Sequences and repertoire of the human T cell receptor alpha and beta chain variable region genes in thymocytes

Skewing of the CD8+ T-cell repertoire in the lungs of patients with systemic sclerosis

Pulmonary parenchymal involvement in SSc is characterized by alveolitis and interstitial fibrosis, with an increased number of CD8+ T cells in BAL fluids. This study analyzed the diversity of the alphabeta T-cell repertoire in peripheral blood and BAL fluids from seven SSc patients, looking for evidence of antigen-driven selection of T cells in the lungs. A reverse transcriptase-polymerase chain reaction technique was used to amplify rearranged TCR transcripts from unfractionated, CD4+, and CD8+ T cells. Nearly all AV and BV gene families were expressed in SSc patients and most had similar levels of expression in blood and BAL samples. Next, the diversity of TCR junctional region lengths was assessed, using sequencing gel electrophoresis. Many V gene families had a Gaussian distribution of their junctional region lengths. However, some V gene families had an abnormal pattern of junctional lengths, with skewing away from a Gaussian distribution, including predominance of one or two lengths. This suggests selected expansion of T cells expressing those V genes. Alterations in TCR junctional region lengths were most prominent in bronchoalveolar CD8+ T cells, with similar patterns of skewing in several patients and in one patient over time. Sequence analysis of AV14 and BV17 junctional regions confirmed the oligoclonal character of expansion of bronchoalveolar CD8+ T cells.

Assessment of T-cell receptor beta-chain diversity by heteroduplex analysis

The aim of this work was to search for a simple and alternative approach to the currently used methodologies for the analysis of T-cell receptor repertoire diversity. To this end we studied whether the heteroduplex analysis could be adapted to study the clonality of the T-cell receptor beta chain (TCRBV). We therefore analyzed, by sequencing, the molecular characteristics of the V-D-J junctions of numerous TCRBV chains from a variety of patients and from normal individuals, and compared the results with those obtained with the heteroduplex analysis. The latter procedure involves the amplification of the target TCRBV chains and the denaturation and renaturation of the amplified product to permit the random association of the distinct DNA strands encoding the different junctional regions. Whereas amplified material from polyclonal lymphoid cells migrates on a polyacrylamide gel as a "smear" of bands composed of different-sized polyclonal PCR fragments, the mismatched chains derived from oligoclonal populations migrate as discrete "heteroduplexes" and can be separated from the matched "homoduplex" obtained from homogeneous clonal cells. Our results provide evidence demonstrating that heteroduplex analysis can successfully be applied to the analysis of T-cell clonality in a variety of samples and can be complementary or substitute for the standard approach of TCR cloning and multiple sequencing of junctional regions. Thus, the procedure should facilitate the implementation of the analysis of TCR in diagnostic routine and should find applications in numerous physiologic and pathologic conditions.

Random suppression of T cells that bear specific T cell receptor V beta sequences in adult T cell leukemia/lymphoma (ATLL) patients at each clinical stage: carrier, smoldering, chronic, and acute

Human T cell leukemia virus type I (HTLV-I) is associated with adult T cell leukemia/lymphoma (ATLL), which is well known as a T cell malignancy. In order to clarify whether HTLV-I plays a role as a virus-encoded superantigen in the neoplastic process, we examined the TCR V beta families in the peripheral blood at four different clinical stages: carrier, smoldering leukemia, chronic leukemia, and acute leukemia. An increased number of CD4 T cells was found in each of the four clinical stages. However, we found neither uniform specific losses nor uniform clonal expansion of particular TCR V beta gene families in any case from the four clinical stages. However, a suppression of the random TCR V beta families was found. Our data did not therefore directly suggest the existence of a common superantigen model of HTLV-I which induces an increase in CD4 T cells. The random suppression in the TCR V beta repertoire is most likely caused by the influence of HTLV-I neoplastic pathogenesis rather than by virus-encoded superantigens. In the patients with acute leukemia, one or two families of the V beta repertoires were very strongly expressed, while in chronic leukemia, no such repertoire of strong expression was observed. The immunological reaction of the hosts might thus be different between the above described groups.

TCR gene polymorphisms and autoimmune disease

Autoimmunity may result from abnormal regulation within the immune system. As the T cell is the principal regulator of the immune system and its normal function depends on immune recognition or self/non-self discrimination, abnormalities of the idiotypic T-cell receptor (TCR) may be one cause of autoimmune disease. The TCR is a clonally distributed, cell-surface heterodimer which binds peptide antigen when complexed with HLA molecules. In order to recognize the variety of antigens it may possibly encounter, the TCR, by necessity, is a diverse structure. As with immunoglobulin, it is the variable domain of the TCR which interacts with antigen and exhibits the greatest amount of amino acid variability. The underlying genetic basis for this structural diversity is similar to that described for immunoglobulin, with TCR diversity relying on the somatic recombination, in a randomly imprecise manner, of smaller gene segments to form a functional gene. There are a large number of gene segments to choose from (particularly the TCRAV, TCRAJ and TCRBV gene segments) and some of these also exhibit allelic variation. Finally, polymorphisms in non-coding regions of TCR genes, leading to biased recombination or expression, are also beginning to be recognized. All these factors contribute to the polymorphic nature of the TCR, in terms of both structure and repertoire formation. It follows that inherited abnormalities in either coding or regulatory regions of TCR genes may predispose to aberrant T-cell function and autoimmune disease. This review will outline the genomic organization of the TCR genes, the genetic mechanisms responsible for the generation of diversity, and the results of investigations into the association between germline polymorphisms and autoimmune disease.

Limited heterogeneity of rearranged T cell receptor V alpha and V beta transcripts in synovial fluid T cells in early stages of rheumatoid arthritis

OBJECTIVE

The identification of activated T cells in synovial fluid and synovium, and the association of rheumatoid arthritis (RA) with specific HLA-DR restriction elements, strongly suggest that these T cells play a critical role in the etiology and pathogenesis of RA. Analysis of the T cell receptor (TCR) repertoire in the early stages of RA might be an approach to identify those T cells involved in the initiation and/or perpetuation of the disease.

METHODS

TCR V alpha and V beta transcripts of synovial T cells, sampled at the early stages of RA, were amplified by reverse transcriptase-polymerase chain reaction. HLA-DR subtyping was determined by serologic analysis and dot-blot hybridization of polymerase chain reaction amplification products using digoxigenin-labeled, sequence-specific oligonucleotide probes.

RESULTS

Our findings showed a limited heterogeneity of V alpha and V beta TCRs in synovial fluid T cells, and a preferential usage of TCR V alpha 17 in early RA. In contrast, in the later stages of RA, a more polyclonal TCR V alpha and V beta gene usage was observed.

CONCLUSION

Our results support the view that induction of RA is driven by an oligoclonal immune response to an unknown antigen. These findings also suggest a pathogenetic role for V alpha 17 T cells in the early stages of RA.

Diversity of human T cell receptor sequences of T cell clones with specificity for Bet v 1 peptide/MHC II complexes

T cell clones (TCC) were raised from the peripheral blood of patients suffering from tree pollen allergy. All TCC were restricted by HLA-DR molecules. In order to investigate possible intervention targets in Type I allergic diseases, we have examined T cell receptor (TCR) alpha- and beta-chain nucleotide sequences of several allergen-reactive human CD4+ TCC specific for four frequently found epitopes of Bet v 1, the major birch pollen allergen. In general, TCC specific for the 4 epitopes investigated, used diverse TCRAV and TCRBV gene segments. Moreover, the junctional regions encoding the third complementarity determining regions (CDR3) of the TCR showed striking heterogeneities in length and amino acid composition. A more restricted use of two J gene segments (TCRBJ1S4 and 2S7) was only observed in the beta-chain of TCR used by TCC specific for epitope 1. In addition, all TCC specific for epitope 4 showed an arginine residue in the N-terminal region of their TCRBV CDR3 loops despite their sequence diversities. In view of the striking heterogeneities found, therapeutical strategies aimed at the clonal deletion of allergen-specific T cell clones, providing help for IgE synthesis, may not be feasible. Moreover, our results cast a doubt on the theory, that the CDR3 exclusively provides the primary contact with the peptide bound in the major histocompatibility (MHC) groove, and suggest additional interaction with MHC class II.

Angiocentric immunoproliferative lesions of the skin show lobular panniculitis and are mainly disorders of large granular lymphocytes

Eleven patients with angiocentric immunoproliferative lesion (AIL) of the skin were studied. Histologically, three patients were grouped into AIL grade II (AIL-II), whereas eight showed angiocentric lymphoma (AIL-III). All the patients' specimens exhibited lobular panniculitis. Infiltrating atypical lymphocytes in nine patients possessed electron-dense membrane bound granules in electron microscopy. Phenotypically, the lymphoid cells in the AIL-II patients were positive for CD3 epsilon; two of these showed a positive reaction to CD2, CD7, and CD8, but lacked natural killer-associated (NKa) antigens CD16, CD56, and CD57. In six AIL-III patients, lymphoma cells were positive for CD2 in all patients, CD56 in five, CD3 epsilon in four, CD7 in four, interleukin-2 beta receptor in four, a pore-forming protein in four, and CD30 in three patients. The remaining two AIL-III patients had B-cell lymphoma. By the Southern blot analysis, three patients with AIL-III showed a rearranged T-cell-receptor beta-gene or a deletion of its germline. The preceding results in nine of 11 patients suggest that abnormal or neoplastic large granular lymphocytes with the characteristics of T and NK cells have an important role in producing the angiocentric/angiodestructive features and lobular panniculitis. Clinically, all three patients with AIL-II and four with AIL-III showed liver dysfunction, cytopenia, and abnormal coagulopathy during the clinical course. Five patients with AIL-III died within 8 months. The histological grading of AIL, patients' age, and limited clinical stage of the disease seem to correlate with response to the treatment and prognosis.

Analysis of T cell receptor beta chain expression by isoelectric focusing following gene amplification and in vitro translation

We describe a new approach to analysis of T cell receptor diversity based on isoelectric focusing of in vitro translation products of amplified V region genes. The method is illustrated by analysis of V beta 2 profiles in peripheral blood lymphocytes from normal donors. The primers used for V beta 2 analysis spanned the V-(D-)J junction and included the segment from amino acid residue position 53 in the variable region to residue 132 of the constant region. The isoelectric focusing patterns display approximately 13-14 bands of varying intensity. Differences in expression of V beta 2-derived peptides were detected in comparisons of the isoelectric focusing profiles from different individuals, suggesting that the method may be useful for detecting genetically determined, immune response related or disease associated differences in Tcr V region expression. The major isoelectric focusing bands have been interpreted as representing groups of V beta 2 sequences sharing J beta region and NDN region charge similarity. Quantitative differences were detected in V beta 2 profiles of CD4 and CD8 T cell subpopulations indicating there may be selection for different charge characteristics in NDNJ sequences in the two T cell subsets. The method provides a new dimension for the detection of perturbations in the T cell repertoire.

TCRBV23 specificity of two monoclonal antibodies revealed by a panel of human V beta chains expressed in mouse cells

Two monoclonal antibodies, HUT78#1 and HUT78#7, were made against the T cell receptor of the T leukemia line HUT78. Their specificity was originally determined as TCRBV1S1 (V beta 1), and they have been used as such in repertoire studies (Rebai et al., 1994, Proc. Natl. Acad. Sci. USA 91, 1529). Here, we report their characterization using a large panel of mouse T cell transfectants expressing various human T cell receptor beta chains at their surface. These transfectants revealed that the true specificity of both monoclonal antibodies was for TCRBV23S1 (V beta 23), a result that was confirmed by several other techniques. We show that the original determination as a V beta 1 specificity was due to a crossreactive oligonucleotide used to type the immunizing cell line. The oligonucleotide amplified the V beta 1 as well as the closely related V beta 23 sequence, while the antibodies, by contrast, react exclusively with the beta chain encoded by the V beta 23 subfamily of the T cell receptor. Both antibodies seem to have identical specificities. These antibodies will be useful for the detection of a new subset of human lymphocytes since, to date, no other reagent with reactivity for the V beta 23 chain of the human T cell receptor has been described so far.

Selective reduction of T cells bearing invariant V alpha 24J alpha Q antigen receptor in patients with systemic sclerosis

A novel subset of T cells characterized by the expression of an invariant T cell antigen receptor (TCR) encoded by V alpha 24J alpha Q gene segments was investigated in patients with systemic sclerosis (SSc). Polymerase chain reaction analysis demonstrated that the V alpha 24 TCR repertoire was selectively used in CD4-CD8- double-negative T cells both in patients and in healthy individuals, while almost all families of TCR V alpha were expressed in single-positive T cell fractions. The V alpha 24+ double-negative T cells were increased by approximately fivefold in patients. However, sequence analysis clearly showed significant differences in the V alpha 24 TCR repertoire dominating in patients and healthy donors. In healthy individuals, the invariant V alpha 24J alpha Q was expanded and comprised 20-50% of the total TCR-alpha, while their selective reduction was observed in SSc patients who also showed expansion of invariant V alpha 24 TCR other than V alpha 24J alpha Q. Analogous to murine invariant V alpha 14J alpha 281 TCR, these results suggest that T cells with invariant V alpha 24J alpha Q TCR would function as regulatory T cells, whereas T cells bearing other invariant V alpha 24 TCR in SSc patients could be autoaggressive T cells in nature.

T-cell receptor J beta gene segment usage in immature and mature human thymocytes

Immature double positive (DP, CD4+CD8+) and mature single positive (SP, CD4+CD8- and CD4-CD8+) human thymocytes from nine thymi were analysed for their complete patterns of relative TCR J beta multigene member usage in relation to six rearranged V beta family exons (V beta 5.1, 6.1-3, 8, 9, 12 and 18). Each sample tested contained mRNA transcripts corresponding to all potential V beta(D beta)J beta combinations. Individual J beta gene segments were expressed in a similar, highly non-random manner both in SP and DP thymocytes, irrespective of original genomic position of the individual associated V beta exon. In addition, ranges of family usage and frequency of individual over-representations of J beta gene segments, as determined in DP and SP thymocyte populations, displayed no significant differences. Upon comparison of DP and SP thymocytes, however, a discrepancy in one aspect of J beta gene utilization was established: decreasing J beta family 1/J beta family 2 ratios were determined to be positively correlated with increasing maturity of thymocytes, a condition further supported by data previously obtained from studies of PBL T cells. At the individual J beta gene level, the observed gradual modification of the relative family usage can largely be explained by a significant shift from a higher J beta 1.1/J beta 2.7 ratio in DP to a higher J beta 2.7/J beta 1.1 ratio in SP thymocytes. Altogether, the present results imply that selectional processes in the thymus appear to have only minor consequences on the distribution pattern of expressed J beta exons. Hence, the disproportionate pattern of TCR J beta gene usage seems to be established mainly at the recombinatorial level followed by minor adjustments during thymic and post-thymic events.

Human T-cell receptor variable gene segment families

Multiple DNA and protein sequence alignments have been constructed for the human T-cell receptor alpha/delta, beta, and gamma (TCRA/D, B, and G) variable (V) gene segments. The traditional classification into subfamilies was confirmed using a much larger pool of sequences. For each sequence, a name was derived which complies with the standard nomenclature. The traditional numbering of V gene segments in the order of their discovery was continued and changed when in conflict with names of other segments. By discriminating between alleles at the same locus versus genes from different loci, we were able to reduce the number of more than 150 different TCRBV sequences in the database to a repertoire of only 47 functional TCRBV gene segments. An extension of this analysis to the over 100 TCRAV sequences results in a predicted repertoire of 42 functional TCRAV gene segments. Our alignment revealed two residues that distinguish between the highly homologous V delta and V alpha, one at a site that in VH contacts the constant region, the other at the interface between immunoglobulin VH and VL. This site may be responsible for restricted pairing between certain V delta and V gamma chains. On the other hand, V beta and V gamma appear to be related by the fact that their CDR2 length is increased by four residues as compared with that of V alpha/delta peptides.

Structure of human T-cell receptors specific for an immunodominant myelin basic protein peptide: positioning of T-cell receptors on HLA-DR2/peptide complexes

T-cell receptors (TCRs) recognize peptide bound within the relatively conserved structural framework of major histocompatibility complex (MHC) class I or class II molecules but can discriminate between closely related MHC molecules. The structural basis for the specificity of ternary complex formation by the TCR and MHC/peptide complexes was examined for myelin basic protein (MBP)-specific T-cell clones restricted by different DR2 subtypes. Conserved features of this system allowed a model for positioning of the TCR on DR2/peptide complexes to be developed: (i) The DR2 subtypes that presented the immunodominant MBP peptide differed only at a few polymorphic positions of the DR beta chain. (ii) TCR recognition of a polymorphic residue on the helical portion of the DR beta chain (position DR beta 67) was important in determining the MHC restriction. (iii) The TCR variable region (V) alpha 3.1 gene segment was used by all of the T-cell clones. TCR V beta usage was more diverse but correlated with the MHC restriction--i.e., with the polymorphic DR beta chains. (iv) Two clones with conserved TCR alpha chains but different TCR beta chains had a different MHC restriction but a similar peptide specificity. The difference in MHC restriction between these T-cell clones appeared due to recognition of a cluster of polymorphic DR beta-chain residues (DR beta 67-71). MBP-(85-99)-specific TCRs therefore appeared to be positioned on the DR2/peptide complex such that the TCR beta chain contacted the polymorphic DR beta-chain helix while the conserved TCR alpha chain contacted the nonpolymorphic DR alpha chain.

Restriction of the T-cell receptor V delta gene repertoire is due to preferential rearrangement and is independent of antigen selection

To determine whether the limited V gene usage by the T-cell receptor delta (TCRD) chain is dictated by preferential rearrangement or by antigen selection, we characterized and compared the TCRDV gene repertoire of the productive with that of the unproductive allele in 80 human TCRG/TCRD clones. Six different V genes were found on the expressed allele; two of them, provisionally named DV7 and DV8, have not been described before on the surface of TCRG/TCRD T cells. Overall, six V genes and six non-V elements were isolated from the unproductive allele. Interestingly, the same set of genes was rearranged both in the productive and in the unproductive chromosome. These findings seem to suggest that antigen-independent mechanisms play a major role in the restriction of the TCRDV gene repertoire.

T cell receptor usage in autoimmune disease

Activated T-cells are believed to play a critical role in the pathogenesis of autoimmune disease. In experimental allergic encephalomyelitis (EAE), an animal model resembling human multiple sclerosis (MS), there is evidence that T cells reactive to myelin basic protein mediate an inflammatory response within the central nervous system leading to demyelination. Furthermore, encephalitogenic T cells express TCR with highly restricted V gene usage and consequently specific forms of immunotherapy directed against V gene products have been successful in preventing and treating EAE. These findings prompted studies into the analysis of TCR repertoire expression in human autoimmune diseases in an attempt to identify the TCR usage of autoreactive and potentially pathogenic T cells. However, this has proved difficult as the autoantigens that drive the T cell response in most human autoimmune disorders are unknown. This review examines the data that have accumulated over the past few years on TCR usage in human autoimmune diseases and is focused largely on rheumatoid arthritis and MS.

A review of T-cell receptors in multiple sclerosis: clonal expansion and persistence of human T-cells specific for an immunodominant myelin basic protein peptide

Understanding the immune response to myelin antigens in regard to the peptide/MHC/TCR complex is important in defining pathogenesis of demyelinating autoimmune diseases and in developing antigen-specific therapies. We previously reported that individual multiple sclerosis patients may use certain dominant TCR V beta chains to recognize immunodominant MBP peptides. In examining the TCR beta chain usage, we observed repeated TCR VDJ sequences among different T-cell lines isolated from the same patient. This suggested that a few expanded T-cell clones may dominate the immune response to immunodominant MBP peptides. Here, we report experiments where TCR rearrangements were used as a probe for the clonal origin of MBP specific T-cells cultured from blood lymphocytes of MS patients and normal subjects. In two patients with the DR2 haplotype that were analyzed in detail, the T-cell response to MBP was focused on the MBP (84-102) peptide and in vivo expanded population(s) dominated the response to the MBP (84-102) peptide. Two MBP (84-102) specific T-cell clones from a normal subject with the DR2 haplotype were also found to have identical TCR sequences. Clonality was proven by demonstrating that independent clones had identical TCR alpha and beta chain sequences as well as identical sequences of a TCR gamma chain or of a second TCR alpha chain rearrangement. These data suggest that the response to human MBP is dominated in at least some subjects by expanded clones that may persist in vivo for relatively long periods of time.

Healthy human T-cell receptor beta-chain repertoire. Quantitative analysis and evidence for J beta-related effects on CDR3 structure and diversity

Analysis of TCR repertoire usage and clonality is of potential value in understanding the pathogenesis of a number of human immune-mediated diseases. In diseases that are likely to be dependent on antigen-driven T cells, it has been suggested that particular TCR junctional region or CDR3 sequences may be critical. Rigorous methods for TCR analysis which are both quantitative and qualitative are therefore required. Of those commonly available, only anchor and inverse PCR are capable of giving high-quality information on V, D, N, and J region usage, but it has not been established whether both methods are quantitatively or analytically equivalent. We show here that both methods detected considerable variability in the usage of V beta and J beta segments in the peripheral blood repertoire of a normal individual. No preferential V-J pairing could be demonstrated. An excess usage of J beta 2 family members was indicated by both methods, although the relative usage of different J beta 2 families differed between the two techniques. The predominantly used V beta usage showed that for some families, estimates of their frequency in the repertoire differed significantly between the anchor and inverse libraries. When sampling relatively few clones the variation between V beta families estimated using the two methods can be considerable. This is likely to be a result of sampling error from a large gene family. Large-scale screening of several thousand clones is recommended to confirm the absolute values obtained from sequencing. Variation in CDR3 length appeared to be normally distributed, suggesting that a statistically optimal junctional region length may have been selected for contact with antigen. CDR3 length distribution differs significantly between receptors, which have rearranged to J beta 1 versus J beta 2 families, with the J beta 2-associated CDR3 on average between 0.5 and 1.2 of an amino acid longer. Thus the TCR beta junctional region repertoire of humans is subject to structural constraints associated with J beta usage. It will be important to establish whether variation in CDR3 length and J beta usage exists between subsets of human T cells in order to interpret TCR repertoire data from disease and control tissues.

T-cell receptor gene structures of HLA-A26-restricted cytotoxic T lymphocyte lines against human autologous pancreatic adenocarcinoma

We isolated two cytotoxic T lymphocyte (CTL) lines, which were independently obtained by mixed lymphocyte-tumor cell culture from tumor-infiltrating lymphocytes of a patient with pancreatic adenocarcinoma. Both lines behaved identically in all the functional aspects tested and appeared to be HLA-A26-restricted. We analyzed their T cell receptor (TCR) gene structures, including V-(D)-J junctional sequences, which are unique to each T-cell clonotype and contribute to TCR diversity. Each line consisted of a clonal T-cell expressing V alpha 18 and V beta 7. The alpha chain gene was composed of V alpha 18/J alpha F/C alpha and the beta-chain gene, of V beta 7.1/D beta/J beta 1.4/C beta 2. The sequences were all in-frame and therefore should yield functional transcripts. The junctional sequences were identical between the two lines. These data suggested that the two CTL clones having the same CDR3 had descended from a common precursor lymphocyte. The clonal expansion of CTL lines with the identical CDR3 implies that they are directed against the same tumor antigen, which seemed to be immunologically dominant in the specific interaction between the CTL and the autologous pancreatic adenocarcinoma.

Structure and diversity of the T-cell receptor alpha chain in rhesus macaque and chimpanzee

We cloned and sequenced cDNA for the TCRAC1 of a healthy rhesus monkey and chimpanzee. TCRAC1 from both nonhuman primates show extensive conservation compared to the human sequence and to other mammals. A possible primate-specific insertion near the hinge region of the TCRAC1 region is described. Characterization of 18 rhesus macaque and eight chimpanzee TCRA chain cDNA clones derived from inverse PCR revealed 12 different TCRAV and 16 different TCRAJ regions which corresponded closely to known human counterparts. One functional rhesus macaque TCRDV-TCRAJ rearrangement was detected, suggesting a genomic organization of the macaque TCRD locus which is similar to humans. At the genomic level, a single TCRAC1 gene segment was detected in rhesus macaque and chimpanzee. The close phylogenetic relationship between primates shown here for TCRA chain components supports the use of these species as animal models of human immune-mediated disease.

Diversity of TCRAV and TCRBV sequences used by human T-cell clones specific for a minimal epitope of Bet v 1, the major birch pollen allergen

T-cell clones (TCC) were raised from the peripheral blood of patients suffering from tree pollen allergy. All TCC were restricted by HLA-DR molecules. In order to investigate possible intervention targets in Type I allergic diseases, we examined T-cell receptor (TCR) alpha and beta chain nucleotide sequences of five allergen-reactive human CD4+ TCC specific for a C-terminal epitope (BV 144) of Bet v 1, the major birch pollen allergen. Proliferation assays using synthetic peptides revealed the 10-mer LRAVESYLLA as minimal epitope for three TCC; two TCC also displayed reactivity with the nonapeptide LRAVESYLL. Two TCC expressed TCRBV2S3, all other BV144-specific TCC used diverse TCRAV and TCRBV gene segments. Moreover, the junctional regions encoding the third complementary determining regions (CDR3) of the TCR showed a striking heterogeneity in length and amino acid composition. Nevertheless, all TCC showed an arginine residue in the N-terminal region of their TCRBV CDR3 loops. Therefore, therapeutical strategies aimed at the clonal deletion of allergen-specific T-cell clones, providing help for IgE synthesis, will not be feasible. Our results cast a doubt on the theory that the CDR3 exclusively provides the primary contact with the peptide bound in the major histocompatibility (MHC) groove, and suggest additional interaction with MHC class II.

T cell receptor repertoire in polymyositis: clonal expansion of autoaggressive CD8+ T cells

In polymyositis (PM), CD8+ T cell receptor (TCR) alpha/beta + cells invade and destroy major histocompatibility complex class I-positive muscle fibers. We combined polymerase chain reaction (PCR) and double-fluorescence immunocytochemistry to analyze the T cell receptor (TCR) repertoire expressed in muscle of PM patients. In patient 1, inverse PCR revealed a preferential usage of TCR V alpha 33.1, V beta 13.1, and V beta 5.1. Six of six TCR V alpha 33.1+ clones and five of seven V beta 13.1+ clones had identical nucleotide sequences. In contrast, the V beta 5.1+ TCRs were more heterogeneous. Similar results were obtained with an independent PCR method using primers specific for TCR V alpha 33, V beta 13, or V beta 5. No TCR sequences could be amplified from noninflammatory control muscle. Furthermore, none of the TCR sequences found in PM muscle could be detected in blood from the same patient or from a normal control subject. Immunohistochemistry confirmed that V beta 5.1 and V beta 13.1 were overrepresented in the muscle lesions of this patient. 32% of all CD8+ T cells were V beta 13.1+, and 16% were V beta 5.1+. However, approximately 60% of the CD8+ T cells that invaded muscle fibers were V beta 13.1+, whereas 10% were V beta 5.1+. In patient 2, 50% of the T cells were V beta 5.1+, and as in patient 1, these T cells were mainly located in interstitial areas. In patient 3, > 75% of the autoinvasive T cells stained with an anti-V beta 3 mAb. Sequence analysis of 15 PCR clones amplified with a V beta 3-specific primer showed that 9 (60%) sequences were identical. The results suggest that (a) a strikingly limited TCR repertoire is expressed in PM muscle; (b) there is a dissociation between the TCR usage of autoinvasive and interstitial T cells; and (c) the autoinvasive T cells are clonally expanded.

Identification of the epitope recognized by the human V beta 5-specific monoclonal antibody 42/1C1. Potential implications for disease therapy

A panel of T-cell clones was generated that was specific for amino acid residues 4-13 of the mycobacterial 65-kd stress protein. All the clones were found to express a member of the V beta 5 family, as defined by PCR. However, the clones could be differentiated on the basis of different staining characteristics with the mAb 42/1C1. This antibody is known to recognize both V beta 5.2 and V beta 5.3, as was the PCR primer pair used in the analysis. Sequencing of the TCRs revealed that those clones which were not stained by 42/1C1 expressed a previously unidentified member of the V beta 5 family. By comparing the sequences of the V beta 5 family members that are recognized by 42/1C1 with those that are not, we were able to identify a probable epitope for the antibody. It is also clear from our data that the TCRs of T cells recognizing identical MHC-peptide combinations, although very similar, may be differentiated by mAbs, thereby posing potential problems in any proposed disease therapy involving treatment with monoclonals.

Limited TCR V beta usage of infiltrating T cells in synovial tissues from patients with HTLV-I associated arthropathy

Human T cell lymphotropic virus type-I (HTLV-I) is the etiologic agent of adult T cell leukemia/lymphoma and recently has also been suggested to be involved in chronic arthritis. The synovia of patients with rheumatoid arthritis (RA) contains activated T lymphocytes, with a restricted expression of T cell receptor (TCR) variable (V) beta gene segments. To characterize the T-cell populations of RA among HTLV-I carriers and noncarriers, we performed the immunohistochemical staining of CD4 and CDB, as well as a reverse transcription polymerase chain reaction (RT-PCR) to estimate the proportion of TCR beta RNA containing any particular V elements on the synovial specimens. In all but one HTLV-I carrier, the proviral DNA and/or RNA expression of HTLV-I was detected in the synovium. The CD4-positive cells proliferated markedly in the HTLV-I carriers compared with the noncarriers. In contrast to mononuclear cells in the peripheral blood, synovial T cells expressed only a few V beta transcripts, and no definite difference was observed between the carriers and the noncarriers. These results suggest that a common major antigen associated with the pathogenesis of RA may thus selectively interact with the V beta component of the TCR. Using RT-PCR, we studied the expression of the recombination-activating gene-1 (RAG-1), which was used in the V(D)J recombination of immunoglobulin and TCR genes. In all cases, RAG-1 was transcripted. The results supported the possibility that the extrathymic development of the selected TCR V beta T cells occurred in the synovia.

Structure and specificity of T cell receptors expressed by potentially pathogenic anti-DNA autoantibody-inducing T cells in human lupus

The production of potentially pathogenic anti-DNA autoantibodies in SLE is driven by special, autoimmune T helper (Th) cells. Herein, we sequenced the T cell receptor (TCR) alpha and beta chain genes expressed by 42 autoimmune Th lines from lupus patients that were mostly CD4+ and represented the strongest inducers of such autoantibodies. These autoimmune TCRs displayed a recurrent motif of highly charged residues in their CDR3 loops that were contributed by N-nucleotide additions and also positioned there by the recombination process. Furthermore, Th lines from four of the five patients showed a marked increase in the usage of the V alpha 8 gene family. Several independent Th lines expressed identical TCR alpha and/or beta chain sequences indicating again antigenic selection. 10 of these Th lines could be tested further for antigenic specificity. 4 of the 10 pathogenic anti-DNA autoantibody-inducing Th lines responded to the non-histone chromosomal protein HMG and two responded to nucleosomal histone proteins; all presented by HLA-DR molecules. Another Th line responded to purified DNA more than nucleosomes. Thus, these autoimmune Th cells of lupus patients respond to charged epitopes in various DNA-binding nucleoproteins that are probably processed and presented by the anti-DNA B cells they selectively help.

T cell repertoire in systemic sclerosis

An increase of certain T cell subsets in systemic sclerosis patients, particularly of V delta 1+ gamma delta T cells in the blood and lungs and CD8+ alpha beta T cells in the lungs, has been shown. The diversity of T cell antigen receptor (TCR) V delta 1, V alpha, and V beta gene repertoires was examined using reverse transcriptase-polymerase chain reaction to amplify rearranged TCR transcripts across the junctional region. This was followed by two methods of analysis. First, the relative expression of V alpha and V beta genes was determined in the blood and bronchoalveolar lavage fluid of the patients. Second, we looked for evidence of restricted diversity of the junctional regions in TCR V delta 1 transcripts and in different V alpha and V beta gene families. Limited V delta 1-C delta junctional region lengths were observed in the patients compared to controls. This was confirmed by sequence analysis of V delta 1-C delta junctional regions after subcloning amplified products in a bacterial vector. A restricted diversity of the junctional region lengths was also detected in a number of V alpha and V beta gene families, particularly within bronchoalveolar CD8+ T cell subset. These data suggest that the oligoclonal expansion of the corresponding alpha beta and gamma delta T cells is antigen-driven and may be important in the pathogenesis of systemic sclerosis.

Endogenous antigen presentation by autoantigen-transfected Epstein-Barr virus-lymphoblastoid cells: T cell receptor N-region hydrophobicity relates to thyroid antigen recognition

Seven human T cell lines from a patient with Graves' disease were raised against endogenously generated human thyroid peroxidase (hTPO) with stimulation indices ranging from 2.1 to 7.6. Clonal expansion within these T cell lines was demonstrated by sequencing multiple bacterial colonies containing RT-PCR-generated fragments derived from the expressed hTcRs. Some lines had more than one human T cell receptor (hTcR) alpha and beta chain mRNAs as judged by RT-PCR. Stopcodons present in several hTcR sequences indicated that only one V alpha and one V beta gene were translated. Both the V alpha/beta gene families and the J alpha/beta gene segments differed amongst the lines and no characteristic recognition sequences were discernable in the CDR3 regions. Using Kyte-Doolittle analysis we found hydrophobic peaks in most N alpha-regions (but not N beta regions) suggesting that hydrophobic interactions may be important in the recognition of hTPO. However, increasing affinity values, as measured by SI, were strongly correlated with decreasing hydrophobicity in the N alpha region (1st order regression, r = -0.93138, p < 0.01). Thus, lower affinity, self-reactive, T cells may be more hydrophobic ('sticky') in their N alpha regions while higher affinity cells may be characterized by TcRs with lower hydrophobicity. These findings demonstrate a substantial role for hydrophobic interactions in hTPO-reactive T cell receptors and further support a role for the TcR alpha chain in the recognition of thyroid autoantigen.

Different TCRBV genes generate biased patterns of V-D-J diversity in human T cells

The aim of this work was to assess whether each T-cell receptor (TCR) BV segment generates a random pattern of junctional diversity or if, alternatively, biased patterns of V-D-J rearrangements limit the number of available TCR specificities. Detailed molecular analysis of T-cell receptors expressed by lymphocytes was obtained by generating a large number of junctional regions sequences from TCRBV3, TCRBV4, TCRBV5S1, TCRBV12, TCRBV13S2, TCRBV17, TCRBV20, and TCRBV22 variable genes. The > 800 sequences analyzed have allowed the characterization of the recombination frequencies of each germline-encoded V, D, and J segments, as well as of the magnitude of exonucleolytic nibbling and of the number of N nucleotides inserted for each group of TCRB segments. The data obtained indicate that the extent of junctional diversity varies considerably depending on the TCRBV gene implicated in the recombination event, due to the occurrence of skewed patterns of J and D region usage. Furthermore, our results show that "illegitimate" rearrangements occur with unexpectedly high incidence, specifically at the level of TCRBD to TCRBJ joining. These findings provide additional information for a more accurate estimation of the size of the TCRBV repertoire and for understanding the well-established biased pattern of TCRBV expression in humans.

Generation and reactivation of T-cell receptor A joining region pseudogenes in primates

Tandemly duplicated T-cell receptor (Tcr) AJ (J alpha) segments contribute significantly to TCRA chain junctional region diversity in mammals. Since only limited data exists on TCRA diversity in nonhuman primates, we examined the TCRAJ regions of 37 chimpanzee and 71 rhesus macaque TCRA cDNA clones derived from inverse polymerase chain reaction on peripheral blood mononuclear cell cDNA of healthy animals. Twenty-five different TCRAJ regions were characterized in the chimpanzee and 36 in the rhesus macaque. Each bears a close structural relationship to an equivalent human TCRAJ region. Conserved amino acid motifs are shared between all three species. There are indications that differences between nonhuman primates and humans exist in the generation of TCRAJ pseudogenes. The nucleotide and amino acid sequences of the various characterized TCRAJ of each species are reported and we compare our results to the available information on human genomic sequences. Although we provide evidence of dynamic processes modifying TCRAJ segments during primate evolution, their repertoire and primary structure appears to be relatively conserved.

Insertion of a short human immunodeficiency virus (HIV)-2 gp36 sequence into an HIV-1 p24 recombinant protein results in a polypeptide with potent and TCRBV-restricted T cell triggering activity

In the present work we investigate whether artificial alterations of the structure of an inactive retrovirus-encoded protein could transform it in a superantigen. As a model system we used a recombinant human immunodeficiency virus (HIV)-1 p24 protein and two of its variants in which a short peptide corresponding to sequences of gp41 of HIV-1 (HIV-1 p24*) or gp36 of HIV-2 (HIV-1-2 p24*) has been inserted nearby the carboxy-terminal end of HIV-1 p24. As expected both HIV-1 p24 and HIV-1 p24* were inactive, while HIV-1-2 p24* was a potent inducer of human, but not murine, T cell proliferation. The possibility that the observed activity was due to contaminants was ruled out since the proliferative response could be specifically inhibited by a monoclonal anti-p24 antibody and by a peptide encompassing the area of HIV-1 p24/HIV-2 gp36 junction. Furthermore, the data exclude the possibility that the gp36 insertion is per se responsible for the observed proliferative activity. The analysis of the functional, phenotypic and molecular properties of the responding cells demonstrated that the response was class II dependent and that the activated cells were predominantly CD4+CD8- expressing a strongly biased repertoire of TCRBV segments. Collectively, these data strongly suggest that the HIV-1-2 p24* fusion protein shares common functional properties typical of superantigen molecules. Thus, our demonstration that a viral protein can be transformed into a superantigen simply by the insertion of a short peptide at the carboxy-terminal end has important implications for understanding the mode of action of retrovirus-encoded superantigens.

Oligoclonality and skewed T cell receptor V beta gene segment expression in in vivo activated human intestinal intraepithelial T lymphocytes

Intraepithelial intestinal T lymphocytes (IEL) bearing alpha beta or gamma delta T cell receptors (TCR) are positioned to serve as a first line of defense against enteric pathogens. To investigate whether intestinal IEL are subject to antigenic selective forces distinct from that influencing (xp T cells in the peripheral blood (PBL), we performed a comparative analysis of V beta gene segment usage in IEL and PBL of immunologically normal donors by quantitative PCR. Primers for 22 different human TCR V beta gene segments of V beta gene segments families were used to analyze the repertoire of TCR beta chain transcripts in colonic IEL (c-IEL), in corresponding colonic lamina propria lymphocytes (c-LPL), and in peripheral blood lymphocytes. In each of the three individuals examined, a limited number (1-4 out of 22) of TCR V beta families predominated and accounted for more than 50% of the total beta chain transcripts from c-IEL, whereas in PBL and c-LPL a more even distribution of V beta gene families was observed. The dominating V beta gene families were V beta 2, V beta 3, V beta 6, V beta 8 and V beta 14. In one individual, V beta 3 comprised more than 40% of the entire repertoire of c-IEL beta chain transcripts. Sequence analysis of the predominant V beta 3 family in this individual revealed identical sequences in 13 of 17 clones analyzed. Human alpha beta TCR+ c-IEL could not be driven to proliferate or exhibit cytotoxic function in vitro however, PCR analysis for detection of lymphokine mRNA revealed constitutive production of several lymphokines known to exert trophic effects on intestinal epithelial cells and pro-inflammatory activities. Taken together, the striking degree of oligoclonality may indicate that the intraepithelial intestinal immune system is targeted to a limited set of hitherto unknown self- or foreign antigens present in the intestine and orchestrates intramucosal inflammatory and regenerative processes.

Characterization of T-cell receptor V beta repertoire in ovarian tumour-reacting CD3+ CD8+ CD4- CTL lines

T cells from tumour infiltrating lymphocytes (TIL) cultured in media containing IL-2 were shown to mediate in vitro and in vivo antitumor responses. To characterize the T-cell antigen receptor (TCR) V beta expression in autologous cytotoxic effectors we isolated CD3+ CD8+ CD4- cells from cultures of TIL and tumour-associated lymphocytes (TAL) and analysed the TCR V beta repertoire of CD3+ CD8+ CD4- lines of known HLA-A, -B and -C phenotype, using polymerase chain reaction (PCR). These lines showed preferential lysis of autologous tumours and lysed, to a much lesser extent, NK and LAK cell-sensitive targets. Tumour lysis was inhibited by antibodies to CD3 and MHC class I antigens indicating that they are cytotoxic T lymphocytes (CTL). These CD8+ CTL lines expressed a broad distribution of TCR V beta repertoire which was dominated by particular groups of V beta families in each CTL line. However, no predominant expression of one or the same V beta segment in all CTL lines was observed although statistical correlations between V beta family usage and magnitude of the antitumour cytolytic response were found. These results suggest that certain TCR V beta families may be selected by antigen in ovarian tumour-reactive T cells and this selection may be affected by Ag expression, and/or host factors. To our knowledge, this is the first documentation of TCR V beta repertoire of human ovarian tumour-reactive CD3+ CD8+ CD4- CTL from different individuals of known HLA types.

Shared amino acid sequences in the ND beta N and N alpha regions of the T cell receptors of tumor-infiltrating lymphocytes within malignant glioma

The purpose of this study was to assess the V-(D)-J junctional region of the T cell receptor (TCR), the CDR3 region, which is responsible for glioma-specific antigen contact in alpha beta TCR-mediated recognition. We sequenced the TCR alpha and beta chains of V alpha 7, and V beta 13.1 cDNA derived from tumor-infiltrating lymphocytes (TIL) of 12 glioma patients and also the corresponding clones from the patients' peripheral blood lymphocytes (PBL). A shared V beta 13.1 DJ sequence of the CDR3 region, ND beta N, was demonstrated in 49 of 66 V beta 13.1+ clones (74.2%) from the glioma TIL, whereas only 4 of 33 clones (12.1%) were observed in the V beta 13.1+ clones from the PBL (p < 0.001). A common VDJ sequence, FCASS (V beta 13.1)-YRLPWGTSDS (ND beta N)-GELFF (J beta 2.2), was observed not only in the gliomas from each patient, but also among all the patients with a preference for V beta 13.1. In contrast, the amino acid sequences of the V beta 13.1+ PBL clones were diverse and random. Next, we sequenced subclones from other V beta subfamilies randomly selected to compare their VDJ region rearrangements (V beta 3 and V beta 5.1). In contrast to V beta 13.1, the amino acid sequences of these junctional regions were completely different in these subclones. The V-J junctional region of the alpha chain is dominated by a few clones in some patients, and no shared amino acid sequences were detected in the TCR V alpha junctional region. However, in the N alpha region of the V alpha 7-bearing TIL clones, arginine was used in 27 of 44 clones (61.4%) compared to only 3 of 12 clones from the PBL (p < 0.05). These results are consistent with the hypothesis that a clonal expansion/accumulation of glioma lineage-specific T cells occurred in vivo at the tumor site and that these T cells may be recognizing glioma-specific antigens.

Analysis of diversity of T cell antigen receptor genes using polymerase chain reaction and sequencing gel electrophoresis

A sensitive, highly resolvable, and quantitative method was designed to analyse the diversity of polymerase chain reaction (PCR)-amplified transcripts which possess length polymorphism. A reverse transcriptase-PCR technique was used to amplify rearranged T cell antigen receptor (TCR) transcripts isolated from human blood. Oligonucleotide primers specific for conserved TCR V and C region sequences were used in PCR, with one of the primers end-labeled with 32P. Amplified cDNA products were analysed by polyacrylamide sequencing gel electrophoresis with an M13mp18 sequencing ladder as a size marker. 32P-labeled products were detected by either autoradiography or PhosphorImager. The method allowed determination of the sizes of PCR products with the precision of one nucleotide. The resolution using this technique was much higher than by electrophoresis in agarose gel with ethidium bromide staining. The sizes of PCR products determined by sequencing gel electrophoresis were consistent with the lengths of nucleotide sequences obtained after subcloning PCR products in competent bacterial cells. Analysis of PCR products by sequencing gel electrophoresis was more rapid and as accurate as nucleotide sequence analysis in determining the relative ratios of TCR mRNA in mixtures of T cell clones. The method is applicable for analysis of both rearranged TCR and immunoglobulin genes.

Superantigen-reactive human T cells express a biased repertoire of T-cell receptor V beta joining regions

A major characteristic of superantigens is their ability to stimulate T cells based predominantly on the type of variable segment of the T-cell receptor (TCR) V beta chain. Recently, however, reports from several laboratories have also implied a role for non-V beta elements in superantigen binding. The goal of the present study was to determine whether TCR V beta-D beta-J beta joining sequences may influence the interaction of superantigens with their target cells. To ascertain how the actual TCR repertoire of superantigen-triggered cells deviates from the theoretical one, we generated a large panel of joining region sequences from TCR carrying the TCR V beta 12 and TCR V beta 5,1 regions. The 245 sequences analysed represent transcripts of T cells from the same donor triggered either with an anti-CD3 monoclonal antibody or with the Staphylococcus aureus enterotoxins. Comparison of the joining sequences of these different groups demonstrates a skewed J beta usage in the sequences derived from superantigen-triggered cells and also provides evidence that ascribes to the putative CDR3 region of V beta segments a role in superantigen recognition. Finally, the data presented give some hints of the regions of the putative CDR3 loop that may play a major role in this function.

Major expansion of CD8+ T cells with a predominant V beta usage during the primary immune response to HIV

A SIGNIFICANT proportion (up to 70%) of individuals experience an acute clinical syndrome of varying severity associated with primary infection with the human immunodeficiency virus (HIV). We report here studies on six individuals who showed an acute HIV syndrome which generally resolved within four weeks, concomitant with a dramatic downregulation of viraemia. To characterize the T-cell-mediated primary immune response to HIV, we used combined semiquantitative polymerase chain reaction assay and cytofluorometry to analyse the T-cell antigen receptor repertoire in sequential peripheral blood mononuclear cells from the patients. We found major oligoclonal expansions in a restricted set of variable-domain beta-chain (V beta) families. Cells expressing the expanded V beta s predominantly expressed the CD8 T-cell differentiation antigen and mediated HIV-specific cytotoxicity. Major oligoclonal expansions of these CD8+ T lymphocytes may represent an important component of the primary immune response to viral infections and may help to clarify both the immunopathogenic and the protective mechanisms of HIV infection.

Structure, diversity, and evolution of the T-cell receptor VB gene repertoire in primates

AB T-cell receptors (TCR) that recognize major histocompatibility complex (MHC)/peptide antigen complexes regulate humoral and cellular arms of the adaptive immune response. Antigen binding sites of MHC and immunoglobulin heavy chain variable regions (Igh-V) are subject to diversity enhancing selection. We sought to establish whether positive Darwinian selection has driven diversity of TCRBV chains in the primate lineage by sequencing rearranged TCR from rhesus monkeys and chimpanzees and comparing them with those of humans. Rates of synonymous (silent) and nonsynonymous (replacement) substitutions indicate selection against amino acid replacements in TCRBV frameworks, and relaxation of these constraints in putative MHC/peptide contact sites. The lack of positive selection for variability in likely ligand contact sites suggests that mechanisms generating somatic diversity in TCR junctional regions have relaxed the pressure for selection of variability in the TCR V region encoded in the germline.

Characterization of horse (Equus caballus) T-cell receptor beta chain genes

Genes encoding the horse (Equus caballus) T-cell receptor beta chain (TCRB) were cloned and characterized. Of 33 cDNA clones isolated from the mesenteric lymph node, 30 had functionally rearranged gene segments, and three contained germline sequences. Sixteen unique variable segments (TCRBV), 14 joining genes (TCRBJ), and two constant region genes (TCRBC) were identified. Horse TCRBV were grouped into nine families based on similarity to human sequences. TCRBV2 and TCRBV12 were the most commonly represented horse families. Analysis of predicted protein structure revealed the presence of conserved regions similar to those seen in TCRB of other species. A decanucleotide promoter sequence homologous to those found in humans and mice was located in the 5' untranslated region of one horse gene. Germline sequences included the 5' region of the TCRBD2 gene with flanking heptamer/nonamer recombination signals and portions of the TCRBJ2-C2 intron. Southern blot hybridizations demonstrated restriction fragment length polymorphisms at the TCRBC locus among different horse breeds.

Degeneracy of T cell receptor recognition of an influenza virus hemagglutinin epitope restricted by HLA-DQ and -DR class II molecules

DT9301-0229737 the TcR are believed to provide the peptide fragments bound to major histocompatibility (MHC) molecules. TcR have an immunoglobulin (Ig)-like structure and, in an analogous manner to antigen recognition by Ig, the third complementarity determining regions (CDR3) of the TcR are believed to provide the primary contact with the peptide lying in the MHC groove. CDR1 and CDR2 are thought to contact the presenting MHC molecule. We have analyzed seven human CD4+ T cell clones that recognize a conserved peptide epitope (residues 255-270) within the influenza virus hemagglutinin (H3) HA1 subunit. Two T cell clones recognized the peptide in the context of HLA-DRB1*1001 and HLA-DQB1*0602/DQA1*0102, respectively, and shared V alpha, V beta and J beta gene segments. Only the junctional regions encoding the CDR3 regions of the two TcR chains were different. This suggests that the CDR3 regions of these TcR interact with the MHC class II molecule. Six of the T cell clones were restricted by the HLA-DRB1*1001. Two of these T cell clones expressed V beta 9.1 and three expressed V beta 13 gene segments; the remaining clone expressed V beta 7.2, a close homologue of V beta 9.1. A diverse selection of V alpha and J gene segments contributed to the junctional heterogeneity of the TcR, indicating a diversity of sequence combinations recognizing the epitope. Nevertheless, five out of six T cell clones bore a motif in the V alpha CDR3 loop consisting of adjacent acidic and polar amino acid residues, eight residues from the carboxyl end of each CDR3.

Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA

We report here the comparative DNA sequence analysis of nearly 100 kilobases of contiguous DNA in the C delta to C alpha region of the alpha/delta T cell receptor loci (TCRAC/TCRDC) of mouse and man. This analysis--the largest genomic sequence comparison so far--provides new insights into the functions of the T cell receptor genes as well as the surrounding chromosome structure through the identification of actively conserved DNA sequences. In this comparison we have identified a very high level of organizational and noncoding sequence similarity (approximately 71%) in contrast to previous findings in the beta-globin gene cluster. This observation begins to question the notion that much of the chromosomal non-coding sequence is junk.

Lack of restricted T-cell receptor beta-chain variable region (V beta) usage of reactive T-lymphocytes in Hodgkin's disease

T-cell response against tumour-associated antigens is mediated by the TCR complex. To determine a possibly restricted TCR-V beta repertoire in reactive T-lymphocytes in Hodgkin's disease (HD), 20 cases (of which 10 were EBV-positive cases) were investigated using 14 monoclonal antibodies (MoAbs) recognizing 11 different TCR-V beta region family products and Northern blot analysis with cDNA probes specific for mRNA transcripts of 11 V beta families that were not detectable by MoAbs. Four V beta families (V beta 5, V beta 6, V beta 8, V beta 19) were investigated using both immunohistochemistry (IHC) with anti-V beta MoAbs and Northern blot analysis. Immunohistochemical and Northern blot findings were correlated with the detection of the Epstein-Barr virus (EBV) genome in Hodgkin's and Reed-Sternberg cells (H-RS). The non-neoplastic lymphocytes in HD were predominantly of T-phenotype (CD3+). Most of these cells were TCR-alpha beta+ (beta F1+) and only a few T-cells were reactive for TCR-delta 1 antibody (TCR-gamma delta+). In the majority of cases helper/inducer T-cells (CD4+) outnumbered suppressor/cytotoxic T-cells (CD8+). Labelling of these samples with the panel of 14 anti-V beta MoAbs showed that only a small percentage (0.2-5.5%) of beta F1+ lymphocytes were positive with each of these MoAbs. The proportion of these cells was comparable to that seen in normal tissues. Most TCR V beta+ cells were randomly distributed, but in virtually all cases occasional V beta+ cells pertaining to the various V beta families were seen in close contact to H-RS cells. Using total RNA extracted from malignant and normal tissues, no visible band was detected with the various V beta probes. As determined in the present study, the percentage of T-cells expressing a given V beta family must be > or = 10% to be detected with Northern blot. Thus, the percentage of V beta+ cells expressing V beta families which were explored only with Northern blot were within the same range as those of the 11 different TCR-V beta region families assessed with IHC, i.e. 1-10% of lymphoid cells. The results of the present study show that in HD there is no restricted T-cell V beta repertoire usage regardless of the detection of EBV. In addition, since the various V beta families are represented in T-cell subpopulations forming rosettes around H-RS cells, we conclude that the T-cells attracted by H-RS cells constitute a polyclonal population.

Usage of TCRAV and TCRBV gene families in human fetal and adult TCR rearrangements

We have investigated fetal and adult T-cell receptor (TCR) A and B V-gene repertoires both by fluorescence-activated cell sorter (FACS) analysis with the available TCR V region-specific mAbs and by the polymerase chain reaction (PCR) with TCR V gene family-specific oligonucleotides. Among the low number of CD3+ T cells, most of the TCR V regions tested for could be detected by FACS analysis in liver, bone marrow, and spleen derived from a 14-week-old fetus and two 15-week-old fetuses. Similarly, the PCR analysis showed that the majority of the TCRAV and TCRBV families were expressed in the peripheral organs of the 13-week-old fetus, although an apparent absence of particular TCR V families was found in liver and bone marrow. This was most probably the consequence of the low number of CD3+ T cells in these organs. In 17-week-old fetal thymi the level of expression of some TCRAV and TCRBV gene families, in particular those that contain a single member, was lower compared to post-partum thymi and adult peripheral blood mononuclear cells. The combined data of FACS and PCR analysis demonstrate that TCR V genes belonging to the majority of TCR V gene families can be used in TCR alpha and beta chain rearrangements during early human fetal life. Our data also suggest that the expression levels of some of the single member TCR V gene families may be influenced by the developmental stage.

Characterization of a novel human T cell receptor beta chain variable region family by transspecies DNA hybridization

One essential component in the generation of diversity of T cell receptor (TcR) alpha and beta chains is the existence of multiple tandemly arranged variable regions in the germ line which are subsequently rearranged to form functional units. In attempting to establish the extent of the human TcR alpha and beta chain repertoire an approach of randomly sequencing cDNA for rearranged receptors has been generally pursued. So far, 24 human V beta families have been characterized and they encompass some 51 transcriptionally active gene segments. Recently, surveys of several hundred TcR beta cDNA clones have failed to establish further V beta families which suggests that if they exist, they are likely to be poorly represented in the peripheral blood repertoire. It is likely, therefore, that the majority of human V beta regions which are rearranged conventionally and are transcriptionally active have already been described. To investigate whether additional V beta families characterize the human TcR repertoire we have examined V beta sequences from an inverse polymerase chain reaction (PCR) TcR beta cDNA library of the chimpanzee, the most closely related creature to man. One clone which could not be assigned to any human V beta family cross-hybridized with human TcR beta chain cDNA. This new human family has been called V beta 25. Comparison of chimpanzee and human V beta 25 sequences using the Lipman-Pearson method gives a similarity index of 94.6% over a consensus length of 112 amino acids. On the evidence of Southern blotting with cDNA probes, V beta 25 segments in human and chimpanzee appear to represent single member gene families and no restriction fragment length polymorphism was evident with the restriction enzymes used. Equalization of TcR beta cDNA followed by family-specific quantitative PCR showed that the gene is expressed at similar levels in the chimpanzee and the human. The actual level of expression in the human is less that 0.5% of the total TcR beta repertoire. Transspecies DNA hybridization using novel sequences from closely related species may be a powerful tool for establishing the full extent of TcR alpha and beta and immunoglobulin repertoires.

A consensus primer to amplify both alpha and beta chains of the human T cell receptor

The use of reverse transcriptase in conjunction with the polymerase chain reaction (RT-PCR) has proven invaluable in the analysis of the T cell receptor (TCR) repertoire of different populations of T cells. However, the presence of a variable region in the T cell receptor has hindered the design of primers for the 5' end of the TCR cDNA. We describe the design and use of a degenerate consensus primer that allows amplification of both the alpha and beta chains of the human TCR. We have used this primer in the analysis of the TCR distribution of T cell clones, peripheral blood lymphocytes and lymphocytes residing in tissue. In addition, the primer has allowed the identification of an alternative splice site in the beta chain constant region which cannot translate into a functional constant region. We have found the primer to be easy to use, sensitive and specific.

T cell receptor V beta gene usage in the recognition of myelin basic protein by cerebrospinal fluid- and blood-derived T cells from patients with multiple sclerosis

Because of its proximity to the central nervous system, the cerebrospinal fluid (CSF) represents an important source of T cells that potentially could mediate putative autoimmune diseases such as multiple sclerosis (MS). To overcome the low CSF cellularity, we evaluated culture conditions that could expand CSF T cells, with a focus on the expression of T-cell receptor V beta genes utilized by T cells specific for the potentially encephalitogenic autoantigen myelin basic protein (BP). Expansion of "activated" CSF cells with IL-2/IL-4 plus accessory cells optimally retained BP-responsive T cells that over-expressed V beta 1, V beta 2, V beta 5, or V beta 18, compared to expansion using supernatants from PHA-stimulated blood cells, or anti-CD3 antibody that led to different V gene bias and rare reactivity to BP. Sequential evaluation of paired CSF and blood samples from a relapsing remitting MS patient indicated that BP-reactive T cells were present in CSF during the period of clinical activity, and the pattern of BP recognition in CSF was partially reflected in blood, even after CSF reactivity had dissipated during remission. Over-expressed V beta genes were not always constant, however, since in three sequential evaluations of a chronic progressive MS patient, V beta genes over-expressed in the first BP-reactive CSF switched to a different V beta gene bias that was present in the second and third CSF samples. Blood samples reflected each pattern of CSF V beta gene bias, but retained the initial bias for at least 4 months after its disappearance from CSF. These data indicate that selective expansion of IL-2/IL-4-responsive CSF cells favors growth of the BP-reactive subpopulation, and, in a limited number of patients studied, reflected clinical disease activity. In comparison, blood T cells provided a partial but longer lasting reflection of the CSF BP reactivity and V beta gene bias.

Preferential usage of T-cell receptor alpha beta variable regions among tumor-infiltrating lymphocytes in primary human malignant melanomas

The usage of T-cell-receptor (TCR) alpha beta variable (V) regions among tumor infiltrating lymphocytes (TILs) in primary human malignant melanomas was characterized using a method based on the polymerase chain reaction (PCR). A panel of 57 different variable-region primers specific for the TCR V alpha I-29 and V beta I-28 was designed, and a semi-quantitative PCR method applicable to formalin-fixed, paraffin-embedded tissues was developed. This semi-quantitative method was demonstrated to be reproducible and to be useful for the assessment of V alpha- and V beta-gene-family usage in formalin-fixed, paraffin-embedded tissue samples. A total of 9 different histopathologically characterized primary tumors were analyzed in this study. The TILs in these tumors were found to preferentially express certain TCR V alpha and V beta regions. The differential usage of certain V alpha regions was very pronounced as illustrated by V alpha 4, which was highly expressed in 3/8 tumors, and V alpha 22, which was highly expressed in 4/8 tumors. For comparison, specific highly expressed V alpha regions in control samples of peripheral-blood lymphocytes rarely exceeded 10%. The most highly expressed V beta region was V beta 8, which was highly expressed in 2/8 tumors. For the highly expressed V alpha 4 and V alpha 22 and V beta 8 regions, the high levels may be explained by the in situ clonal or oligoclonal expansion of TIL. In one specific case, the high expression of V beta 8 was due to expansion of a single clone of TILs, as evidenced by a fully readable sequence of the CDR3 (V-D-J) region, determined by direct sequencing of the PCR product corresponding to V beta 8. In contrast, sequence analysis of V alpha 22, which was expressed in the same tumor sample at similar levels, demonstrated the simultaneous presence of 3 different CDR3 (V-J) sequences derived from V alpha 22 transcripts of exactly the same length. The observed preferential use of TCR V alpha and V beta regions suggests the in situ clonal expansion of specific populations of T-cells, possibly reactive with melanoma-associated peptides presented by HLA molecules. The preferential use of TCR V alpha and V beta regions may imply the involvement of a limited number of shared melanoma-associated peptides.

Cytogenetic and immunogenotypic alterations of blast crisis cells in chronic myelogenous leukemia independently linked to immunophenotypic expression

Chronic myelogenous leukemia (CML) is a disease of the hematopoietic stem cells, which can differentiate into either B-lymphoid or myeloid cells, because most of them develop either lymphoid or myeloid blast crisis. Immunophenotypic, genotypic, and cytogenetic analyses of 22 patients (24 episodes) with Philadelphia (Ph) positive CML in blast crisis were performed to determine the genetic alterations of the blast crisis cells. In B-lymphoid blast crisis, all the five patients had immunoglobulin heavy-chain (IgH) rearrangements and most of them showed normal karyotypes. Among the five patients, T-cell receptor (TCR) genes were rearranged at the following occurrence rates: 20% in TCR-beta, 60% in TCR-gamma, and 40% in TCR-delta chain genes. A high incidence of additional chromosome changes was noted in patients with B-lymphoid/myeloid-mixed blast crisis, but about 80% of them had rearranged IgH and about 40% had TCR rearrangements. In contrast, most of the patients with non-lymphoid blast crisis showed further chromosomal abnormalities, including +8, +19, i(17q), and double Ph, and most of them had germline configurations of IgH and TCR-gamma chain genes. Notably, only one patient (dual lymphoid and myelomegakaryoblast crisis) in this group exhibited IgH rearrangement, and TCR-beta and TCR-delta rearrangements were also rarely noted. Rearrangement of the IgH gene in CML blast crisis might be linked to expression of lymphoid markers, especially CD19.

The extent of the human germline T-cell receptor V beta gene segment repertoire

An assessment of the size of the human TCRBV gene segment repertoire based on the identification of TCRBV gene segments in genomic DNA was undertaken. PCR amplification from cloned and uncloned genomic DNA sources, nucleotide sequencing, Southern blot hybridization, and cosmid cloning were used to identify TCRBV gene segments in multiple unrelated individuals. The key advantages to this approach were: 1) TCRBV gene segments which are expressed only at very low levels in cDNA libraries were still detectable, and 2) it was possible to discriminate between alleles at the same locus vs products of different loci. A total of 63 unique TCRBV gene segments were identified and sequenced. Six of these TCRBV gene segments had not been previously described. Thirty-four cosmid clones containing 51 of the 63 identified TCRBV gene segments were isolated and screened for the presence of additional novel TCRBV subfamily members. These results, obtained by a variety of complementary approaches, indicate that the human TCRBV germline repertoire encodes at least 63 TCRBV gene segments of which 52 are functional. The availability of the majority of these TCRBV gene segments on cosmid clones should facilitate further investigation of germline TCRBV gene segment polymorphism and putative disease associations.

Heterogeneity of T cells specific for a particular peptide/HLA-DQ complex

Whether T cells specific for a particular peptide/HLA-DQ complex are restricted with respect to TCR usage has not been fully established. TCR usage of T cells specific for a peptide presented by a given HLA-DQ molecule has not been studied before. We therefore sequenced the TCR genes of five different TCCs derived from the same donor, which were specific for a p21 ras-derived synthetic peptide presented by the HLA-DQ(alpha 1*0102,beta*0602) (DQ6) molecule. We found that these T cells which recognized the same peptide/HLA-DQ complex used highly diverse TCRs. However, dose-response experiments using various truncations of the p21 ras-derived peptide revealed that the peptide fine specificities of the five TCCs were not completely identical. This may explain the heterogeneity in TCR usage.

Molecular heterogeneity of a Graves' thyroid-infiltrating T cell population rich in CD8+ and gamma delta+ T cells

We report here on the isolation and repertoire characterization of a Graves' thyroid T cell population which, unlike most Graves' thyroid T cell isolates reported before, was rich in CD4-CD8- T cells (16%, all TcR gamma delta+) and CD8+ T cells (75%) [TcR alpha beta+ (59%) and TcR gamma delta+ (16%)]. Only 7% of the isolated T cells were CD4+. By contrast, < 2% of peripheral blood mononuclear cells from the same patient were gamma delta+ and < 14% were CD8+. Sequence analysis of 18 TcR delta cDNAs prepared from these cells indicated the presence of at least 17 different gamma delta+ T cell clonotypes with molecularly heterogeneous antigen-binding site sequences. As opposed to most peripheral blood gamma delta+ T cells (express V delta 2 TcRs), 13 of the 17 different TcR delta clonotypes used a V delta 1 gene, although PCR amplification of TcR gamma- and TcR delta-specific cDNAs with V delta- and V gamma-gene family-specific oligonucleotides confirmed usage of all 4 V gamma and all 6 V delta families. Sequence analysis of 21 TcR alpha cDNAs from a TcR alpha-specific cDNA library indicated the presence of at least 12 different clonotypes, using 8 different V alpha gene families and heterogeneous antigen-binding site sequences. These results are in contrast with the selective V alpha gene usage reported for other intrathyroidal T cell subpopulations in autoimmune thyroid disease.