Structure and function of the pre-T cell receptor

Regulatory Roles of SWI/SNF Chromatin Remodeling Complexes in Immune Response and Inflammatory Diseases

The switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes (also referred to as BAF complexes) are composed of multiple subunits, which regulate the nucleosome translocation and chromatin accessibility. In recent years, significant advancements have been made in understanding mutated genes encoding subunits of the SWI/SNF complexes in cancer biology. Nevertheless, the role of SWI/SNF complexes in immune response and inflammatory diseases continues to attract significant attention. This review presents a summary of the significant functions of SWI/SNF complexes during the overall process from the development to the activation of innate and adaptive immune cells. In addition, the correlation between various SWI/SNF subunits and diverse inflammatory diseases is explored. Further investigations are warranted in terms of the mechanism of SWI/SNF complexes' preference for binding sites and opposite pro-/anti-inflammatory effects. In conclusion, further efforts are needed to evaluate the druggability of targeting SWI/SNF complexes in inflammatory diseases, and we hope this review will inspire the development of novel immune modulators in clinical practice.

Multiple instance learning method based on convolutional neural network and self-attention for early cancer detection

Early cancer detection using T-cell receptor sequencing (TCR-seq) and multiple instances learning methods has shown significant effectiveness. We introduce a multiple instance learning method based on convolutional neural networks and self-attention (MICA). First, MICA preprocesses TCR-seq using word vectors and then extracts features using convolutional neural networks. Second, MICA uses an enhanced self-attention mechanism to extract relational features of instances. Finally, MICA can extract the crucial TCR-seq. After cross-validation, MICA achieves an area under the curve (AUC) of 0.911 and 0.946 on the lung and thyroid cancer datasets, which are 7.1% and 2.1% higher than other methods, respectively.

The partitioning of TCR repertoires by thymic selection

αβ T cells are critical components of the adaptive immune system; they maintain tissue and immune homeostasis during health, provide sterilizing immunity after pathogen infection, and are capable of eliminating transformed tumor cells. Fundamental to these distinct functions is the ligand specificity of the unique antigen receptor expressed on each mature T cell (TCR), which endows lymphocytes with the ability to behave in a cell-autonomous, disease context-specific manner. Clone-specific behavioral properties are initially established during T cell development when thymocytes use TCR recognition of major histocompatibility complex (MHC) and MHC-like ligands to instruct survival versus death and to differentiate into a plethora of inflammatory and regulatory T cell lineages. Here, we review the ligand specificity of the preselection thymocyte repertoire and argue that developmental stage-specific alterations in TCR signaling control cross-reactivity and foreign versus self-specificity of T cell sublineages.

Dendritic cells and antigen-specific immunotherapy in autoimmune rheumatic diseases

Dendritic cells (DCs) are professional antigen-presenting cells and trigger downstream immune responses to antigen while integrating cellular pathogen and damage-associated molecular pattern (PAMP and DAMP) or immunomodulatory signals. In healthy individuals, resting and tolerogenic DCs draining skin and intestine facilitate expansion of regulatory T cells (Treg) to maintain peripheral antigen-specific immune tolerance. In patients with rheumatic diseases, however, DCs activated by PAMPs and DAMPs expand self-reactive effector T cells, including follicular helper T cells that promote the expansion of activated autoreactive B cells, chronic inflammation and end-organ damage. With the development of cellular and nanoparticle (NP)-based self-antigen-specific immunotherapies we here consider the new opportunities and the challenges for restoring immunoregulation in the treatment and prevention of autoimmune inflammatory rheumatic conditions through DCs.

Hyperactive STAT5 hijacks T cell receptor signaling and drives immature T cell acute lymphoblastic leukemia

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T cell cancer. Mutations in IL7R have been analyzed genetically, but downstream effector functions such as STAT5A and STAT5B hyperactivation are poorly understood. Here, we studied the most frequent and clinically challenging STAT5BN642H driver in T cell development and immature T cell cancer onset and compared it with STAT5A hyperactive variants in transgenic mice. Enhanced STAT5 activity caused disrupted T cell development and promoted an early T cell progenitor-ALL phenotype, with upregulation of genes involved in T cell receptor (TCR) signaling, even in absence of surface TCR. Importantly, TCR pathway genes were overexpressed in human T-ALL and mature T cell cancers and activation of TCR pathway kinases was STAT5 dependent. We confirmed STAT5 binding to these genes using ChIP-Seq analysis in human T-ALL cells, which were sensitive to pharmacologic inhibition by dual STAT3/5 degraders or ZAP70 tyrosine kinase blockers in vitro and in vivo. We provide genetic and biochemical proof that STAT5A and STAT5B hyperactivation can initiate T-ALL through TCR pathway hijacking and suggest similar mechanisms for other T cell cancers. Thus, STAT5 or TCR component blockade are targeted therapy options, particularly in patients with chemoresistant clones carrying STAT5BN642H.

Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies

Engineered T cells are at the leading edge of clinical cell therapy. T cell therapies have had a remarkable impact on patient care for a subset of hematological malignancies. This foundation has motivated the development of off-the-shelf engineered cell therapies for a broad range of devastating indications. Achieving this vision will require cost-effective manufacturing of precision cell products capable of addressing multiple process and clinical-design challenges. Pluripotent stem cell (PSC)-derived engineered T cells are emerging as a solution of choice. To unleash the full potential of PSC-derived T cell therapies, the field will require technologies capable of robustly orchestrating the complex series of time- and dose-dependent signaling events needed to recreate functional T cell development in the laboratory. In this article, we review the current state of allogenic T cell therapies, focusing on strategies to generate engineered lymphoid cells from PSCs. We highlight exciting recent progress in this field and outline timely opportunities for advancement with an emphasis on niche engineering and synthetic biology.

Notch Partners in the Long Journey of T-ALL Pathogenesis

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological disease that arises from the oncogenic transformation of developing T cells during T-lymphopoiesis. Although T-ALL prognosis has improved markedly in recent years, relapsing and refractory patients with dismal outcomes still represent a major clinical issue. Consequently, understanding the pathological mechanisms that lead to the appearance of this malignancy and developing novel and more effective targeted therapies is an urgent need. Since the discovery in 2004 that a major proportion of T-ALL patients carry activating mutations that turn NOTCH1 into an oncogene, great efforts have been made to decipher the mechanisms underlying constitutive NOTCH1 activation, with the aim of understanding how NOTCH1 dysregulation converts the physiological NOTCH1-dependent T-cell developmental program into a pathological T-cell transformation process. Several molecular players have so far been shown to cooperate with NOTCH1 in this oncogenic process, and different therapeutic strategies have been developed to specifically target NOTCH1-dependent T-ALLs. Here, we comprehensively analyze the molecular bases of the cross-talk between NOTCH1 and cooperating partners critically involved in the generation and/or maintenance and progression of T-ALL and discuss novel opportunities and therapeutic approaches that current knowledge may open for future treatment of T-ALL patients.

The perception and response of T cells to a changing environment are based on the law of initial value

αβ T cells are critical components of the adaptive immune system and are capable of inducing sterilizing immunity after pathogen infection and eliminating transformed tumor cells. The development and function of T cells are controlled through the T cell antigen receptor, which recognizes peptides displayed on major histocompatibility complex (MHC) molecules. Here, we review how T cells generate the ability to recognize self-peptide-bound MHC molecules and use signals derived from these interactions to instruct cellular development, activation thresholds, and functional specialization in the steady state and during immune responses. We argue that the basic tenants of T cell development and function follow Weber-Fetcher's law of just noticeable differences and Wilder's law of initial value. Together, these laws argue that the ability of a system to respond and the quality of that response are scalable to the basal state of that system. Manifestation of these laws in T cells generates clone-specific activation thresholds that are based on perceivable differences between homeostasis and pathogen encounter (self versus nonself discrimination), as well as poised states for subsequent differentiation into specific effector cell lineages.

Zinc finger protein Zfp335 controls early T cell development and survival through β-selection-dependent and -independent mechanisms

T-cell development in the thymus undergoes the process of differentiation, selective proliferation, and survival from CD4⁻CD8⁻ double negative (DN) stage to CD4⁺CD8⁺ double positive (DP) stage prior to the formation of CD4⁺ helper and CD8⁺ cytolytic T cells ready for circulation. Each developmental stage is tightly regulated by sequentially operating molecular networks, of which only limited numbers of transcription regulators have been deciphered. Here, we identified Zfp335 transcription factor as a new player in the regulatory network controlling thymocyte development in mice. We demonstrate that Zfp335 intrinsically controls DN to DP transition, as T-cell-specific deficiency in Zfp335 leads to a substantial accumulation of DN3 along with reduction of DP, CD4⁺, and CD8⁺ thymocytes. This developmental blockade at DN stage results from the impaired intracellular TCRβ (iTCRβ) expression as well as increased susceptibility to apoptosis in thymocytes. Transcriptomic and ChIP-seq analyses revealed a direct regulation of transcription factors Bcl6 and Rorc by Zfp335. Importantly, enhanced expression of TCRβ and Bcl6/Rorc restores the developmental defect during DN3 to DN4 transition and improves thymocytes survival, respectively. These findings identify a critical role of Zfp335 in controlling T-cell development by maintaining iTCRβ expression-mediated β-selection and independently activating cell survival signaling.

Efficient Generation of iPSC-Derived Hematoendothelial Progenitors and Specification Toward T cell Lineage

One of the major obstacles for adoptive cell transfer (ACT) of T cells is the loss of effector function and proliferative ability of isolated antigen-specific T cells after prolonged ex vivo expansion. To overcome this issue, induced pluripotent stem cells (iPSCs), which have unlimited proliferation and differentiation potential, can be used to generate a large number of antigen-specific T cells. Here, we describe an efficient differentiation protocol for the generation of cytotoxic CD8⁺ T cells from human T cell-derived iPSCs (T-iPSCs). The protocol consists of three main steps including differentiation of T-iPSCs toward hematoendothelial progenitors (HEPs), co-culture of HEPs with OP9-DL1 cells, and stimulation of T cell receptor (TCR) signaling to obtain CD8 single-positive (SP) T cells. This culture system is simple and efficient; therefore, will offer a powerful tool for studying T cell development and applications in adoptive immunotherapy.

T-Cell Immunodeficiencies With Congenital Alterations of Thymic Development: Genes Implicated and Differential Immunological and Clinical Features

Combined Immunodeficiencies (CID) are rare congenital disorders characterized by defective T-cell development that may be associated with B- and NK-cell deficiency. They are usually due to alterations in genes expressed in hematopoietic precursors but in few cases, they are caused by impaired thymic development. Athymia was classically associated with DiGeorge Syndrome due to TBX1 gene haploinsufficiency. Other genes, implicated in thymic organogenesis include FOXN1, associated with Nude SCID syndrome, PAX1, associated with Otofaciocervical Syndrome type 2, and CHD7, one of the genes implicated in CHARGE syndrome. More recently, chromosome 2p11.2 microdeletion, causing FOXI3 haploinsufficiency, has been identified in 5 families with impaired thymus development. In this review, we will summarize the main genetic, clinical, and immunological features related to the abovementioned gene mutations. We will also focus on different therapeutic approaches to treat SCID in these patients.

Recent insights of T cell receptor-mediated signaling pathways for T cell activation and development

T cell activation requires extracellular stimulatory signals that are mainly mediated by T cell receptor (TCR) complexes. The TCR recognizes antigens on major histocompatibility complex molecules with the cooperation of CD4 or CD8 coreceptors. After recognition, TCR-induced signaling cascades that propagate signals via various molecules and second messengers are induced. Consequently, many features of T cell-mediated immune responses are determined by these intracellular signaling cascades. Furthermore, differences in the magnitude of TCR signaling direct T cells toward distinct effector linages. Therefore, stringent regulation of T cell activation is crucial for T cell homeostasis and proper immune responses. Dysregulation of TCR signaling can result in anergy or autoimmunity. In this review, we summarize current knowledge on the pathways that govern how the TCR complex transmits signals into cells and the roles of effector molecules that are involved in these pathways.

CD4 Helper and CD8 Cytotoxic T Cell Differentiation

A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4⁺ helper and CD8⁺ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively. Together with increasing knowledge of epigenetic regulators, these findings have advanced our understanding of the transcription factor network regulating the CD4/CD8 dichotomy. It has also become apparent that CD4⁺ T cells retain developmental plasticity, allowing them to acquire cytotoxic activity in the periphery. Despite such advances, further studies are necessary to identify the molecular links between TCR signaling and the nuclear machinery regulating expression of ThPOK and Runx3.

Long noncoding RNA Malat1 is not essential for T cell development and response to LCMV infection

Long noncoding RNAs (lncRNAs) are emerging as critical mediators of various biological processes in the immune system. The current data showed that the lncRNA Malat1 is highly expressed in T cell subsets, but the function of Malat1 in T cell remains unclear. In this study, we detected the T cell development and both CD8⁺ and CD4⁺ T cell response to LCMV infection using Malat1^-/- mice model. To our surprise, there were no significant defects in thymocytes at different developmental stages and the peripheral T cell pool with ablation of Malat1. During LCMV infection, Malat1^-/- mice exhibited normal effector and memory CD8⁺ T cells as well as T_FH cells differentiation. Our results indicated that Malat1 is not essential for T cell development and T cell-mediated antiviral response though it expresses at very high level in different T cell populations.

Transcription factors and target genes of pre-TCR signaling

Almost 30 years ago pioneering work by the laboratories of Harald von Boehmer and Susumo Tonegawa provided the first indications that developing thymocytes could assemble a functional TCRβ chain-containing receptor complex, the pre-TCR, before TCRα expression. The discovery and study of the pre-TCR complex revealed paradigms of signaling pathways in control of cell survival and proliferation, and culminated in the recognition of the multifunctional nature of this receptor. As a receptor integrated in a dynamic developmental process, the pre-TCR must be viewed not only in the light of the biological outcomes it promotes, but also in context with those molecular processes that drive its expression in thymocytes. This review article focuses on transcription factors and target genes activated by the pre-TCR to drive its different outcomes.

Pre-TCRα supports CD3-dependent reactivation and expansion of TCRα-deficient primary human T-cells

Chimeric antigen receptor technology offers a highly effective means for increasing the anti-tumor effects of autologous adoptive T-cell immunotherapy, and could be made widely available if adapted to the use of allogeneic T-cells. Although gene-editing technology can be used to remove the alloreactive potential of third party T-cells through destruction of either the α or β T-cell receptor (TCR) subunit genes, this approach results in the associated loss of surface expression of the CD3 complex. This is nonetheless problematic as it results in the lack of an important trophic signal normally mediated by the CD3 complex at the cell surface, potentially compromising T-cell survival in vivo, and eliminating the potential to expand TCR-knockout cells using stimulatory anti-CD3 antibodies. Here, we show that pre-TCRα, a TCRα surrogate that pairs with TCRβ chains to signal proper TCRβ folding during T-cell development, can be expressed in TCRα knockout mature T-cells to support CD3 expression at the cell surface. Cells expressing pre-TCR/CD3 complexes can be activated and expanded using standard CD3/CD28 T-cell activation protocols. Thus, heterologous expression of pre-TCRα represents a promising technology for use in the manufacturing of TCR-deficient T-cells for adoptive immunotherapy applications.

Cell competition is a tumour suppressor mechanism in the thymus

Cell competition is an emerging principle underlying selection for cellular fitness during development and disease. Competition may be relevant for cancer, but an experimental link between defects in competition and tumorigenesis is elusive. In the thymus, T lymphocytes develop from precursors that are constantly replaced by bone-marrow-derived progenitors. Here we show that in mice this turnover is regulated by natural cell competition between 'young' bone-marrow-derived and 'old' thymus-resident progenitors that, although genetically identical, execute differential gene expression programs. Disruption of cell competition leads to progenitor self-renewal, upregulation of Hmga1, transformation, and T-cell acute lymphoblastic leukaemia (T-ALL) resembling the human disease in pathology, genomic lesions, leukaemia-associated transcripts, and activating mutations in Notch1. Hence, cell competition is a tumour suppressor mechanism in the thymus. Failure to select fit progenitors through cell competition may explain leukaemia in X-linked severe combined immune deficiency patients who showed thymus-autonomous T-cell development after therapy with gene-corrected autologous progenitors.

TopBP1 deficiency impairs V(D)J recombination during lymphocyte development

TopBP1 was initially identified as a topoisomerase II-β-binding protein and it plays roles in DNA replication and repair. We found that TopBP1 is expressed at high levels in lymphoid tissues and is essential for early lymphocyte development. Specific abrogation of TopBP1 expression resulted in transitional blocks during early lymphocyte development. These defects were, in major part, due to aberrant V(D)J rearrangements in pro-B cells, double-negative and double-positive thymocytes. We also show that TopBP1 was located at sites of V(D)J rearrangement. In TopBP1-deficient cells, γ-H2AX foci were found to be increased. In addition, greater amount of γ-H2AX product was precipitated from the regions where TopBP1 was localized than from controls, indicating that TopBP1 deficiency results in inefficient DNA double-strand break repair. The developmental defects were rescued by introducing functional TCR αβ transgenes. Our data demonstrate a novel role for TopBP1 as a crucial factor in V(D)J rearrangement during the development of B, T and iNKT cells.

Visualization and quantification of monoallelic TCRα gene rearrangement in αβ T cells

T-cell receptor α (TCRα) chain rearrangement is not constrained by allelic exclusion and thus αβ T cells frequently have rearranged both alleles of this locus. Thereby, stepwise secondary rearrangements of both TCRα loci further increase the odds for generation of an α-chain that can be positively selected in combination with a pre-existing TCRβ chain. Previous studies estimated that approximately 2-12% of murine and human αβ T cells still carry one TCRα locus in germline configuration, which must comprise a partially or even fully rearranged TCRδ locus. However, these estimates are based on a relatively small amount of individual αβ T-cell clones and αβ T-cell hybridomas analyzed to date. To address this issue more accurately, we made use of a mouse model, in which a fluorescent reporter protein is introduced into the constant region of the TCRδ locus. In this TcrdH2BeGFP system, fluorescence emanating from retained TCRδ loci enabled us to quantify monoallelically rearranged αβ T cells on a single-cell basis. Via fluorescence-activated cell sorting analysis, we determined the frequency of monoallelic TCRα rearrangements to be 1.7% in both peripheral CD4(+) and CD8(+) αβ T cells. Furthermore, we found a skewed 5' Jα gene utilization of the rearranged TCRα allele in T cells with monoallelic TCRα rearrangements. This is in line with previous descriptions of a tight interallelic positional coincidence of Jα gene segments used on both TCRα alleles. Finally, analysis of T cells from transgenic mice harboring only one functional TCRα locus implied the existence of very rare unusual translocation or episomal reintegration events of formerly excised TCRδ loci.

NFAT5 induction by the pre-T-cell receptor serves as a selective survival signal in T-lymphocyte development

The Rel-like transcription factors nuclear factor kappa B (NF-κB) and the calcineurin-dependent nuclear factor of activated T cells (NFATc) control specific points of thymocyte maturation. Thymocytes also express a distinct member of the Rel family, the calcineurin-independent, osmostress response regulator NFAT5. Here we show that IKKβ regulates the expression of NFAT5 in thymocytes, which in turn contributes to the survival of T-cell receptor αβ thymocytes and the transition from the β-selection checkpoint to the double-positive stage in an osmostress-independent manner. NFAT5-deficient thymocytes had normal expression and proximal signaling of the pre-T-cell receptor but exhibited a partial defect in β-chain allelic exclusion and increased apoptosis. Further analysis showed that NFAT5 regulated the expression of the prosurvival factors A1 and Bcl2 and attenuated the proapoptotic p53/Noxa axis. These findings position NFAT5 as a target of the IKKβ/NF-κB pathway in thymocytes and as a downstream effector of the prosurvival role of the pre-T-cell receptor.

Genetic basis of altered central tolerance and autoimmune diseases: a lesson from AIRE mutations

The thymus is a specialized organ that provides an inductive environment for the development of T cells from multipotent hematopoietic progenitors. Self-nonself discrimination plays a key role in inducing a productive immunity and in preventing autoimmune reactions. Tolerance represents a state of immunologic nonresponsiveness in the presence of a particular antigen. The immune system becomes tolerant to self-antigens through the two main processes, central and peripheral tolerance. Central tolerance takes place within the thymus and represents the mechanism by which T cells binding with high avidity self-antigens, which are potentially autoreactive, are eliminated through so-called negative selection. This process is mostly mediated by medullary thymic epithelia cells (mTECs) and medullary dendritic cells (DCs). A remarkable event in the process is the expression of tissue-specific antigens (TSA) by mTECs driven by the transcription factor autoimmune regulator (AIRE). Mutations in this gene result in autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED), a rare autosomal recessive disease (OMIM 240300). Thus far, this syndrome is the paradigm of a genetically determined failure of central tolerance and autoimmunty. Patients with APECED have a variable pattern of autoimmune reactions, involving different endocrine and nonendocrine organs. However, although APECED is a monogenic disorder, it is characterized by a wide variability of the clinical expression, thus implying a further role for disease-modifying genes and environmental factors in the pathogenesis. Studies on this polyreactive autoimmune syndrome contributed enormously to unraveling several issues of the molecular basis of autoimmunity. This review focuses on the developmental, functional, and molecular events governing central tolerance and on the clinical implication of its failure.

Synergistic effects of interleukin-7 and pre-T cell receptor signaling in human T cell development

The role of IL-7 in pre-T cell receptor (TCR) signaling during human T cell development is poorly understood. To study this, we engineered Molt3, a T cell progenitor T-acute lymphoblastic leukemia cell line, using lentiviral IL-7 receptor α (IL-7Rα) to serve as a model system. IL-7 promoted pre-TCR activation in IL-7Rα(hi) Molt3 as illustrated by CD25 up-regulation after anti-CD3 stimulation. Anti-CD3 treatment activated Akt and Erk1/2 signaling pathways as proven using specific inhibitors, and IL-7 further enhanced both signaling pathways. The close association of IL-7Rα with CD3ζ in the pre-TCR complex was illustrated through live imaging confocal fluorescence microscopy. These results demonstrate a direct and cooperative role of IL-7 in pre-TCR signaling.

Orais and STIMs: physiological mechanisms and disease

The stromal interaction molecules STIM1 and STIM2 are Ca²⁺ sensors, mostly located in the endoplasmic reticulum, that detect changes in the intraluminal Ca²⁺ concentration and communicate this information to plasma membrane store-operated channels, including members of the Orai family, thus mediating store-operated Ca²⁺ entry (SOCE). Orai and STIM proteins are almost ubiquitously expressed in human cells, where SOCE has been reported to play a relevant functional role. The phenotype of patients bearing mutations in STIM and Orai proteins, together with models of STIM or Orai deficiency in mice, as well as other organisms such as Drosophila melanogaster, have provided compelling evidence on the relevant role of these proteins in cellular physiology and pathology. Orai1-deficient patients suffer from severe immunodeficiency, congenital myopathy, chronic pulmonary disease, anhydrotic ectodermal dysplasia and defective dental enamel calcification. STIM1-deficient patients showed similar abnormalities, as well as autoimmune disorders. This review summarizes the current evidence that identifies and explains diseases induced by disturbances in SOCE due to deficiencies or mutations in Orai and STIM proteins.

Purinergic P2X7 receptor drives T cell lineage choice and shapes peripheral γδ cells

TCR signal strength instructs αβ versus γδ lineage decision in immature T cells. Increased signal strength of γδTCR with respect to pre-TCR results in induction of the γδ differentiation program. Extracellular ATP evokes physiological responses through purinergic P2 receptors expressed in the plasma membrane of virtually all cell types. In peripheral T cells, ATP released upon TCR stimulation enhances MAPK activation through P2X receptors. We investigated whether extracellular ATP and P2X receptors signaling tuned TCR signaling at the αβ/γδ lineage bifurcation checkpoint. We show that P2X7 expression was selectively increased in immature γδ(+)CD25(+) cells. These cells were much more competent to release ATP than pre-TCR-expressing cells following TCR stimulation and Ca(2+) influx. Genetic ablation as well as pharmacological antagonism of P2X7 resulted in impaired ERK phosphorylation, reduction of early growth response (Egr) transcripts induction, and diversion of γδTCR-expressing thymocytes toward the αβ lineage fate. The impairment of the ERK-Egr-inhibitor of differentiation 3 (Id3) signaling pathway in γδ cells from p2rx7(-/-) mice resulted in increased representation of the Id3-independent NK1.1-expressing γδ T cell subset in the periphery. Our results indicate that ATP release and P2X7 signaling upon γδTCR expression in immature thymocytes constitutes an important costimulus in T cell lineage choice through the ERK-Egr-Id3 signaling pathway and contributes to shaping the peripheral γδ T cell compartment.

From murine to human nude/SCID: the thymus, T-cell development and the missing link

Primary immunodeficiencies (PIDs) are disorders of the immune system, which lead to increased susceptibility to infections. T-cell defects, which may affect T-cell development/function, are approximately 11% of reported PIDs. The pathogenic mechanisms are related to molecular alterations not only of genes selectively expressed in hematopoietic cells but also of the stromal component of the thymus that represents the primary lymphoid organ for T-cell differentiation. With this regard, the prototype of athymic disorders due to abnormal stroma is the Nude/SCID syndrome, first described in mice in 1966. In man, the DiGeorge Syndrome (DGS) has long been considered the human prototype of a severe T-cell differentiation defect. More recently, the human equivalent of the murine Nude/SCID has been described, contributing to unravel important issues of the T-cell ontogeny in humans. Both mice and human diseases are due to alterations of the FOXN1, a developmentally regulated transcription factor selectively expressed in skin and thymic epithelia.

Notch1 and IL-7 receptor signalling in early T-cell development and leukaemia

Notch receptors are master regulators of many aspects of development and tissue renewal in metazoans. Notch1 activation is essential for T-cell specification of bone marrow-derived multipotent progenitors that seed the thymus, and for proliferation and further progression of early thymocytes along the T-cell lineage. Deregulated activation of Notch1 significantly contributes to the generation of T-cell acute lymphoblastic leukaemia (T-ALL). In addition to Notch1 signals, survival and proliferation signals provided by the IL-7 receptor (IL-7R) are also required during thymopoiesis. Our understanding of the molecular mechanisms controlling stage-specific survival and proliferation signals provided by Notch1 and IL-7R has recently been improved by the discovery that the IL-7R is a transcriptional target of Notch1. Thus, Notch1 controls T-cell development, in part by regulating the stage- and lineage-specific expression of IL-7R. The finding that induction of IL-7R expression downstream of Notch1 also occurs in T-ALL highlights the important contribution that deregulated IL-7R expression and function may have in this pathology. Confirming this notion, oncogenic IL7R gain-of-function mutations have recently been identified in childhood T-ALL. Here we discuss the fundamental role of Notch1 and IL-7R signalling pathways in physiological and pathological T-cell development in mice and men, highlighting their close molecular underpinnings.

An emerging role of RNA-binding proteins as multifunctional regulators of lymphocyte development and function

Sequence-specific RNA-binding proteins (RBP) and the regulation of RNA decay have long been recognized as important regulators of the inflammatory response. RBP influence gene expression throughout the lifespan of the mRNA by regulating splicing, polyadenylation, cellular localization, translation, and decay. Increasing evidence now indicates that these proteins, together with the RNA decay machinery that they recruit, also regulate the development and activation of lymphocytes. The activity of RBP is regulated by the same signal transduction pathways that govern lymphocyte development and differentiation in response to antigen and cytokine receptor engagement. Roles for these proteins in regulating the diverse functions of lymphocytes are becoming increasingly apparent.

Miz-1 is required to coordinate the expression of TCRbeta and p53 effector genes at the pre-TCR "beta-selection" checkpoint

Miz-1 is a Broad-complex, Tramtrack and Bric-à-brac/pox virus zinc finger domain (BTB/POZ)-containing protein expressed in lymphoid precursors that can activate or repress transcription. We report in this article that mice expressing a nonfunctional Miz-1 protein lacking the BTB/POZ domain (Miz-1(ΔPOZ)) have a severe differentiation block at the pre-T cell "β-selection" checkpoint, evident by a drastic reduction of CD4(-)CD8(-) double-negative-3 (DN3) and DN4 cell numbers. T cell-specific genes including Rag-1, Rag-2, CD3ε, pTα, and TCRβ are expressed in Miz-1-deficient cells and V(D)J recombination is intact, but few DN3/DN4 cells express a surface pre-TCR. Miz-1-deficient DN3 cells are highly apoptotic and do not divide, which is consistent with enhanced expression of p53 target genes such as Cdkn1a, PUMA, and Noxa. However, neither coexpression of the antiapoptotic protein Bcl2 nor the deletion of p21(CIP1) nor the combination of both relieved Miz-1-deficient DN3/DN4 cells from their differentiation block. Only the coexpression of rearranged TCRαβ and Bcl2 fully rescued Miz-1-deficient DN3/DN4 cell numbers and enabled them to differentiate into DN4TCRβ(+) and double-positive cells. We propose that Miz-1 is a critical factor for the β-selection checkpoint and is required for both the regulation of p53 target genes and proper expression of the pre-TCR to support the proliferative burst of DN3 cells during T cell development.

The golden anniversary of the thymus

The immunological function of the thymus was first documented 50 years ago by using neonatally thymectomized mice, while studying its role in virus-induced leukaemia. Since then, an enormous wealth of reports has helped to define the importance of this primary lymphoid organ. In this article, I summarize the key advances that have led to our current knowledge of the functions of the thymus and its T cells in immunity.

Appl1 is dispensable for Akt signaling in vivo and mouse T-cell development

Appl1 (Adaptor protein containing pleckstrin homology [PH], phosphotyrosine binding [PTB], and Leucine zipper motifs) is an adaptor that participates in cell signaling by interacting with various signaling molecules including Akt, PI3-kinase (PI3K), Rab5, adiponectin receptor, and TrkA. By using RNA knockdown technology, Appl1 has been implicated in zebrafish development and murine glucose metabolism. To investigate the unambiguous role of Appl1 in vivo, we generated a knockout mouse in which exon1 of the Appl1 gene was disrupted using gene trap methodology. Homozygous Appl1 knockout mice with ubiquitous loss of Appl1 protein expression were viable, grossly normal, and born at expected Mendelian ratios. Moreover, activation of Akt and the downstream effecter Gsk3β was unaffected in vivo. We next performed glucose and insulin tolerance tests and found that glucose metabolism is normal in Appl1-null mice. We also tested the effect of Appl1 loss on Akt signaling in T cells, because we discovered that Appl1 strongly interacts with the p110β subunit of PI3K in T lymphocytes. However, such interaction was found to be dispensable for Akt signaling in thymic T cells and T-cell development. Moreover, Appl1 loss did not affect DNA synthesis in cultured thymocytes, although loss of Appl1 was associated with a slight increase in ConA-stimulated splenic T-cell viability/proliferation. Collectively, our findings indicate that Appl1 is dispensable for Akt signaling in vivo and T-cell differentiation.

Finding their niche: chemokines directing cell migration in the thymus

T lymphocytes are generated throughout life, arising from bone marrow-derived progenitors that complete an essential developmental process in the thymus. Thymic T cell education leads to the generation of a self-restricted and largely self-tolerant peripheral T-cell pool and is facilitated by interactions with thymic stromal cells residing in distinct supportive niches. The signals governing thymocyte precursor migration into the thymus, directing thymocyte navigation through thymic microenvironments and mature T-cell egress into circulation were, until recently, largely unknown, but presumed to be mediated to a large extent by chemokine signalling. Recent studies have now uncovered various specific functions for members of the chemokine superfamily in the thymus. These studies have not only revealed distinct but also in some cases overlapping roles for several chemokine family members in various thymocyte migration events and have also shown that homing and positioning of other cells in the thymus, such as dendritic cells and natural killer T cells is also chemokine-dependent. Here, we discuss current understanding of the role of chemokines in the thymus and highlight key future avenues for investigation in this field.

Notch dimerization is required for leukemogenesis and T-cell development

Notch signaling regulates myriad cellular functions by activating transcription, yet how Notch selectively activates different transcriptional targets is poorly understood. The core Notch transcriptional activation complex can bind DNA as a monomer, but it can also dimerize on DNA-binding sites that are properly oriented and spaced. However, the significance of Notch dimerization is unknown. Here, we show that dimeric Notch transcriptional complexes are required for T-cell maturation and leukemic transformation but are dispensable for T-cell fate specification from a multipotential precursor. The varying requirements for Notch dimerization result from the differential sensitivity of specific Notch target genes. In particular, c-Myc and pre-T-cell antigen receptor α (Ptcra) are dimerization-dependent targets, whereas Hey1 and CD25 are not. These findings identify functionally important differences in the responsiveness among Notch target genes attributable to the formation of higher-order complexes. Consequently, it may be possible to develop a new class of Notch inhibitors that selectively block outcomes that depend on Notch dimerization (e.g., leukemogenesis).

Developmental progression of fetal HEB(-/-) precursors to the pre-T-cell stage is restored by HEBAlt

Gene knockout studies have shown that the E-protein transcription factor HEB is required for normal thymocyte development. We have identified a unique form of HEB, called HEBAlt, which is expressed only during the early stages of T-cell development, whereas HEBCan is expressed throughout T-cell development. Here, we show that HEB(-/-) precursors are inhibited at the β-selection checkpoint of T-cell development due to impaired expression of pTα and function of CD3ε, both of which are necessary for pre-TCR signaling. Transgenic expression of HEBAlt in HEB(-/-) precursors, however, upregulated pTα and allowed development to CD4(+) CD8(+) stage in fetal thymocytes. Moreover, HEBAlt did overcome the CD3ε signaling defect in HEB(-/-) Rag-1(-/-) thymocytes. The HEBAlt transgene did not permit Rag-1(-/-) precursors to bypass β-selection, indicating that it was not acting as a dominant negative inhibitor of other E-proteins. Therefore, our results provide the first mechanistic evidence that HEBAlt plays a critical role in early T-cell development and show that it can collaborate with fetal thymic stromal elements to create a regulatory environment that supports T-cell development past the β-selection checkpoint.

gammadelta and alphabeta T cell lineage choice: resolution by a stronger sense of being

A common bipotent thymocyte precursor gives rise to both lineages of T cells, alphabeta and gammadelta. However, the cell intrinsic and extrinsic factors that influence alphabeta- versus gammadelta-lineage bifurcation remain controversial. gammadelta T cells play a unique and vital role in host defense, from maintaining integrity at epithelial and mucosal barriers to their newly defined role as an important innate source of interleukin-17. Although a T cell receptor (TCR)-independent fate choice may take place, emerging data supports a model in which the differential signaling capacity of alphabeta and gammadeltaTCRs play an instructional role in specifying lineage fate, with strength of signal measured by the amount of ERK/MAPK pathway activation. Here we discuss how the interplay between intrinsic TCR signals and cell extrinsic signals provided by Notch and TCR ligands help to assign and support a final lineage fate decision.

Loss of poly(ADP-ribose) polymerase-2 leads to rapid development of spontaneous T-cell lymphomas in p53-deficient mice

Poly(ADP-ribose) polymerase-2 (Parp-2) belongs to a family of enzymes that catalyse poly(ADP-ribosyl)ation of proteins. Parp-2 deficiency in mice (Parp-2(-/-)) results in reduced thymic cellularity associated with increased apoptosis in thymocytes, defining Parp-2 as an important mediator of T-cell survival during thymopoiesis. To determine whether there is a link between Parp-2 and the p53 DNA-damage-dependent apoptotic response, we have generated Parp-2/p53-double-null mutant mice. We found that p53(-/-) backgrounds completely restored the survival and development of Parp-2(-/-) thymocytes. However, Parp-2-deficient thymocytes accumulated high levels of DNA double-strand breaks (DSB), independently of the p53 status, in line with a function of Parp-2 as a caretaker promoting genomic stability during thymocytes development. Although Parp-2(-/-) mice do not have spontaneous tumours, Parp-2 deficiency accelerated spontaneous tumour development in p53-null mice, mainly T-cell lymphomas. These data suggest a synergistic interaction between Parp-2 and p53 in tumour suppression through the role of Parp-2 in DNA-damage response and genome integrity surveillance, and point to the potential importance of examining human tumours for the status of both genes.

Energy addiction and lymphocyte differentiation: a new role for the liver kinase B1 kinase

Lymphocyte development is a process in which proliferation is coupled to differentiation. In order to undergo efficient proliferation, lymphocytes must coordinate the entry into cell cycle with increased metabolism. The signaling pathways, like those downstream of antigen and cytokine receptors, and specific regulators that directly control cell metabolism are only beginning to be defined. A study in this issue of the European Journal of Immunology, demonstrates that the liver kinase B1 (LKB1) is a regulator of cellular metabolism. Deficiency in LKB1 results in a block in T-cell differentiation, increased apoptosis, as well as impaired survival of mature T cells. This study highlights the importance of LKB1 in T-cell development and function, but as discussed in this Commentary, a number of intriguing questions concerning the regulation and additional functions of LKB1 remain.

Checkpoints in lymphocyte development and autoimmune disease

Antigen receptor-controlled checkpoints in B lymphocyte development are crucial for the prevention of autoimmune diseases such as systemic lupus erythematosus. Checkpoints at the stage of pre-B cell receptor (pre-BCR) and BCR expression can eliminate certain autoreactive BCRs either by deletion of or anergy induction in cells expressing autoreactive BCRs or by receptor editing. For T cells, the picture is more complex because there are regulatory T (T(reg)) cells that mediate dominant tolerance, which differs from the recessive tolerance mediated by deletion and anergy. Negative selection of thymocytes may be as essential as T(reg) cell generation in preventing autoimmune diseases such as type 1 diabetes, but supporting evidence is scarce. Here we discuss several scenarios in which failures at developmental checkpoints result in autoimmunity.

A conserved CXXC motif in CD3epsilon is critical for T cell development and TCR signaling

Structural integrity of the extracellular membrane-proximal stalk region of CD3ε is required for efficient signaling by the T cell antigen receptor complex. The results in this article suggest that receptor aggregation may not be sufficient for a complete T cell receptor signal and that some type of direct allosteric signal may be involved.

Virtually all T cell development and functions depend on its antigen receptor. The T cell receptor (TCR) is a multi-protein complex, comprised of a ligand binding module and a signal transmission module. The signal transmission module includes proteins from CD3 family (CD3ε, CD3δ, CD3γ) as well as the ζ chain protein. The CD3 proteins have a short extracellular stalk connecting their Ig-like domains to their transmembrane regions. These stalks contain a highly evolutionarily conserved CXXC motif, whose function is unknown. To understand the function of these two conserved cysteines, we generated mice that lacked endogenous CD3ε but expressed a transgenic CD3ε molecule in which these cysteines were mutated to serines. Our results show that the mutated CD3ε could incorporate into the TCR complex and rescue surface TCR expression in CD3ε null mice. In the CD3ε mutant mice, all stages of T cell development and activation that are TCR-dependent were impaired, but not eliminated, including activation of mature naïve T cells with the MHCII presented superantigen, staphylococcal enterotoxin B, or with a strong TCR cross-linking antibody specific for either TCR-Cβ or CD3ε. These results argue against a simple aggregation model for TCR signaling and suggest that the stalks of the CD3 proteins may be critical in transmitting part of the activation signal directly through the membrane.

The T cells of the immune system have surface receptors that detect unique features (called antigens) of foreign invaders such as viruses, bacteria and toxins. An encounter between an antigen and the T cell receptor sets off a chain of events that activates the T cell to proliferate and thus call to action the various arms of the immune response that ultimately eliminate the invader. A set of proteins, called CD3, associates with the T cell receptor, spanning the cell membrane. Their function is to deliver a signal to the inside of T cell that its receptor has encountered antigen on the outside of the cell. Two general ideas have been proposed to explain how the CD3 proteins accomplish this: That the engagement of the T cell receptor outside the cell directly causes a change in conformation in the intracellular portion of the associated CD3 proteins that is recognized by the intracellular signaling machinery; and that engagement of the T cell receptor causes clustering of multiple receptor and CD3 proteins such that interactions among the cytoplasmic portions of the many CD3 proteins now attract other proteins to start the chain of intercellular signaling. These two ideas are not mutually exclusive. We show here that mutations in a highly conserved extracellular portion of one of the CD3 proteins can impair the transmission of the activation signal without preventing receptor clustering. These results suggest that direct transmission of a conformational change across the membrane may constitute part of the CD3-mediated activation signal.

ORAI1 and STIM1 deficiency in human and mice: roles of store-operated Ca2+ entry in the immune system and beyond

Store-operated Ca2+ entry (SOCE) is a mechanism used by many cells types including lymphocytes and other immune cells to increase intracellular Ca2+ concentrations to initiate signal transduction. Activation of immunoreceptors such as the T-cell receptor, B-cell receptor, or Fc receptors results in the release of Ca2+ ions from endoplasmic reticulum (ER) Ca2+ stores and subsequent activation of plasma membrane Ca2+ channels such as the well-characterized Ca2+ release-activated Ca2+ (CRAC) channel. Two genes have been identified that are essential for SOCE: ORAI1 as the pore-forming subunit of the CRAC channel in the plasma membrane and stromal interaction molecule-1 (STIM1) sensing the ER Ca2+ concentration and activating ORAI1-CRAC channels. Intense efforts in the past several years have focused on understanding the molecular mechanism of SOCE and the role it plays for cell functions in vitro and in vivo. A number of transgenic mouse models have been generated to investigate the role of ORAI1 and STIM1 in immunity. In addition, mutations in ORAI1 and STIM1 identified in immunodeficient patients provide valuable insight into the role of both genes and SOCE. This review focuses on the role of ORAI1 and STIM1 in vivo, discussing the phenotypes of ORAI1- and STIM1-deficient human patients and mice.

CSL-MAML-dependent Notch1 signaling controls T lineage-specific IL-7R{alpha} gene expression in early human thymopoiesis and leukemia

Notch1 activation is essential for T-lineage specification of lymphomyeloid progenitors seeding the thymus. Progression along the T cell lineage further requires cooperative signaling provided by the interleukin 7 receptor (IL-7R), but the molecular mechanisms responsible for the dynamic and lineage-specific regulation of IL-7R during thymopoiesis are unknown. We show that active Notch1 binds to a conserved CSL-binding site in the human IL7R gene promoter and critically regulates IL7R transcription and IL-7R α chain (IL-7Rα) expression via the CSL–MAML complex. Defective Notch1 signaling selectively impaired IL-7Rα expression in T-lineage cells, but not B-lineage cells, and resulted in a compromised expansion of early human developing thymocytes, which was rescued upon ectopic IL-7Rα expression. The pathological implications of these findings are demonstrated by the regulation of IL-7Rα expression downstream of Notch1 in T cell leukemias. Thus, Notch1 controls early T cell development, in part by regulating the stage- and lineage-specific expression of IL-7Rα.

Oncogenesis of T-ALL and nonmalignant consequences of overexpressing intracellular NOTCH1

Mutations resulting in overexpression of intracellular Notch1 (ICN1) are frequently observed in human T cell acute lymphoblastic leukemia (T-ALL). We have determined the consequences of ICN1 overexpression from retroviral vectors introduced into bone marrow cells. Early consequences are the generation of polyclonal nontumorigenic CD4(+)8(+) T cell receptor (TCR)-alphabeta(+) cells that do not qualify as tumor precursors despite the observation that they overexpress Notch 1 and c-Myc and degrade the tumor suppressor E2A by posttranslational modification. The first tumorigenic cells are detected among more immature CD4(-)8(+)TCR-alphabeta(-) cells that give rise to monoclonal tumors with a single, unique TCR-beta chain and diverse TCR-alpha chains, pinpointing malignant transformation to a stage after pre-TCR signaling and before completion of TCR-alpha rearrangement. In T-ALL, E2A deficiency is accompanied by further transcriptional up-regulation of c-Myc and concomitant dysregulation of the c-Myc-p53 axis at the transcriptional level. Even though the tumors consist of phenotypically heterogeneous cells, no evidence for tumor stem cells was found. As judged by array-based comparative genomic hybridization (array CGH) and spectral karyotype (SKY) analysis, none of the tumors arise because of genomic instability.

TM1 and TM2: two mutant alleles that are involved in the pre-TCR/TCR signaling

It has been shown that the transgene insertional mutations TM1 and TM2 constitute a genetic trait controlling thymocyte development. Here we conducted a detailed analysis of the impact of TM1 and TM2 double mutation on thymocyte development. We found that the hemizygous TM1 and TM2 double transgenic mice possessed much smaller thymi. Flow cytometric analysis revealed a severe blockage of T-cell development at the transition from DN3 to DN4 stage and pre-T-cell receptor (pre-TCR)/TCR signaling appeared to be impaired. We could not identify any known gene that was implicated in a similar function in the chromosomal regions 7E-F1 and 11B5-C, where TM1 and TM2 mutations were mapped to respectively. Thus, TM1 and TM2 mutations represent two novel alleles that define a genetic trait controlling DN3 thymocyte development, possibly through modulating the signals downstream of the pre-TCR.

Early growth response 1 and NF-ATc1 act in concert to promote thymocyte development beyond the beta-selection checkpoint

Development of immature T cell precursors beyond the beta-selection checkpoint is regulated by signals transduced by the pre-TCR complex. The pre-TCR-induced differentiation program is orchestrated by a network of transcription factors that serve to integrate this signaling information. Among these transcription factors are those of the early growth response (Egr) and NF-AT families. In this study, we demonstrate that Egr1 and NF-ATc1 act together to promote development of T cell precursors beyond the beta-selection checkpoint to the CD8 immature single-positive and CD4+ CD8+ double-positive stages. Moreover, we find that Egr1 and NF-AT cooperatively induce the expression of inhibitor of DNA binding 3 (Id3), a regulatory factor known to play an important role in positive selection of thymocytes, but not previously demonstrated to be required for beta-selection. Importantly, we show in this study that Id3 deficiency abrogates the ability of ectopically expressed Egr1 to promote traversal of the beta-selection checkpoint. Id3 is presumably essential for traversal of the beta-selection checkpoint in this context because of the inability of other inhibitor of DNA binding family members to compensate, since transgenic Egr1 does not induce expression of inhibitor of DNA binding 1 (Id1) or 2 (Id2). Taken together, these data demonstrate that Id3 is a cooperatively induced target that is important for Egr-mediated promotion of development beyond the beta-selection checkpoint. Moreover, these data indicate that the ERK and calcium signaling pathways may converge during beta-selection through the concerted action of Egr1 and NF-ATc1, respectively.