Use of variable human V delta genes to create functional T cell receptor alpha chain transcripts

Identification of TRDV-TRAJ V domains in human and mouse T-cell receptor repertoires

Here, we describe the identification of two T-cell receptors (TRs) containing TRDV genes in their TRA chains, the first one in human and the second one in mouse. First, using 5'RACE on a mixed lymphocyte-tumor cell culture (MLTC), we identified TRDV1 5'-untranslated region (UTR) and complete coding sequence rearranged productively to TRAJ24. Single-cell TR RNA sequencing (RNA-seq) of the MLTC, conducted to identify additional clonotypes, revealed that the analysis software detected the hybrid TRDV-TRAJ TRA (TRA) chain but excluded it from the final results. In a separate project, we performed TR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Here, the predominant clonotype contained a TRA chain with a TRDV2-2-TRAJ49 rearrangement. Again, the hybrid TRA chain was not reported in the final results. Transfection of both TR cDNAs resulted in cell surface localization of TR together with CD3, suggesting a productive protein in both cases. Tumor recognition of the Homo sapiens (Homsap) TRDV1-containing TR could be demonstrated by IFN Gamma ELISA ELISpot kit, whereas the Mus musculus (Musmus) TR did not recognize a tumor-derived cell line. To determine whether the TRDV-containing TRA chains we detected were rare events or whether TRDV genes are commonly incorporated into TRA chains, we queried the NCBI Sequence Read Archive for TR single-cell RNA-seq data and analyzed 21 human and 23 murine datasets. We found that especially Homsap TRDV1, Musmus TRDV1, and to some extent Musmus TRDV2-2 are more commonly incorporated into TRA chains than several TRAV genes, making those TRDV genes a relevant contribution to TRA diversity. TRDV-containing TRA chains are currently excluded from the final results of V-(D)-J dataset analyses with the CellRanger software. We provide a work-around to avoid exclusion of those hybrid TRA chains from the final analysis results.

Diversity in recognition and function of human γδ T cells

As interest increases in harnessing the potential power of tissue-resident cells for human health and disease, γδ T cells have been thrust into the limelight due to their prevalence in peripheral tissues, their sentinel-like phenotypes, and their unique antigen recognition capabilities. This review focuses primarily on human γδ T cells, highlighting their distinctive characteristics including antigen recognition, function, and development, with an emphasis on where they differ from their αβ T cell comparators, as well as from γδ T cell populations in the mouse. We review the antigens that have been identified thus far to regulate members of the human Vδ1 population and discuss what players are involved in transducing phosphoantigen-mediated signals to human Vγ9Vδ2 T cells. We also briefly review distinguishing features of these cells in terms of TCR signaling, use of coreceptor and costimulatory molecules and their development. These cells have great potential to be harnessed in a clinical setting, but caution must be taken to understand their unique capabilities and how they differ from the populations to which they are commonly compared.

Generation and molecular recognition of melanoma-associated antigen-specific human γδ T cells

Antigen recognition by T cells bearing αβ T cell receptors (TCRs) is restricted by major histocompatibility complex (MHC). However, how antigens are recognized by T cells bearing γδ TCRs remains unclear. Although γδ T cells can recognize nonclassical MHC, it is generally thought that recognition of antigens is not MHC restricted. Here, we took advantage of an in vitro system to generate antigen-specific human T cells and show that melanoma-associated antigens, MART-1 and gp100, can be recognized by γδ T cells in an MHC-restricted fashion. Cloning and transferring of MART-1-specific γδ TCRs restored the specific recognition of the initial antigen MHC/peptide reactivity and conferred antigen-specific functional responses. A crystal structure of a MART-1-specific γδ TCR, together with MHC/peptide, revealed distinctive but similar docking properties to those previously reported for αβ TCRs, recognizing MART-1 on HLA-A*0201. Our work shows that antigen-specific and MHC-restricted γδ T cells can be generated in vitro and that MART-1-specific γδ T cells can also be found and cloned from the naïve repertoire. These findings reveal that classical MHC-restricted human γδ TCRs exist in the periphery and have the potential to be used in developing of new TCR-based immunotherapeutic approaches.

Genetic variation in MHC proteins is associated with T cell receptor expression biases

Within each individual, a highly diverse T cell receptor (TCR) repertoire interacts with peptides presented by major histocompatibility complex (MHC) molecules. Despite extensive research, it remains controversial whether germline-encoded TCR-MHC contacts promote TCR-MHC specificity and if so, whether there exist differences in TCR V-gene compatibilities with different MHC alleles. We applied eQTL mapping to test for associations between genetic variation and TCR V-gene usage in a large human cohort. We report strong trans associations between variation in the MHC locus and TCR V-gene usage. Fine mapping of the association signals reveals specific amino acids in MHC genes that bias V-gene usage, many of which contact or are spatially proximal to the TCR or peptide. Hence, these MHC variants, several of which are linked to autoimmune diseases, can directly affect TCR-MHC interaction. These results provide the first examples of trans-QTLs mediated by protein-protein interactions, and are consistent with intrinsic TCR-MHC specificity.

Divergent T-cell receptor delta chains from marsupials

Complementary DNAs (cDNAs) encoding T-cell receptor delta (TRD) chains from the northern brown bandicoot, Isoodon macrourus, were identified while sequencing expressed sequence tags (ESTs) from a thymus cDNA library. Surprisingly, the I. macrourus TRD sequences were not orthologous to previously published TRD sequences from another Australian marsupial, the tammar wallaby, Macropus eugenii. Identification of TRD genes in the recently completed whole genome sequence of the South American opossum, Monodelphis domestica, revealed the presence of two highly divergent TRD loci. To determine whether the presence of multiple TRD loci accounts for the lack of orthology between the I. macrourus and M. eugenii cDNAs, additional TRD sequences were obtained from both species of marsupials. The results of this analysis revealed that, unlike eutherian mammals, all three species of marsupials have multiple, highly divergent TRD loci. One group of marsupial TRD sequences was closely related to TR sequences from eutherian mammals. A second group of TRD sequences formed a unique marsupial-specific clade, separate from TR sequences from eutherians. An interesting expression pattern of TRD variable (TRDV) and constant (TRDC) segments was evident in cDNAs from I. macrourus and M. eugenii. TRDV and TRDC sequences that were closely related to TRD genes from eutherian mammals were only found in association with each other in cDNAs from both marsupial species. A similar pattern was seen between TRDV and TRDC sequences that were most closely related to other marsupial TRD genes.

Aberrant T-cell receptor signalling of interferon-gamma- and tumour necrosis factor-alpha-producing cytotoxic CD8+ Vdelta1/Vbeta16 T cells in a patient with chronic neutropenia

We previously found that the peripheral blood (PB) mononuclear cells (MCs) (PBMCs) of a patient with chronic neutropenia contained an expanded population of cytotoxic CD8+ T cells using a variable (V) region delta1 gene product in the T-cell receptor-alpha (TCR-alpha) polypeptide [Vdelta1-constant(C)alpha+ T cells]. Sequencing of polymerase chain reaction (PCR) amplification products have now revealed a productive Vdelta1/joining (J)alphaIGRJa03/Calpha rearrangement of the TCR-alpha gene, predominantly associated with a Vbeta16/Dbeta2.1/Jbeta2.1/Cbeta2 TCR-beta gene, in these cells. Furthermore, we detected a markedly deficient proliferative response of the patient PBMCs to triggering with monoclonal antibodies (MoAbs) to the CD3 molecule, contrasting with a substantial response to the Vbeta3, 12, 14, 15, 17 and 20-specific staphylococcal enterotoxin B (SEB) superantigen, suggesting defective TCR-mediated activation of the Vdelta1+/Vbeta16+ clone. Moreover, whereas triggering of Vdelta1- T cells cultured with interleukin-2 (IL-2) by MoAb to the CD3 molecule enhanced proliferation, Vdelta1-Calpha+ T cells were inhibited by MoAbs to either CD3 or Vdelta1. Vdelta1-Calpha+ T-cell clones spontaneously secrete interferon-gamma (IFN-gamma) and were further induced to release tumour necrosis factor (TNF-alpha) when triggered by anti-CD3 plus phorbol ester. Aberrant signalling by the clonotypic TCR together with the functional properties of the CD8+ Vdelta1+/Vbeta16+ clone may thus contribute to the immunohaematological abnormalities observed in this patient.

T-cell receptor V delta-J alpha rearrangements in human thymocytes: the role of V delta-J alpha rearrangements in T-cell receptor-delta gene deletion

The differentiation mechanisms that force thymocytes into the T-cell receptor (TCR)-alpha beta or TCR-gamma delta lineage are poorly understood, but rearrangement processes in the TCR-alpha/delta locus are likely to play an important role. It is assumed that the TCR-delta gene is deleted prior to V alpha-J alpha rearrangements by rearrangement of the so-called TCR-delta-deleting elements delta Rec and psi J alpha. However, the TCR-delta gene can also be deleted via V delta-J alpha rearrangements. We studied the different TCR-delta-deleting rearrangements of V delta 1, delta Rec, V delta 2 and V delta 3 to J alpha gene segments in human thymocytes and peripheral blood using polymerase chain reaction analysis. The V delta 1 gene segment is the most upstream V delta gene segment tested and appears to rearrange to almost all J alpha gene segments. In contrast, the delta Rec and V delta 2 gene segments only rearrange to the 5'-located J alpha gene segments, thereby preserving an extensive TCR-alpha combinatorial diversity, because most J alpha gene segments are kept available for subsequent V alpha-J alpha rearrangements. Based on our combined data we hypothesize that the different V delta gene segments and the delta Rec gene segment play different roles in T-cell development with regard to TCR-delta deletion.

Comparison of human and mouse T-cell receptor variable gene segment subfamilies

Like the immunoglobulin Igh-V and Igk-V gene families, the human or mouse TCRV gene families may be grouped into subfamilies displaying > 75% nucleic acid sequence similarity among their members. Systematic interspecies sequence comparisons reveal that most mouse Tcr-V subfamilies exhibit clear homology to human TCRV subfamilies (> 60% amino acid sequence similarity). Homologous pairs of TCRV genes in mice and humans show higher sequence similarity than TCRV genes from different subfamilies within either species, indicating transspecies evolution of TCRV genes. Mouse and human homologues show conservation of their relative map order, particularly in the 3' region and a similar sequential and developmentally programmed expression. When the V regions from both species were analyzed together, local length differences and conserved residues in the loop regions were revealed, characteristic of each of the four TCRV families.

Immunopathogenesis of juvenile rheumatoid arthritis: role of T cells and MHC

Juvenile rheumatoid arthritis (JRA) is defined as chronic arthritis of unknown etiology appearing in patients less than 16 years of age. The disease is heterogeneous and is classified as pauciarticular, polyarticular, or systemic-onset disease. A few lines of evidence suggest that T cells are involved in the pathogenesis of the disease. T cells infiltrating the synovial membrane bear markers of activation and produce cytokines. The association of particular subtypes of JRA with certain HLA class II alleles provides strong evidence in favor of T cell involvement through an HLA-peptide-T cell receptor complex. Limited data from a few patients with JRA on T cell receptor transcripts from synovial membrane or synovial fluid cells point towards oligoclonality. This further supports the concept that T cells infiltrating the synovial membrane or extravasating into synovial fluid in patients with JRA reflect antigen-driven T cell proliferation.

T-cell antigen receptors in rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic disease of unknown etiology characterized by chronic inflammation mainly in the joints. Several lines of evidence suggest that T cells are involved in the pathogenesis of the disease. RA is associated with certain HLA-DR alleles. Studies analyzing T-cell receptor transcripts in RA have found biased or preferential usage of certain V alpha and/or V beta gene segments by T cells infiltrating the synovial membrane or extravasating into the synovial fluid compared to peripheral blood. In certain patients few T-cell antigen receptor (TCR) clones dominated the infiltrating T cells, suggesting that T cells from the synovial membrane or the synovial fluid comprise oligoclonal populations of T cells. However, other studies have found a polyclonal population of T cells. In interpreting these results the phase of the disease (early vs. late RA), the source of T cells and the limitations of the methods used in these studies should be taken into consideration. However, it appears that synovial T cells comprise oligoclonal populations of T cells and that there is a bias towards particular TCR gene segments, although a specific TCR gene segment in RA has not emerged.

TCR gene segments from at least one third of V alpha subfamilies rearrange at the delta locus

Using PCR and an experimentally validated V alpha subfamily-specific oligonucleotide panel (V alpha 1-w29), we have investigated whether the TCR delta chain may increase its combinatorial diversity by using V genes considered as alpha chain-specific. We show that at least 10 distinct human V alpha segments rearrange at the J delta locus, leading to scrambling of the two V gene repertoires. Fifty-five per cent of the V alpha/J delta transcripts characterized here were in frame. The 17 V alpha/C delta chains analysed included an extended CDR3 region with up to 18 aa encoded by the junctional region. In addition, a new J delta segment (J delta 4) has been characterized. Together, these findings demonstrate that combinatorial diversity in the human delta locus is larger than previously thought.

In vivo clonal dominance and limited T-cell receptor usage in human CD4+ T-cell recognition of house dust mite allergens

Sensitivity to house dust mite antigens in atopic individuals is a major cause of allergic diseases, ranging from asthma to rhinitis and dermatitis. We have studied the T-cell receptor (TCR) usage of house-dust-mite-specific CD4+ T-cell clones isolated from an atopic individual, by using the anchored polymerase chain reaction, and have analyzed the peripheral TCR repertoire of the same individual. Several T-cell clones had identified TCRs at the sequence level, despite the fact that they had been independently isolated, in some cases, in different years. These data suggest the presence in vivo of long-lived T-cell clones. We have also shown that junctional sequences identical to these clones are present in peripheral blood T cells taken 6 years after the isolation of the T-cell clones. The analysis of TCR genes used by the panel of clones reveals oligoclonality, with the variable (V) region gene segments V alpha 8 and V beta 3 being dominant, although there is minimal conservation of junctional sequences. The results have implications for understanding the TCR recognition of an environmental aeroallergen and the life span of T-cell clones in vivo during a chronic immune response.

Bone marrow cells of athymic nude mice express functional T cell receptor alpha chain transcripts rearranged to V delta 2, 3, 4, 5, 6 genes

From bone marrow cells (BMC) of athymic nude mice, T cell receptor (TcR) alpha chain transcripts were selectively amplified by polymerase chain reaction (PCR) using V delta 2-, V delta 3-, V delta 4-, V delta 5-, V delta 6- and C alpha-specific primers. Amplified DNA fragments were cloned, and 32 randomly selected clones from 5 PCR were sequenced. Twenty-three distinct rearrangement events were detected, of which 87% (20/23) were in-frame. All five tested V delta genes (V delta 2, 3, 4, 5, 6) rearranged in-frame to J alpha-C alpha. N-region diversity in V delta-J alpha junctions present in most clones was limited to two to five nucleotides. P-nucleotide additions in this region were also detected. The V delta 5 gene located 3' of C delta in reversed transcriptional orientation was rearranged to J alpha by inversion. The J alpha usage pattern of the sequenced clones was strongly biased towards rearrangement of the most 5' genes (located nearest to C delta) of the J alpha cluster: the most 5' J alpha (J alpha TA1) was used by 30% of all clones, and 78% of all J alpha rearranged to V delta were located in the 5' 12 kb of the 60-kb J alpha cluster. As distinct V delta/C delta and V alpha/C alpha TcR usage patterns are prevalent in peripheral T cell populations, our data suggest that these TcR usage patterns results from repertoire selections operating in alpha beta and gamma delta T cell lineages, but not from preferential V delta-C delta and V alpha-C alpha rearrangement patterns.