and minor variations observed in this pattern in RSA patients may reflect more recent and/or repeated exposure to nominal antigens or superantigens.

TCR spectratyping revealed T lymphocytes associated with graft-versus-host disease after allogeneic hematopoietic stem cell transplantation

Clonal expansion of T cells after allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been observed, but their characteristics remain to be fully elucidated. We report here that CD8+ T cells were the dominant T lymphocytes seen and T-cell repertoire diversity decreased dramatically during the first 3 months after allo-HSCT. Patients with GVHD grade II – IV had significantly lower T-cell repertoire diversity compared with non-GVHD patients. TCR beta variable gene (TCRBV) subfamily 8, 5.1, 5.2, 4, and 13 were the five most frequently expanded subfamilies among these patients. Among the 49 over-expanded clones identified, clonotype “TCR3-5” and “TCR18-5” were isolated from four patients with HLA-A2 allele and skin GVHD. Their frequencies correlated well with skin symptoms (i.e. rash). Moreover, they were detected in donors but not detected in recipients before transplantation. Lastly, three common TCRBV CDR3 motifs shared by T cells related with GVHD were discovered: TGDS, GLAG, and GGG. These findings suggest that TCR spectratyping is helpful for revealing GVHD-related T cells and may have utility in early diagnosis.

An improved methodology to detect human T cell receptor beta variable family gene expression patterns

Comprehensive gene expression analysis of the T cell receptor repertoire of an individual can be very useful in evaluating the immune response in a variety of conditions. Antibody-based analysis methods can detect approximately 60% of the human T cell receptor beta variable (TCRBV) proteins, while gene expression analysis, primarily through employment of the polymerase chain reaction (PCR), has had somewhat greater success in the detection of additional TCRBV families. Many of these previous PCR methods, however, have been unable to detect all 91 alleles of the human TCRBV genes. This is primarily due to either deficiencies in the amplification of all of the variable beta families, subfamilies, and alleles, or the prior lack of a systematic classification of the TCR variable family gene segment sequences. We describe here a real-time reverse transcription polymerase chain reaction-based method, which allows efficient automation and integration of amplification, detection, and analysis with sequence-specific detection of all T cell receptor beta variable gene families, subfamilies, and alleles. This method, which in itself contributes significant improvements over existing technologies through its comprehensiveness and efficiency, also functions independently of variables such as sample source and sample processing and has the ability to run on multiple real-time PCR platforms, affording one the implementation of personal preferences.

The T-cell receptor beta variable gene promoter is required for efficient V beta rearrangement but not allelic exclusion.

To investigate the role of promoters in regulating variable gene rearrangement and allelic exclusion, we constructed mutant mice in which a 1.2-kb region of the V beta 13 promoter was either deleted (P13(-/-)) or replaced with the simian virus 40 minimal promoter plus five copies of Gal4 DNA sequences (P13(R/R)). In P13(-/-) mice, cleavage, rearrangement, and transcription of V beta 13, but not the flanking V beta gene segments, were significantly inhibited. In P13(R/R) mice, inhibition of V beta 13 rearrangement was less severe and was not associated with any apparent reduction in V beta 13 cleavage. Expression of a T-cell receptor (TCR) transgene blocked cleavages at the normal V beta 13-recombination signal sequence junction and V beta 13 coding joint formation of both wild-type and mutant V beta 13 alleles. However, a low level of aberrant V beta 13 cleavage was consistently detected, especially in TCR transgenic P13(R/R) mice. These findings suggest that the variable gene promoter is required for promoting local recombination accessibility of the associated V beta gene segment. Although the promoter is dispensable for allelic exclusion, it appears to suppress aberrant V beta cleavages during allelic exclusion.

Disruption of the lineage restriction of TCR beta gene rearrangements.

Despite a common lymphoid recombinase, assembly of Ig genes is restricted to B cells, whereas TCR loci rearrange in T cells. Transcriptional promoters and enhancers are critical for the regulation of the recombination process. However, the specific function of such elements in conferring the lineage-restriction of V(D)J recombination remains poorly understood. To gain further insights into the mechanism restricting TCR beta-chain rearrangements to T cells, we generated mice in which an 11 kb region--containing the beta-chain constant region 2 and the TCR beta enhancer (E beta)--was replaced with the B cell specific Ig heavy-chain enhancer (E mu). Unlike the simple E mu to E beta replacement, this mutation allowed significant levels of D beta to J beta as well as V beta to DJ beta rearrangements in both T and B cells. Although the lineage restriction was disrupted, TCR beta allelic exclusion was still efficient in mutated T cells. Together these results demonstrate that changes in the activity of regulatory elements located at the TCR beta constant regions are sufficient to redirect the recombination pattern of TCR beta variable gene segments.

The Human T cell Receptor Beta Variable (TRBV) Genes

‘Human T Cell Receptor Beta Variable (TRBV) Genes’, the seventh report of the ‘IMGT Locus on Focus‘ section, comprises four tables: (1) ‘Number of human germline TRBV genes at 7q35 and potential repertoire’; (2) ‘Human germline TRBV genes at 7q35’; (3) ‘Human TRBV orphons on chromosome 9 (9p21)’, and (4) ‘Human TRBV allele table’. These tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr: 8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

T-cell receptor variable gene analysis of renal allograft-infiltrating cells in biopsy specimens using a nonradioisotopic micromethod.

A sensitive micromethod for T-cell receptor (TCR) analysis is needed for clonality analysis of renal allograft-infiltrating T cells (RAITs) obtained by needle biopsy. TCR cDNA was amplified by the anchored polymerase chain reaction and was hybridized with 28 different TCR beta variable (TCRBV) genes fixed on nylon membranes, and the percentage of each TCRBV gene was measured spectrophotometrically. The specificity and linearity of the hybridization technique and the constancy of the TCRBV percentages over a wide range of sample amounts were demonstrated by control experiments. Analysis of RAITs of biopsy specimens from four patients showed broad or skewed TCRBV usage, indicating the presence of polyclonal and oligoclonal RAIT populations, respectively. In one patient who received OKT3 immunosuppressive treatment, the TCRBV skewness was dramatically reduced after the treatment. We have established a powerful method for analyzing RAIT clonality, which is especially useful for monitoring RAIT dynamics after immunosuppression therapy.

Expression of T-cell receptor Vbeta2, 6 and 8 gene families in chronic adult periodontal disease.

Substantial evidence exists to suggest a role for T-cells in periodontal disease. As yet, however, the T-cell receptors remain to be characterised at the molecular level. The expression and the nucleotide sequence of genes from the T-cell receptor beta variable (TCRBV) gene families 2, 6 and 8 were analyzed in periodontal tissue from 24 patients with chronic adult periodontal disease (CAPD) and peripheral blood lymphocytes (PBL) of 16 of these patients. A restriction in the expression of these TCRBV gene families was detected in periodontal tissue from 14/24 patients with CAPD, and the pattern of gene expression was often different between individual patients; however there was no restriction in TCRBV gene expression in matched PBL samples from 8 of these 14 patients. Quantitative RT PCR analysis of samples from 5 CAPD patients who expressed all 3 TCRBV gene families in their periodontal tissues did not reveal any significant differences in the levels of gene expression in periodontal tissue and PBL. In contrast to the findings with some CAPD patients, genes from all 3 TCRBV families were always expressed in periodontal tissue and PBL from disease-free control subjects. PCR products from both the PBL and periodontal tissue of CAPD patients were cloned and sequenced; analysis of the nucleotide sequence revealed diversity with respect to the expression of TCRB joining (TCRBJ) and TCRB diversity (TCRBD) genes and the sequence of the junctional region in all samples analysed. In conclusion, in CAPD, the pattern of TCRBV gene expression in periodontal tissue is often but not always different from that in PBL and healthy periodontal tissue, which may indicate, in some cases, a local influence on particular T-cell subsets which is relevant to the pathogenesis of periodontal disease. However, the expressed TCRB genes are heterogeneous at the nucleotide level, emphasising the underlying complexity at the molecular level in the local T-cell response in CAPD.

Enhancement of thymopoiesis after bone marrow transplant by in vivo interleukin-7

Bone marrow transplantation (BMT) is followed by a period of profound immune deficiency, during which new T lymphocytes are generated from either stem cells or immature thymic progenitors. Interleukin-7 (IL-7) induces proliferation and differentiation of immature thymocytes. We examined whether the in vivo administration of IL-7 to mice receiving BMT would alter thymic reconstitution. Lethally irradiated C57BL/6 mice received syngeneic BMT, followed by either IL-7 or placebo from days 5 to 18 post-BMT. At day 28, BMT recipients that had not received IL-7 had profound thymic hypoplasia (< 5% of normal), with relative increases in the numbers of immature thymocytes, decreased numbers of mature peripheral (splenic) T lymphocytes, and severely impaired T- and B-cell function. In contrast, transplanted mice treated with IL-7 had normalization of thymic cellularity, with normal proportions of thymic subsets and T-cell receptor beta variable gene (TCRV beta) usage, normal numbers of peripheral CD4+ T lymphocytes, and improved antigen-specific T- and B-cell function. In the BMT-IL-7 mice, there was an eightfold increase in the number of immature CD3-CD4-CD8- thymocytes in G2-M of the cell cycle, indicating that restoration of thymic cellularity was due to enhanced proliferation of immature thymic progenitors. Similar effects following IL-7 administration were also observed when donor bone marrow was depleted of mature T lymphocytes, indicating that IL-7 administration affected immature hematopoietic progenitors. IL-7 promotes thymic reconstitution after BMT, and may be useful in preventing post-BMT immune deficiency.

Enhancement of Thymopoiesis After Bone Marrow Transplant by In Vivo Interleukin-7

Abstract Bone marrow transplantation (BMT) is followed by a period of profound immune deficiency, during which new T lymphocytes are generated from either stem cells or immature thymic progenitors. Interleukin-7 (IL-7) induces proliferation and differentiation of immature thymocytes. We examined whether the in vivo administration of IL-7 to mice receiving BMT would alter thymic reconstitution. Lethally irradiated C57BL/6 mice received syngeneic BMT, followed by either IL-7 or placebo from days 5 to 18 post-BMT. At day 28, BMT recipients that had not received IL-7 had profound thymic hypoplasia (&lt; 5% of normal), with relative increases in the numbers of immature thymocytes, decreased numbers of mature peripheral (splenic) T lymphocytes, and severely impaired T- and B-cell function. In contrast, transplanted mice treated with IL-7 had normalization of thymic cellularity, with normal proportions of thymic subsets and T-cell receptor beta variable gene (TCRV beta) usage, normal numbers of peripheral CD4+ T lymphocytes, and improved antigen- specific T- and B-cell function. In the BMT-IL-7 mice, there was an eightfold increase in the number of immature CD3-CD4-CD8- thymocytes in G2-M of the cell cycle, indicating that restoration of thymic cellularity was due to enhanced proliferation of immature thymic progenitors. Similar effects following IL-7 administration were also observed when donor bone marrow was depleted of mature T lymphocytes, indicating that IL-7 administration affected immature hematopoietic progenitors. IL-7 promotes thymic reconstitution after BMT, and may be useful in preventing post-BMT immune deficiency.