PCR-based genotyping and haplotype analysis of human TCRBV gene segment polymorphisms

T-large granular lymphocyte leukemia: current molecular concepts

T-large granular lymphocyte (T-LGL) leukemia is a chronic and often indolent T cell lymphoproliferation characterized by extreme expansion of a semi-autonomous cytotoxic T lymphocyte (CTL) clone. Clinically, T-LGL can be associated with various cytopenias; neutropenia constitutes the most frequent manifestation. LGL clone represents a pathologic counterpart of the cytotoxic effector T cell but an abnormal memory CD8 cell seems to provide the supply of the matured LGL population. Analysis of clonal T cell receptor (TCR) rearrangement and complementarity determining region 3 (CDR3) of the TCR beta-chain is a useful tool to investigate clonal expansions, track the frequency of expanded clones and also clinically useful to monitor the response to therapy. The lessons learned from molecular analysis of clonal repertoire support a clinically-derived conclusion that the LGL clone arises in the context of an initially polyclonal immune response or an autoimmune process. Consequently, specific manifestations of T-LGL may be a result of the recognition spectrum of the transformed clone and the cytokines it produces. Due to the often monoclonal manifestation, T-LGL constitutes a suitable model to investigate polyclonal CTL-mediated processes. Application of new technologies, including TCR repertoire analysis by sequencing, clonotypic quantitative PCR and VB flow cytometry facilitate clinical diagnosis and may allow insights into the regulation of TCR repertoire and consequences resulting from the contraction of clonal diversity.

Variability in TRBV haplotype frequency and composition in Caucasian, African American, Western African and Chinese populations

The polymorphic T-cell receptor Vbeta (TRBV) genes encode much of the variable region of the T-cell receptor beta chain. Analysis of allele frequencies of three closely linked polymorphic TRBV genes, TRBV7-3, TRBV9 and TRBV6-4, was undertaken in several populations. The frequencies of these alleles are not significantly different in populations of Caucasians, African Americans and Western Africans. However, Chinese population is extremely homogenous at all three loci. The current study identifies the existence of haplotypic relationships between alleles of these genes in the Caucasian population. The ORF allele TRBV7-3*A3 is found exclusively on chromosomes bearing TRBV9*A2 and TRBV6-4*A2 in this cohort. In contrast, TRBV7-3*A1 and the null allele TRBV7-3*A2 are associated only with TRBV9*A1 and TRBV6-4*A1. This pattern of linkage disequilibrium (LD) is altered in the African American and Western African populations. In these cohorts, there is a marked reduction in LD between alleles of TRBV7-3 and TRBV9. This study is consistent with previous population genetic studies wherein African-derived samples have a greater level of genetic diversity compared to Caucasians. These data also demonstrate that patterns of LD are not consistent across the entire TRBV locus.

T-cell receptor BV gene segment polymorphisms in healthy elderly individuals from the south of Brazil

The ageing of the immune system (immunosenescence) is believed to be involved in both morbidity and mortality in elderly humans due to a higher incidence of infections, autoimmune diseases, cancers and other pathological situations. As any specific immune response involves recognition of antigens by T cells, the ability to develop a given immune response is also dependent on the T-cell repertoire available at a given time point. Different T-cell receptor beta variable segment (BV) (TCRBV) gene segment alleles have been associated with diseases in various human populations. In the present work we analysed the allelic frequencies of four biallelic polymorphisms in TCRBV gene segments (TCRBV3S1, TCRBV13S5, TCRBV13S6 and TCRBV18) in healthy elderly human subjects (80 years old or more) from the south of Brazil, where life expectancies reach similar levels to those observed in developed countries. Except for allele 2 of the TCRBV13S6 polymorphism, which was more frequent in elderly than in young individuals (P = 0.0105), there were no differences in allele or genotype frequencies between young and elderly individuals. The data suggest that there is no direct correlation between the TCRBV3S1, TCRBV13S5 and TCRBV18 polymorphisms analysed and healthy senescence in this particular group of elderly individuals. The higher frequency of TCRBV13S6 allele 2 in healthy elderly individuals should be confirmed in other samples to establish the significance of this finding.

Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus

The T-cell receptor (TCR) plays a central role in the immune system, and > 90% of human T cells present a receptor that consists of the alpha TCR subunit (TCRA) and the beta subunit (TCRB). Here we report an analysis of 63 variable genes (BV), spanning 553 kb of TCRB that yielded 279 single-nucleotide polymorphisms (SNPs). Samples were drawn from 10 individuals and represent four populations-African American, Chinese, Mexican, and Northern European. We found nine variants that produce nonfunctional BV segments, removing those genes from the TCRB genomic repertoire. There was significant heterogeneity among population samples in SNP frequency (including the BV-inactivating sites), indicating the need for multiple-population samples for adequate variant discovery. In addition, we observed considerable linkage disequilibrium (LD) (r(2) > 0.1) over distances of approximately 30 kb in TCRB, and, in general, the distribution of r(2) as a function of physical distance was in close agreement with neutral coalescent simulations. LD in TCRB showed considerable spatial variation across the locus, being concentrated in "blocks" of LD; however, coalescent simulations of the locus illustrated that the heterogeneity of LD we observed in TCRB did not differ markedly from that expected from neutral processes. Finally, examination of the extended genotypes for each subject demonstrated homozygous stretches of >100 kb in the locus of several individuals. These results provide the basis for optimization of locuswide SNP typing in TCRB for studies of genotype-phenotype association.

A new coding region polymorphism of human IgLC2

A new allelic form of the human IgLC2 gene is described. The marker involves a T to C substitution in the C lambda 2 constant region gene, a silent substitution at amino acid coding position 178 (YAASSYLSL) and two substitutions in the 3'-flanking region. Analysis of IgLC2 alleles in a total of 60 individuals has indicated a frequency of 0.32 for the new allele, which has been designated IgLC2*B2. The *B1 and *B2 alleles encode T and C, respectively, at nucleotide position 212 in the IgLC2 coding region. Both the *B1 and *B2 alleles are found in individuals homozygous for the single-copy RFLP allele of IgLC2/IgLC3 (8 kb EcoRI). Knowledge of alleles of this marker will be important for studies on the expression of the IgLC2 and IgLC3 isotypes in normal and autoimmune lymphocyte populations, as the coding regions of the two isotypes differ only at this position. The marker will also be useful in further studies of linkage with other IgLV and IgLC markers and to establish possible correlations with susceptibility to autoimmune disorders.

The nonfunctional allele TCRBV6S1B is strongly associated with Helicobacter pylori infection

To determine genetic susceptibility factors for Helicobacter pylori infection, polymorphic T-cell receptor gene elements were investigated in 203 H. pylori-infected individuals and 180 uninfected individuals (controls). H. pylori infection is highly associated with individuals homozygous for the nonfunctional TCRBV6S1B element (odds ratio = 5.9; chi(2) = 13; P = 0.00032; P value corrected for multiple comparisons [Bonferroni correction] = 0. 00063).

Analysis of TCRAV and TCRBV repertoires in healthy individuals by microplate hybridization assay

We have developed an adaptor ligation PCR-based microplate hybridization assay (MHA) for analysis of T cell receptor alpha chain variable region (TCRAV) and T cell receptor beta chain variable region (TCRBV) repertoires. Forty three TCRAV and thirty eight TCRBV-specific probes were immobilized onto microplate wells in water-soluble carbodiimide. After hybridization of 5'-biotinylated PCR products, quantitative ELISA was carried out and followed by automated colorimetric reading. The conditions for immobilization and hybridization were optimized using representative TCRBV-specific probes. The sensitivity of MHA allows us to detect as low as 40 pg of biotinylated PCR products. The frequencies of individual V segments obtained by MHA were consistent with those obtained by FACS analysis and reverse dot blot assays. Analysis of the entire TCRAV and TCRBV repertoires could be done using a single 96-well plate, and completed in less than 6 h. Simplicity and reproducibility of this method make it suitable for routine laboratory use. The expression of TCRAV and TCRBV segments was next studied in peripheral blood mononuclear cells (PBMC) of 14 healthy donors using the newly developed MHA method. TCRAV8S1, TCRAV23S1, TCRBV2S1, TCRBV3S1, TCRBV4S1, and TCRBV6S5 were highly expressed in PBMC. Further, the TCRAV repertoires among individuals were less variable compared to the TCRBV repertoires. Interestingly, considerable variations in the expression levels of BV3S1, BV4S1, and BV17S1 were observed among individuals. One polymorphic site was found at the coding region of BV4S1, and there were two alleles. These results suggest that variable expression among individuals may be associated with unknown allelic polymorphism in coding and/or regulatory regions of these TCRBV segments, or with disparity in HLA genes.

Synergy between T cell receptor beta gene polymorphism and HLA-DR4 in susceptibility to rheumatoid arthritis

OBJECTIVE

To investigate the etiologic significance of germline polymorphisms in the T cell receptor beta variable region 6S7 (TCRBV6S7) gene segment and adjacent loci in susceptibility to rheumatoid arthritis (RA).

METHODS

Ten TCRB allelic polymorphisms were analyzed from 3 groups of white women: 112 with RA, 72 with systemic lupus erythematosus, and 70 healthy controls. All participants were also HLA typed.

RESULTS

HLA-DR4+ RA patients showed significantly increased frequencies of TCRBV6S7*1, 13S5P*1 (an allelic variant of BV13S5 promoter), and 12S4*2, compared with healthy controls. The combination of DR4 with either BV6S7*1, 13S5P*1, or 12S4*2 conferred greater risk for RA than HLA-DR4 alone. Pairwise analyses showed a high degree of linkage disequilibrium (P = 10(-5)-10(-8)) between these 3 TCRBV loci that span 47 kilobases (kb).

CONCLUSION

Our data suggest that a TCR gene segment in or linked to this 47-kb region may be involved in genetic susceptibility to RA through an interaction with HLA-DR4.

Comparison of human and mouse T-cell receptor variable gene segment subfamilies

Like the immunoglobulin Igh-V and Igk-V gene families, the human or mouse TCRV gene families may be grouped into subfamilies displaying > 75% nucleic acid sequence similarity among their members. Systematic interspecies sequence comparisons reveal that most mouse Tcr-V subfamilies exhibit clear homology to human TCRV subfamilies (> 60% amino acid sequence similarity). Homologous pairs of TCRV genes in mice and humans show higher sequence similarity than TCRV genes from different subfamilies within either species, indicating transspecies evolution of TCRV genes. Mouse and human homologues show conservation of their relative map order, particularly in the 3' region and a similar sequential and developmentally programmed expression. When the V regions from both species were analyzed together, local length differences and conserved residues in the loop regions were revealed, characteristic of each of the four TCRV families.