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Results for “TCR specificity prediction”

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PubMed2002

Epitope mapping of neutralizing TSST-1 specific antibodies induced by immunization with toxin or toxoids.

Toxic shock syndrome toxin-1 (TSST-1), a superantigen produced by Staphylococcus aureus, is a potent stimulator of the immune system. T-cells are activated by crosslinking of MHC class II molecules on antigen presenting cells with T-cell receptors (TCR). TSST-1 is associated with the majority of the cases of menstrual staphylococcal toxic shock, a severe and life-threatening multisystem disorder. Even though antibody mediated protection has been studied, information on antibody specificity directed to individual antigenic determinants of the protein is incomplete. To obtain immunogens with low toxicity, we generated a double-site mutant (dmTSST-1), modified at solvent-exposed residues predicted to be important for both MHC class II and TCR binding, and detoxified recombinantly expressed TSST-1 (rTSST-1) as well as native TSST-1 (nTSST-1) isolated from Staphylococcus aureus by treatment with formaldehyde. Rabbits were immunized with rTSST-1, nTSST-1, dmTSST-1, and formaldehyde inactivated toxoids. The sera obtained were used to map the antigen-reactive regions of the molecule and to identify specificities of antibodies induced by immunization with the different antigens. To detect linear antigenic epitopes of TSST-1 the reactivity of the sera with 11-meric peptides having an overhang of four residues, covering the entire molecule of TSST-1, have been studied. We found that sera of TSST-1 immunized rabbits predominantly reacted with N-terminal residues 1-15, while sera generated with formaldehyde inactivated toxoid recognized a total of 7 regions located at the N- and C-terminus and internal sites of TSST-1. Despite different specificities all sera were able to inhibit TSST-1 induced proliferation of human mononuclear cells.

Amino Acid Sequence↗

PubMed1993

Protein tyrosine kinase p56lck controls allelic exclusion of T-cell receptor beta-chain genes.

During T-cell development, site-specific DNA rearrangements mediating assembly of beta- and alpha-chain genes of the T-cell receptor (TCR) are developmentally ordered. In particular, assembly and expression of a complete beta-chain gene blocks further rearrangements at the beta-locus (a process referred to as allelic exclusion) and drives the generation and expansion of CD4+8+ cells. Although the mechanism used by TCR beta chains to deliver such signals is unknown, studies in transgenic animals have suggested that the lymphocyte-specific protein tyrosine kinase p56lck may impinge on a similar signalling pathway. The hypothesis that TCR beta chains deliver intracellular signals via p56lck makes an explicit prediction: that interference with p56lck function will mitigate the effects of a simultaneously expressed TCR beta chain. Here we confirm this prediction through examination of allelic exclusion in mice expressing both a functional TCR beta chain transgene and a catalytically inactive form of p56lck.

Alleles↗

PubMed1991

The human T cell receptor beta-chain gene complex contains at least 57 variable gene segments. Identification of six V beta genes in four new gene families.

The human TCR beta-chain gene complex includes at least 57 variable (V) gene segments, a number estimated using a combination of Southern blots of conventional and pulsed field gels, sequence analysis of cDNA clones, and from the analysis of genomic cosmid and phage clones. This number includes six TCR beta-chain V genes in four new families identified here by sequence analysis of clones derived from a human TCR beta-chain specific cDNA library. Comparison of the sequences of the new V beta genes with previously reported V beta sequences reveals predicted similarities but less than 75% nucleic acid identity that establishes them as new V beta families. One of the new V beta gene families includes three genes and the other three are single member families. Identification of these six new V beta genes falling into four V beta families brings the total number of transcribed human V beta families to 24 and makes it possible to refine the estimate of the total number of human TCR V beta genes to 57.

Amino Acid Sequence↗

PubMed2002

Modeling alternative binding registers of a minimal immunogenic peptide on two class II major histocompatibility complex (MHC II) molecules predicts polarized T-cell receptor (TCR) contact positions.

Several major histocompatibility complex class II (MHC II) complexes with known minimal immunogenic peptides have now been solved by X-ray crystallography. Specificity pockets within the MHC II binding groove provide distinct peptide contacts that influence peptide conformation and define the binding register within different allelic MHC II molecules. Altering peptide ligands with respect to the residues that contact the T-cell receptor (TCR) can drastically change the nature of the ensuing immune response. Here, we provide an example of how MHC II (I-A) molecules may indirectly effect TCR contacts with a peptide and drive functionally distinct immune responses. We modeled the same immunogenic 12-amino acid peptide into the binding grooves of two allelic MHC II molecules linked to distinct cytokine responses against the peptide. Surprisingly, the favored conformation of the peptide in each molecule was distinct with respect to the exposure of the N- or C-terminus of the peptide above the MHC II binding groove. T-cell clones derived from each allelic MHC II genotype were found to be allele-restricted with respect to the recognition of these N- vs. C-terminal residues on the bound peptide. Taken together, these data suggest that MHC II alleles may influence T-cell functions by restricting TCR access to specific residues of the I-A-bound peptide. Thus, these data are of significance to diseases that display genetic linkage to specific MHC II alleles, e.g. type 1 diabetes and rheumatoid arthritis.

Alleles↗

PubMed2005

A unique Vgamma5-T-cell population in the murine mammary gland.

Mammary epithelia and the epidermis share a common embryologic origin. Like resident epidermal T cells (ETC), a significant number of murine mammary gland T cells (MTC) express Vgamma5-T-cell receptors (TCR). MTC were assessed to see if they express the same invariant Vgamma5/Vdelta1-TCRs as those of ETC. MTC-derived hybridomas, positive for Vgamma5-TCRs, expressed Vdelta5 instead of Vdelta1. Additionally, they showed non-germline additions in the gamma-TCR and delta-TCR junctions, sharing among them an identical 19-nucleotide N-region in the delta-TCR junctions. Vgamma5-TCR and Vdelta5-TCR gene sequences from fresh peripartum MTC also contained variable N-regions, including a 7-nucleotide N-region similar to one found in the hybridomas. Thus, Vgamma5-TCR+ MTC are distinct from Vgamma5-TCR+ ETC by expressing variable non-canonical TCRs, predicting differences in the two T-cell populations in ligand specificity and in function.

Animals↗

PubMed1993

Reactions of anti-immunoglobulin sera with synthetic T cell receptor peptides: implications for the three-dimensional structure and function of the TCR beta chain.

The derived amino acid sequence of the human TCR beta chain shows considerable homology to lg lambda light chains in its variable (V) and constant (C) domains, and in its joining segment (J). We assessed the cross-reactivity between TCR beta chains and lg light chains by synthesizing a set of nested, overlapping 16-mer peptides that duplicated the sequence that corresponds to the continuous VDJC sequence of TCR beta chain and determining the capacity of rabbit antisera to human or murine lgs to react with these peptides. The reactivities we observed were consistent with homologies to lambda and kappa light chains. The strongest reactivity in ELISA binding and competitive inhibition was with a peptide that corresponds to the 'switch peptide' of light chains. The sequence is encoded by the C-terminal region of the J segment (Fr4) and the N-terminus of the C region. Other regions reactive with anti-light chain sera corresponded respectively to CDR1 and Fr3 segments of the V region, and a segment of the constant region predicted to loop out of the tight globular structure. The peptide immunochemical results, coupled with the identification of specific regions of sequence correspondence between TCR beta and the characterized lambda light chain Mcg, allowed us to develop a three-dimensional model of the beta chain consistent with its role in antigen recognition and response to superantigens.

Amino Acid Sequence↗

PubMed1999

Developing antigen-specific therapies in multiple sclerosis: a tale of Tantalus or Ulysses?

Autoreactive T-cell responses directed to myelin proteins in the central nervous system are widely believed to be crucial in the pathology of multiple sclerosis (MS). However, effective ways of selectively targeting these T-cells in order to alter the clinical course of MS in a predictable manner has yet to be demonstrated. This review discusses two recent developments of crucial importance to the rational development of antigen-specific therapy in MS. The very idea of antigen-specific therapy in MS has long faced the challenge of determinant spreading, i.e., the development of novel autoimmune responses as the consequence of tissue damage. This phenomenon has led many to expect that in ongoing MS, many different pathogenic specificities would accumulate. Obviously, this would render antigen-specific therapy very difficult. Recent data now suggest that determinant spreading is most likely to be a transient phenomenon limited only to the first stages of tissue damage. A second development has changed our perspective on the specificity of individual T-cells and, thus, on the suitability of various ways to implement antigen-specific therapy. Evidence is rapidly accumulating that T-cell receptors are much more cross-reactive than previously assumed. This notion poses unexpected challenges to therapeutic approaches in MS that are based on selective targeting of autoreactive TCR. Vaccination with TCR peptides, administration of anti-TCR antibodies and development of therapeutically altered peptide ligands all depend on a significant level of predictability of pathogenic TCR. With such predictability now turning out to be much lower than was previously hoped, selective TCR-directed strategies for intervention may therefore turn out to be much less effective than anticipated. In the development of antigen-specific therapies, the use of whole protein tolerogens now seems to be the most promising route. Oral, intranasal or iv. administration of antigen remain viable options to re-establish selective tolerance that ought to be further developed for the benefit of MS patients.

Journal Article↗

PubMed1993

Simultaneous involvement of all six predicted antigen binding loops of the T cell receptor in recognition of the MHC/antigenic peptide complex.

The TCR is predicted to resemble the Fab fragment of an Ig molecule and by analogy to possess six Ag binding loops that contact MHC proteins bound with antigenic peptides. We have identified residues in the predicted Ag binding loops (beta 1, beta 2, and beta 3) on a TCR beta-chain that are important in the recognition of the MHC/antigenic peptide complex. Using site-directed mutagenesis, we altered the residues forming the predicted Ag binding site on the beta-chain expressed by the T lymphocyte clone D5, which specifically recognizes p-azobenzenearsonate-conjugated peptides presented by the class II MHC molecule I-Ad. Amino acid substitution of individual residues in each loop affected Ag recognition, demonstrating that all three putative Ag binding loops of the D5 TCR beta-chain are important in interaction with I-Ad/arsonate-conjugated Ag. Taken together with our previous work on the D5 TCR alpha-chain (Nalefski et al., J. Exp. Med. 175:1553), these results suggest that all six Ag binding loops of the D5 TCR alpha- and beta-chains interact simultaneously with the MHC/peptide complex. Consequently, the area of interaction between the TCR and the MHC/antigenic peptide complex is predicted to be extensive.

Amino Acid Sequence↗

PubMed2006

Identification of HLA class I dependent immunogenic peptides from clonotypic TCRbeta expressed in cutaneous T-cell lymphoma.

The clonotypic T-cell receptor (TCR) is a potential target antigen for specific immunotherapy of cutaneous T-cell lymphoma (CTCL). We identified T-cell epitopes from the rearranged TCR beta chain of the malignant T-cell population by the "reverse immunology" approach. Peptide-specific T-cell lines were generated against predicted epitopes and tested for the recognition of tumor cells and cells transfected with the full-length DNA coding for TCRV beta chain. Two peptides derived from the clonotypic TCRVbeta of a HLA-A2 positive patient could induce peptide-specific T cells from peripheral blood mononuclear cells of healthy donors and the patient as assessed by IFN-gamma ELISpot assay. Furthermore, the reactive CTLs efficiently recognized autologous Sézary tumor cells, as well as HLA-A2 positive 293 cells transfected with recombinant plasmid expressing the corresponding TCRVbeta29 protein. Similar results were obtained in a HLA-A3+ patient for TCRVbeta7-Jbeta2.7. In conclusion, our experiments show that the TCR beta chain harbors epitopes suitable as targets for specific vaccination which might be a promising approach for the specific immunotherapy of cutaneous T-cell lymphoma patients.

Epitopes↗

PubMed1995

Autoregulation of Tcr V region epitopes in autoimmune disease.

Normal individuals possess low levels of autoantibodies specific for certain peptide defined regions of T-cell receptor (Tcr) variable regions, particularly CDR1 and Fr3. These regions are predicted to be exposed on the surface of the native molecule and, by analogy and comparison with immunoglobulins, correspond to public idiotype determinants. The anti-Tcr idiotype antibodies appear to be ubiquitous and we propose that they play a role in the regulation of T-cell function. To delineate the parameters of expression of these antibodies, we characterized anti-Tcr antibody activity in normal individuals, in those suffering from the autoimmune diseases rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), and in patients with non-autoimmune arthritis (osteoarthritis) as a disease control. There were significant increases in autoantibody levels in the autoimmune patients. There was also variation in isotype and the particular variable regions recognized. IgM autoantibodies directed against a few peptide defined determinants were elevated in RA, whereas SLE patient sera showed high levels of IgG binding to a broad spectrum of Tcr peptides.

Arthritis, Rheumatoid↗

PubMed1994

Definition of TCR recognition sites on Ld-tum- complexes.

The P911 variant of the P815 mastocytoma was shown by Lurquin et al. (Cell 58:293, 1989) to elicit rapid tumor rejection in a syngeneic host. This rejection was mediated by Ld-restricted cytotoxic T lymphocytes (CTL) for which targets could be sensitized by the synthetic peptide designated tum- (P91A-.12-24). In a previous study, T cell clones specific for Ld-tum- complexes displayed very restricted TCR usage and a characteristic TCR motif in the V alpha CDR3 region, predicted to interact with peptide. However, in contrast to the majority of Ld peptide ligands that are nonamers, the tum- peptide is a 13-mer and its sequence does not fit the Ld binding motif. Thus, to define shorter versions of the tum- 13-mer and residues involved in TCR recognition, nonamer derivatives were synthesized and compared in several different binding and functional assays. From these comparisons, the peptide TQNHRALDL was found to be the optimal nonamer. CTL recognition of Ala-substituted analogues of this peptide indicated that the His and Arg residues at positions 4 and 5 are important for TCR contact. We propose that these basic residues of the tum- peptide interact with the previously defined acidic residues in the CDR3 region of several TCR known to recognize Ld-tum- complexes.

Amino Acid Sequence↗

PubMed2006

Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity.

Why some virus-specific CD8 TCR repertoires are diverse and others restricted or "oligoclonal" has been unknown. We show here that oligoclonality and extreme clonal dominance can be a consequence of T cell cross-reactivity. Lymphocytic choriomeningitis virus (LCMV) and Pichinde virus (PV) encode NP(205-212) epitopes that induce different but highly cross-reactive diverse TCR repertoires. Homologous viral challenge of immune mice only slightly skewed the repertoire and enriched for predictable TCR motifs. However, heterologous viral challenge resulted in a narrow oligoclonal repertoire with dominant clones with unpredictable TCR sequences. This shift in clonal dominance varied with the private, i.e., unique, specificity of the host's TCR repertoire and was simulated using affinity-based computer models. The skewing differences in TCR repertoire following homologous versus heterologous challenge were observed within the same private immune system in mice adoptively reconstituted with memory CD8 T cell pools from the same donor. Conditions driving oligoclonality resulted in an LCMV epitope escape variant in vivo resembling the natural Lassa virus sequence. Thus, T cell oligoclonality, including extremes in clonal dominance, may be a consequence of heterologous immunity and lead to viral escape. This has implications for the design of peptide-based vaccines, which might unintentionally prime for skewed TCR responses to cross-reactive epitopes.

Animals↗

PubMed2001

Caspase-dependent cleavage of the hematopoietic specific adaptor protein Gads alters signalling from the T cell receptor.

Gads is a SH2 and SH3 domain-containing, hematopoietic-specific adaptor protein that functions in signalling from the T cell receptor. Gads acts by linking SLP-76, bound by the carboxy-terminal Gads SH3 domain, to tyrosine phosphorylated LAT which contains binding sites for the Gads SH2 domain. Gads is distinguished from Grb2 and the closely related Grap protein by the presence of a 120 amino acid unique region between the SH2 domain and the carboxy terminal SH3 domain. Here we demonstrate that the unique region of Gads contains a capase cleavage site. Induction of apoptosis in lymphocytes results in detectable Gads cleavage by 60 min. Gads cleavage is blocked in vivo by treating cells with a caspase 3 inhibitor. A putative caspase 3 cleavage site was identified within the unique region and mutation of this site prevented Gads cleavage in vitro, and in vivo. The Gads cleavage products retained the predicted binding specificity for SLP-76 and LAT. Expression of the Gads cleavage products in Jurkat T cells inhibited NFAT activation following TCR cross linking. These findings indicate that cleavage of Gads in vivo could function to alter signalling downstream of the T cell receptor by disrupting cross talk between SLP-76 and LAT.

Adaptor Proteins, Signal Transducing↗

PubMed1991

Profound alteration in an alpha beta T-cell antigen receptor repertoire due to polymorphism in the first complementarity-determining region of the beta chain.

Amino acid residues that are critical in maintaining the framework structure of immunoglobulin heavy- and light-chain variable (V) regions are strongly conserved in the V alpha and V beta proteins of the alpha beta T-cell antigen receptor (TCR alpha beta). Consequently, it has been proposed that TCR alpha beta has a conformation similar to that of an immunoglobulin Fab fragment and that the regions of the TCR homologous to the three immunoglobulin complementarity-determining regions (CDRs 1, 2, and 3) bind to the peptide antigen-major histocompatibility complex (MHC) molecule ligand. A single amino acid substitution in the predicted CDR1 of the V beta 3 protein of certain mouse strains dramatically altered TCR alpha beta usage in an antigen-specific MHC-restricted immune response but did not abrogate V beta 3 specificity for the superantigens minor lymphocyte stimulatory locus (Mls)c and staphylococcal enterotoxin A (SEA). The results confirm the importance of the V beta CDR1 in antigen-MHC molecule recognition, supporting the Fab-like structural model of TCR alpha beta, and provide further evidence that conventional antigen-MHC recognition and superantigen recognition are mediated by distinct regions of the TCR beta chain. They also suggest that allelic polymorphism may be a significant source of diversity in the TCR repertoire.

Animals↗

PubMed1993

Biased T cell receptor usage by Ld-restricted, tum- peptide-specific cytotoxic T lymphocyte clones.

We have investigated the TCR gene usage in a panel of H-2Ld-restricted, tum- peptide-specific CTL clones. These clones possess identical MHC restriction and peptide specificity, yet they vary dramatically in the amount of peptide required to sensitize targets for recognition. We previously demonstrated a precise quantitative correlation between the determinant density requirement of a given clone and the CD8 dependency. In this study we sequenced polymerase chain reaction copies of the TCR mRNA used by these clones, not only to correlate TCR structure with recognition of a specific class I/peptide complex, but also to determine if the functional affinity differences between these clones is reflected in the TCR gene products used. The number of TCR V beta, V alpha, and J alpha region gene segments expressed by these clones is very limited. Twelve of 17 clones express V beta 8 at comparable levels on the cell surface. Using PCR amplification of cDNA templates, cloning, and dideoxy sequencing, we have obtained the nucleotide sequence of the TCR V-(D)-J regions in seven of the V beta 8+ clones. Two of the clones use V beta 8.2 and identical J alpha gene segments. Three of the five V beta 8.3+ clones express identical V alpha and J alpha gene products and the other two use similar V alpha chains and J alpha chains with a shared motif in the predicted CDR3 region. Although no clear correlation between TCR gene usage and CD8 dependency was seen, the range of TCR gene usage in the tum- peptide-specific, Ld-restricted immune response is strikingly narrow and suggests a coselection of the alpha- and beta- chains for recognition of the class I/peptide complex.

Amino Acid Sequence↗

PubMed2002

T-cell epitope prediction with combinatorial peptide libraries.

T cell receptors (TCR) recognize antigenic peptides in complex with the major histocompatibility complex (MHC) molecules and this trimolecular interaction initiates antigen-specific signaling pathways in the responding T lymphocytes. For the study of autoimmune diseases and vaccine development, it is important to identify peptides (epitopes) that can stimulate a given TCR. The use of combinatorial peptide libraries has recently been introduced as a powerful tool for this purpose. A combinatorial library of n-mer peptides is a set of complex mixtures each characterized by one position fixed to be a specified amino acid and all other positions randomized. A given TCR can be fingerprinted by screening a variety of combinatorial libraries using a proliferation assay. Here, we present statistical models for elucidating the recognition profile of a TCR using combinatorial library proliferation assay data and known MHC binding data.

Combinatorial Chemistry Techniques↗

PubMed1991

Limited regions of the alpha 2-domain alpha-helix control anti-A2 allorecognition: an analysis using a panel of A2 mutants.

The regions of the HLA-A2 molecule controlling anti-A2 alloreactivity were explored using naturally occurring allelic variants of HLA-A, and a panel of transfectants expressing the products of A2.1 genes that had been mutated at multiple positions encoding residues in the alpha 2 domain alpha-helix. As a means of detecting distant conformational effects, these altered A2.1 molecules were also examined serologically. Amino acid substitutions at the carboxy-terminal end of the alpha 2 domain alpha-helix led to diminished staining with the monoclonal antibody (mAb) MA2.1. The epitope for this antibody has previously been mapped to the alpha 1 domain alpha-helix (residues 62-65). This suggests that interdomain contacts may cause conformational alteration, and that mutants can have distant, as well as local effects. Of the 24 positions where substitutions were made, only six led to loss of the anti-A2 alloresponse by the three clones and three lines that were tested. In addition, the mutations that altered the MA2.1 epitope, located on the alpha 1 domain alpha-helix, did not inhibit allorecognition. This suggests that a limited number of regions on the A2.1 molecule are responsible for allodeterminant expression. The most influential substitutions were those at positions 152, 154, 162, and 166. It is notable that three of these are predicted to be T-cell receptor (Tcr)-contacting residues, and one (152) to contribute to peptide binding. These results suggest that the specificity of alloreactive T cells is determined by exposed polymorphisms, directly contacted by the Tcr, and by concealed polymorphisms which influence peptide binding.

Cell Line↗

PubMed2002

The relationship between predicted peptide-MHC class II affinity and T-cell activation in a HLA-DRbeta1*0401 transgenic mouse model.

The HLA-DRB1*0401 MHC class II molecule (DR4) is genetically associated with rheumatoid arthritis. It has been proposed that this MHC class II molecule participates in disease pathogenesis by presenting arthritogenic endogenous or exogenous peptides to CD4+ T cells, leading to their activation and resulting in an inflammatory response within the synovium. In order to better understand DR4 restricted T cell activation, we analyzed the candidate arthritogenic antigens type II collagen, human aggrecan, and the hepatitis B surface antigen for T-cell epitopes using a predictive model for determining peptide-DR4 affinity. We also applied this model to determine whether cross-reactive T-cell epitopes can be predicted based on known MHC-peptide-TCR interactions. Using the HLA-DR4-IE transgenic mouse, we showed that both T-cell proliferation and Th1 cytokine production (IFN-gamma) correlate with the predicted affinity of a peptide for DR4. In addition, we provide evidence that TCR recognition of a peptide-DR4 complex is highly specific in that similar antigenic peptide sequences, containing identical amino acids at TCR contact positions, do not activate the same population of T cells.

Aggrecans↗