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Thymic negative selection of the T cell receptor (TCR) repertoire is essential for establishing self-tolerance and acquired allograft tolerance following organ transplantation. However, it is unclear whether and how peripheral clonal deletion of alloreactive T cells induces transplantation tolerance. Here, we establish that programmed cell death protein 1 (PD-1) is a hallmark of alloreactive T cells and is associated with clonal expansion after alloantigen encounter. Moreover, we found that diphtheria toxin receptor (DTR)–mediated ablation of PD-1+ cells reshaped the TCR repertoire through peripheral clonal deletion of alloreactive T cells and promoted tolerance in mouse transplantation models. In addition, by using PD-1–specific depleting antibodies, we found that antibody-mediated depletion of PD-1+ cells prevented heart transplant rejection and the development of experimental autoimmune encephalomyelitis (EAE) in humanized PD-1 mice. Thus, these data suggest that PD-1 is an attractive target for peripheral clonal deletion and induction of immune tolerance. Editor's summary: Although solid organ transplantation is often the best therapy after irreversible organ damage, graft rejection remains a major limitation to long-term success. Using mouse models of MHC-mismatched organ transplantation, Cui et al. found that programmed cell death protein 1 (PD-1) is selectively induced on alloreactive T cells during transplant rejection. Genetic or antibody-mediated ablation of PD-1+ cells eliminated donor-reactive T cells and prolonged heart allograft survival. Cui et al. also developed a depleting antibody targeting human PD-1 that prevented heart transplant rejection in humanized mice. These findings indicate that selective removal of PD-1+ cells is a promising approach for inducing organ transplant tolerance. —Claire Olingy [ABSTRACT FROM AUTHOR]

Mitochondrial antiviral signaling protein (MAVS)–mediated cytosolic RNA sensing plays a central role in tumor immunogenicity. However, the effects of host MAVS signaling on antitumor immunity remain unclear. Here, we demonstrate that the host MAVS pathway supports tumor growth and impairs antitumor immunity, whereas MAVS deficiency in dendritic cells (DCs) promotes tumor-reactive CD8+ T cell responses. Specifically, CD8+ T cell priming capacity was enhanced by MAVS ablation in a type I interferon–independent, but IL-12–dependent, manner. Mechanistically, loss of the RIG-I/MAVS cascade activated the noncanonical NF-κB pathway and in turn induced IL-12 production by DCs. MAVS-restrained IL-12 promoted cross-talk between CD8+ T cells and DCs, which was licensed by IFN-γ. Moreover, ablation of host MAVS sensitized tumors to immunotherapy and attenuated radiation resistance, thereby facilitating the maintenance of effector CD8+ T cells. These findings demonstrate that the host MAVS pathway acts as an immune regulator of DC-driven antitumor immunity and support the development of immunotherapies that antagonize MAVS signaling in DCs. Editor's summary: Intratumoral activation of innate immune sensing pathways generates a viral mimicry response that enhances tumor immunogenicity and can be leveraged for cancer immunotherapy. Cytosolic sensing of viral RNA by RIG-I–like receptors leads to activation of their adaptor protein mitochondrial antiviral signaling protein (MAVS) and production of type I interferon (IFN-I). Using genetically engineered mice, Wu et al. found that ablation of DC-intrinsic MAVS in tumor-bearing hosts enhanced antitumor immunity and slowed tumor growth. These effects were independent of IFN-I signaling and instead involved induction of IL-12 by MAVS-deficient DCs. Tumors in MAVS-deficient mice were more responsive to PD-L1 blockade and radiation therapy. These findings demonstrate that MAVS signaling in DCs restrains antitumor immunity, contrasting its tumor cell–intrinsic functions in promoting tumor immunogenicity. —Claire Olingy [ABSTRACT FROM AUTHOR]

Some hematological malignancies such as multiple myeloma are inherently resistant to immune-mediated antitumor responses, the cause of which remains unknown. Allogeneic bone marrow transplantation (alloBMT) is the only curative immunotherapy for hematological malignancies due to profound graft-versus-tumor (GVT) effects, but relapse remains the major cause of death. We developed murine models of alloBMT where the hematological malignancy is either sensitive [acute myeloid leukemia (AML)] or resistant (myeloma) to GVT effects. We found that CD8+ T cell exhaustion in bone marrow was primarily alloantigen-driven, with expression of inhibitory ligands present on myeloma but not AML. Because of this tumor-independent exhaustion signature, immune checkpoint inhibition (ICI) in myeloma exacerbated graft-versus-host disease (GVHD) without promoting GVT effects. Administration of post-transplant cyclophosphamide (PT-Cy) depleted donor T cells with an exhausted phenotype and spared T cells displaying a stem-like memory phenotype with chromatin accessibility present in cytokine signaling genes, including the interleukin-18 (IL-18) receptor. Whereas ICI with anti–PD-1 or anti–TIM-3 remained ineffective after PT-Cy, administration of a decoy-resistant IL-18 (DR-18) strongly enhanced GVT effects in both myeloma and leukemia models, without exacerbation of GVHD. We thus defined mechanisms of resistance to T cell–mediated antitumor effects after alloBMT and described an immunotherapy approach targeting stem-like memory T cells to enhance antitumor immunity. Flipping the switch on graft-versus-tumor effects: Allogeneic bone marrow transplantation (alloBMT) is a potentially curative treatment for hematological malignancies but is prone to tumor relapse due to escape from graft-versus-tumor (GVT) effects, especially when accompanied by systemic immunosuppression. Using a mouse model of myeloma resistant to treatment with alloBMT, Minnie et al. found that alloBMT-derived donor T cells become functionally exhausted from exposure to alloantigen rather than tumor antigen. Post-transplant cyclophosphamide depleted alloantigen-driven exhausted T cells, leaving a population bearing a stem cell memory–like gene signature. In leukemia-bearing mice receiving a haploidentical transplant, agonist immunotherapy with an engineered IL-18 resistant to endogenous inhibitors enhanced the antitumor immunity and improved survival. These results demonstrate that immunotherapy targeting residual T cell populations can improve the GVT response of alloBMT during systemic immunosuppression. [ABSTRACT FROM AUTHOR]

T cells become functionally exhausted in tumors, limiting T cell–based immunotherapies. Although several transcription factors regulating the exhausted T (Tex) cell differentiation are known, comparatively little is known about the regulators of Tex cell survival. Here, we reported that the regulator of G protein signaling 16 (Rgs-16) suppressed Tex cell survival in tumors. By performing lineage tracing using reporter mice in which mCherry marked Rgs16-expressing cells, we identified that Rgs16+CD8+ tumor-infiltrating lymphocytes (TILs) were terminally differentiated, expressed low levels of T cell factor 1 (Tcf1), and underwent apoptosis as early as 6 days after the onset of Rgs16 expression. Rgs16 deficiency inhibited CD8+ T cell apoptosis and promoted antitumor effector functions of CD8+ T cells. Furthermore, Rgs16 deficiency synergized with programmed cell death protein 1 (PD-1) blockade to enhance antitumor CD8+ T cell responses. Proteomics revealed that Rgs16 interacted with the scaffold protein IQGAP1, suppressed the recruitment of Ras and B-Raf, and inhibited Erk1 activation. Rgs16 deficiency enhanced antitumor CD8+ TIL survival in an Erk1-dependent manner. Loss of function of Erk1 decreased antitumor functions of Rgs16-deficient CD8+ T cells. RGS16 mRNA expression levels in CD8+ TILs of patients with melanoma negatively correlated with genes associated with T cell stemness, such as SELL, TCF7, and IL7R, and predicted low responses to PD-1 blockade. This study uncovers Rgs16 as an inhibitor of Tex cell survival in tumors and has implications for improving T cell–based immunotherapies. Rgs16 is exhausting: Many cancer therapies are limited by T cell exhaustion; thus, understanding the mechanisms by which T cells become exhausted in tumors is crucial for improving cancer therapies. Weisshaar et al. found that Rgs16, a regulator of G protein signaling, was linked to CD8+ T cell dysfunction and death in an Erk1-mediated manner in melanoma tumors. Knocking out Rgs16 rescued CD8+ T cell functionality and survival in tumors, leading to slower tumor growth and improving the efficacy of immune checkpoint blockade. Last, Rgs16 correlated to exhausted T cells and predicted poor responses to PD-1 blockade in patients with melanoma. Thus, Rgs16 regulates CD8+ T cell function in tumors and is a potential target to improve cancer therapies. [ABSTRACT FROM AUTHOR]

The response of naive CD8+ T cells to their cognate antigen involves rapid and broad changes to gene expression that are coupled with extensive chromatin remodeling, but the mechanisms governing these changes are not fully understood. Here, we investigated how these changes depend on the basic leucine zipper ATF-like transcription factor Batf, which is essential for the early phases of the process. Through genome scale profiling, we characterized the role of Batf in chromatin organization at several levels, including the accessibility of key regulatory regions, the expression of their nearby genes, and the interactions that these regions form with each other and with key transcription factors. We identified a core network of transcription factors that cooperated with Batf, including Irf4, Runx3, and T-bet, as indicated by their colocalization with Batf and their binding in regions whose accessibility, interactions, and expression of nearby genes depend on Batf. We demonstrated the synergistic activity of this network by overexpressing the different combinations of these genes in fibroblasts. Batf and Irf4, but not Batf alone, were sufficient to increase accessibility and transcription of key loci, normally associated with T cell function. Addition of Runx3 and T-bet further contributed to fine-tuning of these changes and was essential for establishing chromatin loops characteristic of T cells. These data provide a resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells and for investigating the interdependency between transcription factors and its effects on the epigenome and transcriptome of primary cells. [ABSTRACT FROM AUTHOR]

Immune checkpoint blockade has demonstrated success in treating cancer but can lead to immune-related adverse events (irAEs), illustrating the centrality of these pathways in tolerance. Here, we describe programmed cell death protein 1 (PD-1) control of T cell responses, focusing on its unique restraint of regulatory T cell function. We examine successes and limitations of checkpoint blockade immunotherapy and review clinical and mechanistic features of irAEs. Last, we discuss strategies to modulate PD-1 blockade to enhance antitumor immunity while limiting autoimmunity. [ABSTRACT FROM AUTHOR]

The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified antigen-reactive T cell enrichment assay, from 39 patients with COVID-19 and 10 healthy participants. Patients with COVID-19 were segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was "exhausted" or "non-exhausted." SARS-CoV-2–reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in patients with COVID-19 experiencing mild compared with severe illness. In contrast, SARS-CoV-2–reactive cells in the dominant nonexhausted subset from patients with severe disease showed enrichment of transcripts linked to costimulation, prosurvival NF-κB signaling, and antiapoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy participants displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2–reactive cells from both patients with COVID-19 and healthy controls nonexposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Tumor-infiltrating lymphocyte lessons: The presence of intratumoral CD8+ tumor-infiltrating lymphocytes (TILs) is associated with better outcomes for patients with non–small cell lung cancer (NSCLC). These TILs consist of multiple subpopulations, and Gueguen et al. use single-cell RNA and T cell receptor sequencing to examine the origins and functional organization of TILs in NSCLC. They identified two precursor CD8+ TIL subpopulations with memory-like gene signatures. One of these subpopulations is detected in peripheral blood, whereas the other population is detected in juxtatumor tissue. Both subsets differentiate through a similar transitional stage into terminal effector TILs, which appear to be actively cycling within the tumor. Together, these results better define the origins and differentiation of CD8+ TILs associated with NSCLC. Tumor-infiltrating lymphocytes (TILs), in general, and especially CD8+ TILs, represent a favorable prognostic factor in non–small cell lung cancer (NSCLC). The tissue origin, regenerative capacities, and differentiation pathways of TIL subpopulations remain poorly understood. Using a combination of single-cell RNA and T cell receptor (TCR) sequencing, we investigate the functional organization of TIL populations in primary NSCLC. We identify two CD8+ TIL subpopulations expressing memory-like gene modules: one is also present in blood (circulating precursors) and the other one in juxtatumor tissue (tissue-resident precursors). In tumors, these two precursor populations converge through a unique transitional state into terminally differentiated cells, often referred to as dysfunctional or exhausted. Differentiation is associated with TCR expansion, and transition from precursor to late-differentiated states correlates with intratumor T cell cycling. These results provide a coherent working model for TIL origin, ontogeny, and functional organization in primary NSCLC. [ABSTRACT FROM AUTHOR]

A path to innate lymphoid cells: Mature innate lymphoid cell (ILC) subsets develop from ILC progenitors that have differentiated from early hematopoietic progenitors, but the regulation of this process is not well understood. Liu et al. show that basic leucine zipper ATF-like transcription factor (Batf) is a critical regulator of ILC development. IL-7 induces Batf expression in α-lymphoid progenitors, and Batf activates transcription of the Nfil3 gene, which induces ILC hematopoiesis. The presence of Batf is needed for maintenance of early and late ILC bone marrow progenitors and peripheral homeostasis of ILC1, ILC2, ILC3, and NK cells. Batf deficiency is associated with ILC lymphopenia and defective ILC responses, including inflammation and inadequate protection against enteric bacteria. These findings define the critical role of Batf in ILC development. Early hematopoietic progenitors undergo sophisticated developmental processes to become committed innate lymphoid cell (ILC) progenitors and ultimately mature ILC subsets in the periphery. Basic leucine zipper ATF-like transcription factor (Batf) plays important roles in lymphocyte biology. We report here that Batf regulates the production of bone marrow ILC progenitors and maintenance of peripheral ILCs. The expression of Batf is induced during ILC development at the α-lymphoid progenitor stage in response to the cytokine IL-7. As a potential mechanism, up-regulated Batf binds and activates transcription of the Nfil3 gene to promote ILC hematopoiesis. Batf is necessary to maintain normal numbers of early and late ILC progenitors in the bone marrow and mature ILC1, ILC2, ILC3, and NK cells in most peripheral tissues. Batf deficiency causes ILC lymphopenia, leading to defective ILC responses to inflammatory cytokines and defective immunity to enteric bacterial infections. Thus, Batf plays critical roles in bone marrow hematopoiesis, peripheral homeostasis, and effector functions of ILCs. [ABSTRACT FROM AUTHOR]

The TOX profiles of T cells: Transcription factors TOX and TCF-1 have emerged as key drivers of exhaustion and stemness programs in CD8+ T cells. Using bulk and single-cell transcriptome analyses and flow cytometric analyses, Sekine et al. have generated a detailed map of TOX and TCF-1 expression in human CD8+ T cells. TOX is generally expressed by effector memory CD8+ T cells and is not restricted to exhausted T cells, whereas TCF-1 demarcates early-differentiated, memory CD8+ T cells. Using tetramers to examine the specificity of antigen-specific CD8+ T cells, they found that cytotoxic memory CD8+ T cells targeting both pathogenic and well-controlled chronic infections are more likely to express TOX. Their results propose that TOX-dependent transcriptional wiring is not restricted to exhausted CD8+ T cells. CD8+ T cell exhaustion is a hallmark of many cancers and chronic infections. In mice, T cell factor 1 (TCF-1) maintains exhausted CD8+ T cell responses, whereas thymocyte selection-associated HMG box (TOX) is required for the epigenetic remodeling and survival of exhausted CD8+ T cells. However, it has remained unclear to what extent these transcription factors play analogous roles in humans. In this study, we mapped the expression of TOX and TCF-1 as a function of differentiation and specificity in the human CD8+ T cell landscape. Here, we demonstrate that circulating TOX+ CD8+ T cells exist in most humans, but that TOX is not exclusively associated with exhaustion. Effector memory CD8+ T cells generally expressed TOX, whereas naive and early-differentiated memory CD8+ T cells generally expressed TCF-1. Cytolytic gene and protein expression signatures were also defined by the expression of TOX. In the context of a relentless immune challenge, exhausted HIV-specific CD8+ T cells commonly expressed TOX, often in clusters with various activation markers and inhibitory receptors, and expressed less TCF-1. However, polyfunctional memory CD8+ T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) also expressed TOX, either with or without TCF-1. A similar phenotype was observed among HIV-specific CD8+ T cells from individuals who maintained exceptional immune control of viral replication. Collectively, these data demonstrate that TOX is expressed by most circulating effector memory CD8+ T cell subsets and not exclusively linked to exhaustion. [ABSTRACT FROM AUTHOR]