TCR repertoire evolution during maintenance of CMV-specific T-cell populations

During infections and cancer, the composition of the T-cell receptor (TCR) repertoire of antigen-specific CD8⁺ T cells changes over time. TCR avidity is thought to be a major driver of this process, thereby interacting with several additional regulators of T-cell responses to form a composite immune response architecture. Infections with latent viruses, such as cytomegalovirus (CMV), can lead to large T-cell responses characterized by an oligoclonal TCR repertoire. Here, we review the current status of experimental studies and theoretical models of TCR repertoire evolution during CMV infection. We will particularly discuss the degree to which this process may be determined through structural TCR avidity. As engineered TCR-redirected T cells have moved into the spotlight for providing more effective immunotherapies, it is essential to understand how the key features of a given TCR influence T-cell expansion and maintenance in settings of infection or malignancy. Deeper insights into these mechanisms will improve our basic understanding of T-cell immunology and help to identify optimal TCRs for immunotherapy.     

Disease etiology and diagnosis by TCR repertoire analysis goes viral

The importance of T‐cell receptor (TCR) repertoire diversity is highlighted in murine models of immunodeficiency and in many human pathologies. However, the true extent of TCR diversity and how this diversity varies in health and disease is poorly understood. In a previous issue of the European Journal of Immunology, Lossius et al. [Eur. J. Immunol. 2014. 44: 3439–3452] dissected the composition of the TCR repertoire in the context of multiple sclerosis (MS) using high‐throughput sequencing of TCR‐β chains in cerebrospinal fluid samples and blood. The authors demonstrated that the TCR repertoire of the CSF was largely distinct from the blood and enriched in EBV‐reactive CD8⁺ T cells in MS patients. Studies of this kind have long been hindered by technical limitations and remain scarce in the literature. However, TCR sequencing methodologies are progressing apace and will undoubtedly shed light on the genetic basis of T‐cell responses and the ontogeny of T‐cell‐mediated diseases, such as MS.     

T cell receptor repertoire and function in patients with DiGeorge syndrome and velocardiofacial syndrome

DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS) are associated with chromosome 22q11.2 deletion. Limited information is available on the T cell receptor (TCR) Vbeta repertoire. We therefore investigated TCR Vbeta families in lymphocytes isolated from blood and thymic samples of seven patients with DGS and seven patients with VCFS, all with 22q11.2 deletion. We also studied activities related to TCR signalling including in vitro proliferation, anti-CD3-induced protein tyrosine phosphorylation, and susceptibility to apoptosis. Reduced CD3+ T cells were observed in most patients. Spontaneous improvement of T cell numbers was detected in patients, 3 years after the first study. Analysis of CD4+ and CD8+ TCR Vbeta repertoire in peripheral and thymic cells showed a normal distribution of populations even if occasional deletions were observed. Lymphoproliferative responses to mitogens were comparable to controls as well as anti-CD3-induced protein tyrosine phosphorylation. Increased anti-CD3-mediated apoptosis was observed in thymic cells. Our data support the idea that in patients surviving the correction of cardiac anomalies, the immune defect appears milder than originally thought, suggesting development of a normal repertoire of mature T cells.     

Characterization of peripheral blood TCR repertoire in patients with ankylosing spondylitis by high-throughput sequencing

Ankylosing spondylitis (AS) is a chronic and progressive autoimmune disease affecting the invasion of the spine, sacroiliac joints and peripheral joints. T cells play a vital role in the underlying pathogenesis of AS, which mediated autoimmune and inflammatory responses via specific recognition of autoantigen peptides presented by susceptibility HLA. Antigen-specific T cells triggered by HLA/antigen complexes will undergo a massive expansion that forming an uneven T cell repertoire. To enhance our understanding of T-cell-mediated autoimmune in AS, we applied TCR β chains high-throughput sequencing to AS patients for in-depth TCR repertoire analysis. A significantly lower TCR repertoire diversity was observed in peripheral blood of AS patients relative to controls. And severe patients in our AS cohort have a more restricted TCR repertoire than mild patients, suggesting that the TCR repertoire diversity might be associated with the clinical severity of disease. No V, J and VJ pairs with significant biased usage were identified, which indicated that the usage frequency deviation of certain V/J/V-J genes in AS patients is little. This is a pilot study with potentially interesting observation on reduced diversity of T cells repertoire in peripheral blood of AS patients and further studies are needed.     

Numbers and odds: TCR repertoire size and its age changes impacting on T cell functions

A vast array of αβ T cell receptors (TCRs) is generated during T cell development in the thymus through V(D)J recombination, which involves the rearrangement of multiple V, D, and J genes and the pairing of α and β chains. These diverse TCRs provide protection to the human body against a multitude of foreign pathogens and internal cancer cells. The entirety of TCRs present in an individual's T cells is referred to as the TCR repertoire. Despite an estimated 4 × 10¹¹ T cells in the adult human body, the lower bound estimate for the TCR repertoire is 3.8 × 10⁸. While the number of circulating T cells may slightly decrease with age, the changes in the diversity of the TCR repertoire is more apparent. Here, I review recent advancements in TCR repertoire studies, the methods used to measure it, how richness and diversity change as humans age, and some of the known consequences associated with these changes.     

Post-thymic in vivo proliferation of naive CD4+ T cells constrains the TCR repertoire in healthy human adults

In spite of thymic involution early in life, the numbers of naive CD4(+) T cells only slowly decline in ageing humans implying peripheral post-thymic naive CD4(+) T cell expansion. This proliferation may compensate for continuous activation and death of naive CD4(+) T cells but may also have negative consequences for protective immunity. Here we show that naive CD4(+) T cells that have proliferated in the periphery are characterized by a highly restricted oligoclonal TCR repertoire. Additionally these cells, which constitute the majority of naive CD4(+) T cells in the elderly, display signatures of recent TCR engagement. Our results demonstrate for the first time that peripheral post-thymic proliferation of naive CD4(+) T cells in healthy human individuals causes a significant contraction of the peripheral TCR repertoire. This age-dependent deterioration of CD4(+) T cell immunity could entail ageing-associated autoimmunity, increased susceptibility to infection or cancer and decreased efficiency of vaccination.     

Analysis of T cell repertoire and function in mice transgenic for the human V{beta}3 TCR

We have constructed mice containing the human V_ß3TCR gene from the influenza virus haemagglutinin specific humanCD4⁺ T cell clone HA1.7. Similar cell yields were obtained fromtransgenic and non-transgenic lymphoid tissue, with normal levelsof T cells and with no unusual bias of the CD4 or CD8 subpopulations.Immunostaining and FACS analysis of transgenic thymocytes, spleen,and mesenteric lymph nodes revealed that the majority of T cellsexpressed the human V_ß3 TCR on the cell surface. Smallnumbers of cells expressing murine TCR_ßchain werealso detected. Polymerase chain reaction analysis revealed thatan extensive V TCR repertoire was used in the human V_ß3transgenic mice. Lymphocytes from the spleen and bmesentericlymph nodes of transgenic mice were assessed for functionalactivity in vitro. Isolated cells were stimulated with mitogenor superantigen, as well as directly through the TCR-CD3 complex,and their ability to proliferate and secrete lymphokines analysed.Cells from transgenic mice responded well after stimulationwith phytohaemagglutinin, concanavalin A, anti-CD3 antibody,anti-CD3 antibody with phorbol ester, and Staphylococcus aureusenterotoxin B, and also showed alloreactivity in a mixed lymphocytereaction. Minimal levels of response were detected after stimulationwith murine TCRß antibody. Together, these data suggestthat a human TCRß chain is able to associate witha murine TCR chain, to form a fully functional surface TCR-CD3complex.     

Onset of promiscuous gene expression in murine fetal thymus organ culture

T-cell differentiation and induction of tolerance to self-antigens occurs mainly in the thymus. Thymic stromal cells, specifically medullary thymic epithelial cells, express a diverse set of genes encoding parenchymal organ-specific proteins. This phenomenon has been termed promiscuous gene expression (PGE) and has been implicated in preventing organ-specific autoimmunity by inducing T-cell tolerance to self antigens. Early thymopoiesis and the critical factors involved in T-cell differentiation can be reproduced in vitro by murine fetal thymus organ culture (FTOC), which mimics the natural thymic microenvironment. To evaluate the occurrence of PGE in FTOC, gene expression profiling during in vitro thymic development in BALB/c mice was performed using a set of nylon cDNA microarrays containing 9216 sequences. The statistical analysis of the microarray data (sam program) revealed the temporal repression and induction of 57 parenchymal and seven lymphoid organ-specific genes. Most of the genes analysed are repressed during early thymic development (15-17 days post-coitum). The expression of the autoimmune regulator (AIRE) gene at 16 days post-coitum marks the onset of PGE. This precedes the induction of parenchymal organ genes during the late developmental phase at 20 days post-coitum. The mechanism of T-cell tolerance induction begins during fetal development and continues into adulthood. Our findings are significant because they show a fine demarcation of PGE onset, which plays a central role in induction of T-cell tolerance.     

Isolation and phenotypical characterization of mesenchymal stem cells from human fetal thymus

Stem cells from human fetal thymus ectomesenchyma capable of forming colonies during in vitro culturing were isolated and characterized. Selection of culturing conditions showed that the growth and phenotypical characteristics of these cultures depended on seeding density and presence of basic fibroblast growth factor in the medium. After nonspecific inhibition of proliferation clonogenic cultures of thymic mesenchymal stem cells differentiated into myoblasts, formed characteristic myotubes, and expressed specific myogenesis markers. Colonies of thymic mesenchymal stem cells differentiated into chondrogenic, osteogenic, and adipogenic lines under conditions described for bone marrow mesenchymal stem cells. Cytofluorometric analysis of surface epitopes of thymic mesenchymal stem cells showed that the majority of cells expressed mesenchymal markers Thy-1, CD44, and CD105. Testing for CD34, CD38, CD45, and HLA-DR were negative in all cases. The main cell population (70–95%) did not express MHCl antigens during long-term culturing.__________This revised version was published online in July 2005 with the addition of the issue title and article categoryTranslated from Kletochnye Tekhnologii v Biologii i Meditsine, Vol. 1, No. 1, pp. 34–41, January, 2005     

Non-random employment of V{beta}6 and J{beta} gene elements and conserved amino acid usage profiles in CDR3 regions of human fetal and adult TCR {beta} chain rearrangements

We have studied the usage of V_ß36, D_ß, andJ_ß elements, and the composition of the CDR3 regionsof human fetal TCR ß chain rearrangements In a 17week old fetal thymus and In fetal liver, bone marrow, spleen,and cord blood at 11 and 13 weeks of gestation. These fetalsequences were compared with TCR ß chain rearrangementsobtained from post-partum thymus, adult spleen, and adult peripheralblood mononuclear cells. Both fetal and adult TCR V_ß6rearrangements exhibited a non-random usage of V_ßand J_ß elements. Up to 90% of the sequences obtainedat 11 weeks of gestation used J_ß2 elements, most notablyJ_ß2.1. In the 13 and 17 week old fetal and in theadult tissues, J_ß1 elements were used In 30% of therearrangements while, within the J_ß2 rearrangements,J_ß2.1 and J_ß2.7 were used most frequently.Both fetal and adult TCR ß chain CDR3 regions showednon-random usage of amlno acids. However, the early fetal repertoirewas further limited due to the relative absence of N-reglonsin up to 60% of the 11 and 13 week old TCR ß chainrearrangements, resulting In smaller antigen binding sites.In fetal and adult TCR ß chain rearrangements thedistribution patterns of the length of N-regions and the usageprofiles of J_ß elements were similar in hematopoletlcand peripheral organs, suggesting no apparent preference forparticular TCR ß chain rearrangements. On the whole,the data showed that both the available fetal and adult TCRV_ß6 repertoires are seemingly smaller than expectedon the basis of random usage of V_ß and J_ßelements and amlno acid composition of the CDR3 regions.     

The majority of murine VH12-expressing B cells are excluded from the peripheral repertoire in adults

We have previously demonstrated that at birth most productive (P) V_H12 rearrangements in B10.H-2^aH-4^bp/Wts (2^a4^b) mice encode a ten-amino acid CDR3, and that a significant fraction of the expected repertoire is absent. We have now examined the adult V_H12 CDR3 repertoire involving all four J_H gene segments in both peritoneum and spleen. Of the 74 P V_H12 rearrangements from these tissues 67 encode a CDR3 of ten amino acids and include a Gly in the fourth position (designated 10/G4). Most of these rearrangements appear to derive from phosphatidylcholine (PtC)-specific B cells, which also have a 10/G4 V_HCDR3, since few 10/G4 P rearrangements were present in spleen cells depleted of PtC-specific B cells. Thus, the V_H12 B cell repertoire in adult mice is largely restricted to the use of a single CDR3 motif and to a single antigen specificity. This bias results from two selection events: (1) selective exclusion of most V_H12 B cells from the peripheral repertoire, and (2) clonal expansion in the periphery of V_H12 B cells that have a 10/G4 V_HCDR3 and bind PtC. Analysis of V_H12-J_H1 rearrangements in viable motheaten (me^vJme^v) mice, which have an abnormal B cell repertoire due to a defective phosphatase (Hcph) and have barely detectable numbers of PtC-specific B cells, indicates that selective exclusion of V_H12 B cells from the peripheral repertoire occurs normally, but that clonal expansion of 10/G4 V_H12 B cells is minimal. This is evidence that the selective exclusion of V_H12 B cells from the peripheral repertoire and the clonal expansion of V_H12 B cells with a 10/G4 CDR3 are due to independent signaling events.     

Pervasive and stochastic changes in the TCR repertoire of regulatory T-cell-deficient mice

We hypothesize that regulatory T-cell (Treg)-deficient strainshave an altered TCR repertoire in part due to the expansionof autoimmune repertoire by self-antigen. We compared the Vβfamily expression profile between B6 and Treg-lacking B6.Cg-Foxp3^sf/Y(B6.sf) mice using fluorescent anti-Vβ mAbs and observedno changes. However, while the spectratypes of 20 Vβ familiesamong B6 mice were highly similar, the Vβ family spectratypesof B6.sf mice were remarkably different from B6 mice and fromeach other. Significant spectratype changes in many Vβfamilies were also observed in Treg-deficient IL-2 knockout(KO) and IL-2R KO mice. Such changes were not observed withanti-CD3 mAb-treated B6 mice or B6 CD4⁺CD25^– T cells.TCR transgenic (OT-II.sf) mice displayed dramatic reductionof clonotypic TCR with concomitant increase in T cells bearingnon-transgenic Vβ and V families, including T cells withdual receptors expressing reduced levels of transgenic V andendogenous V. Collectively, the data demonstrate that Treg deficiencyallows polyclonal expansion of T cells in a stochastic manner,resulting in widespread changes in the TCR repertoire.     

Positive selection of CD4+ T cells by TCR-specific antibodies requires low valency TCR cross-linking: implications for repertoire selection in the thymus

The developmental fate of immature CD4⁺ 8⁺ thymocytes is determined by intrathymic signals transduced by surface TCR complexes. In particular, TCR signals are required for immature CD4⁺ 8⁺ thymocytes to further differentiate into CD4⁺ 8⁻ or CD4⁻ 8⁺ T cells, a process referred to as positive selection. It is generally thought that positive selection results from low affinity TCR interactions with self antigens which engage the relatively few surface TCR complexes that are on immature CD4⁺ 8⁺ thymocytes. However, we now demonstrate with TCR-specific antibodies that positive selection of CD4⁺ T cells requires low valency cross-linking of surface TCR complexes on immature thymocytes. That is, positive selection signals are only generated within a narrow range of TCR cross-linking: cross-linking either too few or too many surface TCR complexes fails to signal positive selection. We interpret these results as indicating that positive selection of CD4⁺ T cells is not signaled by low affinity TCR interactions per se, but rather can be signaled by any combination of TCR affinity and ligand density that induces low valency TCR cross-linking on immature thymocytes.     

FT-2 antigen for distinguishing lymphocyte subpopulations in the developing thymus

The surface phenotypes of lymphoid cells in the developing embryonic thymus were characterized by using monoclonal antibodies. FT-2 antigen thus defined was predominantly expressed on thymocytes in the earlier embryonic stages in all the inbred mouse strains tested. The immunofluorescence and immunoperoxidase tests indicated that, like FT-1 antigen, the proportion of FT-2+ fetal thymocytes rapidly decreased with increase in gestation time, and these cells disappeared by day 19 of gestation. The treatment of fetal thymocytes with anti-FT-1 plus complement eliminated not only FT-1+, but also FT-2+ cells, whereas the treatment with anti-FT-2 failed to eliminate approximately 40% of FT-1+ cells, suggesting that embryonic thymocytes can be provisionally divided into at least three subpopulations, FT-1+2+, FT-1+2- and FT-1-2-.     

Longitudinal analysis of T cells responding to tetanus toxoid in healthy subjects as well as in pediatric patients after bone marrow transplantation: the identification of identical TCR-CDR3 regions in time suggests long-term stability of at least part of the antigen-specific TCR repertoire

To understand the nature of long-term Th immune responses, we investigated in the present study the TCRBV gene repertoire of CD4(+) T cells specific for the recall antigen tetanus toxoid (TT) in recipients of an allogeneic bone marrow transplantation (allo-BMT) at several time points after transplantation and in their BM donors. We observed that the TCR repertoire of TT-specific CD4(+) Th cells was heterogeneous, and differed between allo-BMT recipients and their respective donors. Some individuals, however, used similar TCR-complementarity-determining region (CDR) 3 motifs that could reflect recognition of and selection by similar promiscuous epitopes of TT. Longitudinal analysis of this TT-specific T cell response revealed that T cells with completely identical TCR were present at several time points after the first analysis in allo-BMT recipients, most probably reflecting long-term stability of at least part of the antigen-specific TCR repertoire. Similar stability of the TT-specific TCR repertoire in time was also noted in the allo-BMT donors. These observations reveal that within a given individual the dominant antigen-specific T cell clones persist in time in an otherwise diverse TT-specific CD4(+) T cell immune response.     

TCR function analysis using a novel system reveals the multiple unconventional tumor-reactive T cells in human breast cancer-infiltrating lymphocytes

Tumor-infiltrating lymphocytes (TILs) are a potent source for obtaining tumor-reactive T cell receptors (TCRs). Although comprehensive methods to analyze the TCR repertoire in TILs have been reported, the evaluation system for TCR-reactivity to endogenously expressed antigen in tumor cells remains laborious and time consuming. Consequently, very limited numbers of TCRs in TILs have been analyzed for their reactivity to tumor cells. In this study, we developed an efficient evaluation system for TCR function designated c-FIT (c omprehensive f unctional i nvestigation of T CRs) to analyze TCR reactivity. The c-FIT system enabled us to analyze up to 90 TCRs for their reactivity to tumor cells by a single assay within a month. Using c-FIT, we analyzed 70 TCRs of CD8⁺ TILs derived from two breast cancer patients and obtained 23 TCRs that reacted to tumor cells. Surprisingly, although two TCRs were HLA class I-restricted, the remaining 21 TCRs were non-HLA-restricted. Thus, c-FIT can be applied for monitoring multiple conventional and unconventional antigen-specific killer T cells in TILs, leading to the development of new designs for more effective T-cell-based immunotherapies.     

T Cell Receptor (TCR) Repertoire in Alloimmune Responses

A large number of alloantigenic determinants could be generated by both the direct and indirect alloantigen presentation pathways. Hence, a heterogeneous population of T cells expressing a wide variety of receptors would be expected to respond to this diverse array of alloantigenic determinants. However, T cells expressing highly restricted T cell receptor (TCR) variable genes have been reported in a variety of alloimmune responses. A similar phenomenon has been observed in a wide variety of other immune responses, from those induced by superantigens, to very specific responses induced by a single peptide presented by a single MHC molecule. Given this scenario, the limited number of T cell clones which dominate an allograft rejection response, or for that matter an autoimmune response or a tumor specific response, could be therapeutically targeted by virtue of the selected TCR expression.