Influence of human leukocyte antigen genes on TCR V gene segment frequencies

Human leukocyte antigen (HLA)-dependent selection mechanisms exerted during thymic maturation are supposed to be main contributing factors to the genetic predetermination of the TCR repertoire and may have a detectable effect on adult peripheral blood lymphocyte V segment frequencies. Here, we analyzed whether polymorphic or non-polymorphic HLA determinants are associated with selected expression of some V gene segment specificities. We first examined the reactivity of 17 V segment specific mAb on purified CD4+ and CD8+ cell fractions in 10 unrelated people. We found a significant overexpression of only three V segment products (V beta 2, V beta 5.1 and V beta 6.7) in CD4+ and none in CD8+ cell fractions in most individuals. Skewing of certain V beta segments by non-polymorphic HLA determinants (i.e. class II for CD4+ and class I for CD8+ cells) is therefore more limited (3/17) than previously thought. Considering the effects of polymorphic HLA determinants, we compared TCR V segment frequencies in HLA-identical siblings to sibling pairs who differ at one or both HLA haplotypes, using 13 V beta specific mAb. In pairwise comparisons, we found that the HLA complex had no detectable effect on TCR repertoire in five large families with multiple siblings. Together, these observations suggest that HLA-predicted selection mechanisms exerted during thymic maturation might not have a predominant influence shaping the TCR repertoire of normal adults.

TCR gene segments from at least one third of V alpha subfamilies rearrange at the delta locus

Using PCR and an experimentally validated V alpha subfamily-specific oligonucleotide panel (V alpha 1-w29), we have investigated whether the TCR delta chain may increase its combinatorial diversity by using V genes considered as alpha chain-specific. We show that at least 10 distinct human V alpha segments rearrange at the J delta locus, leading to scrambling of the two V gene repertoires. Fifty-five per cent of the V alpha/J delta transcripts characterized here were in frame. The 17 V alpha/C delta chains analysed included an extended CDR3 region with up to 18 aa encoded by the junctional region. In addition, a new J delta segment (J delta 4) has been characterized. Together, these findings demonstrate that combinatorial diversity in the human delta locus is larger than previously thought.

Limited T-cell receptor diversity in liver-infiltrating lymphocytes from patients with primary biliary cirrhosis

Primary biliary cirrhosis is associated with the presence of high-titer anti-mitochondrial autoantibodies as well as T-cell infiltration of the liver, suggesting the involvement of autoimmune mechanisms. We have studied here the sequences of T-cell receptor alpha and beta chains expressed by T-cell clones derived from liver-infiltrating lymphocytes of two patients with primary biliary cirrhosis. Among the eight clones studied from the first patient, four expressed the same member of the V beta 6 subfamily, associated with either V alpha 4 (three clones) or V alpha 21 (one clone) gene segment. Two other clones expressed an identical V beta 12 transcript, and two in-frame alpha chain transcripts, involving V alpha 2 and V alpha 7 gene segments. From the second patient, eight out of the nine clones were found to rearrange V beta 17-J beta 2.1 and V alpha 3 gene segments. The remaining clone expressed distinct T-cell receptor chains, involving V beta 9 and V alpha 11 gene segments. As deduced from the analysis of their junctional regions, the eight T-cell clones expressing V beta 17/V alpha 3 gene segments derived from only three different T cells. Furthermore, conserved amino acid motifs were found to be encoded in both the alpha and the beta-chain junctional regions. Together, these data show a local amplification of unique T lymphocytes in both patients. The use of identical V beta J beta and V alpha gene segments with similar junctional sequences by three different cells, evidenced in one of the two cases, strengthens the view that liver-infiltrating T lymphocytes are selected locally by autoantigens in PBC.

The use of anchored polymerase chain reaction for the study of large numbers of human T-cell receptor transcripts

Anchored-PCR (A-PCR) is an approach designed to amplify and clone sequences with unknown 5' or 3' extremities. A-PCR is therefore appropriate for studying variable region of T-cell receptors (TCRs) expressed in polyclonal T-cell populations since it does not prejudge which variable gene segments are actually being used. We report here some critical modifications in the initial procedure to make it easy to clone and sequence large series of TCR transcripts. They have been introduced to improve both the yield and specificity of TCR amplified products and include re-amplification, size selections of the material combined with the successive use of nested TCR constant region specific primers. This procedure has been successfully applied to the study of the repertoire of both TCR alpha/beta+ and gamma/delta+ human T-cells. The efficiency of the present A-PCR protocol will help to precisely analyze TCR usage in normal and pathological situations.

Fine specificity of monoclonal antibodies directed at human T cell receptor variable regions: comparison with oligonucleotide-driven amplification for evaluation of V beta expression

Seven distinct anti-human T cell receptor (TcR) V region monoclonal antibodies (mAb) were generated by immunizing mice with either human T cell lines or transfected murine cells expressing human TcR V beta genes. The specificity of these reagents was determined as follows: T cells recognized by each mAb were purified from the peripheral blood of healthy donors and TcR transcripts expressed in these cells were analyzed using oligonucleotide-driven amplification and cDNA sequencing. Four mAb were found to delineate the V beta 3, V beta 8, V beta 17 and V beta 19 subfamilies, respectively. The remaining reagents recognize subsets within the V beta 2, V beta 5 and V beta 13 subfamilies. Reactivity of the mAb with circulating T cells from 18 unrelated healthy individuals was determined. Limited variability was found from an individual to another. In four donors, mAb staining was compared to oligonucleotide-driven amplification for evaluation of V beta 3, V beta 8, V beta 17 and V beta 19 subfamily expression in the peripheral blood. Although the V gene subfamily-specific oligonucleotides used in this study belong to a carefully controlled series, our results show that this method does not give an accurate estimate of the percentage of peripheral T cells expressing a given TcR beta chain. The present data confirm the necessity to establish a complete set of well-characterized monoclonal reagents to study human T cell responses.

Analysis of T-cell-receptor variable gene segment usage in peripheral-blood lymphocytes of advanced cancer patients

Advanced cancer patients generally display impaired T-cell immune functions. The underlying mechanisms are not well understood. The aim of this study was to analyze whether major alterations of TCR variable gene segment usage could be detected in the blood of these patients. Seventeen individuals with various malignancies were tested using PCR and a panel of V-gene-segment-sub-family-specific (V alpha 1-w29/V beta 1-w24) oligonucleotide primers. The results indicate that these cancer patient lymphocytes expressed most V alpha and V beta sub-family specificities, similarly to the lymphocytes of healthy donors (n = 10). This suggests that immunodepression in advanced cancer patients is not related to major deletions in their T-cell repertoires. We also compared the mean relative expression of each V-sub-family specificity of patients and healthy donors by quantitative densitometric analysis. We found significant differences in 4 V beta specificities (and no V alpha). Our analysis identified unique T-cell sub-sets putatively involved in the mechanisms leading to immunodepression in advanced cancer patients. Alternatively, the observed differences in terms of V beta specificity expression may reflect the host response against the tumor.

Analysis of T cell receptor variability in tumor-infiltrating lymphocytes from a human regressive melanoma. Evidence for in situ T cell clonal expansion

Malignant melanomas are often infiltrated by T lymphocytes. It is postulated that the presence of tumor-infiltrating lymphocytes (TIL) reflects ongoing immune responses against transformed cells. Such "responses" appear generally inefficient with the potential exception of infrequent clinical situations characterized by spontaneous tumor regression. We have characterized here the molecular structure of the T cell receptor beta chain expressed by TILs in a case of regressive melanoma. Advantage was taken of the PCR technology to study T lymphocytes directly without cell culture. Experimentally validated V beta subfamily specific primers were used to evaluate the V beta usage in TILs and control samples. Our results reveal that clonal T cell populations, precisely defined by their V-D-J junctional sequences, are amplified at the tumor site. The existence of such local antigen-driven selections support the hypothesis that antitumor responses may indeed take place in regressive melanoma.

An experimentally validated panel of subfamily-specific oligonucleotide primers (V alpha 1-w29/V beta 1-w24) for the study of human T cell receptor variable V gene segment usage by polymerase chain reaction

We report here the characterization of a series of T cell receptor (TcR) V alpha or V beta subfamily-specific oligonucleotide primers. Criteria that have guided the design of each oligonucleotide include appropriate thermodynamic parameters as well as differential base-pairing scores with related and unrelated target sequences. The specificity of the oligonucleotides for each V alpha or V beta subfamily was tested by polymerase chain reaction (PCR) on both a series of TcR encoding plasmid DNA and clonal T cell populations. Unexpected cross-reactivities were observed with plasmid cDNA sequences corresponding to unrelated subfamily gene segments. This led to the synthesis of additional series of oligonucleotides to obtain a relevant panel. A series of V alpha 1-w29/V beta 1-w24 TcR subfamily-specific oligonucleotides was eventually selected which generates little, if any, cross-reactivity. The use of C alpha or C beta primers for the amplification of internal positive control templates (i.e. C beta for the V alpha series and C alpha for the V beta series) has been tested in PCR performed with cDNA derived from peripheral blood lymphocytes; it was shown not to alter the amplification of the V subfamily-specific DNA fragments. This panel of oligonucleotides will be helpful in the study of TcRV gene segment usage and, thus, may lead to a better characterization of T cell responses in physiological and pathological situations.

Studies on the human T cell receptor alpha/beta variable region genes. I. Identification of 7 additional V alpha subfamilies and 14 J alpha gene segments

The anchored-polymerase chain reaction has been used to study further the diversity of the human T cell receptor alpha chain. The analysis of 308 cDNA transcripts from human peripheral lymphocytes hybridizing with a C alpha probe led to the identification of a series of additional V alpha and J alpha gene segments. The sequences of seven V alpha gene segments which individually define a novel V alpha subfamily (termed V alpha w23 to V alpha w29) are reported. The sequences of some previously described V alpha 1, V alpha 2, V alpha 5, V alpha 7 and V alpha 22 gene segments are also extended. In addition, we report 14 novel J alpha gene segment sequences. Taken together, these data indicate that the contribution of the alpha chain combinatorial diversity to the human T cell receptor alpha/beta variability has not yet been fully appreciated.

The T-cell receptor V delta genes predominantly used by human peripheral gamma/delta+ T lymphocytes are not rearranged in CD3- natural killer cells

We have analyzed, in 19 CD3- natural killer cell clones, the genomic organization of the T-cell receptor delta locus with two distinct V delta probes, V delta 1 and V delta 2. These two V delta genes code for surface proteins expressed in more than 90% of peripheral blood T-cell receptor gamma/delta+ lymphocytes, as shown by double color immunofluorescence analysis with anti-TCR delta 1, anti-BB3, and anti-delta TCS1 monoclonal antibodies. The V delta 1 and V delta 2 genes were found to be in germline position in all these clones, which are distinct phenotypically and represent a variety of the corresponding peripheral natural killer cell populations. We also studied in these cloned cell lines the transcriptional activity of the T-cell receptor delta locus with a C delta probe: short transcripts (1.7 and 0.8 kb) were found exclusively. These experiments further suggest that CD3- natural killer peripheral cells are likely to constitute a unique lineage distinct from T lymphocytes.

A novel human V delta gene expressed predominantly in the Ti gamma A fraction of gamma/delta+ peripheral lymphocytes

We have characterized a functional T cell receptor (TcR) delta transcript in a Ti gamma A+ human cloned cell line derived from peripheral blood. This cDNA includes a novel V gene (V-AB12), whose expression was initially studied in a series of TcR gamma/delta+ clones. Nine Ti gamma A+ clones derived independently from distinct donors have been tested: each of them was found to possess a unique V-AB12/J-IDP2 5.5-kb Eco RI rearrangement, which was constantly transcribed. Surface expression of the protein encoded by this unique rearranged gene was demonstrated by immunoprecipitations performed on three Ti gamma A+ polyclonal cell lines using a specific rabbit heteroantiserum. Further analysis strongly suggested that a monoclonal antibody (mAb), designated anti-BB3, detects a V-AB12-encoded antigenic determinant on the cell surface. Double-color immunofluorescence analysis of peripheral blood lymphocytes from ten donors indicated that most BB3+ cells are recognized by anti-Ti gamma A mAb. In previous studies, we have shown that a majority of TcR gamma/delta+ peripheral T cells expresses a gamma chain including V9 (Ti gamma A) and most frequently JP-encoded peptides. Given the present results on the delta chain, it can be concluded that, in many individuals, a predominant fraction (V gamma 9+/V-AB12+) of circulating CD3+ TcR alpha/beta- T lymphocytes expresses a receptor with little, if any, combinatorial diversity.