V delta repertoire during thymic ontogeny suggests three novel waves of gamma delta TCR expression

Tcrd Rearrangement Redirects a Processive Tcra Recombination Program to Expand the Tcra Repertoire

Adaptive immunity depends on diverse T cell receptor repertoires generated by variable, diversity, and joining (V[D]J) recombination. Here, we define the principles by which combinatorial diversity is generated in the murine Tcra repertoire. Tcra and Tcrd gene segments share the Tcra-Tcrd locus, with interspersed V_α and V_δ segments undergoing V_δ-D_δ-J_δ rearrangement in CD4^-CD8^- thymocytes and then multiple rounds of V_α-J_α rearrangement in CD4⁺CD8⁺ thymocytes. We document stepwise, highly coordinated proximal-to-distal progressions of V_α and J_α use on individual Tcra alleles, limiting combinatorial diversity. This behavior is supported by an extended chromatin conformation in CD4⁺CD8⁺ thymocytes, with only nearby V_α and J_α segments contacting each other. Tcrd rearrangements can use distal V_δ segments due to a contracted Tcra-Tcrd conformation in CD4^-CD8^- thymocytes. These rearrangements expand the Tcra repertoire by truncating the V_α array to permit otherwise disfavored V_α-J_α combinations. Therefore, recombination events at two developmental stages with distinct chromatin conformations synergize to promote Tcra repertoire diversity.

Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development

T cell antigen receptor δ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination events in developing γδ thymocytes. Here, we use linear amplification-mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in CD4(-)CD8(-) double-negative thymocyte progenitors differentiated in vitro from bone marrow-derived hematopoietic stem cells. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, whereas Trdd1 joining is ordered with joining to Trdd2, a prerequisite for further rearrangement. We also find frequent, previously unappreciated, Trdd1 and Trdd2 rearrangements that inactivate Tcrd, including sequential rearrangements from V(D)J recombination signal sequence fusions. Moreover, we find dozens of RAG off-target sequences that are generated via RAG tracking both upstream and downstream from the Trdd2 recombination center across the Tcrd loop domain that is bounded by the upstream INT1-2 and downstream TEA elements. Disruption of the upstream INT1-2 boundary of this loop domain allows spreading of RAG on- and off-target activity to the proximal Trdv domain and, correspondingly, shifts the Tcrd V(D)J recombination landscape by leading to predominant V(D)J joining to a proximal Trdv3 pseudogene that lies just upstream of the normal boundary.

Expression of the inhibitory Ly49E receptor is not critically involved in the immune response against cutaneous, pulmonary or liver tumours

Natural killer (NK) lymphocytes are part of the innate immune system and are important in immune protection against tumourigenesis. NK cells display a broad repertoire of activating and inhibitory cell surface receptors that regulate NK cell activity. The Ly49 family of NK receptors is composed of several members that recognize major histocompatibility complex class I (MHC-I) or MHC-I-related molecules. Ly49E is a unique inhibitory member, being triggered by the non-MHC-I-related protein urokinase plasminogen activator (uPA) in contrast to the known MHC-I-triggering of the other inhibitory Ly49 receptors. Ly49E also has an uncommon expression pattern on NK cells, including high expression on liver DX5⁻ NK cells. Furthermore, Ly49E is the only Ly49 member expressed by epidermal γδ T cells. As γδ T cells and/or NK cells have been shown to be involved in the regulation of cutaneous, pulmonary and liver malignancies, and as uPA is involved in tumourigenesis, we investigated the role of the inhibitory Ly49E receptor in the anti-tumour immune response. We demonstrate that, although Ly49E is highly expressed on epidermal γδ T cells and liver NK cells, this receptor does not play a major role in the control of skin tumour formation or in lung and liver tumour development.

A discrete chromatin loop in the mouse Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires

The Tcra-Tcrd locus undergoes V(D)J recombination in CD4⁻CD8⁻double-negative thymocytes and CD4⁺CD8⁺ double-positive thymocytes to generate diverse TCRδ and TCRα repertoires, respectively. Here we reveal a Tcra-Tcrd locus chromatin interaction network in double-negative thymocytes that was formed by interactions between CTCF-binding elements. Disruption of a discrete chromatin loop encompassing Tcrd diversity, joining and constant gene segments allowed a single variable gene segment to frequently contact and rearrange to diversity and joining gene segments and dominate the adult TCRδ repertoire. Disruption of this loop also narrowed the TCRα repertoire, which, we believe, follows as a consequence of the restricted TCRδ repertoire. Hence, a single CTCF-mediated chromatin loop directly regulates TCRδ diversity and indirectly regulates TCRα diversity.

Specification of Vδ and Vα usage by Tcra/Tcrd locus V gene segment promoters

The Tcra/Tcrd locus undergoes V-Dδ-Jδ rearrangement in CD4(-)CD8(-) thymocytes to form the TCRδ chain of the γδ TCR and V-Jα rearrangement in CD4(+)CD8(+) thymocytes to form the TCRα-chain of the αβ TCR. Most V segments in the locus participate in V-Jα rearrangement, but only a small and partially overlapping subset participates in V-Dδ-Jδ rearrangement. What specifies any particular Tcra/Tcrd locus V gene segment as a Vδ, a Vα, or both is currently unknown. We tested the hypothesis that V segment usage is specified by V segment promoter-dependent chromatin accessibility in developing thymocytes. TRAV15/DV6 family V gene segments contribute to both the Tcrd and the Tcra repertoires, whereas TRAV12 family V gene segments contribute almost exclusively to the Tcra repertoire. To understand whether the TRAV15/DV6 promoter region specifies TRAV15/DV6 as a Vδ, we used gene targeting to replace the promoter region of a TRAV12 family member with one from a TRAV15/DV6 family member. The TRAV15/DV6 promoter region conferred increased germline transcription and histone modifications to TRAV12 in double-negative thymocytes and caused a substantial increase in usage of TRAV12 in Tcrd recombination events. Our results demonstrate that usage of TRAV15/DV6 family V gene segments for Tcrd recombination in double-negative thymocytes is regulated, at least in part, by intrinsic features of TRAV15/DV6 promoters, and argue that Tcra/Tcrd locus Vδ gene segments are defined by their local chromatin accessibility in CD4(-)CD8(-) thymocytes.

Long-distance regulation of fetal V(δ) gene segment TRDV4 by the Tcrd enhancer

Murine Tcra and Tcrd gene segments are organized into a single genetic locus (Tcra/Tcrd locus) that undergoes V(D)J recombination in CD4(-)CD8(-) double-negative (DN) thymocytes to assemble Tcrd genes and in CD4(+)CD8(+) double-positive thymocytes to assemble Tcra genes. Recombination events are regulated by two developmental stage-specific enhancers, E(δ) and E(α). Effects of E(α) on Trca/Tcrd locus chromatin have been well documented, but effects of E(δ) have not. In this regard, E(α) acts over long distances to activate many V(α) and J(α) segments for recombination in double-positive thymocytes. However, in DN thymocytes, it is unclear whether E(δ) functions over long distances to regulate V(δ) gene segments or functions only locally to regulate D(δ) and J(δ) gene segments. In this study, we analyzed germline transcription, histone modifications, and recombination on wild-type and E(δ)-deficient alleles in adult and fetal thymocytes. We found that E(δ) functions as a local enhancer whose influence is limited to no more than ∼10 kb in either direction (including D(δ), J(δ), and TRDV5 gene segments) in adult DN thymocytes. However, we identified a unique long-distance role for E(δ) promoting accessibility and recombination of fetal V(δ) gene segment TRDV4, over a distance of 55 kb, in fetal thymocytes. TRDV4 recombination is specifically repressed in adult thymocytes. We found that this repression is enforced by a developmentally regulated loss of histone acetylation. Constitutively high levels of a suppressive modification, histone H3 lysine 9 dimethylation, may contribute to repression as well.

Distribution and development of the postnatal murine Vδ1 T-cell receptor repertoire

Murine γ/δ T cells express canonical Vγ5Vδ1 chains in the epidermis and Vγ6Vδ1 chains at reproductive sites. Both subsets carry an identical Vδ1-Dδ2-Jδ2 chain which completely lacks junctional diversity. These cells are thought to monitor tissue integrity via recognition of stress-induced self antigens. In this study, we showed by reverse transcription-polymerase chain reaction (RT-PCR), complementarity determining region 3 (CDR3) spectratyping and sequencing of the junctional regions of Vδ1 chains from C57BL/6 mice (aged 1 day to 14 months) that the canonical Vδ1-Dδ2-Jδ2 chain is also consistently present at other sites such as the thymus, gut, lung, liver, spleen and peripheral blood. In addition, we found multiple Vδ1 chains with fetal type rearrangements which were also shared among organs and among animals. These Vδ1 chains were typically characterized by a conserved amino acid motif, 'GGIRA'. Furthermore, by analysing the early postnatal period at days 10 and 16, we demonstrated that the diversification of the thymic Vδ1 repertoire is not paralleled by a diversification of extrathymic Vδ1+γ/δ T cells. This indicates that only fetal type rearrangements survive at extrathymic sites. In conclusion, γ/δ T cells expressing the canonical Vδ1-Dδ2-Jδ2 chain are not unique to the skin and reproductive sites. Furthermore, we found other γ/δ T cells expressing fetal type Vδ1 chains which were shared among different organs and animals. Thus, γ/δ T cells expressing conserved Vδ1 chains are likely to have important functions. We suggest a model in which this subset continuously recirculates throughout the organism and rapidly responds to stress-induced self antigens.

Recombination signal sequence-associated restriction on TCRdelta gene rearrangement affects the development of tissue-specific gammadelta T cells

Assembly of TCRalpha and TCRdelta genes from the TCRalpha/delta locus is tightly controlled for the proper generation of alphabeta and gammadelta T cells. Of >100 shared variable gene segments in the TCRalpha/delta locus, only a few are predominantly used for the TCRdelta gene assembly, while most are for TCRalpha. However, the importance and mechanisms of the selective variable gene rearrangement for T cell development are not fully understood. We report herein that the development of a tissue-specific gammadelta T cell population is critically affected by recombination signal sequence-associated restriction on the variable gene usage for TCRdelta assembly. We found that the development of substitute skin gammadelta T cells in mice deficient of the TCRgamma3 gene, which is used in wild-type skin gammadelta T cells, was drastically affected by the strain background. A Vgamma2(+) skin gammadelta T cell population developed in mice of the B6 but not the 129 strain backgrounds, due to a difference in the rearrangement of endogenous Vdelta7(+) TCRdelta genes, which paired with the Vgamma2(+) TCRgamma gene to generate the Vgamma2/Vdelta7(+) skin gammadelta T cell precursors in fetal thymi of the B6 background mice. The defective TCRdelta rearrangement of the 129-"Vdelta7" gene was associated with specific variations in its recombination signal sequence, which renders it poorly compatible for rearrangement to Ddelta genes. These findings provide the first direct evidence that recombination signal sequence-associated restriction on the variable gene usage for TCRalpha/delta gene assembly plays an important role in T cell development.

Vdelta1+ T cells are crucial for repertoire formation of gammadelta T cells in the lung

The pulmonary resident T lymphocytes (RPLs) expressing a nearly invariant T cell receptor gammadelta heterodimer (gammadeltaTCR) migrate from fetal thymus to the lung epithelium, followed by RPL subsets expressing diverse sets of gammadeltaTCRs after birth. However, it remains unclear whether the fetal type Vgamma6/Vdelta1+ RPLs are essential for gammadelta T cell repertoire formation in the lung epithelium. In this study, we found a marked decrease in the number of gammadeltaRPLs at 4 weeks of age in Vdelta1-/- mice and they predominantly expressed Vgamma6 and Vdelta4 genes. The skewed diversity towards the Vdelta4-(Ddelta1)-Ddelta2-Jdelta2 junctional region was observed only in gammadelta RPLs from 4-week-old Vdelta1-/- mice, compared with those from 8-week-old Vdelta1-/- mice and the both ages of wild-type mice. These results suggest that the invariant Vdelta1+ T cells are crucial not only for optimal gammadelta T cell expansion but also for affecting the migration or microenvironment for other gammadelta T cells in the lung epithelium.

T cells developing in fetal thymus of T-cell receptor alpha-chain transgenic mice colonize gammadelta T-cell-specific epithelial niches but lack long-term reconstituting potential

The gammadelta T cells generated during mouse fetal development are absolutely dependent on their invariant T-cell receptors (TCRs) for their function. However, there is little information on whether the epithelial homing properties of fetal T cells might also be developmentally induced by factors unrelated to TCR specificity. We have previously described TCR alpha-chain transgenic (2B4 TCR-alpha TG) mice, in which the transgenic TCR alpha-chain is expressed early, already at embryonic day 14 (E14). These mice have a large population of 'gammadelta T-cell-like' CD4- CD8- (double-negative; DN) alphabeta T cells, some of which develop during E14-E18 contemporarily to intraepithelial lymphocytes (IELs) expressing invariant TCR-gammadelta. Using the 2B4 TCR-alpha TG mouse model we have been able to more precisely study the impact of a variant TCR expression on IEL development and homing. In this study we show that TCR-alpha TG and TCR-alpha TG crossed to TCR-delta-deficient mice (TCR-alpha TG x TCR-delta-/-) carry TG TCR-alpha+ dendritic epidermal T cells (DETCs) and TCR-alpha TG+ IELs in the small intestine. The TG+ DETCs develop and seed the epidermis with similar kinetics as Vgamma5+ DETCs of normal mice, in contrast to the TCR-alphabeta+ DETCs found in TCR-delta-/- mice. However, whereas the intestinal TCR-alpha TG+ IELs persist in old mice (> 20 months), the TCR-alpha TG+ DETCs do not. The data in this study indicate that the timing of TCR expression and thereby development during ontogeny regulates the specific homing potential for fetal T cells but not their subsequent functions and properties.

Identification of three new bovine T-cell receptor delta variable gene subgroups expressed by peripheral blood T cells

To understand the biology of gammadelta T cells in ruminants, it is necessary to have a comprehensive picture of gammadelta T-cell receptor gene diversity and expression. In this study, three new subgroups of bovine T-cell receptor delta (TRD) variable genes were identified by RT-PCR and sequencing and homology with TRDV genes from other mammals determined. Previously unidentified TRDV subgroup genes described in this study include the bovine homologues of ovine TRDV2, TRDV3, and TRDV4 which were named accordingly. TRDV2 subgroup has two genes (TRDV2-1 and TRDV2-2) while we found the previously identified TRDV1 has at least eight genes corresponding to separate genomic sequences. Nucleotide and amino acid sequences for particular gene subgroups between cattle and sheep were more than 87% identical but identities among TRDV subgroups within a species were much less, with bovine TRDV4 having <45% identity to the other three bovine TRDV gene subgroups. Analysis of circulating bovine gammadelta T cells revealed that genes from all four TRDV subgroups were expressed in combination with TRDJ1, TRDJ3, and TRDC, although TRDV4 was the least represented, and all displayed a variety of CDR3 junctional lengths. Finally, some genes within the TRDV1, TRDV2, and TRDV3 subgroups recombined with TRAV incorporating TRAJs, suggesting dual use.

Stage-specific and differential notch dependency at the alphabeta and gammadelta T lineage bifurcation

Signals transduced by Notch receptors are indispensable for T cell specification and differentiation of alphabeta T lineage cells. However, the role of Notch signals during alphabeta versus gammadelta T lineage decision remains controversial. Here, we addressed this question by employing a clonal analysis of CD4(-)CD8(-) (DN) progenitor potential to position the divergence of alphabeta and gammadelta T cell lineages to the late DN2 to DN3 developmental stages. Accordingly, alphabeta and gammadelta precursor frequencies within these T cell progenitor subsets were determined, both in the presence and absence of Notch signaling through Delta-like 1. Notch signals were found to be critical for the DN to CD4(+)CD8(+) (DP) transition, irrespective of the identity (pTalphabeta or gammadelta) of the inducing T cell receptor complex, whereas gammadelta T cells developed from gammadeltaTCR-expressing T cell progenitors in the absence of further Notch ligand interaction. Collectively, our findings demonstrate a differential, stage-specific requirement for Notch receptor-ligand interactions in the differentiation of alphabeta and gammadelta T cells from T cell progenitors.

Journey through the thymus: stromal guides for T-cell development and selection

Lympho-stromal interactions in multiple microenvironments within the thymus have a crucial role in the regulation of T-cell development and selection. Recent studies have implicated that chemokines that are produced by thymic stromal cells have a pivotal role in positioning developing T cells within the thymus. In this Review, I discuss the importance of stroma-derived chemokines in guiding the traffic of developing thymocytes, with an emphasis on the processes of cortex-to-medulla migration and T-cell-repertoire selection, including central tolerance.

Cellular and molecular events during early thymus development

The thymic stromal compartment consists of several cell types that collectively enable the attraction, survival, expansion, migration, and differentiation of T-cell precursors. The thymic epithelial cells constitute the most abundant cell type of the thymic microenvironment and can be differentiated into morphologically, phenotypically, and functionally separate subpopulations of the postnatal thymus. All thymic epithelial cells are derived from the endodermal lining of the third pharyngeal pouch. Very soon after the formation of a thymus primordium and prior to its vascularization, thymic epithelial cells orchestrate the first steps of intrathymic T-cell development, including the attraction of lymphoid precursor cells to the thymic microenvironment. The correct segmentation of pharyngeal epithelial cells and their subsequent crosstalk with cells in the pharyngeal arches are critical prerequisites for the formation of a thymus anlage. Mutations in several transcription factors and their target genes have been informative to detail some of the complex mechanisms that control the development of the thymus anlage. This review highlights recent findings related to the genetic control of early thymus organogenesis and provides insight into the molecular basis by which lymphocyte precursors are attracted to the thymus.

Regulation of TCR delta and alpha repertoires by local and long-distance control of variable gene segment chromatin structure

Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4- CD8- (double negative [DN]) and CD4+ CD8+ (double positive [DP]) thymocytes, respectively. TcraTcrd locus variable gene segments are subject to complex regulation. Only a small subset of approximately 100 variable gene segments contributes substantially to the adult TCRdelta repertoire. Moreover, although most contribute to the TCRalpha repertoire, variable gene segments that are Jalpha proximal are preferentially used during primary Tcra recombination. We investigate the role of local chromatin accessibility in determining the developmental pattern of TcraTcrd locus variable gene segment recombination. We find variable gene segments to be heterogeneous with respect to acetylation of histones H3 and H4. Those that dominate the adult TCRdelta repertoire are hyperacetylated in DN thymocytes, independent of their position in the locus. Moreover, proximal variable gene segments show dramatic increases in histone acetylation and germline transcription in DP thymocytes, a result of super long-distance regulation by the Tcra enhancer. Our results imply that differences in chromatin accessibility contribute to biases in TcraTcrd locus variable gene segment recombination in DN and DP thymocytes and extend the distance over which the Tcra enhancer can regulate chromatin structure to a remarkable 525 kb.

Enforcing order within a complex locus: current perspectives on the control of V(D)J recombination at the murine T-cell receptor alpha/delta locus

V(D)J recombination proceeds according to defined developmental programs at T-cell receptor (TCR) and immunoglobulin loci as a function of cell lineage and stage of differentiation. Although the molecular details are still lacking, such regulation is thought to occur at the level of accessibility of chromosomal recombination signal sequences to the recombinase. The unique and complex organization of the TCRalpha/delta locus poses intriguing regulatory challenges in this regard: embedded TCRalpha and TCRdelta gene segments rearrange at distinct stages of thymocyte development, there is a highly regulated progression of primary followed by secondary rearrangements involving Jalpha segments, and there are important developmental constraints on V gene segment usage. The locus therefore provides a fascinating laboratory in which to explore the basic mechanisms underlying developmental control. We provide here a current view of cis-acting mechanisms that enforce the TCRalpha/delta locus developmental program, and we emphasize the unresolved issues that command the attention of our and other laboratories.

Both TCR alpha and TCR delta chain diversity are regulated during thymic ontogeny

TCRalpha and TCRdelta chains are coded by a common genetic locus using a single set of V gene segments (ADV segments). This article addresses the question of regulation of the use of the ADV segments by the TCRalpha and TCRdelta chains. Using both qualitative and quantitative analyses we have studied the use of 23 ADV gene families as part of TCRalpha and TCRdelta transcripts. A number of previously undetected rearrangement and transcription events are described, indicating that the intrathymic TCRdelta repertoire is much more diverse than previously supposed. Repertoire analysis at several developmental time points allowed the description of regulated waves of ADV gene use, not only for TCRdelta chains, but also for TCRalpha chains, during thymic ontogeny. Control of these waves appears to be linked directly to the ADV segments and their local chromatin environment, which may change over the course of T cell differentiation.

Expression of functional CD8alpha Beta heterodimer on rat gamma delta T cells does not correlate with the CDR3 length of the TCR delta chain predicted for MHC class I-restricted antigen recognition

In accordance with their lack of MHC restriction, most mouse and human gamma delta T cells express neither the CD4 nor CD8(alpha beta) coreceptor. In striking contrast, up to 80% of splenic rat gamma delta T cells express the CD8alpha beta isoform of CD8, which for the alpha beta T cell subset serves as a marker for MHC class I-restricted cells. We compared CD8 on alpha beta and gamma delta T cells with regard to co-stimulatory function and correlation of CD8 expression with TCRDV usage and CDR3delta length. In both subsets, CD8 acted as a co-stimulatory molecule in vitro and was found to bind the kinase lck efficiently. No differences between the CDR3delta length spectra of CD8+ and CD8- gamma delta T cells or between unselected thymic and peripheral gamma delta T cells were found. As seen in man and mice, CDR3delta were rather long, a structural feature which can be expected to interfere with an alpha beta TCR-like mode of MHC class I binding. In summary, CD8 expressed by rat gamma delta T cells is a molecule with the potential to act as a coreceptor, but its expression gives no indication for antigen recognition analogous to that of MHC class I-restricted alpha beta T cells.