A fetal wave of human type 3 effector gamma delta cells with restricted TCR diversity persists into adulthood

Accumulating evidence suggests that the mouse embryonic thymus produces distinct waves of innate effector gamma delta T cells. However, it is unclear whether this process occurs similarly in humans and whether it comprises a dedicated subset of innate-like type 3 effector gamma delta T cells. Here, we present a protocol for high-throughput sequencing of TRG and TRD pairs that comprise the clonal gamma delta TCR. In combination with single-cell RNA sequencing, multiparameter flow cytometry, and TCR sequencing, we reveal a high heterogeneity of gamma delta T cells sorted from neonatal and adult blood that correlated with TCR usage. Immature gamma delta T cell clusters displayed mixed and diverse TCRs, but effector cell types segregated according to the expression of either highly expanded individual V delta 1(+) TCRs or moderately expanded semi-invariant V gamma 9V delta 2(+) TCRs. The V gamma 9V delta 2(+) T cells shared expression of genes that mark innate-like T cells, including ZBTB16 (encoding PLZF), KLRB1, and KLRC1, but consisted of distinct clusters with unrelated V gamma 9V delta 2(+) TCR clones characterized either by TBX21, FCGR3A, and cytotoxicity-associated gene expression (type 1) or by CCR6, RORC, IL23R, and DPP4 expression (type 3). Effector gamma delta T cells with type 1 and type 3 innate T cell signatures were detected in a public dataset of early embryonic thymus organogenesis. Together, this study suggests that functionally distinct waves of human innate-like effector gamma delta T cells with semi-invariant V gamma 9V delta 2(+) TCR develop in the early fetal thymus and persist into adulthood

Alpaka, Gürteltier und Baumwollratte als neue Tiermodelle für nichtkonventionelle T-Zellen: Identifikation von Zellpopulationen und Analyse von Antigenrezeptoren und Liganden

In this thesis, three species were investigated for the conservation of two non-conventional T cell systems, the CD1d/ iNKT cell system and the BTN3/ Vγ9Vδ2 T cell system. Non-conventional T cells are αβ or γδ T cells that do not fit into the classical mode of antigen recognition and adaptive responses. These T cells recognize antigens different from classical peptide antigens and are not restricted to the polymorphic MHC molecules but rather to non-polymorphic antigen-presenting molecules. The iNKT cell subset is restricted by the lipid antigen-presenting molecule CD1d and carries out immunomodulatory functions by rapid cytokine secretion. The molecular basis of this system, the semi-invariant iNKT TCR chains and CD1d were proven to be expressed and compared to homologs in human and rodents. Cotton rats possess multiple members of the AV14 and BV8 family and only one isoform of CD1d which is comparable to findings in the rat. Moreover, the reactivity of primary cells to glycolipid antigens could be shown, and an iNKT cell-like population was detected in primary cells using newly developed cotton rat CD1d oligomers. These were also applied to test the capacity of CD1d to present typical glycolipid antigens to iNKT TCR transductants. In addition, expression of cotton rat iNKT TCR α and β chains in TCR-negative cell lines was used to show successful pairing and detection of glycolipids in the context of CD1d. In summary, the conservation of a functional CD1d/iNKT cell system in the cotton rat could be shown, and tools were developed to study this cell subset in the course of infectious diseases. The Vγ9Vδ2 T cell subset is the major γδ T cell subset in human peripheral blood and has the unique ability to contribute to immune surveillance by detecting pyrophosphorylated metabolites of isoprenoid synthesis that indicate cell stress, transformation or infection. Up to this date, phosphoantigen-reactive γδ T cells have only been shown in primate species. However, evidence for the existence and functional conservation of the genes implied in the BTN3/Vγ9Vδ2 T cell system was found in several placental mammal species, and two candidate species were chosen for further investigation. The nine-banded armadillo, a valuable model for leprosy research, was shown to possess homologous genes to TRGV9, TRDV2 and BTN3. In this study, the expression of productive rearrangements of TRDV2 gene segments could be shown in peripheral blood samples, but no evidence was found for the expression of a functional TRGV9 rearrangement or BTN3 molecules. Moreover, determinants of phosphoantigen-reactive Vγ9Vδ2 T cells and functional BTN3 molecules were found to still be prevalent in armadillo genes. This makes the armadillo an interesting model to study the structural determinants that allow phosphoantigen recognition by a functional Vγ9Vδ2 T cell subset although this species is merely a witness for a functional system in a placental mammal ancestor. In contrast, alpacas were shown to express functional Vγ9Vδ2 T cells which conserved many features of the human counterpart. Expression of Vγ9Vδ2 pairings could be shown by single-cell PCR and functional phosphoantigenreactive pairings were observed. This phosphoantigen reactivity was also shown in PBMC cultures with a newly developed antibody specific for alpaca Vδ2Jδ4 chains. Moreover, a more detailed study of the alpaca TCR repertoire showed similarities to “γδ high” species like camelids and cattle which possess an extended family of TRDV genes. The γ and δ loci of alpaca TCR genes were drafted based on genomic information and cDNA studies and provide an overview for more detailed studies. Conservation of phosphoantigen recognition by the single BTN3 molecule of alpacas was shown in 293T knock out cell lines, and BTN3 detection on PBMCs was investigated with a newly developed alpaca BTN3-specific antibody. These findings prove the existence of a functional BTN3-dependent phosphoantigen-reactive Vγ9Vδ2 T cell subset and provide a basis for the future study of this cell system in a non-primate species. Moreover, as the first non-primate candidate species with the BTN3/Vγ9Vδ2 T cell system the alpaca is an important outgroup for research in this field. The use of a single BTN3 variant in contrast to three human isoforms that work together renders the alpaca a unique and to this date indispensable model for Vγ9Vδ2 T cells. In conclusion, this study provides an overview of the applicability of new animal models in the study of the non-conventional T cell subsets iNKT cells and Vγ9Vδ2 T cells and leads the way for a better understanding of structural and functional relationships.In dieser Arbeit wurden drei Spezies hinsichtlich ihrer Konservierung von unkonventionellen T-Zellen und ihren Interaktionspartnern, dem CD1d/iNKT-Zellsystem und dem BTN3/Vγ9Vδ2 T-Zellsystem, untersucht. Nicht-konventionelle T-Zellen sind αβ oder γδ T-Zellen, die nicht in das klassische Schema der adaptiven Immunantwort und Peptidantigenerkennung via MHC passen. Diese speziellen T-Zellen erkennen andere Antigene und unterliegen nicht der MHC-Restriktion, sondern interagieren mit meist nicht-polymorphen antigenpräsentierenden Molekülen. iNKT-Zellen erkennen Lipide, die von CD1d präsentiert werden, und führen immunmodulatorische Funktionen durch schnelle Zytokinproduktion aus. Charakteristisch ist die Expression einer semi-invarianten TCR α-Kette mit einer AV14/AJ18-Umlagerung in Mäusen und Ratten und der homologen Umlagerung AV24/AJ18 im Menschen. Diese α-Kette liegt gepaart mit bestimmten β-Ketten vor, die Diversität in der CDR3 Region aufweisen. Die Erforschung von iNKT-Zellen in der Baumwollratte, einem Modellorganismus für Infektionen mit humanen Viren, war bislang durch das Fehlen von genomischen Daten und Methoden eingeschränkt. Daher wurde die Konservierung von iNKT-Zellen und ihrem antigenpräsentierenden Molekül CD1d in der Baumwollratte untersucht. Die Expression der molekularen Bestandteile dieses Systems, die iNKT α-Kette, typische β-Ketten und CD1d, konnte bestätigt werden und mit den homologen Molekülen in Menschen und Nagern verglichen werden. Baumwollratten besitzen, vergleichbar mit Ratten, mehrere Mitglieder der AV14- und BV8-Familie und nur eine CD1d Variante. Zudem konnte die Reaktivität von primären Baumwollrattenzellen gegenüber typischen iNKT-Zell-Antigenen gezeigt werden und iNKT-Zellpopulationen in primären Zellen wurden mithilfe von CD1d-Multimeren gefärbt. Diese wurden auch zum Test der Funktionalität von CD1d herangezogen. Zusätzlich wurden iNKT TCR-Ketten in TCR-negativen Zelllinien exprimiert und so Paarung und Glykolipiderkennung gezeigt. Zusammenfassend konnte die Konservierung des CD1d/iNKT-Zellsystems in der Baumwollratte bewiesen werden Methoden entwickelt werden, die eine Erforschung der Bedeutung von iNKT-Zellen in Virusinfektionen in diesem Modellorganismus ermöglichen. Vγ9Vδ2 T-Zellen sind die Hauptpopulation von γδ T-Zellen im Blut des Menschen und haben die einzigartige Fähigkeit Metabolite des Isoprenoidstoffwechsels zu erkennen und dadurch zur Immunüberwachung beizutragen. Diese Moleküle sind ein Indiz für Zellstress, Transformation oder Infektionen. Bis jetzt wurden funktionelle Vγ9Vδ2 T-Zellen nur in Vertretern der Primaten gezeigt, die Gene dieses Systems sind allerdings in mehreren höheren Säugetieren konserviert. Zwei Kandidaten für ein funktionelles BTN3/Vγ9Vδ2 T-Zellsystem wurden in dieser Arbeit näher betrachtet. Das Neunbinden-Gürteltier ist ein Modellorganismus der Lepraforschung und die Konservierung von TRGV9, TRDV2 und BTN3 Homologen wurde in dieser Spezies gezeigt. Die Expression von produktiven TRDV2-Umlagerungen konnte im Blut dieser Tiere nachgewiesen werden, es wurde jedoch kein Hinweis auf die Expression von γ-Ketten mit TRGV9 Gensegmenten oder BTN3 Transkripten gefunden. Zusätzlich konnten charakteristische Merkmale von Phosphoantigen-reaktiven menschlichen Vγ9Vδ2 T-Zellen und BTN3 gefunden werden, die immer noch im Gürteltier angelegt sind. Dadurch bietet sich das Neunbinden-Gürteltier als Modell für die Erforschung von strukturellen Faktoren an, die Phosphoantigen-Erkennung durch funktionelle Vγ9Vδ2 T Zellen ermöglichen. Generell ist dieser Modellorganismus aber eher ein Zeuge für ein funktionelles BTN3/VγVδ2 T-Zellsystem in einem gemeinsamen Vorfahren. Im Gegensatz dazu wurden in Alpakas funktionelle Vγ9Vδ2 T-Zellen nachgewiesen, die viele Charakteristiken menschlicher phosphoantigen-reaktiver Vγ9Vδ2 T-Zellen, z.B. TRGJP Verwendung und CDR3 Längenrestriktion, aufweisen. Die Expression von Vγ9Vδ2 Paarungen im Alpaka konnte durch Einzelzell-PCR gezeigt werden und einige Paarungen waren in der Lage Phosphoantigene zu erkennen. Diese Reaktivität wurde, mithilfe von neu entwickelten Vδ2Jδ4-spezifischen Antikörpern, auch in PBMC Kulturen nachgewiesen. Weiterhin wurden Ähnlichkeiten des Alpakas mit „γδ high“ Spezies, z. B. Kamele und Rinder, durch eine erweiterte Untersuchung des TCR-Repertoires aufgezeigt. Schematische Darstellungen der TCR-γ und -δ Loci wurden basierend auf genomischen Daten und cDNA Analysen angefertigt und ermöglichen eine Übersicht für genauere Untersuchungen. Die Konservierung der Phosphoantigen-Bindung zu Alpaka BTN3 konnte durch Gen Knock-out Zelllinien bestätigt werden und die BTN3 Expression wurde mit neuen Alpaka BTN3-spezifischen Antikörpern untersucht. Diese Ergebnisse beweisen die Existenz einer BTN3-abhängigen Phosphoantigen-reaktiven Vγ9Vδ2 T-Zellpopulation im Alpaka und liefern eine Basis für zukünftige Studien dieses Systems. Weiterhin ist das Alpaka als erste nicht-Primaten Spezies eine wichtige Außengruppe für die Forschung in diesem Feld und ein bis jetzt einzigartiges und unersetzliches Modell für die Verwendung nur einer BTN3 Isoform in einem funktionellen BTN3/Vγ9Vδ2 T-Zellsystem. Abschließend lässt sich sagen, dass in dieser Arbeit eine Übersicht der Eignung von neuen Tiermodellen für die Untersuchung zweier nicht-konventioneller T-Zellpopulationen, der iNKT und Vγ9Vδ2 T-Zellen, geschaffen wurde. Dies ermöglicht weitere Untersuchungen zum besseren Verständnis von strukturellen und funktionellen Interaktionen

Human γδ TCR Repertoires in Health and Disease

The T cell receptor (TCR) repertoires of γδ T cells are very different to those of αβ T cells. While the theoretical TCR repertoire diversity of γδ T cells is estimated to exceed the diversity of αβ T cells by far, γδ T cells are still understood as more invariant T cells that only use a limited set of γδ TCRs. Most of our current knowledge of human γδ T cell receptor diversity builds on specific monoclonal antibodies that discriminate between the two major subsets, namely Vδ2+ and Vδ1+ T cells. Of those two subsets, Vδ2+ T cells seem to better fit into a role of innate T cells with semi-invariant TCR usage, as compared to an adaptive-like biology of some Vδ1+ subsets. Yet, this distinction into innate-like Vδ2+ and adaptive-like Vδ1+ γδ T cells does not quite recapitulate the full diversity of γδ T cell subsets, ligands and interaction modes. Here, we review how the recent introduction of high-throughput TCR repertoire sequencing has boosted our knowledge of γδ T cell repertoire diversity beyond Vδ2+ and Vδ1+ T cells. We discuss the current understanding of clonal composition and the dynamics of human γδ TCR repertoires in health and disease

An Update on the Molecular Basis of Phosphoantigen Recognition by Vγ9Vδ2 T Cells

About 1–5% of human blood T cells are Vγ9Vδ2 T cells. Their hallmark is the expression of T cell antigen receptors (TCR) whose γ-chains contain a rearrangement of Vγ9 with JP (TRGV9JP or Vγ2Jγ1.2) and are paired with Vδ2 (TRDV2)-containing δ-chains. These TCRs respond to phosphoantigens (PAg) such as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), which is found in many pathogens, and isopentenyl pyrophosphate (IPP), which accumulates in certain tumors or cells treated with aminobisphosphonates such as zoledronate. Until recently, these cells were believed to be restricted to primates, while no such cells are found in rodents. The identification of three genes pivotal for PAg recognition encoding for Vγ9, Vδ2, and butyrophilin (BTN) 3 in various non-primate species identified candidate species possessing PAg-reactive Vγ9Vδ2 T cells. Here, we review the current knowledge of the molecular basis of PAg recognition. This not only includes human Vγ9Vδ2 T cells and the recent discovery of BTN2A1 as Vγ9-binding protein mandatory for the PAg response but also insights gained from the identification of functional PAg-reactive Vγ9Vδ2 T cells and BTN3 in the alpaca and phylogenetic comparisons. Finally, we discuss models of the molecular basis of PAg recognition and implications for the development of transgenic mouse models for PAg-reactive Vγ9Vδ2 T cells

Species Specific Differences of CD1d Oligomer Loading In Vitro

CD1d molecules are MHC class I-like molecules that present glycolipids to iNKT cells. The highly conserved interaction between CD1d:α-Galactosylceramide (αGC) complexes and the iNKT TCR not only defines this population of αβ T cells but can also be used for its direct identification. Therefore, CD1d oligomers are a widely used tool for iNKT cell related investigations. To this end, the lipid chains of the antigen have to be inserted into the hydrophobic pockets of the CD1d binding cleft, often with help of surfactants. In this study, we investigated the influence of different surfactants (Triton X-100, Tween 20, Tyloxapol) on in vitro loading of CD1d molecules derived from four different species (human, mouse, rat and cotton rat) with αGC and derivatives carrying modifications of the acyl-chain (DB01-1, PBS44) and a 6-acetamido-6-deoxy-addition at the galactosyl head group (PBS57). We also compared rat CD1d dimers with tetramers and staining of an iNKT TCR transductant was used as readout for loading efficacy. The results underlined the importance of CD1d loading efficacy for proper analysis of iNKT TCR binding and demonstrated the necessity to adjust loading conditions for each oligomer/glycolipid combination. The efficient usage of surfactants as a tool for CD1d loading was revealed to be species-specific and depending on the origin of the CD1d producing cells. Additional variation of surfactant-dependent loading efficacy between tested glycolipids was influenced by the acyl-chain length and the modification of the galactosyl head group with PBS57 showing the least dependence on surfactants and the lowest degree of species-dependent differences

Maximum binding of differently loaded CD1d dimers.

<p>(A+B) Highest relative staining reached with each CD1d dimer loaded with indicated glycolipid as presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.g002" target="_blank">Fig 2</a>. Presented (A) as absolute or (B) as relative to the highest value reached for each CD1d. Human CD1d: Binding maxima are for all glycolipids are reached with Tyloxapol as surfactant. Mouse CD1d: Binding maxima with αGC and PBS57 are reached with Tween 20, forDB01-1 with Triton X-100 and for PBS44 with Tyloxapol. Rat CD1d: Binding maxima for αGC, DB01-1 and PBS44 are reached with Triton X-100, and for PBS57 with Tyloxapol. Cotton Rat: All maxima reached using Tyloxapol. Statistical analysis can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.s003" target="_blank">S2 Table</a>. Hierarchy of surfactant efficacy between experiments are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.s001" target="_blank">S1 Fig</a>. Data were computed from results shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.g002" target="_blank">Fig 2</a>.</p

<i>In vitro</i> loading analysis of CD1d dimers.

<p>CD1d dimers were incubated with 40x molar excess of indicated glycolipid in presence of 0.05% of indicated surfactant or without surfactant o.n. at 37°C. After <i>in vitro</i> loading, the indicated amount of CD1d dimers was used for staining of 10⁵ iNKT TCR transduced cells, dimer binding was revealed by staining with PE labeled donkey F(ab′)₂ fragment anti-mouse IgG (H+L). Binding presented as relative staining, i.e. ratio between geometric means of CD1d dimer and CD3 antibody staining was performed simultaneously. In total, staining was performed three times independently using oligomers derived from two independent loadings. Hierarchy of surfactant efficacy between experiments is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.s001" target="_blank">S1 Fig</a>. Note that scales differ in order to facilitate visualization different hierarchies of binding caused by the different surfactants.</p

<i>In vitro</i> loading analysis of rat CD1d tetramers.

<p>PE conjugated CD1d tetramers were incubated with 40x molar excess of indicated glycolipid in presence of 0.05% indicated surfactant or without surfactant o.n. at 37°C. After <i>in vitro</i> loading, the indicated amount of CD1d tetramers was used for staining of 10⁵ iNKT TCR transduced cells. Binding presented as relative staining, i.e. ratio between geometric means of CD1d tetramer and CD3 antibody staining performed simultaneously. In total, staining was performed three times independently using oligomers derived from two independent loadings. Hierarchy of surfactant efficacy between experiments is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143449#pone.0143449.s001" target="_blank">S1 Fig</a>.</p