Highly biased CDR3 usage in restricted sets of beta chain variable regions during viral superantigen 9 response

Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients

Allogeneic hematopoietic stem cell transplantation (HSCT) is one of curative treatment options for patients with hematologic malignancies. Although GVHD mediated by the donor's T lymphocytes remains the most challenging toxicity of allo-HSCT, graft-versus-leukemia (GVL) effect targeting leukemic cells, has an important role in affecting the overall outcome of patients with AML. Here we comprehensively characterized the TCR repertoire in patients who underwent matched donor or haplo-cord HSCT using next-generation sequencing approach. Our study defines the functional kinetics of each TCRA and TCRB clone, and changes in T-cell diversity (with identification of CDR3 sequences) and the extent of clonal expansion of certain T-cells. Using this approach, our study demonstrates that higher percentage of cord-blood cells at 30 days after transplant was correlated with higher diversity of TCR repertoire, implicating the role of cord-chimerism in enhancing immune recovery. Importantly, we found that GVHD and relapse, exclusive of each other, were correlated with lower TCR repertoire diversity and expansion of certain T-cell clones. Our results highlight novel insights into the balance between GVHD and GVL effect, suggesting that higher diversity early after transplant possibly implies lower risks of both GVHD and relapse following the HSCT transplantation.

MMTV superantigens coerce an unconventional topology between the TCR and MHC class II

Mouse mammary tumor virus superantigens (vSAGs) are notorious for defying structural characterization, and a consensus has yet to be reached regarding their ability to bridge the TCR to MHC class II (MHCII). In this study, we determined the topology of the T cell signaling complex by examining the respective relation of vSAG7 with the MHCII molecule, MHCII-associated peptide, and TCR. We used covalently linked peptide/MHCII complexes to demonstrate that vSAG presentation is tolerant to variation in the protruding side chains of the peptide, but can be sensitive to the nature of the protruding N-terminal extension. An original approach in which vSAG was covalently linked to either MHCII chain confirmed that vSAG binds outside the peptide binding groove. Also, whereas the C-terminal vSAG segment binds to the MHCII α-chain in a conformation-sensitive manner, the membrane-proximal N-terminal domain binds the β-chain. Because both moieties of the mature vSAG remain noncovalently associated after processing, our results suggest that vSAG crosslinks MHCII molecules. Comparing different T cell hybridomas, we identified key residues on the MHCII α-chain that are differentially recognized by the CDR3β when engaged by vSAG. Finally, we show that the highly conserved tyrosine residue found in the vSAg TGXY motif is required for T cell activation. Our results reveal a novel SAG/MHCII/TCR architecture in which vSAGs coerce a near-canonical docking between MHCII and TCR that allows eschewing of traditional CDR3 binding with the associated peptide in favor of MHCII α-chain binding. Our findings highlight the plasticity of the TCR CDRs.

Substantial proportions of identical β-chain T-cell receptor transcripts are present in epithelial ovarian carcinoma tumors

To determine whether clonally expanded T cells are present in tumor specimens from patients with epithelial ovarian carcinoma (EOC) we amplified by the non-palindromic adaptor PCR (NPA-PCR) or by Vbeta-specific PCR beta-chain T-cell receptor (TCR) transcripts from these tumor specimens. The amplified transcripts were cloned and sequenced. Sequence analysis revealed the presence of substantial proportions of multiple identical copies of beta-chain TCR transcripts, suggesting the presence of clonal expansions of T cells in these patients, which were statistically significant by the binomial distribution in seven of nine patients. Independent amplification in separate experiments of beta-chain TCR transcripts from one patient by either NPA-PCR or by Vbeta-specific PCR, followed by cloning and sequencing, revealed identical clonal expansions irrespectively of the amplification method used. Multiple identical copies of beta-chain TCR transcripts can be derived only by specific antigen-driven proliferation and clonal expansion of the T-cell clones which recognize these antigens. Because of the very large size of the TCR repertoire, the probability of finding by chance multiple identical copies of these transcripts within an independent sample of T cells is negligible. These results demonstrate that T cells infiltrating solid tumor specimens or malignant ascites of patients with EOC contain monoclonal/oligoclonal populations of T cells.

Zinc-binding sites in the N terminus of Mycoplasma arthritidis-derived mitogen permit the dimer formation required for high affinity binding to HLA-DR and for T cell activation

Zinc-dependent superantigens can be divided into two subfamilies based on how they use zinc ions for interactions with major histocompatibility complex (MHC) class II molecules. Members of the first subfamily use zinc ions for interactions with histidine 81 on the beta-chain of MHC class II molecules, whereas members of the second subfamily use zinc ions for dimer formation. The zinc-binding motif is located in the C terminus of the molecule in both subfamilies. While our recent studies with Mycoplasma arthritidis-derived mitogen (MAM) have provided the first direct evidence demonstrating the binding to MHC class II molecules in a zinc-dependent manner, it still not known how zinc coordinates the interaction. Data presented here show that the zinc ion is mainly required to induce MAM/MAM dimer formation. Residues in the N terminus of MAM are involved in dimer formation and MHC class II binding, while histidine 14 and aspartic acid 31 of the MAM sequence are the major residues mediating MAM/MAM dimerization. Zinc-induced dimer formation is necessary for MAM binding, MHC class II-induced cell-cell adhesion, and efficient T cell activation. Together these results depict the unique mode of interaction of MAM in comparison with other superantigens.

Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes

Superantigens (SAGs) crosslink MHC class II and TCR molecules, resulting in an overstimulation of T cells associated with human disease. SAGs interact with several different surfaces on MHC molecules, necessitating the formation of multiple distinct MHC-SAG-TCR ternary signaling complexes. Variability in SAG-TCR binding modes could also contribute to the structural heterogeneity of SAG-dependent signaling complexes. We report crystal structures of the streptococcal SAGs SpeA and SpeC in complex with their corresponding TCR beta chain ligands that reveal distinct TCR binding modes. The SpeC-TCR beta chain complex structure, coupled with the recently determined SpeC-HLA-DR2a complex structure, provides a model for a novel T cell signaling complex that precludes direct TCR-MHC interactions. Thus, highly efficient T cell activation may be achieved through structurally diverse strategies of TCR ligation.

So many ways of getting in the way: diversity in the molecular architecture of superantigen-dependent T-cell signaling complexes

Superantigens (SAGs) elicit massive T-cell proliferation through simultaneous interaction with MHC and TCR molecules. SAGs have been implicated in toxic shock syndrome and food poisoning, and they may also play a pathogenic role in autoimmune diseases. The best-characterized group of SAGs are the pyrogenic bacterial SAGs, which utilize a high degree of genetic variation on a common structural scaffold to achieve a wide range of MHC-binding and T-cell-stimulating effects while assisting pathogen evasion of the adaptive immune response. Several new structures of SAG-MHC and SAG-TCR complexes have significantly increased understanding of the molecular bases for high-affinity peptide/MHC binding by SAGs and for TCR Vbeta domain specificity of SAGs. Using the currently available SAG-MHC and SAG-TCR complex structures, models of various trimolecular MHC-SAG-TCR complexes may be constructed that reveal wide diversity in the architecture of SAG-dependent T-cell signaling complexes, which nevertheless may result in similar signaling outcomes.

Mixed immune response induced in rodents by two naked DNA genes coding for mycobacterial glycosylated proteins

Two genes of Mycobacterium tuberculosis, apa (Rv1860) and pro (Rv1796), coding for two glycosylated excreted proteins have been injected to mice and guinea pigs. They produce an extended immunological response of Th1 and Th2 types. Despite the fact that mycobacterial glycosylation is necessary for a high level of delayed-type hypersensitivity (DTH) reaction, plasmids bearing each of the two genes induced an elevated level of DTH sensitization. An inverse relation between the CpG-N hexamer cluster frequency and the protective effect of injected genes is described. A comparison of the strength of several eukaryotic promoters based on the diameter of the DTH reaction shows that CMVIE followed by the ubiquitin promoter are the most efficient among those tested. A significant protective effect (0.7 log unit CFU) in mice was found for the apa gene while the pro gene had no effect.

Limited CD4 T-cell diversity associated with colitis in T-cell receptor alpha mutant mice requires a T helper 2 environment

BACKGROUND & AIMS

T-cell receptor alpha mutant (TCRalpha(-/-)) mice spontaneously develop chronic colitis mediated by CD4(+) TCRalpha(-)beta(+) T cells. The aim of this study was to analyze the mechanisms of expansion of these cells by characterization of the TCRbeta repertoire.

METHODS

TCRbeta repertoire was analyzed by reverse-transcription polymerase chain reaction/Southern blot and DNA sequencing. Clonality of T cells was examined in the lymphoid tissues and colons of TCRalpha(-/-) mice and interleukin 4-deficient TCRalpha(-/-) mice. In addition, an in vitro culture system using syngeneic colonic epithelial cells as antigens was used.

RESULTS

The clonal expansion of a restricted subset of Vbeta8.2(+) T cells was characterized by conservation of a single negatively charged amino acid residue in the second position of the complementarity-determining region 3 (CDR3). These T cells were observed in the diseased colon and appendix (cecal patch) of TCRalpha(-/-) mice, but not germfree TCRalpha(-/-) mice. Culture of polyclonal T cells from young TCRalpha(-/-) mice with colonic epithelial cells under T helper 2 conditions resulted in the survival of Vbeta8.2(+) T cells characterized by the same CDR3 pattern. In addition, the transfer of the cultivated T cells induced mild colitis in recombination-activating gene 1 mutant mice.

CONCLUSIONS

In the TCRalpha(-/-) mice, the development of colitis is associated with the presence of a restricted diversity of Vbeta8. 2(+) T-cell subsets characterized by a specific TCR motif. The limited diversity of lamina propria T cells that are derived from naive T cells expanded by reacting with luminal bacterial antigens is likely caused by the survival of these T cells after stimulation with self-antigens in the presence of a T helper 2 environment.

Murine gamma-herpesvirus infection causes V(beta)4-specific CDR3-restricted clonal expansions within CD8(+) peripheral blood T lymphocytes

Infection of mice with the gamma-herpesvirus MHV-68 results in lytic infection in the lung cleared by CD8(+) cells and establishment of lifelong latency. An Epstein-Barr virus (EBV)-like infectious mononucleosis (IM) syndrome emerges approximately 3 weeks after infection. In human IM, the majority of T cells in the peripheral blood are monoclonal or oligoclonal and are frequently specific for lytic or latent viral epitopes. However, a unique feature of MHV-68-induced IM is a prominent MHC haplotype-independent expansion of CD8(+) T cells, the majority of which utilize V(beta)4 chains in their alphabetaTCR. The ligand driving the V(beta)4 expansion is unknown, but the V(beta) bias and MHC haplotype independence raised the possibility that these cells were responding to a virally encoded or a virally induced endogenous superantigen (sAg). The aim of this study was to determine whether this rapidly proliferating subset is composed of polyclonally or clonally expanded T cells. Complementarity-determining region (CDR)-3 size analysis of V(beta)4(+)CD8(+) cells in infected mice demonstrated CDR3-restricted expansions in the V(beta)4 family as a whole. More refined analysis demonstrated major distortions in every J(beta) subfamily. V-D-J junctional region sequencing indicated that these CDR3 size-restricted expansions were composed of clonal or oligoclonal populations. The sequences were largely unique in individual mice, although evidence for 'public' or highly conserved T cell expansions was also seen between different mice. Taken together with previous studies showing an apparent MHC independence, the data suggest that a novel ligand, distinct from conventional sAg and peptide-MHC, drives proliferation of V(beta)4(+)CD8(+) T cells.

Mouse xenoantigens contribute to rat T-cell Vbeta repertoire generation in mixed xenogeneic bone marrow chimeras

We previously demonstrated that rat bone-marrow-derived cells in mixed xenogeneic chimeras (rat + mouse --> mouse) contribute to peripheral selection of mouse T-cell receptor (TCR) variable betas (Vbetas) repertoire. In this study, we analysed rat T cells that developed in the chimeras to assess the contribution of mouse xenoantigens to the development of rat TCR repertoire. The expression of rat Vbetas was analysed using flow cytometry and a reverse transcription-polymerase chain reaction (RT-PCR) method that allows for both semiquantitative analysis of rat Vbeta gene expression and size heterogeneity of the complementarity determining region 3 (CDR3) domain. Three distinct patterns of Vbeta expression were detected. Partial deletion was observed for Vbeta5, 7, 12, 14, 16, 17 and 20 that exhibited reduced levels of peripheral expression by 3.4-, 1.8-, 8.7-, 2.0-, 7.8-, 9.5- and 1.8-fold, respectively, compared with the levels of Vbetas in naYve rats. Higher levels of peripheral expression were detected for three rat Vbeta genes; Vbeta6 (2.2-fold), Vbeta8.2 (3.2-fold), and Vbeta9 (1.7-fold). The relative expression of the other 10 known rat Vbeta families in chimeras was unchanged as compared with that of normal rats. We did not observe detectable changes in the pattern of CDR3 expression in chimeras, suggesting that the mouse xenogeneic environment exerted its influence on the development of rat T cells via the Vbeta-encoded CDR1/2 domains. Our data demonstrate that the rat T-cell repertoire in chimeras is shaped by both contractions as well as expansions of selected Vbetas and suggest that mouse xenoantigens and/or superantigens of endogenous mouse retroviruses may contribute as ligands for these selection processes

Mapping the energy of superantigen Staphylococcus enterotoxin C3 recognition of an alpha/beta T cell receptor using alanine scanning mutagenesis

Binding of the T cell receptor (TCR) to a bacterial superantigen (SAG) results in stimulation of a large population of T cells and subsequent inflammatory reactions. To define the functional contribution of TCR residues to SAG recognition, binding by 24 single-site alanine substitutions in the TCR Vbeta domain to Staphylococcus aureus enterotoxin (SE) C3 was measured, producing an energy map of the TCR-SAG interaction. The results showed that complementarity determining region 2 (CDR2) of the Vbeta contributed the majority of binding energy, whereas hypervariable region 4 (HV4) and framework region 3 (FR3) contributed a minimal amount of energy. The crystal structure of the Vbeta8.2-SEC3 complex suggests that the CDR2 mutations act by disrupting Vbeta main chain interactions with SEC3, perhaps by affecting the conformation of CDR2. The finding that single Vbeta side chain substitutions had significant effects on binding and that other SEC3-reactive Vbeta are diverse at these same positions indicates that SEC3 binds to other TCRs through compensatory mechanisms. Thus, there appears to be strong selective pressure on SAGs to maintain binding to diverse T cells.

The structural basis of T cell activation by superantigens

Superantigens (SAGs) are a class of immunostimulatory and disease-causing proteins of bacterial or viral origin with the ability to activate large fractions (5-20%) of the T cell population. Activation requires simultaneous interaction of the SAG with the V beta domain of the T cell receptor (TCR) and with major histocompatibility complex (MHC) class II molecules on the surface of an antigen-presenting cell. Recent advances in knowledge of the three-dimensional structure of bacterial SAGs, and of their complexes with MHC class II molecules and the TCR beta chain, provide a framework for understanding the molecular basis of T cell activation by these potent mitogens. These structures along with those of TCR-peptide/MHC complexes reveal how SAGs circumvent the normal mechanism for T cell activation by peptide/MHC and how they stimulate T cells expressing TCR beta chains from a number of different families, resulting in polyclonal T cell activation. The crystal structures also provide insights into the basis for the specificity of different SAGs for particular TCR beta chains, and for the observed influence of the TCR alpha chain on SAG reactivity. These studies open the way to the design of SAG variants with altered binding properties for TCR and MHC for use as tools in dissecting structure-activity relationships in this system.

Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B

Superantigens (SAGs) are a class of immunostimulatory proteins of bacterial or viral origin that activate T cells by binding to the V beta domain of the T cell antigen receptor (TCR). The three-dimensional structure of the complex between a TCR beta chain (mouse V beta8.2) and the SAG staphylococcal enterotoxin B (SEB) at 2.4 A resolution reveals why SEB recognizes only certain V beta families, as well as why only certain SAGs bind mouse V beta8.2. Models of the TCR-SEB-peptide/MHC class II complex indicate that V alpha interacts with the MHC beta chain in the TCR-SAG-MHC complex. The extent of the interaction is variable and is largely determined by the geometry of V alpha/V beta domain association. This variability can account for the preferential expression of certain V alpha regions among T cells reactive with SEB.

Structure-function studies of T-cell receptor-superantigen interactions

Superantigens (SAGs) are a class of disease-causing and immunostimulatory proteins of bacterial or viral origin that activate T cells by binding to the V beta domain of the T-cell antigen receptor (TCR). The three-dimensional structure of the complex between a TCR beta chain (mouse V beta 8.2-J beta 2.1-C beta 1) and the SAG staphylococcal enterotoxin C3 (SEC3) has been recently determined. The complementarity-determining region 2 (CDR2) of the beta chain and, to lesser extents, CDR1 and hypervariable region 4 (HV4) bind in a cleft between the small and large domains of the SAG. A model of the TCR-SAG-peptide/MHC complex constructed from available crystal structures reveals how the SAG acts as a wedge between the TCR and MHC, thereby displacing the antigenic peptide away from the TCR and circumventing the normal mechanism for T-cell activation by peptide/MHC. To evaluate the actual contribution of individual SAG residues to stabilizing the V beta C beta-SEC3 complex, as well as to investigate the relationship between the affinity of SAGs for TCB and MHC and their ability to activate T cells, we measured the binding of a set of SEC3 mutants to a soluble recombinant TCR beta chain and to the human MHC class II molecule HLA-DR1. We show that there is direct correlation between affinity and ability to stimulate T cells, with SAGs having the highest affinity for the TCR being the most biologically active. We also find that there is an interplay between TCR-SAG and SAG-MHC interactions in determining mitogenic potency, such that a small increase in the affinity of a SAG for MHC can overcome a large decrease in the SAG's affinity for the TCR. Finally, we observe that those SEC3 residues that make the greatest energetic contribution to stabilizing the V beta C beta-SEC3 complex are strictly conserved among enterotoxins reactive with mouse V beta 8.2, thereby explaining why SAGs having other residues at these positions show different V beta-binding specificities.