CCR7 defines a precursor for murine iNKT cells in thymus and periphery

The precise steps of iNKT subset differentiation in the thymus and periphery have been controversial. We demonstrate here that the small proportion of thymic iNKT and mucosal associated invariant T cells that express CCR7 represent a multi-potent progenitor pool that gives rise to effector subsets within the thymus. Using intra-thymic labeling, we also showed that CCR7+ iNKT cells emigrate from the thymus in a Klf2 dependent manner, and undergo further maturation after reaching the periphery. Ccr7 deficiency impaired differentiation of iNKT effector subsets and localization to the medulla. Parabiosis and intra-thymic transfer showed that thymic NKT1 and NKT17 were resident-they were not derived from and did not contribute to the peripheral pool. Finally, each thymic iNKT effector subset produces distinct factors that influence T cell development. Our findings demonstrate how the thymus is both a source of iNKT progenitors and a unique site of tissue dependent effector cell differentiation.

The purinergic receptor P2RX7 directs metabolic fitness of long-lived memory CD8+ T cells

Extracellular ATP (eATP) is an ancient 'danger signal' used by eukaryotes to detect cellular damage¹. In mice and humans, the release of eATP during inflammation or injury stimulates both innate immune activation and chronic pain through the purinergic receptor P2RX7^2-4. It is unclear, however, whether this pathway influences the generation of immunological memory, a hallmark of the adaptive immune system that constitutes the basis of vaccines and protective immunity against re-infection^5,6. Here we show that P2RX7 is required for the establishment, maintenance and functionality of long-lived central and tissue-resident memory CD8⁺ T cell populations in mice. By contrast, P2RX7 is not required for the generation of short-lived effector CD8⁺ T cells. Mechanistically, P2RX7 promotes mitochondrial homeostasis and metabolic function in differentiating memory CD8⁺ T cells, at least in part by inducing AMP-activated protein kinase. Pharmacological inhibitors of P2RX7 provoked dysregulated metabolism and differentiation of activated mouse and human CD8⁺ T cells in vitro, and transient P2RX7 blockade in vivo ameliorated neuropathic pain but also compromised production of CD8⁺ memory T cells. These findings show that activation of P2RX7 by eATP provides a common currency that both alerts the nervous and immune system to tissue damage, and promotes the metabolic fitness and survival of the most durable and functionally relevant memory CD8⁺ T cell populations.

Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development

The thymus is responsible for generating a diverse yet self-tolerant pool of T cells1. Although the thymic medulla consists mostly of developing and mature AIRE+ epithelial cells, recent evidence has suggested that there is far greater heterogeneity among medullary thymic epithelial cells than was previously thought2. Here we describe in detail an epithelial subset that is remarkably similar to peripheral tuft cells that are found at mucosal barriers3. Similar to the periphery, thymic tuft cells express the canonical taste transduction pathway and IL-25. However, they are unique in their spatial association with cornified aggregates, ability to present antigens and expression of a broad diversity of taste receptors. Some thymic tuft cells pass through an Aire-expressing stage and depend on a known AIRE-binding partner, HIPK2, for their development. Notably, the taste chemosensory protein TRPM5 is required for their thymic function through which they support the development and polarization of thymic invariant natural killer T cells and act to establish a medullary microenvironment that is enriched in the type 2 cytokine, IL-4. These findings indicate that there is a compartmentalized medullary environment in which differentiation of a minor and highly specialized epithelial subset has a non-redundant role in shaping thymic function.

How Lipid-Specific T Cells Become Effectors: The Differentiation of iNKT Subsets

In contrast to peptide-recognizing T cells, invariant natural killer T (iNKT) cells express a semi-invariant T cell receptor that specifically recognizes self- or foreign-lipids presented by CD1d molecules. There are three major functionally distinct effector states for iNKT cells. Owning to these innate-like effector states, iNKT cells have been implicated in early protective immunity against pathogens. Yet, growing evidence suggests that iNKT cells play a role in tissue homeostasis as well. In this review, we discuss current knowledge about the underlying mechanisms that regulate the effector states of iNKT subsets, with a highlight on the roles of a variety of transcription factors and describe how each subset influences different facets of thymus homeostasis.

Intravenous Labeling and Analysis of the Content of Thymic Perivascular Spaces

Following development in the thymus, T cells are thought to exit into the periphery predominantly through perivascular spaces (PVS). This exit route is used by conventional T cells, and likely also applies to unconventional T cell subsets, such as precursors of CD8αα and TCRγδ intraepithelial lymphocytes, regulatory T cells and natural killer T cells. Additional cell types might also be found in the PVS and initiate interactions with exiting T cells. The exact content of the PVS, and the processes within, are not well studied. To distinguish vascular from resident cells within various tissues by flow cytometry, intravenous (i.v.) labeling is becoming a commonly employed method. We recently used anti-CD45.2 antibodies and magnetic enrichment to further evaluate this technique, and compared labeled and unlabeled cells in the thymus and blood. This assay can be used to specifically investigate hematopoietic cell subsets within the PVS of the thymus.

Directing T cell fate: How thymic antigen presenting cells coordinate thymocyte selection

The development of a self-tolerant and effective T cell receptor repertoire is dependent on interactions coordinated by various antigen presenting cells (APC) within the thymus. T cell receptor-self-peptide-MHC interactions are essential for determining T cell fate, however different cytokine and co-stimulatory signals provided by the diverse APCs within the thymus are also critical. Here, we outline the different localization and functional capabilities of thymic APCs. We also discuss how these distinct APCs work collectively to facilitate the establishment of a diverse T cell receptor repertoire that is tolerant to an array of different self-antigens.

Cutting Edge: Dual TCRα Expression Poses an Autoimmune Hazard by Limiting Regulatory T Cell Generation

Despite accounting for 10-30% of the T cell population in mice and humans, the role of dual TCR-expressing T cells in immunity remains poorly understood. It has been hypothesized that dual TCR T cells pose an autoimmune hazard by allowing self-reactive TCRs to escape thymic selection. We revisited this hypothesis using the NOD murine model of type 1 diabetes. We bred NOD mice hemizygous at both TCRα and β (TCRα^+/- β^+/-) loci, rendering them incapable of producing dual TCR T cells. We found that the lack of dual TCRα expression skewed the insulin-specific thymocyte population toward greater regulatory T (T_reg) cell commitment, resulting in a more tolerogenic T_reg to conventional T cell ratio and protection from diabetes. These data support a novel hypothesis by which dual TCR expression can promote autoimmunity by limiting agonist selection of self-reactive thymocytes into the T_reg cell lineage.

CD8αα intraepithelial lymphocytes arise from two main thymic precursors

TCRαβ⁺CD4^-CD8α⁺CD8β^- intestinal intraepithelial lymphocytes (CD8αα IELs) are an abundant population of thymus-derived T cells that protect the gut barrier surface. We sought to better define the thymic IEL precursor (IELp) through analysis of its maturation, localization and emigration. We defined two precursor populations among TCRβ⁺CD4^-CD8^- thymocytes by dependence on the kinase TAK1 and rigorous lineage-exclusion criteria. Those IELp populations included a nascent PD-1⁺ population and a T-bet⁺ population that accumulated with age. Both gave rise to intestinal CD8αα IELs after adoptive transfer. The PD-1⁺ IELp population included more strongly self-reactive clones and was largely restricted by classical major histocompatibility complex (MHC) molecules. Those cells localized to the cortex and efficiently emigrated in a manner dependent on the receptor S1PR1. The T-bet⁺ IELp population localized to the medulla, included cells restricted by non-classical MHC molecules and expressed the receptor NK1.1, the integrin CD103 and the chemokine receptor CXCR3. The two IELp populations further differed in their use of the T cell antigen receptor (TCR) α-chain variable region (V_α) and β-chain variable region (V_β). These data provide a foundation for understanding the biology of CD8αα IELs.

T cell progenitor therapy-facilitated thymopoiesis depends upon thymic input and continued thymic microenvironment interaction

Infusion of in vitro-derived T cell progenitor (proT) therapy with hematopoietic stem cell transplant aids the recovery of the thymus damaged by total body irradiation. To understand the interaction between proTs and the thymic microenvironment, WT mice were lethally irradiated and given T cell-deficient (Rag1-/-) marrow with WT in vitro-generated proTs, limiting mature T cell development to infused proTs. ProTs within the host thymus led to a significant increase in thymic epithelial cells (TECs) by day 21 after transplant, increasing actively cycling TECs. Upon thymus egress (day 28), proT TEC effects were lost, suggesting that continued signaling from proTs is required to sustain TEC cycling and cellularity. Thymocytes increased significantly by day 21, followed by a significant improvement in mature T cell numbers in the periphery by day 35. This protective surge was temporary, receding by day 60. Double-negative 2 (DN2) proTs selectively increased thymocyte number, while DN3 proTs preferentially increased TECs and T cells in the spleen that persisted at day 60. These findings highlight the importance of the interaction between proTs and TECs in the proliferation and survival of TECs and that the maturation stage of proTs has unique effects on thymopoiesis and peripheral T cell recovery.

Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst γδ T, Innate Lymphoid, and Th Cells

Invariant NKT cells differentiate into three predominant effector lineages in the steady state. To understand these lineages, we sorted undifferentiated invariant NK T progenitor cells and each effector population and analyzed their transcriptional profiles by RNAseq. Bioinformatic comparisons were made to effector subsets among other lymphocytes, specifically Th cells, innate lymphoid cells (ILC), and γδ T cells. Myc-associated signature genes were enriched in NKT progenitors, like in other hematopoietic progenitors. Only NKT1 cells, but not NKT2 and NKT17 cells, had transcriptome similarity to NK cells and were also similar to other IFN-γ-producing lineages such as Th1, ILC1, and intraepithelial γδ T cells. NKT2 and NKT17 cells were similar to their analogous subsets of γδ T cells and ILCs, but surprisingly, not to Th2 and Th17 cells. We identified a set of genes common to each effector lineage regardless of Ag receptor specificity, suggesting the use of conserved regulatory cores for effector function.

IL-4 sensitivity shapes the peripheral CD8+ T cell pool and response to infection

Homeostatic levels of IL-4 are necessary for normal development of memory phenotype CD8⁺ T cells and naive CD8⁺ T cells and for a robust CD8⁺ T cell response to LCMV infection.

Previous studies have revealed that a population of innate memory CD8⁺ T cells is generated in response to IL-4, first appearing in the thymus and bearing high expression levels of Eomesodermin (Eomes) but not T-bet. However, the antigen specificity and functional properties of these cells is poorly defined. In this study, we show that IL-4 regulates not only the frequency and function of innate memory CD8⁺ T cells, but also regulates Eomes expression levels and functional reactivity of naive CD8⁺ T cells. Lack of IL-4 responsiveness attenuates the capacity of CD8⁺ T cells to mount a robust response to lymphocytic choriomeningitis virus infection, with both quantitative and qualitative effects on effector and memory antigen-specific CD8⁺ T cells. Unexpectedly, we found that, although numerically rare, memory phenotype CD8⁺ T cells in IL-4Rα–deficient mice exhibited enhanced reactivity after in vitro and in vivo stimulation. Importantly, our data revealed that these effects of IL-4 exposure occur before, not during, infection. Together, these data show that IL-4 influences the entire peripheral CD8⁺ T cell pool, influencing expression of T-box transcription factors, functional reactivity, and the capacity to respond to infection. These findings indicate that IL-4, a canonical Th2 cell cytokine, can sometimes promote rather than impair Th1 cell–type immune responses.

CCR7+ naive iNKT serve as precursors for iNKT effector subsets and distinct mechanisms are involved in their thymic retention

Invariant natural killer T cells (iNKT) are CD1d restricted, lipid recognizing αβ T cells that modulate immunity under various contexts. iNKT are comprised of distinct effector subsets, NKT1, NKT2 and NKT17, characterized by long term retention in the thymus. However, the developmental steps of iNKT cell effector differentiation have been controversial, and mechanisms underlying their thymic retention are unclear. Specifically, the markers historically used to define stage 1 and 2 precursors also include mature effector NKT2 and NKT17 cells. Using RNAseq, we identified CCR7 as a candidate marker for undifferentiatied or naïve iNKT precursor. We demonstrate here that CCR7+ iNKT cells, distinguished from stage 0 iNKT by low CD24 expression, migrate from thymic cortex to medulla to give rise to iNKT effector subsets. CCR7+ iNKT express higher Rag2GFP, indicating they are “younger” than other thymic iNKT cells. Moreover, iNKT recent thymic emigrants in the periphery, identified by intrathymic labeling, are predominantly CCR7+ iNKT that express both Rag2GFP and KLF2, and are Qa2 negative. Busulfan chimeras confirmed that CCR7+ naive iNKT emigrate from thymus well before the accumulation of thymic effector iNKT cells. Type I and II interferon signals synergistically up-regulate CD69 in NKT1, and contribute to their retention in thymus. NKT17 highly express CD103 that might be critical for their thymic retention. Although it remains unclear how NKT2 are retained, their selective expression of IL-4 and RANK ligand influence effector CD8 T cell, as well as thymic DC and medullary epithelial cells (mTEC) development. Our findings provide novel insights into the developmental pathway of iNKT cells and the mechanisms of their thymic retention.

Absence of dual TCR T cells protects NOD mice from diabetes due to an increased insulin-specific Treg:Teff ratio

Due to allelic exclusion, most αβ T cells express only a single αβ TCR specificity. However, around 10% of human and mouse T cells express two different α chains with the potential for dual specificities. Dual β-expressing T cells also exist and account for ~1% of all T cells. Expression of two different TCR specificities by a single T cell is one hypothesized mechanism by which self-reactive TCRs escape central tolerance to initiate autoimmunity. While peripheral tolerance mechanisms typically control any self-reactive T cells in healthy animals, these mechanisms are hypo-functional in NOD mice. We hypothesized that eliminating dual TCR T cells would protect NOD mice from diabetes. To test this hypothesis we generated NOD mice hemizygous at both the TCRα and β loci (TCRα+/−β+/−). Indeed, we found that NOD mice incapable of generating dual TCR T cells were protected from diabetes with both lower diabetes incidence than wildtype (WT) NOD mice (0% versus 70% at 30 weeks of age) and also lower insulitis scores at 10 weeks of age. Examination of the insulin-specific T cell population in the pancreas-draining lymph node revealed a lower Treg:Teff ratio in WT NOD mice compared to single TCR T cell NOD mice. Anti-PD-1 treatment resulted in the rapid development of diabetes in 100% of WT NOD mice but in only 30% of single TCR T cell mice, suggesting that the diabetes resistance phenotype of single TCR T cell mice is not primarily due to increased anergy. These data support the hypothesis that the presence of dual TCR T cells increases the risk of diabetes in NOD mice by altering the insulin-specific Treg:Teff ratio.

Specific patterns of self-antigen expression determine the mechanisms by which polyclonal self-reactive CD4+ T cells are tolerized

Understanding how self-tolerance is maintained requires the ability to track rare, self-reactive T cells of known specificity in normal individuals. However, due to technical limitations much of our knowledge has relied on the study of T cell receptor transgenic cells that recognize model antigens. While this work has identified numerous modes of tolerance, it is unclear which mechanisms operate in normally diverse repertoires and how this decision is made. We studied polyclonal CD4+ T cells specific for an epitope from green fluorescent protein (GFP) in fourteen different mouse strains that express GFP under the control of tissue-specific promoters. We found that clonal deletion was the key tolerance mechanism for self-antigens that were uniformly expressed by thymic antigen-presenting cells. In contrast, self-antigens that were absent from the thymus were ignored. A more complex form of tolerance regulated CD4+ T cells specific for self-antigens with limited expression by thymic antigen-presenting cells. These populations showed partial clonal deletion and impaired effector T cell potential but enhanced regulatory T cell potential of remaining cells. Furthermore, these tolerance mechanisms were also found to regulate CD4+ T cells specific for endogenously expressed self-antigens. Thus, self-antigen expression patterns dictate the tolerance mechanisms by which self-reactive polyclonal CD4+ T cells are regulated.

CD4(+) T cell anergy prevents autoimmunity and generates regulatory T cell precursors

The role of anergy, an acquired state of T cell functional unresponsiveness, in natural peripheral tolerance remains unclear. In this study, we found that anergy was selectively induced in fetal antigen-specific maternal CD4(+) T cells during pregnancy. A naturally occurring subpopulation of anergic polyclonal CD4(+) T cells, enriched for self antigen-specific T cell antigen receptors, was also present in healthy hosts. Neuropilin-1 expression in anergic conventional CD4(+) T cells was associated with hypomethylation of genes related to thymic regulatory T cells (Treg cells), and this correlated with their ability to differentiate into Foxp3(+) Treg cells that suppressed immunopathology. Thus, our data suggest that not only is anergy induction important in preventing autoimmunity but also it generates the precursors for peripheral Treg cell differentiation.

Tolerance is established in polyclonal CD4(+) T cells by distinct mechanisms, according to self-peptide expression patterns

Studies of mouse monoclonal CD4⁺ T cell repertoires have revealed several mechanisms of self-tolerance, however, which mechanisms operate in normal repertoires is unclear. Here, polyclonal CD4⁺ T cells specific for green fluorescent protein expressed in different organs were studied, allowing determination of the effects of specific expression patterns on the same epitope-specific T cells. Peptides presented uniformly by thymic antigen-presenting cells were tolerated by clonal deletion, whereas thymus-excluded peptides were ignored. Peptides with limited thymic expression induced partial clonal deletion and impaired effector but enhanced regulatory T cell potential. These mechanisms were also active for T cell populations specific for endogenously expressed self-antigens. Thus, immune tolerance of polyclonal CD4⁺ T cells is maintained by distinct mechanisms, according to self-peptide expression patterns.

Bi-Allelic TCRα or β Recombination Enhances T Cell Development but Is Dispensable for Antigen Responses and Experimental Autoimmune Encephalomyelitis

Dual TCRα-expressing T cells outnumber dual TCRβ-expressing cells by ~10:1. As a result, efforts to understand how dual TCR T cells impact immunity have focused on dual TCRα expression; dual TCRβ expression remains understudied. We recently demonstrated, however, that dual TCRβ expression accelerated disease in a TCR transgenic model of autoimmune arthritis through enhanced positive selection efficiency, indicating that dual TCRβ expression, though rare, can impact thymic selection. Here we generated mice hemizygous for TCRα, TCRβ, or both on the C57BL/6 background to investigate the impact bi-allelic TCR chain recombination has on T cell development, repertoire diversity, and autoimmunity. Lack of bi-allelic TCRα or TCRβ recombination reduced αβ thymocyte development efficiency, and the absence of bi-allelic TCRβ recombination promoted γδ T cell development. However, we observed no differences in the numbers of naïve and expanded antigen-specific T cells between TCRα^+/-β^+/- and wildtype mice, and TCR repertoire analysis revealed only subtle differences in Vβ gene usage. Finally, the absence of dual TCR T cells did not impact induced experimental autoimmune encephalomyelitis pathogenesis. Thus, despite more stringent allelic exclusion of TCRβ relative to TCRα, bi-allelic TCRβ expression can measurably impact thymocyte development and is necessary for maintaining normal αβ/γδ T cell proportions.

T Cell Adolescence: Maturation Events Beyond Positive Selection

Single-positive thymocytes that successfully complete positive and negative selection must still undergo one final step, generally termed T cell maturation, before they gain functional competency and enter the long-lived T cell pool. Maturation initiates after positive selection in single-positive thymocytes and continues in the periphery in recent thymic emigrants, before these newly produced T cells gain functional competency and are ready to participate in the immune response as peripheral naive T cells. Recent work using genetically altered mice demonstrates that T cell maturation is not a single process, but a series of steps that occur independently and sequentially after positive selection. This review focuses on the changes that occur during T cell maturation, as well as the molecules and pathways that are critical at each step.

Tissue-Specific Distribution of iNKT Cells Impacts Their Cytokine Response

Three subsets of invariant natural killer T (iNKT) cells have been identified, NKT1, NKT2, and NKT17, which produce distinct cytokines when stimulated, but little is known about their localization. Here, we have defined the anatomic localization and systemic distribution of these subsets and measured their cytokine production. Thymic NKT2 cells that produced interleukin-4 (IL-4) at steady state were located in the medulla and conditioned medullary thymocytes. NKT2 cells were abundant in the mesenteric lymph node (LN) of BALB/c mice and produced IL-4 in the T cell zone that conditioned other lymphocytes. Intravenous injection of α-galactosylceramide activated NKT1 cells with vascular access, but not LN or thymic NKT cells, resulting in systemic interferon-γ and IL-4 production, while oral α-galactosylceramide activated NKT2 cells in the mesenteric LN, resulting in local IL-4 release. These findings indicate that the localization of iNKT cells governs their cytokine response both at steady state and upon activation.

Impaired Epstein-Barr Virus-Specific Neutralizing Antibody Response during Acute Infectious Mononucleosis Is Coincident with Global B-Cell Dysfunction

Here we present evidence for previously unappreciated B-cell immune dysregulation during acute Epstein-Barr virus (EBV)-associated infectious mononucleosis (IM). Longitudinal analyses revealed that patients with acute IM have undetectable EBV-specific neutralizing antibodies and gp350-specific B-cell responses, which were associated with a significant reduction in memory B cells and no evidence of circulating antibody-secreting cells. These observations correlate with dysregulation of tumor necrosis factor family members BAFF and APRIL and increased expression of FAS on circulating B cells.

Cytokine-Mediated Loss of Blood Dendritic Cells During Epstein-Barr Virus-Associated Acute Infectious Mononucleosis: Implication for Immune Dysregulation

Acute infectious mononucleosis (IM) is associated with altered expression of inflammatory cytokines and disturbed T-cell homeostasis, however, the precise mechanism of this immune dysregulation remains unresolved. In the current study we demonstrated a significant loss of circulating myeloid and plasmacytoid dendritic cells (DCs) during acute IM, a loss correlated with the severity of clinical symptoms. In vitro exposure of blood DCs to acute IM plasma resulted in loss of plasmacytoid DCs, and further studies with individual cytokines showed that exposure to interleukin 10 could replicate this effect. Our data provide important mechanistic insight into dysregulated immune homeostasis during acute IM.

The transcription factor KLF2 restrains CD4⁺ T follicular helper cell differentiation

T follicular helper (Tfh) cells are essential for efficient B cell responses, yet the factors that regulate differentiation of this CD4⁺ T cell subset are incompletely understood. Here we found that the KLF2 transcription factor serves to restrain Tfh cell generation. Induced KLF2 deficiency in activated CD4⁺ T cells led to increased Tfh cell generation and B cell priming, while KLF2 overexpression prevented Tfh cell production. KLF2 promotes expression of the trafficking receptor S1PR1, and S1PR1 downregulation is essential for efficient Tfh cell production. However, KLF2 also induced expression of the transcription factor Blimp-1, which repressed transcription factor Bcl-6 and thereby impaired Tfh cell differentiation. Furthermore, KLF2 induced expression of the transcription factors T-bet and GATA3 and enhanced Th1 differentiation. Hence, our data indicate KLF2 is pivotal for coordinating CD4⁺ T cell differentiation through two distinct and complementary mechanisms: via control of T cell localization, and by regulation of lineage-defining transcription factors.