Human T-cell Receptor Research Articles

Compositional characteristics of human peripheral TRBV pseudogene rearrangements

The diversity of the T cell receptor (TCR) complementarity determining region 3 (CDR3) repertoire is the result of random combinations, insertions and deletions during recombination of the germline V, D and J gene fragments. During evolution, some human TCR beta chain variable (TRBV) pseudogenes have been retained. Many previous studies have focused on functional TRBV genes, while little attention has been given to TRBV pseudogenes. To describe the compositional characteristics of TRBV pseudogene rearrangements, we compared and analysed TRBV pseudogenes, TRBV open reading frames (ORFs) and functional TRBV genes via high-throughput sequencing of DNA obtained from the peripheral blood of 4 healthy volunteers and 4 patients. Our results revealed several differences in J and D gene usage. The V deletion distribution profile of the pseudogenes was significantly different from that of the ORFs and functional genes. In addition, arginine, lysine and cysteine were more frequently used in putative CDR3 pseudogene rearrangements, while functional rearrangements used more leucine. This study presents a comprehensive description of the compositional characteristics of peripheral TRBV pseudogene rearrangements, which will provide a reference for further research on TRBV pseudogenes.

Long-amplicon TCRβ repertoire sequencing to reveal human T-cell receptor variable gene polymorphism: Implications for the prediction and interpretation of immunotherapy outcome.

129 Background: Human T cell antigen receptors play a critical role in protective immune responses but are also implicated in autoimmune disease and immune-mediated adverse events during immunotherapy. The antigen specificity of the T cell receptor is determined in part by the sequence of the CDR and Framework regions encoded by the TCRB variable gene. Previous studies of population sequencing data indicate that current antigen receptor allele databases, such as IMGT, fail to capture a significant portion of human variation. Here we use long-amplicon multiplex sequencing of rearranged TCRB receptors to validate putative novel human variable gene alleles previously recovered from 1000 genomes data. Methods: TCRB rearrangements were amplified from cDNA from 85 Caucasians undergoing treatment for melanoma using AmpliSeq-based multiplex Framework 1 and Constant gene primers to produce ~330bp amplicons. Samples were sequenced using the Ion Torrent S5 530 chip to produce ~1.5M raw reads per sample. Ion Reporter was used for clonotyping and identification of variable gene sequences absent from the IMGT database. Putatively novel sequences were compared to those reported in the Lym1k database of alleles recovered from 1000 genomes data. Results: We identified 15 novel variable gene alleles that are absent from the IMGT database and result in amino acid changes to the CDR or Framework regions of the TCR. Typically, a single individual was found to be heterozygous for a novel variant, though we note two instances where multiple individuals possessed a novel variant. We also identified novel variable gene alleles that are absent from the Lym1k database, potentially due to challenges in inferring receptor alleles from short-read population sequencing studies. Conclusions: We find evidence for significant human diversity in TCRB variable gene alleles beyond what is currently represented in the IMGT database. TCRB sequencing using multiplex Framework 1 and Constant gene targeting primers is ideally suited for studying the role of TCRB polymorphism in autoimmune disease and immune-mediated adverse events during immunotherapy.

Profiling the pattern of the human T-cell receptor γδ complementary determinant region 3 repertoire in patients with lung carcinoma via high-throughput sequencing analysis.

γδ T cells function as sentinels in early host responses to infections and malignancies. Specifically, γδ T cells recognize tumor-associated stress antigens via T-cell receptor (TCR) γδ and play important roles in the antitumor immune response. In this study, we characterized the pattern of the human TCR γδ complementary determinant region 3 (CDR3) repertoire in patients with lung carcinoma (LC) via high-throughput sequencing. The results showed that the diversity of CDR3δ was significantly reduced, and that of CDR3γ was unchanged in LC patients compared with healthy individuals; in addition, LC patients shared significantly more CDR3δ sequences with each other than healthy individuals. The CDR3 length distribution and N-addition length distribution did not significantly differ between LC patients and healthy individuals. In addition, the CDR3 repertoire tended to use more Vδ2 and fewer Vδ1 germline gene fragments among LC patients. Moreover, we found a combination of four TCR γδ repertoire features that focus on CDR3δ and can be used as a biomarker for LC diagnosis. Our research suggests that the TCR γδ CDR3 repertoire changed in LC patients due to the antitumor immune response by γδ T cells in vivo, and these changes primarily focus on the amplification of certain tumor-specific CDR3δ clones among patients. This study demonstrates the role of γδ T cells from the TCR γδ CDR3 repertoire in tumor immunity and lays the foundation for elucidating the mechanism underlying the function of γδT cells in antitumor immunity.

Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity

Most affinity-maturation campaigns for antibodies and T-cell receptors (TCRs) operate on the residues at the binding site, located within the loops known as complementarity-determining regions (CDRs). Accordingly, mutations in contact residues, or so-called "second shell" residues, that increase affinity are typically identified by directed evolution involving combinatorial libraries. To determine the impact of residues located at a distance from the binding site, here we used single-codon libraries of both CDR and non-CDR residues to generate a deep mutational scan of a human TCR against the cancer antigen MART-1·HLA-A2. Non-CDR residues included those at the interface of the TCR variable domains (Vα and Vβ) and surface-exposed framework residues. Mutational analyses showed that both Vα/Vβ interface and CDR residues were important in maintaining binding to MART-1·HLA-A2, probably due to either structural requirements for proper Vα/Vβ association or direct contact with the ligand. More surprisingly, many Vα/Vβ interface substitutions yielded improved binding to MART-1·HLA-A2. To further explore this finding, we constructed interface libraries and selected them for improved stability or affinity. Among the variants identified, one conservative substitution (F45βY) was most prevalent. Further analysis of F45βY showed that it enhanced thermostability and increased affinity by 60-fold. Thus, introducing a single hydroxyl group at the Vα/Vβ interface, at a significant distance from the TCR·peptide·MHC-binding site, remarkably affected ligand binding. The variant retained a high degree of specificity for MART-1·HLA-A2, indicating that our approach provides a general strategy for engineering improvements in either soluble or cell-based TCRs for therapeutic purposes.

Abstract IA22: Targeting CARs to the TRAC locus enhances T-cell potency

Abstract Chimeric antigen receptors (CARs) are synthetic receptors that redirect and reprogram T cells to mediate tumor rejection. The most successful CARs used to date are those targeting CD19, which offer the prospect of complete remissions in patients with chemorefractory/relapsed B cell malignancies. CARs are typically transduced into patient T cells using γ-retroviral or other randomly-integrating retroviral vectors (RVs), which may result in variegated CAR expression and transcriptional silencing. Recent advances in genome editing enable efficient sequence-specific modifications in human primary cells, including site-specific transgene integration into the CCR5 and AAVS1 loci in T lymphocytes. Using CRISPR/Cas9 to edit human T cells, we have established conditions yielding efficient target gene disruption and CAR insertion in a single step. We have found that directing a CD19 CAR to the human T-cell receptor (TCR) alpha chain (TRAC) locus not only results in efficient and uniform CAR expression in human peripheral blood T cells, but, remarkably, also enhances T-cell potency, vastly outperforming that of conventionally generated CAR T cells. We further show that CAR gene expression under the control of the TCR alpha promoter minimizes tonic signaling and allows effective regulation of CAR expression. These findings provide important insights into CAR immunobiology and highlight the potential of CRISPR/Cas9 genome editing to advance immunotherapies. Citation Format: Michel Sadelain, Justin Eyquem. Targeting CARs to the TRAC locus enhances T-cell potency [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA22.

Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information.

Inter-sample comparisons of T-cell receptor (TCR) repertoires are crucial for gaining a better understanding of the immunological states determined by different collections of T cells from different donor sites, cell types, and genetic and pathological backgrounds. For quantitative comparison, most previous studies utilized conventional methods in ecology, which focus on TCR sequences that overlap between pairwise samples. Some recent studies attempted another approach that is categorized into Poisson abundance models using the abundance distribution of observed TCR sequences. However, these methods ignore the details of the measured sequences and are consequently unable to identify sub-repertoires that might have important contributions to the observed inter-sample differences. Moreover, the sparsity of sequence data due to the huge diversity of repertoires hampers the performance of these methods, especially when few overlapping sequences exist. In this paper, we propose a new approach for REpertoire COmparison in Low Dimensions (RECOLD) based on TCR sequence information, which can estimate the low-dimensional structure by embedding the pairwise sequence dissimilarities in high-dimensional sequence space. The inter-sample differences between repertoires are then quantified by information-theoretic measures among the distributions of data estimated in the embedded space. Using datasets of mouse and human TCR repertoires, we demonstrate that RECOLD can accurately identify the inter-sample hierarchical structures, which have a good correspondence with our intuitive understanding about sample conditions. Moreover, for the dataset of transgenic mice that have strong restrictions on the diversity of their repertoires, our estimated inter-sample structure was consistent with the structure estimated by previous methods based on abundance or overlapping sequence information. For the dataset of human healthy donors and Sézary syndrome patients, our method also showed robust estimation performance even under the condition of high sparsity in TCR sequences, while previous studies failed to estimate the structure. In addition, we identified the sequences that contribute to the pairwise-sample differences between the repertoires with the different genetic backgrounds of mice. Such identification of the sequences contributing to variation in immune cell repertoires may provide substantial insight for the development of new immunotherapies and vaccines.

Streamlined Single Cell TCR Isolation and Generation of Retroviral Vectors for In Vitro and In Vivo Expression of Human TCRs.

Although, several methods for sequencing of paired T cell receptor (TCR) alpha and beta chains from single T cells have been developed, none so far have been conducive to downstream in vivo functional analysis of TCR heterodimers. We have developed an improved protocol based on a two-step multiplex-nested PCR, which results in a PCR product that spans entire variable regions of a human TCR alpha and beta chains. By identifying unique restriction sites and incorporating them into the PCR primers, we have made the PCR product compatible with direct sub-cloning into the template retroviral vector. The resulting retroviral construct encodes a chimeric human/mouse TCR with a mouse intracellular domain, which is functional in mouse cells or in in vivo mouse models. Overall, the protocol described here combines human single cell paired TCR alpha and beta chain identification with streamlined generation of retroviral vectors readily adaptable for in vitro and in vivo TCR expression. The video and the accompanying material are designed to give a highly detailed description of the single cell PCR, so that the critical steps can be followed and potential pitfalls avoided. Additionally, we provide a detailed description of the cloning steps necessary to generate the expression vector. Once mastered, the whole procedure from single cell sorting to TCR expression could be performed in a short two-week period.

Human TCR-MHC coevolution after divergence from mice includes increased nontemplate-encoded CDR3 diversity.

For thymic selection and responses to pathogens, T cells interact through their αβ T cell receptor (TCR) with peptide-major histocompatibility complex (MHC) molecules on antigen-presenting cells. How the diverse TCRs interact with a multitude of MHC molecules is unresolved. It is also unclear how humans generate larger TCR repertoires than mice do. We compared the TCR repertoire of CD4 T cells selected from a single mouse or human MHC class II (MHC II) in mice containing the human TCR gene loci. Human MHC II yielded greater thymic output and a more diverse TCR repertoire. The complementarity determining region 3 (CDR3) length adjusted for different inherent V-segment affinities to MHC II. Humans evolved with greater nontemplate-encoded CDR3 diversity than did mice. Our data, which demonstrate human TCR-MHC coevolution after divergence from rodents, explain the greater T cell diversity in humans and suggest a mechanism for ensuring that any V-J gene combination can be selected by a single MHC II.

Research on the diversity of T cell receptor repertoire in the process of malignant transformation of HBV chronic infection.

e23086 Background: The progression of liver inflammation resulted from HBV infection is the main cause of HBV-related liver cancer. T cells play a central role in anti-HBV and anti-tumor specific immune response during disease progression, and the T cell receptor (TCR) repertoire can quantitatively reflect the immune function of T cells. The accurate information of TCR repertoire change in the progression from chronic hepatitis B to tumor was obtained in this study. Methods: CD4+ T cells from the spleens of mice and CD8+ T cells from 50ml peripheral blood of the patients with chronic hepatitis B and liver cancer were sorted by flow cytometry for establishing next generation sequencing (NGS) and the related bioinformatics research system of TCR repertoire. The sequence in V region of TCR was amplified bu using 5 'RACE technology with the mRNA as template. The sequences of TCRα and TCRβ were determined by the NGS technology, and the sequence data with 6Gb were obtained for each chain of each individual. Results: Acoording to analysis of TCR repertoire in mouse CD4+ T cells, the V-J pairing and diversity of CDR3 sequence in TCRβ were higher than TCRα; With the increasing of the recombination number in D gene fragments in the TCRβ chain, a higher diversity of V-J pairing could be introduced in TCRβ.Acoording to analysis of TCR repertoire in human CD8+ T cells, the effects of chronic hepatitis and HCC condition on the overall diversity of TCR receptor repertoire were not significant; The level of receptor repertoire in patients with chronic hepatitis and HCC showed major difference only at the level of low frequency ratio compared with healthy volunteers; the distinctive V-J paring and CDR3 could be detected in the group of patients with chronic hepatitis and HCC based on the above TCR clone at the level of low frequency. Conclusions: NGS sequencing and the related bioinformatics research system of mouse and human TCR repertoire were established. The level of receptor repertoire in patients with chronic hepatitis and HCC showed major difference only at the level of low frequency ratio compared with healthy volunteers.

Aging-related changes in human T-cell repertoire over 20 years delineated by deep sequencing of peripheral T-cell receptors

Recent deep sequencing studies on T-cell receptor (TCR) repertoire have provided robust data to characterize diversity of T-cell immune responsiveness to a wide variety of peptide antigens, including viral and tumor antigens. The human TCR repertoire declines with age, but this decline has not been fully investigated longitudinally in individuals. Using a deep sequencing approach, we analyzed TCRβ repertoires longitudinally over approximately 20years, with ages ranging from 23 to 50years at the start (23 to 65years overall), in peripheral-blood CD4 and CD8 T-cell populations that were collected and cryopreserved 3 times at intervals of approximately 10years from each of 6 healthy adults (3 men and 3 women). Sequence data at the hypervariable complementarity determining region 3 (CDR3) in the TCRB gene locus were evaluated by applying a random-coefficient statistical regression model. Two outcomes were analyzed: total number of distinct TCRB CDR3 sequences as a TCR diversity metric, and clonality of the T-cell populations. TCR repertoire diversity decreased (p<0.001) and frequencies of clonal populations increased (p=0.003) with age in CD8 T cells, whereas CD4 T cells retained fairly diverse TCR repertoires along with relatively low clonality. We also found that approximately 10–30% and 30–80% of read sequences in CD4 and CD8 T cells, respectively, overlapped at different ages within each individual, indicating long-term stable maintenance of T-cell clonal composition. Moreover, many of the most frequent TCRB CDR3 sequences (i.e., top T-cell clones) persisted over 20years, and some of them expanded and exerted a dominating influence on clonality of peripheral T-cell populations. It is thus possible that persistence or expansion of top T-cell clones is a driver of T-cell immunity aging, and therefore represents a potential interventional target.

Investigating Structural Drivers of Antigen Specificity

Cellular immunity and new immunotherapeutic approaches rely on interactions between T‐cell receptors (TCRs) and the peptide‐major histocompatibility complex (pMHC) to initiate successful immune responses. Achieving peptide specificity by the TCR while simultaneously engaging the pMHC is critical for proper recognition and T‐cell activation. Although early studies emphasized the role of CDR3α and CDR3β loops in determining antigen specificity, more recent work has shown that antigen specificity arises from a cooperative interplay between germline and hypervariable loops and the pMHC surface. To better understand the determinants of TCR specificity, we have been studying engineered variants of the human TCR A6, which recognizes the viral peptide Tax presented by the class I MHC HLA‐A2, but has also been re‐engineered to recognize the tumor associated antigen MART‐1 with high specificity. An additional variant shows a surprising loss of specificity, recognizing a large range of structurally and chemically distinct peptide/HLA‐A2 complexes with high affinity. Here, we describe the structural and biochemical features that correlate with this loss in specificity and discuss the implications for how TCRs achieve specificity and how it can be manipulated.

Rltpr Is a Central Scaffold Protein Regulating Human TCR Co-Signaling and Cytoskeletal Dynamics

T cells are central players in adaptive immunity and T cell receptor (TCR) signaling and co-signaling govern immune defense, immune homeostasis and immune surveillance. Upon antigen encounter, the TCR becomes engaged and in concert with context-sensitive co-receptors, such as CD28, T cell activation, differentiation and function are achieved. Whereas TCR-dependent signaling has been subject to intense investigations, knowledge about CD28-dependent signal cascades is rather incomplete.In murine T cells, Rltpr was discovered to play an important role in CD28 co-signaling. We identified four patients from two consanguineous families presenting with generalized EBV-associated smooth muscle cell tumors and susceptibility to recurrent viral, bacterial, and fungal infections. All patients had homozygote loss-of-function mutations in RLTPR (c.489insG and c.871+1G>T respectively) and did not express RLTPR protein. Primary RLTPR-mutated T cells were characterized by deficiency to signal via CD28. In addition, the cells showed disturbed cytoskeletal microtubule network and defective migratory pattern with increased spontaneous motility in 2D and 3D, but reduced migratory persistence.To determine the protein interactome of human RLTPR, we designed CRISPR/Cas9 constructs and targeted the RLTPR locus in Jurkat cells. We derived five RLTPR-defective Jurkat clones, as determined by Western blot analysis and Sanger sequencing studies. Next, these clones were engineered via retroviral vectors to re-express a GFP-tagged human RLTPR protein. Jurkat T-cell clones expressing RLTPR with N-terminal-GFP, RLTPR with C-terminal-GFP or GFP only were stimulated with anti-CD3/CD28 or left unstimulated and lysed after 15 minutes. Upon pull-down using GFP-Trap, the RLTPR interactome was comprehensively investigated by nano liquid chromatography tandem mass spectrometry (LC-MS/MS) and analyzed using Maxquant. Confirmation by immunoprecipitation and western blotting was performed for selected proteins. In seven independent experiments, 903 different proteins were detected in total, 192 proteins repeatedly in at least half of the RLTPR-GFP samples. Quantitative analysis and statistical evaluation yielded 26 proteins significantly enriched in the RLTPR-GFP compared to the control samples (permutation-based q-values < 0.05).The interactome of RLTPR in genetically modified Jurkat cells primarily included cytoskeletal proteins such as capping proteins and (co)chaperones. In addition, RLTPR also interacted with a metabolic enzyme involved in nucleotide synthesis and with vesicle transport proteins involved in the initiation of TCR signaling. Known TCR or CD28 signaling molecules were not detected indicating an indirect contribution of RLTPR in these pathways.In summary, studying rare patients with EBV-associated smooth-muscle cell tumors has allowed us to define RLTPR-deficiency as a novel human primary immunodeficiency disorder and to define RLTPR as a central scaffolding molecule for CD28-mediated TCR co-signaling, cytoskeletal dynamics and metabolic signaling. DisclosuresNo relevant conflicts of interest to declare.

284 HLA-C*06:02 mediates an autoimmune response against melanocytes in psoriasis

Psoriasis vulgaris is a human leukocyte antigen (HLA)-C*06:02-associated skin disease. Because of a strong linkage disequilibrium with other genes of the HLA-locus the role of HLA-C*06:02 in psoriasis pathogenesis as well as the mechanisms leading to lesional psoriatic T-cell activation were still unresolved. Accordingly, an autoimmune pathogenesis of psoriasis had remained hypothetical. We addressed these two interrelated questions using a Vα3S1/Vβ13S1 T-cell receptor (TCR) obtained directly from a tissue infiltrating CD8+ T-cell clone of an HLA-C*06:02-positive psoriasis patient by single-cell TCR analysis. Through reconstitution of this TCR in a reporter T-hybridoma cell line, we generated a reliable tool to determine the specificity of the lesional psoriatic T-cell response. Using this TCR hybridoma in a coculture system with other cell types, we discovered that the Vα3S1/Vβ13S1 TCR specifically recognized melanocytes in an HLA-C*06:02 restricted manner. By combinatorial peptide library screening, we identified ADAMTS-like protein 5 (ADAMTSL5) as an HLA-C*06:02-presented melanocytic autoantigen of the Vα3S1/Vβ13S1 TCR. Consistent with the Vα3S1/Vβ13S1-TCR reactivity, double/triple immunofluorescence staining revealed CD8+ T cells in psoriasis lesions attacking melanocytes that express ADAMTSL5. Thus, HLA-C*06:02 mediates an autoimmune response against melanocytes through autoantigen presentation and likely predisposes to psoriasis via this newly identified autoimmune pathway. Our study represents the first occasion where the unbiased analysis of a human TCR from tissue-infiltrating T cells could uncover HLA restriction, target cells, and an autoantigen in a human autoimmune disease. Exploring the specificity of the Vα3S1/Vβ13S1 TCR we demonstrate that the pathogenic relevance of an autoantigenic peptide has to be proven in the context of the full-length parent protein. This may require expression in the actual target cell type. Overall, our data provide conclusive evidence for the autoimmune nature of psoriasis.

Phase 1 Dose Escalation Study of MEDI-565, a Bispecific T-Cell Engager that Targets Human Carcinoembryonic Antigen, in Patients With Advanced Gastrointestinal Adenocarcinomas

IntroductionMEDI-565, a bispecific, single-chain antibody targeting human carcinoembryonic antigen on tumor cells and the CD3 epsilon subunit of the human T-cell receptor complex, showed antitumor activity in carcinoembryonic antigen-expressing tumors in murine models. Patients and MethodsThis phase I, multicenter, open-label dose escalation study enrolled adults with gastrointestinal adenocarcinomas. MEDI-565 was given intravenously over 3 hours on days 1 through 5 in 28-day cycles, with 4 single-patient (0.75-20 μg) and 5 standard 3 + 3 escalation (60 μg-3 mg; 1.5-7.5 mg with dexamethasone) cohorts. Primary objective was determining maximum tolerated dose; secondary objectives were evaluating pharmacokinetics, antidrug antibodies, and antitumor activity. ResultsThirty-nine patients were enrolled (mean age, 59 years; 56% male; 72% colorectal cancer). Four patients experienced dose-limiting toxicities (2 at 3 mg; 2 at 7.5 mg + dexamethasone): hypoxia (n = 2), diarrhea, and cytokine release syndrome (CRS). Five patients reported grade 3 treatment-related adverse events: diarrhea, CRS, increased alanine aminotransferase, hypertension (all, n = 1), and hypoxia (n = 2); 6 experienced treatment-related serious adverse events: diarrhea, vomiting, pyrexia, CRS (all, n = 1), and hypoxia (n = 2). MEDI-565 pharmacokinetics was linear and dose-proportional, with fast clearance and short half-life. Nineteen patients (48.7%) had antidrug antibodies; 5 (12.8%) had high titers, 2 with decreased MEDI-565 concentrations. No objective responses occurred; 11 (28%) had stable disease as best response. ConclusionsThe maximum tolerated dose of MEDI-565 in this patient population was 5 mg administered over 3 hours on days 1 through 5 every 28 days, with dexamethasone. Pharmacokinetics were linear. No objective responses were observed.

Genetically modified human CD4(+) T cells can be evaluated invivo without lethal graft-versus-host disease.

Adoptive cell immunotherapy for human diseases, including the use of T cells modified to express an anti-tumour T-cell receptor (TCR) or chimeric antigen receptor, is showing promise as an effective treatment modality. Further advances would be accelerated by the availability of a mouse model that would permit human T-cell engineering protocols and proposed genetic modifications to be evaluated invivo. NOD-scid IL2rγ(null) (NSG) mice accept the engraftment of mature human T cells; however, long-term evaluation of transferred cells has been hampered by the xenogeneic graft-versus-host disease (GVHD) that occurs soon after cell transfer. We modified human primary CD4(+) T cells by lentiviral transduction to express a human TCR that recognizes a pancreatic beta cell-derived peptide in the context of HLA-DR4. The TCR-transduced cells were transferred to NSG mice engineered to express HLA-DR4 and to be deficient for murine class II MHC molecules. CD4(+) T-cell-depleted peripheral blood mononuclear cells were also transferred to facilitate engraftment. The transduced cells exhibited long-term survival (up to 3months post-transfer) and lethal GVHD was not observed. This favourable outcome was dependent upon the pre-transfer T-cell transduction and culture conditions, which influenced both the kinetics of engraftment and the development of GVHD. This approach should now permit human T-cell transduction protocols and genetic modifications to be evaluated invivo, and it should also facilitate the development of human disease models that incorporate human T cells.

Suppression of inducible CD4 regulatory cells by MHC class I-restricted human tumor epitope specific TCR engineered multifunctional CD4 T cells

Regulatory T cells (Treg) can interfere with the generation and function of anti-tumor immune effectors. Accordingly, ways that could block Treg function would be useful in cancer immunotherapy. We have previously shown that incorporation of CD4+CD25-ve T cells in an in vitro cytolytic T lymphocyte (CTL) generation assay leads to generation of induced regulatory T cells (iTregs), and that these iTreg block the generation of productive CTL response (Chattopadhyay et al., 2006). We here show that human CD4 T cells engineered to express MHC class I-restricted human melanoma associated epitope, MART-127–35, specific T cell receptor (TCR), that can simultaneously exhibit helper as well as cytolytic effector functions (Chhabra et al., 2008, Ray et al., 2010), can interfere with the generation of inducible Treg, block iTreg-mediated suppression, and allow the activation and expansion of MART-127–35 specific CTL responses, in vitro. We also show that mitigation of Treg generation by TCR engineered CD4 T cells is not mediated by a soluble factor and may involve “licensing/conditioning” of the dendritic cells (DC). Our data offer novel insights on the biology of MHC class I restricted TCReng CD4 T cells and have translational implications.

Multiple sclerosis: Molecular mimicry of an antimyelin HLA class I restricted T-cell receptor.

Objective:To identify target antigens presented by human leukocyte antigen (HLA)–A*02:01 to the myelin-reactive human T-cell receptor (TCR) 2D1, which was originally isolated from a CD8+ T-cell clone recognizing proteolipid protein (PLP) in the context of HLA-A*03:01, we employed a new antigen search technology.Methods:We used our recently developed antigen search technology that employs plasmid-encoded combinatorial peptide libraries and a highly sensitive single cell detection system to identify endogenous candidate peptides of mice and human origin. We validated candidate antigens by independent T-cell assays using synthetic peptides and refolded HLA:peptide complexes. A molecular model of HLA-A*02:01:peptide complexes was obtained by molecular dynamics simulations.Results:We identified one peptide from glycerolphosphatidylcholine phosphodiesterase 1, which is identical in mice and humans and originates from a protein that is expressed in many cell types. When bound to HLA-A*02:01, this peptide cross-stimulates the PLP-reactive HLA-A3-restricted TCR 2D1. Investigation of molecular details revealed that the peptide length plays a crucial role in its capacity to bind HLA-A*02:01 and to activate TCR 2D1. Molecular modeling illustrated the 3D structures of activating HLA:peptide complexes.Conclusions:Our results show that our antigen search technology allows us to identify new candidate antigens of a presumably pathogenic, autoreactive, human CD8+ T-cell-derived TCR. They further illustrate how this TCR, which recognizes a myelin peptide bound to HLA-A*03:01, may cross-react with an unrelated peptide presented by the protective HLA class I allele HLA-A*02:01.

Severe cutaneous adverse drug reactions

The clinical manifestations of drug eruptions can range from mild maculopapular exanthema to severe cutaneous adverse drug reactions (SCAR), including drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms, Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) which are rare but occasionally fatal. Some pathogens may induce skin reactions mimicking SCAR. There are several models to explain the interaction of human leukocyte antigen (HLA), drug and T-cell receptor (TCR): (i) the "hapten/prohapten" theory; (ii) the "p-i concept"; (iii) the "altered peptide repertoire"; and (iv) the "altered TCR repertoire". The checkpoints of molecular mechanisms of SCAR include specific drug antigens interacting with the specific HLA loci (e.g. HLA-B*15:02 for carbamazepine-induced SJS/TEN and HLA-B*58:01 for allopurinol-induced SCAR), involvement of specific TCR, induction of T-cell-mediated responses (e.g. granulysin, Fas ligand, perforin/granzyme B and T-helper 1/2-associated cytokines) and cell death mechanism (e.g. miR-18a-5p-induced apoptosis; annexin A1 and formyl peptide receptor 1-induced necroptosis in keratinocytes). In addition to immune mechanism, metabolism has been found to play a role in the pathogenesis of SCAR, such as recent findings of strong association of CYP2C9*3 with phenytoin-induced SCAR and impaired renal function with allopurinol SCAR. With a better understanding of the mechanisms, effective therapeutics and prevention for SCAR can be improved.

A novel, rapid and efficient method of cloning functional antigen-specific T-cell receptors from single human and mouse T-cells

T-cell receptor (TCR) gene therapy is a promising approach for the treatment of infectious diseases and cancers. However, the paired cloning and functional assays of antigen-specific TCRα and TCRβ is time-consuming and laborious. In this study, we developed a novel, rapid and efficient antigen-specific TCR-cloning system by combining three technologies: multiplex one-step RT-PCR, transcriptionally active PCR (TAP) and luciferase reporter assays. Multiplex one-step RT-PCR with leader primers designed from leader peptide sequences of TCRs enabled us to amplify cDNAs of TCRα and β pairs from single T-cells with remarkably high efficiency. The combination of TAP fragments and HEK293T-based NFAT-luciferase reporter cells allowed for a rapid functional assay without the need to construct expression vectors. Using this system, we cloned human TCRs specific for Epstein-Barr virus BRLF-1-derived peptide as well as mouse TCRs specific for melanoma-associated antigen tyrosinase-related protein 2 (TRP-2) within four days. These results suggest that our system provides rapid and efficient cloning of functional antigen-specific human and mouse TCRs and contributes to TCR-based immunotherapy for cancers and infectious diseases.

A SMARTer approach to profiling the human T-cell receptor repertoire

Abstract Profiling T-cell receptor (TCR) repertoires involves characterizing the diversity of TCR nucleotide sequences in a sample, and is an increasingly popular approach for analyzing the composition of the adaptive immune system. While low-throughput approaches have yielded important insights concerning TCR repertoire dynamics, development of next-generation sequencing (NGS) technologies has dramatically expanded research prospects. Using SMART® technology, we have developed an NGS library preparation kit for TCR profiling that employs a 5′ RACE-like approach to capture full-length variable regions of TCR-α and/or TCR-β subunits. With this approach, 10 ng–3 μg of input RNA or 50–10,000 purified T cells undergo reverse transcription using dT priming. Following first-strand cDNA synthesis, semi-nested PCR is used to amplify TCR-specific sequences and add Illumina® sequencing adapters. Starting with peripheral blood RNA, libraries containing TCR-α and TCR-β sequences were generated and sequenced. For each replicate &amp;gt;70% of reads were on-target, and the most highly represented clonotypes remained consistent across a range of input amounts. A separate sensitivity assay demonstrated that RNA corresponding to a single clonotype could be detected above background levels when spiked into input RNA at a relative concentration of 0.1 %. Our approach enables the user to obtain sequencing-ready TCR libraries from RNA in ~2.5 hours of hands-on time. Whereas approaches that utilize genomic DNA as starting material require multiplexed PCR strategies, RNA based amplification of TCR sequences use single primer pairs for each subunit. In this way, our approach minimizes the likelihood of sample misrepresentation due to amplification biases.