A novel and rapid cloning method for the T-cell receptor variable region sequences

Use of a Pan-Vbeta primer permits the amplification and sequencing of TCRbeta chains expressed by bovine T-cell clones following a single semi-nested PCR reaction

We report in this study the design and validation of a Pan-Vbeta primer that in combination with Cbeta-specific primers enables the amplification, in a single semi-nested PCR, of TCRbeta chains expressed by bovine T-cell clones irrespective of the expressed Vbeta sequence. Using the Pan-Vbeta primer we examined the TCRbeta chains expressed by 16 Theileria parva-specific clones that had not been previously analysed. TCRbeta chain sequence was obtained from 15 of the clones following direct sequencing of the PCR product, whilst the other clone appeared to express 2 different TCRbeta chains which were characterised following sub-cloning of the PCR product. We have also successfully used the Pan-Vbeta primer to amplify the TCRbeta chains expressed by 19 T-cell clones, on which previous analysis using Vbeta-subfamily-specific primers had failed to do. Sequencing of these TCRbeta chains has identified members of 2 novel bovine Vbeta subfamilies-Vbeta5 and VbetaX. This method offers a simple and rapid method of analyzing the TCRbeta chains of bovine T-cell clones that has many potential applications in the investigation of bovine T-cell responses.

Highly diverse TCR delta chain repertoire in bovine tissues due to the use of up to four D segments per delta chain

Tissue-specific distribution of gammadelta TCRs with limited TCR diversity is a common phenomenon in species with a low percentage of gammadelta T cells like humans and mice. We set out to investigate whether this is also the case in cattle (Bos taurus), a species with high percentages of gammadelta T cells. Using a method that was independent of variable (V) segment-specific primers, we generated 65 unique TCR delta chain sequences. We found no evidence for preferential use of certain Vdelta segments in lymph node, skin, spleen, small intestine, large intestine, and blood. The delta chain CDR3 length distribution was very wide in each tissue, which was confirmed by spectratyping. The highly variable CDR3 length was due to the use of up to four diversity (D) segments by one bovine delta chain. Human and murine delta chains contain only one or two D segments. The five functional Ddelta segments that we describe here were identified at cDNA and genomic level, and are the first ruminant D segments described. Fourteen TCR delta chain sequences used novel Vdelta1 segments, and one expressed a novel member of the Vdelta3 family. The number of known functional Vdelta segments in cattle including these new ones is 42 now, but the total number may be much higher. A high number of Vdelta segments in combination with the use of up to four out of five D segments, and the possibility of using non-template encoded (N) nucleotides on either side of these, makes the potential bovine delta chain repertoire much bigger than any known TCR chain. This situation is quite different from the situation in humans and mice, and suggests that the differences between gammadelta high and gammadelta low species in distribution, diversity, and function of gammadelta T cells may be substantial.

Expansion of CD4 T cells expressing a highly restricted TCR structure specific for a single parasite epitope correlates with high pathology in murine schistosomiasis

The hepatic immunopathology in schistosomiasis mansoni is mediated by CD4 T cells specific for egg antigens and varies considerably among mouse strains. Previous studies in high pathology C3H mice suggested that a strong T cell response was due to the recognition of an immunodominant epitope within the major egg antigen Sm-p40 (Sm-p40(234-246)). Using a panel of T cell hybridomas, we have now examined the egg antigen-specific TCR repertoire in two high pathology strains, C3H and CBA. We found that nearly half of the hybridomas responded to the Sm-p40(234-246 )epitope and, of these, nearly all expressed Valpha11.3 associated with Vbeta8. Furthermore, in response to egg antigen stimulation, transcript levels of Valpha11.3J36 (the most prevalent rearrangement expressed by Sm-p40(234-246)-specific hybridomas), increased in high pathology (CBA) but not in low pathology BALB/c strains. Our findings suggest that exacerbated schistosome egg-induced immunopathology can be driven by T cells expressing a highly restricted TCR structure specific for a single parasite epitope.

Simplified fluorescent multiplex PCR method for evaluation of the T-cell receptor V beta-chain repertoire

RATIONALE

Evaluation of the T-cell receptor (TCR) V beta-chain repertoire by PCR-based CDR3 length analysis allows fine resolution of the usage of the TCR V beta repertoire and is a sensitive tool to monitor changes in the T-cell compartment. A multiplex PCR method employing 24 labeled upstream V beta primers instead of the conventionally labeled downstream C beta primer is described.

METHOD

RNA was isolated from purified CD4 and CD8 T-cell subsets from umbilical cord blood and clinical samples using TRI reagent followed by reverse transcription using a C beta primer and an Omniscript RT kit. The 24 V beta primers were multiplexed based on compatibility and product sizes into seven reactions. cDNA was amplified using 24 V beta primers (labeled with tetrachloro-6-cardoxyfluorescein, 6-carboxyfluorescein, and hexachloro-6-carboxyfluorescein), an unlabeled C beta primer, and Taqgold polymerase. The fluorescent PCR products were resolved on an automated DNA sequencer and analyzed using the Genotyper 2.1 software.

RESULTS

V beta spectratypes of excellent resolution were obtained with RNA amounts of 250 ng using the labeled V beta primers. The resolution was superior to that obtained with the labeled C beta primer assay. Also the numbers of PCRs were reduced to 7 from the 12 required in the C beta labeling method, and the sample processing time was reduced by half.

CONCLUSION

The method described for T-cell receptor V beta-chain repertoire analysis eliminates tedious dilutions and results in superior resolution with small amounts of RNA. The fast throughput makes this method suitable for automation and offers the feasibility to perform TCR V beta repertoire analyses in clinical trials.

Production of functional antibodies generated in a nonlytic insect cell expression system

A monoclonal antibody directed against the type 2 adenovirus (Ad2) penton base protein was cloned and expressed in Spodoptera frugiperda (Sf9) cells using a nonlytic vector system. The coding sequences for the immunoglobulin light and heavy chains were placed under the control of the Orgyia pseudotsugata multicapsid nucleopolyhedrosis virus immediate-early 2 (OpIE2) promoter. Transfected Sf9 cells continuously secreted the antibody which retained the ability to recognize both native and recombinant Ad2 penton base proteins. Bifunctional penton base antibodies were also generated by fusing a gene for a growth factor or a cytokine at the 3' end of the Ig constant heavy chain domain. The quantity and activity of recombinant antibodies generated in the nonlytic insect cell system could be determined relatively quickly compared to other expression systems. Moreover, these recombinant proteins were not subjected to proteolytic degradation as frequently occurs during baculovirus-mediated cell lysis and the levels of recombinant antibodies produced in the nonlytic system were comparable to those reported for cytolytic baculovirus vectors.

Identification of the T-cell receptor alpha variable (TRAV) gene(s) in T-cell malignancies

Due to the lack of a complete range of monoclonal antibodies (mAb) it is often impossible to rapidly identify by flow cytometry the T-cell receptor variable genes in patients suffering from T-cell malignancies. This applies especially to the alpha variable genes (TRAV), since only very few anti-TcR variable alpha mAb are available. We describe a very rapid method for inverse PCR amplification of the TcR alpha chain without prior purification of the double-stranded cDNA, provide the sequences for appropriate oligonucleotides, and describe a buffer system that dramatically enhances the amplification efficiency as compared to standard conditions.

Signaling antibodies complexed with adenovirus circumvent CAR and integrin interactions and improve gene delivery

Current adenoviral (Ad) vectors cannot be targeted to specific cell types due to the widespread distribution of the Ad receptor (CAR). Moreover, CAR and/or internalization receptors (alphav integrins) are absent or present at low levels on some cell types, rendering them resistant to Ad-mediated gene delivery. To address these problems, we have developed a novel vector targeting approach that takes advantage of the common cell signaling pathways initiated by ligation of alphav integrins and growth factor receptors. Recombinant growth factor/cytokines (TNF-alpha, IGF-1, EGF) which trigger phosphatidylinositol-3-OH kinase (PI3K) activation, a signaling molecule involved in adenovirus internalization, were fused to a monoclonal antibody specific for the viral penton base. Ad vectors complexed with these bifunctional mAbs increased gene delivery 10 to 50-fold to human melanoma cells lacking alphav integrins. The bifunctional mAbs also enhanced gene delivery by fiberless adenovirus particles which cannot bind to CAR. Improved gene delivery correlated with increased virus internalization and attachment as well as PI3K activity. The use of bifunctional mAbs to trigger specific cell signaling pathways offers a widely applicable method for bypassing the normal Ad receptors in gene delivery and potentially increasing the selectivity of gene transfer.

Rapid screening of T-cell receptor (TCR) variable gene usage by multiplex PCR: application for assessment of clonal composition

The selection of various T-cell receptor (TCR) gene families and complex rearrangements during intra-thymic differentiation provide the basis for the expression of antigen specificity by mature T cells. TCR beta variable (TCRBV) transcripts can be identified by RT-PCR, but multiple reactions are required to detect all genes of the TCRBV subfamilies. We describe here a multiplex PCR method that amplifies 46 functional genes comparing 23 TCRBV families in 5 reactions where each reaction contains 4 to 7 specific primers together with a single fluorescence-tagged TCR beta constant region primer. Between 8 and 10 distinct subtypes within each of the 23 TCRBV families can be identified by analysis of the CDR3 length. Multiplex PCR products isolated from agarose gels can be subjected to direct sequencing for confirmation and definitive clonotyping if necessary. The data illustrated here show that the multiplex PCR technique is useful for screening TCRBV usage and can be easily adapted for analysis of clonal composition in T-cell populations.

Intron retention may regulate expression of Epstein-Barr virus nuclear antigen 3 family genes

The nuclear antigen 3 family genes (EBNA-3, EBNA-4, and EBNA-6) of Epstein-Barr virus (EBV) are important for EBV-induced immortalization and survival of B lymphocytes. However, little is known about how the expression of these genes is regulated. Each of the EBNA-3, EBNA-4, and EBNA-6 genes consists of two exons separated by a small intron. Reverse transcriptase PCR assays revealed that the vast majority of the EBNA-3, EBNA-4, and EBNA-6 mRNA, expressed in transfected and EBV-infected B cells, retained intron sequences. Northern blot and S1 protection assays confirmed that most of the EBNA-3 mRNA contained intron. Examination of deletion mutants of EBNA-3 indicated that the EBNA-3 protein was not necessary for intron retention and that there was no splicing silencing element encoded in the EBNA-3 mRNA. Cell fractionation and RNA gradient analysis revealed that the unspliced EBNA 3 family mRNAs were transported into the cytoplasm and associated with the polysomes. However, Western blot analysis of FLAG-epitope tagged EBNA-3 gave no indication of the presence of splice variant protein forms of EBNA-3. In contrast, transiently transfected cells expressing EBNA-3 revealed a sixfold increase in EBNA-3 protein expression from the genomic EBNA-3 gene compared to EBNA-3 cDNA. These data show that the intronic sequences can influence EBNA-3 protein expression and suggest that intron retention may provide a means for the fine-tuning of expression of the individual EBNA 3 family genes.

Molecular recognition of lipid antigens by T cell receptors

The T cell antigen receptor (TCR) mediates recognition of peptide antigens bound in the groove of major histocompatibility complex (MHC) molecules. This dual recognition is mediated by the complementarity-determining residue (CDR) loops of the alpha and beta chains of a single TCR which contact exposed residues of the peptide antigen and amino acids along the MHC alpha helices. The recent description of T cells that recognize hydrophobic microbial lipid antigens has challenged immunologists to explain, in molecular terms, the nature of this interaction. Structural studies on the murine CD1d1 molecule revealed an electrostatically neutral putative antigen-binding groove beneath the CD1 alpha helices. Here, we demonstrate that alpha/beta TCRs, when transferred into TCR-deficient recipient cells, confer specificity for both the foreign lipid antigen and CD1 isoform. Sequence analysis of a panel of CD1-restricted, lipid-specific TCRs reveals the incorporation of template-independent N nucleotides that encode diverse sequences and frequent charged basic residues at the V(D)J junctions. These sequences permit a model for recognition in which the TCR CDR3 loops containing charged residues project between the CD1 alpha helices, contacting the lipid antigen hydrophilic head moieties as well as adjacent CD1 residues in a manner that explains antigen specificity and CD1 restriction.

T-Cell Receptor Analysis in Omenn’s Syndrome: Evidence for Defects in Gene Rearrangement and Assembly

Patients with Omenn’s syndrome have a form of severe immune deficiency that is associated with pathological features of graft-versus-host disease, except for the lack of foreign engraftment. It has been hypothesized that the disease’s unique clinical features are mediated by an expanded population of autologous self-reactive T cells of limited clonality. In the current study, an investigation of the T-cell receptor (TCR) repertoire was undertaken to identify defects in T-cell rearrangement and development. The TCR repertoire in this group of patients was exquisitely restricted in the number of different TCR clonotypes, and some of these clonotypes seemed to have similar recognition motifs in the antigen-binding region, indicating antigen-driven proliferation of T lymphocytes. The TCRs from some patients lacked N- or P-nucleotide insertions and used proximal variable and joining gene segments, suggesting abnormal intrathymic T-cell development. Finally, abnormal assembly of gene segments and truncated rearrangements within nonproductive alleles suggested abnormalities in TCR rearrangement mechanisms. Overall, the findings suggest that inefficient and/or abnormal generation of TCRs may be a consistent feature of this disease.

T-Cell Receptor Analysis in Omenn’s Syndrome: Evidence for Defects in Gene Rearrangement and Assembly

Patients with Omenn’s syndrome have a form of severe immune deficiency that is associated with pathological features of graft-versus-host disease, except for the lack of foreign engraftment. It has been hypothesized that the disease’s unique clinical features are mediated by an expanded population of autologous self-reactive T cells of limited clonality. In the current study, an investigation of the T-cell receptor (TCR) repertoire was undertaken to identify defects in T-cell rearrangement and development. The TCR repertoire in this group of patients was exquisitely restricted in the number of different TCR clonotypes, and some of these clonotypes seemed to have similar recognition motifs in the antigen-binding region, indicating antigen-driven proliferation of T lymphocytes. The TCRs from some patients lacked N- or P-nucleotide insertions and used proximal variable and joining gene segments, suggesting abnormal intrathymic T-cell development. Finally, abnormal assembly of gene segments and truncated rearrangements within nonproductive alleles suggested abnormalities in TCR rearrangement mechanisms. Overall, the findings suggest that inefficient and/or abnormal generation of TCRs may be a consistent feature of this disease.

High-resolution analysis of T-cell receptor beta-chain repertoires using DNA heteroduplex tracking: generally stable, clonal CD8+ expansions in all healthy young adults

The accurate measurement of T-cell receptor (TCR) repertoire changes requires the analysis of a representative sampling of complex T-cell populations. The number and frequency of clonally expanded TCR beta-chain transcripts bearing distinct CDR3 sequences were accurately determined using a simple DNA heteroduplex tracking assay. This method allowed major and minor clonal expansions (> or = 1% of a Vbeta subfamily's transcripts) to be rapidly and reproducibly quantified. Oligoclonal CD8 + cell expansions were detected in all young adults tested, while CD4 + cells generally expressed more polyclonal beta-chain repertoires. The same pattern of CD8 + cells oligoclonality and CD4 + cells polyclonality was observed in asymptomatic HIV-1 infected individuals with high CD4 + cell counts. CD8 + CD45RA + and CD8 + CD45RO + cell fractions both displayed oligoclonal, although distinct, TCR beta chain repertoires while CD8 + cells from umbilical cord blood were generally polyclonal. Oligoclonal CD8 + cell repertoires from young adults were generally stable over a period of weeks, although minor, transient, clonal expansions could also be detected in the absence of symptomatic infections. DNA heteroduplex tracking analysis provided a higher level of sensitivity for the detection of TCR beta chain transcript expansions than CDR3 length (spectrotyping/immunoscope) analysis. DNA heteroduplex tracking of TCR beta-chain transcripts is therefore a simple and sensitive method for assessing the level of clonality and for measuring changes in the TCR beta chain repertoire of different T-cell populations.

A restricted T cell response to myelin basic protein (MBP) is stable in multiple sclerosis (MS) patients

The close resemblance of MS to the animal model experimental autoimmune encephalomyelitis (EAE) has provided compelling data sustaining a pathogenic role of circulating T cells reactive against MBP. T cell antigen receptor (TCR) usage in EAE is commonly considered restricted; nevertheless, dynamic changes of TCR usage correlate with the course of EAE, resulting in a limited repertoire during early stages of disease activity followed by the recruitment of other T cells reactive against new determinants. Although a broader TCR repertoire mediates the response to MBP in humans, a restricted intraindividual heterogeneity may occur in some MS patients. In the present study we characterize the response to MBP in MS subjects with relapsing remitting disease from two sampling time points 12 months apart. MBP-specific T cell lines (TCL) were first generated from eight MS individuals and two healthy subjects. New TCL were obtained after 12 months from one control and three MS patients whose response, at the first time point, was directed against a single epitope. Interestingly, these three subjects had a stable and mild disease. Few TCL obtained at two time points from the MS individuals recognized the same immunodominant epitope and shared identical TCR Vbeta sequences. In the control we could not detect a restriction of the repertoire. These findings suggest that in some MS patients with benign disease a predominant T cell response to a single determinant may be detectable at different moments and is mediated by clonally expanded populations.

Analysis of the alpha/beta T-cell receptor repertoire by competitive and quantitative family-specific PCR with exogenous standards and high resolution fluorescence based CDR3 size imaging

The characterization of the human T-cell receptor (TCR) repertoire in various physiological and pathological conditions has become an important tool in studies of the immune response. Therefore, a number of PCR based strategies for the semiquantitative analysis of the TCR repertoire have been described. Family specific amplification of TCR cDNA has been employed in a number of studies often with contradictory results. We have developed a strategy utilizing exogenous standards with homologous primer binding sites for the quantitative analysis of the alpha/beta T-cell receptor repertoire. This system allows the detection of even minute differences in T-cell populations based on quantitative PCR (Q-PCR) and competitive PCR (C-PCR). Results presented here demonstrate that expansions of T-cell subsets as defined by the specificity of the variable gene segments can be readily monitored when exceeding 1% of the total repertoire. In addition, the proposed method reveals direct information of CDR3 size heterogeneity and can be used to estimate the T-cell repertoire complexity and monitor clonal expansions. We discuss variables such as cell number and experimental conditions influencing accuracy and reproducibility of the analyses. We have used this protocol based on non-radioactive techniques for characterization of the fine specificity of the T-cell repertoire in peripheral and organ-infiltrating T-lymphocytes. The analyses revealed information about polyclonal or clonal expansion of T-cells in vivo and in vitro following various stimuli such as superantigenic stimulation of T-cell subsets as well as antigen-driven shaping of the alpha/beta T-cell repertoire in autoimmune and infectious diseases.

Inverse PCR amplification of low-abundancy message of gamma delta T cell receptor genes

The technique of inverse PCR permits the rapid amplification and identification of unknown DNA segments adjacent to well characterized core regions. In the field of immunology anchored PCR and inverse PCR are useful methods for examining junctional diversity and unknown variable gene segments of rearranged T cell receptor genes. We have applied an improved inverse PCR protocol to study the repertoire of gamma delta T cell receptor genes in the developing thymus of the mouse.

Cloning of an unidentified T-cell receptor alpha chain gene from a vesicular stomatitis virus-specific helper T-cell clone

A vesicular stomatitis virus glycoprotein-specific, class II restricted, CD4+ T-cell clone was obtained and the unidentified T-cell receptor alpha chain cloned in order to establish a T-cell receptor (TCR) alpha chain transgenic mouse line. Polymerase chain reaction (PCR) strategies have been developed to clone TCR chain genes starting from T-cell cDNA. There remain difficulties, however, in cloning the functional TCR alpha chain due to the complexity of the protocols applied if the variable (V) alpha region rearranged is not known. The strategy described here allows the identification and cloning of alpha chains that are not recognized by any of the anti-V alpha monoclonal antibodies available: three 5' consensus V alpha primers designed from all known V alpha gene sequences and a primer specific for the constant (C) alpha region were used and the PCR product sequenced. The T-cell clone displayed two alpha gene rearrangements, only one of which giving rise to a functional protein. The alpha chain used by the T-cell clone contained a V alpha 3.1 and a J alpha region which has been described only at the genomic level, but never in a functional TCR. The complete alpha chain gene was cloned by enriching the alpha chain-encoding cDNA by ligation-anchored PCR and using an alpha specific primer pair. The use of the present method, even if the sequence of the 5' untranslated (UT) region of the alpha chain is not known, is also discussed.

Quantitative assessment of the human TCRBV repertoire by competitive PCR

A novel quantitative protocol was developed for the measurement of the relative expression levels of the human TCRBV genes based on reverse transcription (RT) and subsequent competitive polymerase chain reaction (cPCR). Competitor DNA templates for the analysis of 24 different TCRBV families were generated by a simple and rapid one-step PCR procedure with a special PCR primer, which introduces a deletion in the constant region gene segment. A defined amount of TCRBV family-specific competitor DNA and the reverse transcribed cDNA of interest were amplified in the same tube with the same primer pair in a competitive way. The resulting fragments were separated on agarose gels and the densitometrical values were evaluated directly without the requirement for additional hybridization steps. For all of the 24 different TCRBV family-specific cPCRs equal amplification efficiencies were demonstrated by titration experiments for wild-type and competitor templates. For TCRBV repertoire studies, a short form of the cPCR assay was performed, requiring only one cPCR for quantitation of each TCRBV family. The exact initial amount of wild-type template in each cPCR was interpolated from TCRBV family-specific reference calibration curves. The RT-cPCR assay was applied for the quantitative assessment of the TCRBV repertoire of CD4+ and CD8+ T cell subsets in unstimulated PBMC and compared to flow cytometric analyses with a panel of monoclonal antibodies specific for TCRBV determinants. The RT-cPCR experiments revealed a differential expression of several BV families in either the CD4+ or the CD8+ fraction. The TCRBV family-specific cPCR assay presented here combines the simplicity and speed of conventional TCRBV family-specific PCR with the quantitative features of competitive PCR. TCRBV family-specific RT-cPCR has a broad application for all kinds of quantitative T cell repertoire studies and could be easily adapted for the usage with different BV-specific primer sets.

Zfp60, a mouse zinc finger gene expressed transiently during in vitro muscle differentiation

The complete cDNA coding sequence of the zinc finger gene Zfp60 is reported. The predicted amino acid sequence of the Zfp60 protein has been found to contain 19 zinc finger motives clustered at the C-terminus. At its N-terminus, Zfp60 shares with other members of the zinc finger gene family two additional conserved amino acid modules named Kruppel Associated Boxes (KRAB). The expression patterns of Zfp60, MyoD and MHC mRNAs have been followed during in vitro myogenic differentiation of C2 cells. We show that the bacterial produced Zfp60 protein binds DNA only in presence of zinc ions. Zfp60 locus has been mapped in chromosome 7, where other Zfp loci are localised.

PCR strategies for isolation of the 5' end of an immunoglobulin-encoding bovine cDNA

We have employed two in vitro amplification strategies in our attempts to characterise the variable region of bovine immunoglobulin heavy chains (VH). Products derived by 5' RACE (rapid amplification of cDNA ends) spanned the coding sequence, but diversity in the complementarity determining regions was highly restricted, indicating that a limited subset of the heavy-chain repertoire had been recovered. In contrast, unique, full-length VH determinants were obtained with ease by an inverse application of the polymerase chain reaction. The strength of this approach is considerable: it is straightforward to perform, requiring none of the tailing procedures inherent to RACE strategies, yet it enables the rapid isolation of uncharacterized regions of genes for which limited sequence data are available. Our findings suggest strongly that the heavy-chain repertoire of cattle is highly dependent upon a very limited number of germline VH and JH (joining region) gene families.

The delta T cell receptor repertoire in human colon and peripheral blood is oligoclonal irrespective of V region usage

The majority of gamma/delta T cell receptors (TCR) in the human intestinal mucosa are thought to use the TCRDV1 (V delta 1) variable region gene segment, whereas gamma/delta T cells in the circulation predominantly express the TCRDV2 (V delta 2) gene segment. delta T cell receptors that use the TCRDV2 variable region gene segment generally have been regarded as highly diverse, whereas those that use the TCRDV1 gene segment are oligoclonal, whether present in the intestinal tract or in peripheral blood. We report herein that oligoclonality is a general feature of the peripheral delta T cell receptor repertoire in healthy human adults, irrespective of the variable region used and regardless of whether gamma/delta T cells reside in the intestinal mucosa or in peripheral blood. In addition, the delta T cell receptor repertoire is shown to be highly compartmentalized between such sites as the colon and peripheral blood, relatively stable over at least a 10-16-mo period, and unique in each individual. Further, the spectrum of variable region genes used by delta T cell receptor transcripts in the human colon is greater than previously recognized. Thus, in addition to the TCRDV1 and TCRDV2 variable region gene segments, delta T cell receptors in normal intestinal mucosa can use TCRDV3 (V delta 3) and TCRAV (V alpha) gene segments which, in some individuals, comprise a significant component of the mucosal delta T cell receptor repertoire. Our studies indicate that the potential of delta T cell receptors for extensive diversity is not reflected in the mature human repertoire. Moreover, these findings suggest a model wherein the delta T cell receptor repertoire in the colon and peripheral blood is shaped by selection and clonal expansion of gamma/delta T cells that ultimately seed throughout the length of the colon mucosa and populate the circulation.

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.

Human V gamma 9-V delta 2 cells are stimulated in a cross-reactive fashion by a variety of phosphorylated metabolites

Many different pathogens stimulate cells bearing the V gamma 9-V delta 2 T cell receptor (TCR), which represent the most abundant population of human gamma delta cells. The antigens responsible for the stimulation of these gamma delta cells are not well characterized. Here, we describe six non-peptidic molecules which share this property: isopentenylpyrophosphate, dimethylallylpyrophosphate, 2,3-diphosphoglyceric acid, glycerol-3-phosphoric acid, xylose-1-phosphate, and ribose-1-phosphate. All these molecules are naturally occurring metabolites in prokaryotic and eukaryotic cells, and stimulate freshly isolated gamma delta cells from peripheral blood of different donors as well as established gamma delta clones. Comparison of their structure with that of similar but inactive molecules showed that both the number and position of the phosphate groups, as well as the residues connected with the carbon backbone are required for stimulation. The CD3-TCR complex is involved in cell triggering as shown by inhibition with anti-CD3 Fab fragments. However, all gamma delta clones were broadly cross-reactive and we could not isolate cells specific for only one ligand. The capacity of this frequent subset of gamma delta cells to recognize common bacterial metabolites confers the advantage to react rapidly to different invading pathogens.

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.

T-cell repertoire diversity and clonal expansions in normal and clinical samples

Improved polymerase chain reaction (PCR)-based methods now permit a more in-depth analysis of the repertoire of T cells recovered in biological samples from mice and humans. At a certain level of resolution, the diversity of the T-cell repertoire can be readily estimated and clonal expansions become easily detectable. As discussed here by Christophe Pannetier, Jos Even and Philippe Kourilsky, these improvements allow a better appreciation of the degree of reproducibility of immune responses, both in mice and humans, and should have a significant impact on clinical investigations.

Inverse PCR amplification of rare T cell receptor delta messages from mucosal biopsy specimens

Reverse transcription (RT) PCR is an important tool in studies of the repertoire of T cell antigen receptors (TCR). In combination with inverse PCR, it can be used to amplify TCR transcripts whose V regions are unknown. Little is currently known regarding the delta TCR repertoire in human intestine. Here, RT inverse PCR was adapted to efficiently amplify low abundance delta TCR sequences from human colonic mucosal biopsy specimens. In this protocol, high yields of PCR products were obtained by optimizing the conditions at which cDNA autoligation was performed.

Engineered Fv fragments as a tool for the one-step purification of integral multisubunit membrane protein complexes

The preparation of pure and homogeneous membrane proteins or membrane protein complexes is time consuming, and the yields are frequently insufficient for structural studies. To circumvent these problems we established an indirect immunoaffinity chromatography method based on engineered Fv fragments. cDNAs encoding the variable domains of hybridoma-derived antibodies raised against various membrane proteins were cloned and expressed in Escherichia coli. The Fv fragments were engineered to serve as bifunctional adaptor molecules. The Fv fragment binds to the epitope of the membrane protein, while the Strep tag affinity peptide, which was fused to the carboxy-terminus of the VH chain, immobilizes the antigen-Fv complex on a streptavidin sepharose column. The usefulness of this technique is illustrated with membrane protein complexes from Paracoccus denitrificans, namely, the cytochrome c oxidase (EC 1.9.3.1), the ubiquinol:cytochrome c oxidoreductase (EC 1.10.2.2), and subcomplexes or individual subunits thereof. These membrane proteins were purified simply by combining the crude P. denitrificans membrane preparation with the E. coli periplasmic cell fraction containing the corresponding Fv fragment, followed by solubilization and streptavidin affinity chromatography. Pure and highly active membrane protein complexes were eluted in the Fv-bound form using diaminobiotin for mild competitive displacement of the Strep tag. The affinity column could thus be reused under continuous operation for several months. Five to 10 mg of membrane protein complexes could be obtained without any detectable impurities within five hours.

T cell receptor gamma delta repertoire is skewed in cerebrospinal fluid of multiple sclerosis patients: molecular and functional analyses of antigen-reactive gamma delta clones

To study the relevance of gamma delta T cells in multiple sclerosis (MS) we analyzed the T cell receptor (TCR) gamma delta repertoire and the antigen reactivity of gamma delta clones isolated from cerebrospinal fluid (CSF). In T cell cultures derived from CSF we found an increased percentage of V delta 1+ cells as compared to peripheral blood of the same donors. Phenotypic analysis of cells from MS CSF with V gamma- and V delta-specific monoclonal antibodies (mAb) showed that the V delta 1 chain is most frequently associated with gamma chains belonging to the V gamma 1 family. Sequence analysis of TCR genes revealed heterogeneity of junctional regions in both delta and gamma genes indicating polyclonal expansion. gamma delta clones were established and some recognized glioblastoma, astrocytoma or monocytic cell lines. Stimulation with these targets induced serine esterase release and lymphokine expression characteristic of the TH0-like phenotype. Remarkably, these tumor-reactive gamma delta cells were not detected in the peripheral blood using PCR oligotyping, but were found in other CSF lines independently established from the same MS patient. Altogether, these results demonstrate that in the CSF there is a skewed TCR gamma delta repertoire and suggest that gamma delta cells reacting against brain-derived antigens might have been locally expanded.

Encephalitogenic, myelin basic protein-specific T cells from naive rat thymus: preferential use of the T cell receptor gene V beta 8.2 and expression of the CD4-CD8- phenotype

Using a primary limiting dilution approach to generate T cell lines, we compared myelin basic protein (MBP)-specific T cell clones from naive unprimed Lewis rat thymuses with the corresponding T cell repertoire of primed rats. We found that in the native thymus repertoire MBP-specific, encephalitogenic T cell clones preferentially use T cell receptor V beta 8.2 genes, along with CDR3 sequences typical for the primed Lewis anti-MBP response. In contrast to T cells from primed immune organs, which all display the CD4+CD8- phenotype, the majority of naive thymus-derived T cell clones expressed reduced levels of the CD4 co-receptor. Some clones were completely CD4-CD8-, while others included CD4-CD8- subpopulations along with CD4+CD8- T cells. In the one mixed population examined in detail, the CD4-CD8- and CD4+CD8-T cell subpopulations used a T cell receptor with identical beta chain sequence. The data suggest that in the Lewis rat the biased T cell receptor gene usage by encephalitogenic T cells is a property of the natural thymic T cell repertoire, possibly as a consequence of positive selection. The unusually low expression of CD4 in the major histocompatibility complex class II-restricted autoreactive T cells could be related to their escape from negative selection within the thymus.

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.

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.

Analysis of the V beta specificity of superantigen activation with a rapid and sensitive method using RT PCR and an automatic DNA analyser

Polymerase chain reaction (PCR) by the specific amplification of a DNA target sequence has been shown to permit analysis of T cell receptor usage. The complete repertoire is amplified using oligonucleotide primers specific for each of the known V alpha or V beta regions of the T cell receptor. One of the methods currently used to appreciate the relative quantity of different V chains of the TCR is by coamplifying in the same reaction tube the variable region of one chain together with the constant region of the other chain. We have optimised PCR conditions and analysed PCR products on an automatic DNA analyser facilitating the quantification of the amplified products, avoiding the use of radioisotopes, and allowing the determination of the sizes of CDR3 regions, thus giving new information on the modification of the T cell repertoire. This method was used to analyse the precise V beta specificity of the T cell activation with the superantigen SEB.

PCR amplification of antibody variable regions using primers that anneal to constant regions

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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.

Evidence of antigen receptor-influenced oligoclonal B lymphocyte expansion in the synovium of a patient with longstanding rheumatoid arthritis

Plasma cell infiltration of synovium is common in longstanding rheumatoid arthritis (RA). The mechanism(s) underlying synovial B cell proliferation remains unclear. One theory invokes nonspecific polyclonal stimuli; another implicates antigen as the driving force. Antigen-driven repertoires are characteristically enriched for related sets of V gene segments containing similar sequence in the antigen binding site (complementarity-determining regions; CDRs). To study the forces shaping B cell proliferation, we analyzed V kappa transcripts expressed in the synovium of an RA patient. We found Humkv325, a developmentally regulated V kappa III gene segment associated with autoantibody reactivity, in > 10% of randomly-chosen synovial C kappa cDNAs. Two sets of sequences contained identical charged amino acid residues at the V kappa-J kappa join, apparently due to N region addition. We generated "signature" oligonucleotides from these CDR3s and probed PCR amplified V kappa products from the synovium and PBLs of the same patient, and from PBLs and spleen of individuals without rheumatic disease. Significant expression of transcripts containing these unique CDR3 sequences occurred only in the patient's synovium. Thus, in this synovium there is expansion of a limited set of B cell clones expressing antigen receptors that bear evidence of antigen selection.

T cell receptor (TCR) structure of autologous melanoma-reactive cytotoxic T lymphocyte (CTL) clones: tumor-infiltrating lymphocytes overexpress in vivo the TCR beta chain sequence used by an HLA-A2-restricted and melanocyte-lineage-specific CTL clone

HLA-A2+ melanomas express common melanoma-associated antigens (Ags) recognized in vitro by autologous cytotoxic T lymphocytes (CTL). However, it is not known whether tumor Ags can drive in vivo a selective accumulation/expansion of Ag-specific, tumor-infiltrating T lymphocytes (TIL). Therefore, to evaluate this possibility, 39 CTL clones isolated from several independent mixed lymphocyte tumor cultures (MLTC) of TIL and peripheral blood lymphocytes (PBL) of an HLA-A2+ melanoma patient and selected for T cell receptor (TCR)-dependent, HLA-restricted tumor lysis, were used for analysis of TCR alpha and beta chain structure by the cDNA polymerase chain reaction (PCR) technique with variable gene-specific primers followed by sequencing. Despite absence of oligoclonality in fresh TIL and PBL, as well as in T cells of day 28 MLTC (day of cloning), sequence analysis of TCR alpha and beta chains of TIL clones revealed a dominance of a major category of melanoma-specific, HLA-A2-restricted T cells expressing a V alpha 8.2/J alpha AP511/C alpha and V beta 2.1/D beta 1/J beta 1.1/C beta 1 TCR. The same TCR was also found in 2 out of 14 PBL clones. The other PBL clones employed a V alpha 2.1 gene segment associated with either V beta 13.2, 14, or w22. Clones A81 (V alpha 2.1/J alpha IGRJ alpha 04/C alpha and V beta 14/D beta 1/J beta 1.2/C beta 1) and A21 (V alpha 8.2/J alpha AP511/C alpha and V beta 2.1/D beta 1/J beta 1.1/C beta 1), representative of the two most frequent TCR of PBL and TIL, respectively, expressed different lytic patterns, but both were HLA-A2 restricted and lysed only HLA-A2+ melanomas and normal melanocytes, thus indicating recognition of two distinct HLA-A2-associated and tissue-related Ags. Finally, by the inverse PCR technique, the specific TCR beta chain (V beta 2.1/D beta 1/J beta 1.1/C beta 1) expressed by the dominant TIL clone was found to represent 19 and 18.4% of all V beta 2 sequences expressed in the fresh tumor sample and in the purified TIL, respectively, but < 0.19% of V beta 2+ sequences expressed in PBL. These results are consistent with the hypothesis that a clonal expansion/accumulation of a melanocyte-lineage-specific and HLA-A2-restricted T cell clone occurred in vivo at the site of tumor growth.

Compartmentalization of T lymphocytes to the site of disease: intrahepatic CD4+ T cells specific for the protein NS4 of hepatitis C virus in patients with chronic hepatitis C

The adult liver is an organ without constitutive lymphoid components. Therefore, any intrahepatic T cell found in chronic hepatitis should have migrated to the liver after infection and inflammation. Because of the little information available on the differences between intrahepatic and peripheral T cells, we used recombinant proteins of the hepatitis C virus (HCV) to establish specific T cell lines and clones from liver biopsies of patients with chronic hepatitis C and compared them with those present in peripheral blood mononuclear cells (PBMC). We found that the protein nonstructural 4 (NS4) was able to stimulate CD4+ T cells isolated from liver biopsies, whereas with all the other HCV proteins we consistently failed to establish liver-derived T cell lines from 16 biopsies. We then compared NS4-specific T cell clones obtained on the same day from PBMC and liver of the same patient. We found that the 22 PBMC-derived T cell clones represent, at least, six distinct clonal populations that differ in major histocompatibility complex restriction and response to superantigens, whereas the 27 liver-derived T cell clones appear all identical, as further confirmed by cloning and sequencing of the T cell receptor (TCR) variable and hypervariable regions. Remarkably, none of the PBMC-derived clones has a TCR identical to the liver-derived clone, and even with polymerase chain reaction oligotyping we did not find the liver-derived clonotypic TCR transcript in the PBMC, indicating a preferential intrahepatic localization of these T cells. Functionally, the liver-derived T cells provided help for polyclonal immunoglobulin (Ig)A production by B cells in vitro that is 10-fold more effective than that provided by the PBMC-derived clones, whereas there is no difference in the help provided for IgM and IgG production. Altogether these results demonstrate that the protein NS4 is highly immunogenic for intrahepatic CD4+ T cells primed by HCV in vivo, and that there can be compartmentalization of some NS4-specific CD4+ T cells to the liver of patients with chronic hepatitis C.

Clonal V alpha 12.1+ T cell expansions in the peripheral blood of rheumatoid arthritis patients

Rheumatoid arthritis (RA) represents a heterogenous disease characterized by chronic polyarthritis. Most patients with adult RA inherit HLA-DR4 or -DR1 major histocompatibility complex (MHC) genes. While the molecular basis for this genetic predisposition is unknown, the major function of these MHC-encoded molecules is to present peptides to T lymphocytes. It is hypothesized that an endogenous or environmental antigen initiates a MHC-restricted immune response mediated by T lymphocytes, which is followed by a chronic inflammatory reaction involving many cell types. In chronic RA, previous or ongoing antigenic activation might result in detectable skewing of the peripheral alpha/beta T cell receptor (TCR) repertoire. Here we demonstrate a marked expansion of V alpha 12.1-bearing CD8+ T cells in the peripheral blood (mean, 22%; range, 10-43%) of > 15% of RA patients. A major proportion of these patients shared HLA-DQ2 in addition to the expected high frequency DR1 and DR4 alleles. Detailed molecular analysis in three of the RA patients with elevated V alpha 12.1+ T cells identified repeated TCR alpha chain sequences consistent with clonal V alpha 12.1+,CD8+ T cell expansion. In addition to shared TCR V alpha 12.1 germline gene usage among unrelated subjects, a conserved J alpha motif was also detected. Together, these results suggest an antigen-driven mechanism of T cell expansion in these patients and may offer a new approach in examining specific antigen that stimulate T cells in RA.

A single universal primer for the T-cell receptor (TCR) variable genes enables enzymatic amplification and direct sequencing of TCR beta cDNA of various T-cell clones

We designed a primer for the PCR directed against a highly conserved sequence of the TCR V beta gene. The V beta-universal primer, in combination with a constant region-specific primer, enabled us to amplify TCR beta cDNA of allo-HLA class-II-reactive T-cell clones by PCR without prior knowledge of their V beta sequences. The amplified TCR cDNA was purified by agarose gel electrophoresis and subjected to direct sequencing. In nine of ten T-cell clones analyzed, direct TCR sequencing gave readable sequence ladders, including two-thirds of V beta, junctional, and J beta regions. One T-cell clone gave an unreadable mixed-profile sequence ladder, indicating that this clone expressed more than one major TCR beta transcript. Even in this case, however, it was possible to determine two different TCR beta sequences separately using sequence primers specific to one of the 13 J beta segments deduced from the mixed ladder. Thus, direct sequencing utilizing the single V beta-universal primer enabled a simple, rapid, and reliable sequence determination of TCR beta cDNA of all T-cell clones analyzed.

A general method for chimerization of monoclonal antibodies by inverse polymerase chain reaction which conserves authentic N-terminal sequences

Chimerization of antibodies (Ab) by cloning the V (variable) regions encoding the light and heavy chains with degenerate oligodeoxyribonucleotide primers matching to framework region 1 and to the joining regions, leads to Ab with altered amino acids at the N-terminus compared to those of the parental Ab. This is due to N-terminal framework 1 sequences in the expression vectors [Larrick et al., Bio/Technology 7 (1989) 937-938; Le Boeuf et al., Gene (1989) 371-377; Orlandi et al., Proc. Natl. Acad. Sci. USA 86 (1989) 3833-3837]. This might lead to Ab with altered affinity to the antigen due to interaction of framework sequences with complementarity determining regions. Moreover, some V regions may be refractory to cloning by this procedure. Here, we describe a method to circumvent these potential problems. The V regions for both chains of the Ab are cloned by inverse polymerase chain reaction (PCR) with primers matching the known constant region sequences of the Ab. After sequencing, PCR fragments corresponding to the V regions of both chains are inserted in-frame into appropriate expression vectors leading to Ab with unaltered N-terminal sequences after expression in mammalian cells. The procedure is illustrated with an Ab directed against the beta chain of the human interleukin-2 receptor.

The polymerase chain reaction for detection of T-cell antigen receptor expression

Applications of the polymerase chain reaction have revolutionized the field of immunogenetics, particularly in studies of human leukocyte antigen class II polymorphism, and more recently in the analysis of T-cell receptor usage. However, the enormous diversity and variability of the T-cell receptor complex have made the amplification of the complete repertoire difficult. Several methods have been devised to address this problem. Each system is described with recent examples of its use and an assessment of its advantages and disadvantages. The use of quantitative polymerase chain reaction in T-cell receptor analysis is also discussed. The elucidation of the T-cell repertoire involved in a pathogenic process can have therapeutic implications, given the success of reversing experimental autoimmune disorders by directing specific forms of immunotherapy against V region gene products.