T cell receptor CDR3 loop length repertoire is determined primarily by features of the V(D)J recombination reaction

The third complementarity-determining region (CDR) of the TCR alpha and beta chains forms loops that engage amino acid residues of peptides complexed with MHC. This interaction is central to the specific discrimination of antigenic-peptide-MHC complexes by the TCR. The TCRbeta chain CDR3 loop is encoded by the Dbeta gene segment and flanking portions of the Vbeta and Jbeta gene segments. The joining of these gene segments is imprecise, leading to significant variability in the TCRbeta chain CDR3 loop length and amino acid composition. In marked contrast to other pairing antigen-receptor chains, the TCR beta and alpha chain CDR3 loop size distributions are relatively narrow and closely matched. Thus, pairing of TCR alpha and beta chains with relatively similar CDR3 loop sizes may be important for generating a functional repertoire of alpha beta TCR. Here we show that the TCRbeta chain CDR3 loop size distribution is minimally impacted by TCRbeta chain or alpha beta TCR selection during thymocyte development. Rather, this distribution is determined primarily at the level of variable-region gene assembly, and is critically dependent on unique features of the V(D)J recombination reaction that ensure Dbeta gene segment utilization.     

T-cell receptor variable beta genes show differential expression in CD4 and CD8 T cells.

Studies in transgenic and inbred strains of mice have shown that the critical molecular interactions controlling positive selection involve major histocompatibility complex (MHC), T-cell receptor (TCR), and CD4 or CD8 coreceptor molecules. Correlations have been established between MHC gene products and the percentage of CD4 or CD8 T cells that express specific variable (V) beta-gene products as part of the alpha beta heterodimer. These studies have important implications regarding potential mechanisms of HLA-linked autoimmune diseases in humans. If similar interactions are required for positive selection in humans, one would predict that the TCR repertoire expressed by mature, peripheral blood CD4 and CD8 T cells would vary. To test this hypothesis the expression of specific TCR V beta-region genes by CD4 and CD8 T cells from healthy individuals was compared using both triple-color flow cytometry and polymerase chain reaction based experimental approaches. The results show that the TCR repertoire does vary as a function of CD4 and CD8 T-cell subsets. Among unrelated individuals certain V beta genes were consistently overrepresented in the CD4 population (V beta-5.1, -6.7a, and -18); some were skewed to the CD8 population (V beta-14) while others showed variable patterns (V beta-12 and -17). Deletion of entire V beta gene families was not observed suggesting that this is a rare event in humans. Attempts to correlate the expressed TCR repertoire in humans with HLA alleles will require consideration of these differences in expression as a function of subset.     

HLA-DRB1 molecules and antigenic experience shape the repertoire of CD4 T cells

Forces influencing the composition of the mature TCR repertoire have been well studied in the mouse. In particular, the contribution of MHC molecules in negative and positive selection events of T lymphocytes has been established. To understand whether the allelic polymorphism of HLA-DRB1 molecules can shape the human TCR repertoire, we compared the usage of TCR Vβ segments in two cohorts of unrelated individuals who were selected for the expression of HLA-DRB1 alleles. To investigate the potential role of antigenic experience in shaping the TCR repertoire, we compared the usage of Vβ gene elements in CD45RO⁻ CD4⁺ (naive) T cells versus CD45RO⁺ CD4⁺ (memory) T cells. A correlation between Vβ gene segment usage and HLA-DRB1 alleles could be demonstrated for the repertoire of the naive CD4⁺ T cells, suggesting a shaping force of the HLDRB1 allele on the peripheral TCR repertoire. While the HLA-DRB1 imposed profile in Vβ distribution was maintained in CD45RO⁺ CD4⁺ T cells, it was less pronounced, indicating that antigenic experience modulates the functional TCR repertoire.     

Population study of T cell receptor V beta gene usage in peripheral blood lymphocytes: differences in ethnic groups.

The T cell receptor (TCR) V beta repertoire in peripheral blood lymphocytes (PBL) of a large number of healthy individuals was analysed by quantifying V beta-specific mRNA using the method of anchored multiprimer DNA amplification and a reverse dot blot assay. Among 16 V beta gene families examined, particular V beta genes were noted to be unequally expressed in the PBL of 70 healthy donors. The frequently used genes belong to the V beta 4, 5, 6, 8 and 13 (12) families, while V beta 1, 9 and 15 were the least frequently used gene families. This bias in gene usage was observed in all individuals. Marked deviation from the mean percentage usage was noted for some V beta genes in individuals when their PBL were examined serially, but the common pattern of biased usage was not grossly distorted. When the TCR repertoire of different ethnic groups was examined, a lower mean frequency of V beta 3.2 was seen in the repertoire of 19 Caucasians compared with 25 age-matched Samoans (P < 0.003). Conversely, the expression of V beta 5.1 and V beta 5.3 was higher in Caucasians than in 51 age-matched Polynesians (Maoris and Samoans, P < 0.003). Considering the 20% co-efficient of variation in the estimate of V beta gene usage, our data from 70 unrelated individuals suggest that in PBL, individual variations in the TCR repertoire were superimposed upon a common biased usage of V beta genes in the general population.     

Silent allelic variants of a T-cell receptor V beta 12 gene are present in diverse human populations.

Amino acid substitutions in variable regions of the T-cell receptor (TCR) can alter T-cell reactivity; however, relatively little is known about the extent of allelic variation in human TCR coding sequences. In the present studies, coding region variation in the human TCR V beta 12.2 gene was examined in detail. Virtually the entire V beta 12.2 coding region was screened for nucleotide substitutions by single-stranded conformational polymorphism analysis. Four alleles were identified in a sample population of 90 unrelated people from diverse genetic backgrounds. Three of the alleles were common, with estimated frequencies of 0.32, 0.47, and 0.20. Sequence analyses revealed that variation between the alleles was confined to three single-base differences in codons 24, 31, and 45; none of these changes altered the amino acid sequence. No evidence for other coding region differences in this gene were found. This analysis suggests that coding region variation in V beta 12.2 is limited, and amino acid sequence is highly conserved.     

T cell receptor DJ but not VDJ rearrangement within a recombination substrate introduced into a pre-B cell line

To elucidate mechanisms that regulate ordered and tissue-specific assembly of Ig and TCR variable region gene segments, we have introduced a recombination substrate comprised of germline TCR beta V, D, and J gene segments into an Abelson murine leukemia virus-transformed pre-B cell line that actively rearranges endogenous Ig H chain variable region gene segments but does not rearrange endogenous light chain or TCR variable region gene segments. We find that these cells efficiently join D beta segments to J beta segments within the mini-locus, but that they do not make any detectable site-specific rearrangements of the introduced V beta segment even though it is closely linked in the same construct to the D beta. These findings suggest that factors necessary for V beta to (D beta)J beta joining may be absent in these pre-B cells and also imply that the order in which TCR V beta, D beta, and J beta segments are rearranged can be influenced by factors other than the 12/23 recombination rule. Furthermore, in agreement with the an accessibility model of VDJ recombinase control, the D beta region of the construct was found to be relatively more sensitive to DNAase I digestion in isolated nuclei when compared to the unrearranged V beta region.     

Analysis of the TCR alpha-chain rearrangement profile in human T lymphocytes

The size of the available human alphabeta T cell repertoire is difficult to determine and is open to debate. Empirical analysis of TCR beta-chain diversity reveals approximately 10(6) different beta chains in peripheral blood. Due in part to locus complexity, comparable information for TCR alpha is lacking. Rather, current estimates for human TCR alpha diversity, and hence, total repertoire diversity, are based on theoretical analyses that assume equal probabilities of rearrangement between any V alpha gene and J alpha gene. Here, we report on a systematic locus-wide rearrangement analysis of the TCR alpha-chain in human T cells. We first demonstrate that the V-J alpha recombination in the thymus is not random but depends on the reciprocal V alpha and J alpha position within the locus. Characterization of the frequency of gene usage combined with identification of five previously unrecognized pseudogenes enables us to empirically estimate the human TCR alpha combinatorial repertoire. The number of V-J alpha combinations achieved is approximately 44-56% of the total combinatorial possibilities, significantly lower than theoretical estimates. We also demonstrate that TCR alpha-chain diversity in peripheral T lymphocytes mimics the same general patterns of rearrangement as observed in the thymus, and these patterns appear conserved among different individuals. This unexpected observation indicates that, unlike the TCR beta locus, the human TCR alpha-chain repertoire is primarily predetermined by genetic recombination and its size is restricted by limits on the combinatorial repertoire rather than post-thymic selection.     

Fractal Organization of the Human T Cell Repertoire in Health and after Stem Cell Transplantation

T cell repertoire diversity is generated in part by recombination of variable (V), diversity (D), and joining (J) segments in the T cell receptor β (TCR) locus. T cell clonal frequency distribution determined by high-throughput sequencing of TCR β in 10 stem cell transplantation (SCT) donors revealed a fractal, self-similar frequency distribution of unique TCR bearing clones with respect to V, D, and J segment usage in the T cell repertoire of these individuals. Further, ranking of T cell clones by frequency of gene segment usage in the observed sequences revealed an ordered distribution of dominant clones conforming to a power law, with a fractal dimension of 1.6 and 1.8 in TCR β DJ and VDJ containing clones in healthy stem cell donors. This self-similar distribution was perturbed in the recipients after SCT, with patients demonstrating a lower level of complexity in their TCR repertoire at day 100 followed by a modest improvement by 1 year post-SCT. A large shift was observed in the frequency distribution of the dominant T cell clones compared to the donor, with fewer than one third of the VDJ-containing clones shared in the top 4 ranks. In conclusion, the normal T cell repertoire is highly ordered with a TCR gene segment usage that results in a fractal self-similar motif of pattern repetition across levels of organization. Fractal analysis of high-throughput TCR β sequencing data provides a comprehensive measure of immune reconstitution after SCT.     

Human T‐cell receptor V gene segment of alpha and beta families: A revised primer design strategy

The application of human TCR in cancer immunotherapy has gained momentum with developments in tumor killing strategies using endogenous adaptive immune responses. The successful coverage of a diverse TCR repertoire is mainly attributed to the primer design of the human TCR V genes. Here, we present a refined primer design strategy of the human TCR V gene by clustering V gene sequence homolog for degenerate primer design based on the data from IMGT. The primers designed were analyzed and the PCR efficiency of each primer set was optimized. A total of 112 alpha and 160 beta sequences were aligned and clustered using a phylogram yielding 32 and 27 V gene primers for the alpha and beta family. The new primer set was able to provide 93.75% and 95.63% coverage for the alpha and beta family, respectively. A semi‐qualitative approach using the designed primer set was able to provide a relative view of the TCR V gene diversity in different populations. Taken together, the new primers provide a more comprehensive coverage of the TCR gene diversity for improved TCR library generation and TCR V gene analysis studies.     

Evolution of antibody and T-cell receptor V genes--the antibody repertoire might have evolved abruptly

Structural homology present between antibody genes and T-cell antigen receptor (TCR) genes include not only V genes but also D and J segments. This may indicate that the gene duplication occurred involving a large chromosomal region containing all these genes and segments. It is conceivable, however, that the TCR gene complex is the ancestor, as effective selective forces to diversity V gene sequences are provided by MHC polymorphism only for TCR V genes. Consequently, we argue that the antibody repertoire may have emerged rather abruptly in evolution.     

In vivo selection of a TCR Vbeta repertoire directed against an immunodominant influenza virus CTL epitope

Little is known about the mechanisms governing TCR repertoire selection in response to foreign antigens. Here, we evaluate the molecular features of the murine C57BL/6 (B6) TCR Vbeta repertoire directed at the NP(366-374) immunodominant epitope of the influenza virus nucleoprotein. Common or 'public' beta chains are shared among individuals following either primary or secondary infection. Importantly, repertoire diversity decreases substantially after a second viral exposure due to enrichment of TCRs sharing Vbeta CDR3 loops of identical length and highly related amino acid sequences. TCRs from these secondary T cell populations possess greater overall avidity for the NP(366-374)/D(b) complex compared to those from the primary repertoire. Thus, expansion of CD8(+) T cells expressing a favored germline Vbeta gene segment in the primary response and further selection for CDR3beta loops during the secondary response, contribute to optimization of immune recognition against certain viral epitopes.     

T-cell receptor V delta-J alpha rearrangements in human thymocytes: the role of V delta-J alpha rearrangements in T-cell receptor-delta gene deletion.

The differentiation mechanisms that force thymocytes into the T-cell receptor (TCR)-alpha beta or TCR-gamma delta lineage are poorly understood, but rearrangement processes in the TCR-alpha/delta locus are likely to play an important role. It is assumed that the TCR-delta gene is deleted prior to V alpha-J alpha rearrangements by rearrangement of the so-called TCR-delta-deleting elements delta Rec and psi J alpha. However, the TCR-delta gene can also be deleted via V delta-J alpha rearrangements. We studied the different TCR-delta-deleting rearrangements of V delta 1, delta Rec, V delta 2 and V delta 3 to J alpha gene segments in human thymocytes and peripheral blood using polymerase chain reaction analysis. The V delta 1 gene segment is the most upstream V delta gene segment tested and appears to rearrange to almost all J alpha gene segments. In contrast, the delta Rec and V delta 2 gene segments only rearrange to the 5'-located J alpha gene segments, thereby preserving an extensive TCR-alpha combinatorial diversity, because most J alpha gene segments are kept available for subsequent V alpha-J alpha rearrangements. Based on our combined data we hypothesize that the different V delta gene segments and the delta Rec gene segment play different roles in T-cell development with regard to TCR-delta deletion.     

Polymorphism of the human T cell receptor alpha chain variable genes: identification of a highly polymorphic V gene probe

In this study, we report the RFLP of the human T cell receptor (TCR) alpha chain variable gene segments. Using DNA samples from 20 individuals and three restriction endonucleases (BamHI, EcoRI and HindIII), the degree of RFLP of a number of different V gene segments was defined. Half of the V alpha subfamilies (6/12) were characterized by a predominant hybridization pattern, with only a few individuals displaying a second pattern. However, one particular V gene family, V alpha 6, has at least five allelic forms that segregated consistently in familial studies. The V alpha polymorphisms revealed in this study, together with those exhibited by V beta gene subfamilies, should prove useful in studying possible associations between TCR gene usage and disorders of the immune system.     

T-Cell Receptor Identification of an Oligodendrocyte-Specific Autoreactive Cytotoxic T-Cell Clone Without Self Restriction

In addition to myelin basic protein (MBP) and proteolipid protein (PLP), oligodendrocyte (Od) membrane autoantigens, such as the glycoprotein M2/MOG, could participate in the pathogenesis of autoimmune demyelinating diseases of the central nervous system (CNS), such as experimental allergic encephalomyelitis (EAE) or multiple sclerosis (MS). We have described an Od-specific autoreactive and cytotoxic T-cell clone, named C2, which recognized M2/MOG without conventional MHC restriction. In order to analyse the Od/C2 interaction, we determined the alpha/beta T-cell receptor (TCR) variable region usages and structures of C2. Monoclonal antibody stainings of C2 and nucleotide sequences show that the alpha chain is composed of a V alpha 5 and a J alpha identical to J alpha 18BBM142 gene segments, and that the TCR beta chain is composed of V beta 17a, D beta 2.1 and J beta 2.2 gene segments indicating that C2 used a conventional alpha/beta TCR for M2/MOG recognition.     

Systematic study of human αβ T cell receptor V segments shows allelic variations resulting in a large number of distinct T cell receptor haplotypes

The variation of the αβ T cell receptor (TCR) results mainly from rearrangements of germ-line V, D and J elements combined with the processes of N- and P-region addition. In addition to this extensive diversity, diallelic polymorphism is also recognized in V regions of β loci. Four such polymorphisms have previously been defined, but the full extent of such variation has not yet been established. To investigate allelic polymorphism, we used a strategy based on V locus-specific polymerase chain reaction and single-strand conformation polymorphisms. Studying the two Vβ 2 loci and the Vα8.1 locus, we found that all exhibited a coding polymorphism. One of the Vβ 2 loci proved to be the first multiallele segment to be recognized, with three common variants. The second Vβ 2 locus, for which none of the two alleles has been identified in cDNA, appeared in fact to be a Vβ orphon, in abnormal location on the chromosome 9. A yeast artificial chromosome containing part of the TCRB locus allowed us to place the first Vβ 2 segment on the known map to define haplotypes with two other polymorphic segments: Vβ 1 and Vβ 6.7. Multiple distinct haplotypes result from combinations between these polymorphic loci, showing that Vβ regions are highly variable between individuals. Two alleles exist at the Vα8.1 segment and both are expressed. This represents the first example of a frequent coding polymorphism for TCRA gene. The distribution of allele frequencies for these segments suggest the action of balancing selection. These data add a further dimension to TCR polymorphism and suggest new candidates to explore TCR-encoded susceptibility to autoimmune diseases.     

Biased T cell receptor V alpha region repertoire in the synovial fluid of rheumatoid arthritis patients.

Synovial T lymphocytes seem to contribute to the pathogenesis of rheumatoid arthritis (RA). Since very little is known about the structural heterogeneity of their T cell antigen receptors (TcR), we analyzed TcR alpha chain mRNA of synovial fluid T cells from two RA patients. TcR alpha chain cDNA was amplified by the polymerase chain reaction with single-sided specificity for the alpha chain constant (C alpha) gene segment, and the nucleotide sequences of 51 functionally rearranged cDNA clones were determined. Twenty different V alpha genes and 26 different J alpha gene segments were utilized in these cDNA clones. Three of the V alpha gene segments which are frequently (8%-17% total) expressed in synovial fluid T cells have rarely been found in the TcR repertoire of peripheral blood T cells from healthy individuals. The T cell responses in the rheumatic synovia analyzed here are not oligoclonal, but the usage of TcR V alpha genes is biased.     

Polymorphism in human T cell receptor alpha chain variable region genes

Polymorphism of human T cell antigen receptor (TCR)alpha genes was detected by restriction fragment length polymorphism (RFLP). Individual TCR alpha gene segments showed limited polymorphism in that few restriction enzymes revealed polymorphism in genomic DNA samples and when RFLP were detected only two or three allelic forms were observed. A rabbit TCR alpha cDNA clone (VJR5) detected polymorphism in human DNA samples digested with PvuII or MspI. In order to characterize the human V alpha genes detected by the rabbit probe, genomic clones hybridizing with the VJR5 probe were isolated and characterized. A probe derived from a human genomic clone (HUTAVR5) hybridized with some but not all fragments detected by the rabbit VJR5 probe. The data suggest that the rabbit probe hybridized with two distinct human TCR alpha V genes and that polymorphism of each gene was detectable by only one restriction enzyme. In contrast to the limited polymorphism of TCR alpha genes detected by individual markers, extensive heterogeneity of TCR alpha genes was observed in the combination of markers present in haplotypes. Six RFLP were used as TCR alpha markers to define haplotypes in 20 parents and 53 offspring from 10 families and 17 different combinations of markers were observed. The observation that TCR alpha haplotypes include numerous combinations of markers that individually show limited polymorphism suggests that recombination may occur frequently within the TCR alpha gene complex.