Bovine T cell receptors and γδ WC1 co-receptor transcriptome analysis during the first month of life

Defining the caprine γδ T cell WC1 multigenic array and evaluation of its expressed sequences and gene structure conservation among goat breeds and relative to cattle

Workshop cluster 1 (WC1) molecules are part of the scavenger receptor cysteine-rich (SRCR) superfamily and act as hybrid co-receptors for the γδ T cell receptor and as pattern recognition receptors for binding pathogens. These members of the CD163 gene family are expressed on γδ T cells in the blood of ruminants. While the presence of WC1⁺ γδ T cells in the blood of goats has been demonstrated using monoclonal antibodies, there was no information available about the goat WC1 gene family. The caprine WC1 multigenic array was characterized here for number, structure and expression of genes, and similarity to WC1 genes of cattle and among goat breeds. We found sequence for 17 complete WC1 genes and evidence for up to 30 SRCR a1 or d1 domains which represent distinct signature domains for individual genes. This suggests substantially more WC1 genes than in cattle. Moreover, goats had seven different WC1 gene structures of which 4 are unique to goats. Caprine WC1 genes also had multiple transcript splice variants of their intracytoplasmic domains that eliminated tyrosines shown previously to be important for signal transduction. The most distal WC1 SRCR a1 domains were highly conserved among goat breeds, but fewer were conserved between goats and cattle. Since goats have a greater number of WC1 genes and unique WC1 gene structures relative to cattle, goat WC1 molecules may have expanded functions. This finding may impact research on next-generation vaccines designed to stimulate γδ T cells.

The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla

The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda, and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC “cassettes”, each containing the basic V-J-J-C unit. Eighteen genes arranged in four TRGC cassettes, form the pig TRG locus. All the functional TRG genes were expressed, and the TRGV genes preferentially rearrange with the TRGJ genes within their own cassette, which correlates the diversity of the γ-chain repertoire with the number of cassettes. Among them, the TRGC5, located at the 5′ end of the locus, is the only cassette that retains a marked homology with the corresponding TRGC cassettes of all the analyzed species. The preservation of the TRGC5 cassette for such a long evolutionary time presumes a highly specialized function of its genes, which could be essential for the survival of species. Therefore, the maintenance of this cassette in pigs confirms that it is the most evolutionarily ancient within Cetartiodactyla, and it has undergone a process of duplication to give rise to the other TRGC cassettes in the different artiodactyl species in a lineage-specific manner.

Transcriptional programming and gene regulation in WC1+ γδ T cell subpopulations

γδ T cells represent a high proportion of lymphocytes in the blood of ruminants with the majority expressing lineage-specific glycoproteins from the WC1 family. WC1 receptors are coded for by a multigenic array whose genes have variegated but stable expression among cells in the γδ T cell population. WC1 molecules function as hybrid pattern recognition receptors as well as co-receptors for the TCR and are required for responses by the cells. Because of the variegated gene expression, WC1⁺ γδ T cells can be divided into two main populations known as WC1.1⁺ and WC1.2⁺ based on monoclonal antibody reactivity with the expressed WC1 molecules. These subpopulations differ in their ability to respond to specific pathogens. Here, we showed these populations are established in the thymus and that WC1.1⁺ and WC1.2⁺ subpopulations have transcriptional programming that is consistent with stratification towards Tγδ1 or Tγδ17. WC1.1⁺ cells exhibited the Tγδ1 phenotype with greater transcription of Tbx21 and production of more IFNγ while the WC1.2⁺ subpopulation tended towards Tγδ17 programming producing higher levels of IL-17 and had greater transcription of Rorc. However, when activated both WC1⁺ subpopulations' cells transcribed Tbx21 and secreted IFNγ and IL-17 reflecting the complexity of these subpopulations defined by WC1 gene expression. The gene networks involved in development of these two subpopulations including expression of their archetypal genes wc1-3 (WC1.1⁺) and wc1-4 (WC1.2⁺) were unknown but we report that SOX-13, a γδ T cell fate-determining transcription factor, has differential occupancy on these WC1 gene loci and suggest a model for development of these subpopulations.

Subpopulations of swine γδ T cells defined by TCRγ and WC1 gene expression

γδ T cells constitute a major portion of lymphocytes in the blood of both ruminants and swine. Subpopulations of swine γδ T cells have been distinguished by CD2 and CD8α expression. However, it was not clear if they have distinct expression profiles of their T-cell receptor (TCR) or WC1 genes. Identifying receptor expression will contribute to understanding the functional differences between these subpopulations and their contributions to immune protection. Here, we annotated three genomic assemblies of the swine TCRγ gene locus finding four gene cassettes containing C, J and V genes, although some haplotypes carried a null TRGC gene (TRGC4). Genes in the TRGC1 cassette were homologs of bovine TRGC5 cassette while the others were not homologous to bovine genes. Here we evaluated three principal populations of γδ T cells (CD2⁺/SWC5^-, CD2^-/SWC5⁺, and CD2^-/SWC5^-). Both CD2^- subpopulations transcribed WC1 co-receptor genes, albeit with different patterns of gene expression but CD2⁺ cells did not. All subpopulations transcribed TCR genes from all four cassettes, although there were differences in expression levels. Finally, the CD2⁺ and CD2^- γδ T-cell populations differed in their representation in various organs and tissues, presumably at least partially reflective of different ligand specificities for their receptors.

Special features of γδ T cells in ruminants

Ruminant γδ T cells were discovered in the mid-1980's shortly after a novel T cell receptor (TCR) gene from murine cells was described in 1984 and the murine TCRγ gene locus in 1985. It was possible to identify γδ T cell populations early in ruminants because they represent a large proportion of the peripheral blood mononuclear cells (PBMC). This null cell population, γδ T cells, was designated as such by its non-reactivity with monoclonal antibodies (mAb) against ovine and bovine CD4, CD8 and surface immunoglobulin (Ig). γδ T cells are non-conventional T cells known as innate-like cells capable of using both TCR as well as other types of receptor systems including pattern recognition receptors (PRR) and natural killer receptors (NKR). Bovine γδ T cells have been shown to respond to stimulation through toll-like receptors, NOD, and NKG2D as well as to cytokines alone, protein and non-protein antigens through their TCR, and to pathogen-infected host cells. The two main populations of γδ T cells are distinguished by the presence or absence of the hybrid co-receptor/PRR known as WC1 or T19. These two populations not only differ by their proportional representation in various tissues and organs but also by their migration into inflamed tissues. The WC1⁺ cells are found in the blood, skin and spleen while the WC1^- γδ T cells predominate in the gut, mammary gland and uterus. In ruminants, γδ T cells may produce IFNγ, IL-17, IL-10 and TGFβ, have cytotoxic activity and memory responses. The expression of particular WC1 family members controls the response to particular pathogens and correlates with differences in cytokine responses. The comparison of the WC1 gene families in cattle, sheep and goats is discussed relative to other multigenic arrays that differentiate γδ T cells by function in humans and mice.

The WC1 γδ T cell pathogen receptor of ruminants is preserved in the genome of ancient extinct auroch

The work reported here investigated the γδ T cell-specific cell surface receptor known as workshop cluster 1 (WC1) in the extinct Auroch and compared the gene sequences to those in modern cattle breeds. These molecules function as hybrid pattern recognition receptors (PRR), binders of microbial pathogens, and as signaling co-receptors of the T cell antigen receptor (TCR), directing the immune responses by γδ T cell subsets. Sequences in the Auroch genome included both WC1.1 and WC1.2-like a-patterned scavenger receptor cytsteine-rich (SRCR) domains as well as the more conserved b, c, d, and e-patterned SRCR domains. While there was much sequence homology with bovine WC1 genes, there are also unique Auroch genes based on the signature a1 SRCR domain sequences that are used to identify individual WC1 genes. There was also conservation of genes coding for Type I and II intracytoplasmic endodomains although no evidence for gene sequences for Type III endodomains or the extracellular 6 SRCR domains that are associated with this endodomain. This particular WC1 molecule has been proposed to represent the most ancient WC1, and thus, it is particularly interesting that it is apparently missing in the Auroch genome although it could be due to incomplete sequencing. Overall, the results suggest that while WC1 genes have been preserved from Ancient Auroch to modern cattle, they may have co-evolved perhaps as a result of differing pathogen or environmental antigen exposure.

Gene characterization and expression of the γδ T cell co-receptor WC1 in sheep

Sheep are known to express the hybrid co-receptor/pattern recognition receptor WC1 on their γδ T cells but details of the ovine WC1 multigenic array and gene expression were unknown. Annotation of the sheep genome assembly (Oar_rambouillet_v1.0) yielded 15 complete and 42 partial WC1 genes predicted to code for six different protein structures. RT-PCR amplification of the most distal scavenger receptor cysteine rich (SRCR) domain known as a1, which serves as the gene signature, from genomic and cDNA templates verified the majority of annotated genes. As for cattle and goats, sheep a1 domain sequences included WC1.1 and WC1.2 types. A unique ovine gene, WC1-16, had multiple SRCR a-pattern domains in tandem similar to one found in goats. Intracytoplasmic domains of WC1 transcripts had splice variants that may affect signal transduction. The larger number of WC1 genes in sheep and differences in structures and splice variants relative to cattle could have implications in expression patterns and engagement of γδ T cells by pathogens or vaccine constructs.

Bovine neonate is deficient in innate immunity at birth

With an objective to understand acquisition of innate immunity in bovine neonates, we analyzed perinatal expression of cytokine, adhesion molecule and complement component genes involved in innate and adaptive immune functions. Statistically robust transcriptomic analysis of 27 cytokines showed low IL1B, IL2 and IL7 but high IL23, TGFB1 and TGFB2 expression in bovine neonates post-birth. Unlike mice and humans, no T_H2 polarizing cytokine expression occurs in bovine neonates. Further, T_H17 and Treg differentiation in bovine neonates may differ from other species like mice and humans. Decreased IL7, IL23R, CXCR3 and increased TGFB1 and TGFB2 expression provides an immunosuppressive environment in the bovine neonate at birth. Transcriptomic analysis of 31 adhesion molecules showed rapid increase in ITGAL expression within a week post-birth in bovine neonates that permits acquisition of innate cytotoxic functions by granulocytes (antibody-mediated), cytotoxic T and NK cells. However, innate immune functions involving phagocytosis and platelet aggregation are deficient in bovine neonates at birth. Of twenty-seven, 18 complement component genes show no significant differential gene expression in neonates post-birth. But low expression of C1QA, C1QB, CQC, C1R and C2 compromises classical and lectin complement pathways mediated lytic function in bovine neonates. The complement-mediated cytotoxic functions, however, normalize between days 7 and 28 post-birth. To conclude, bovine neonate is immunosuppressed and deficient in innate immune competence at birth. Such differences with regard to global innate immune deficiency and lack of T_H2 polarization in bovine neonates have profound implications for designing vaccines to prevent neonatal infections. To conclude, species-specific unique characteristics of developing innate and adaptive immune system need to be taken into consideration while designing new immunization strategies to prevent neonatal mortality from infections.

Characterization of the domestic goat γδ T cell receptor gene loci and gene usage

Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1⁺ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1⁺ γδ T cells. In contrast, caprine WC1⁺ and WC1^- γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle.

Evolution of the T-Cell Receptor (TR) Loci in the Adaptive Immune Response: The Tale of the TRG Locus in Mammals

T lymphocytes are the principal actors of vertebrates' cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response.

Comprehensive genomic analysis of the dromedary T cell receptor gamma (TRG) locus and identification of a functional TRGC5 cassette

The emergent availability in public databases of more complete genome assemblies allows us to improve genomic data obtained by classical molecular cloning. The main goal of this study was to refine the genomic map of the dromedary TRG locus by integrating our previous genomic data with the analysis of recent genomic assemblies. We identified an additional TRGC cassette, defined as a V-J-C recombination unit, located at the 5' of the locus and made up of five TRGV genes followed by three TRGJ genes and one TRGC gene. Hence, the complete dromedary TRG locus spans about 105 Kb and consists of three in tandem TRGC cassettes delimited by AMPH and STARD3NL genes at the 5' and 3' end, respectively. An expression assay carried out on peripheral blood showed the functional competency for the dromedary TRGC5 cassette and confirmed the presence of the somatic hypermutation mechanism able to enlarge the repertoire diversity of the dromedary γδ T cells.

γδ T cells in livestock: Responses to pathogens and vaccine potential

The immediate objective of our research is to understand the molecular mechanisms underlying activation and potentiation of the protective functional response of WC1⁺ γδ T cells to pathogens afflicting livestock species. The long-term goal is to incorporate stimulation of these cells into the next generation of vaccine constructs. γδ T cells have roles in the immune response to many infectious diseases including viral, bacterial, protozoan and worm infections, and their functional responses overlap with those of canonical αβ T cells, for example they produce cytokines including interferon-γ and IL-17. Stimulation of non-conventional lymphocytes including γδ T cells and αβ natural killer T (NKT) cells has been shown to contribute to protective immunity in mammals, bridging the gap between the innate and adaptive immune responses. Because of their innate-like early response, understanding how to engage γδ T-cell responses has the potential to optimize strategies of those that aim to induce pro-inflammatory responses as discussed here.