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Combes, A. J.

Publications and source records attributed to Combes, A. J..

At least 19 recordsLinked to original sources

Spatial Orchestration of Skin Fibrosis by a CD8+ T cell-Myofibroblast Axis

Fibrosing skin diseases are highly morbid conditions with diverse clinical and histopathologic features. Prior work, primarily in systemic sclerosis (SSc), has yielded mixed data regarding the immune drivers of fibrosis, as well as the identity and spatial localization of pro-fibrotic fibroblast cell subsets. Here, we focus on morphea and eosinophilic fasciitis (EF), which cause more acutely inflammatory skin fibrosis. Using multimodal single-nucleus and spatial transcriptomics, we find that effector CD8+ T cells are highly enriched in fibrotic skin. These cells are particularly abundant in inflammatory tissue domains bordering fibrotic stroma, which are marked by expression of interferon-{gamma} stimulated genes. Inflammatory domains feature a loss of local homeostatic fibroblast populations and replacement with ADAM12-expressing inflammatory fibroblasts and myofibroblasts, which co-localize closely with CD8+ T cells. All subtypes of morphea featured similar patterns of CD8+ T-cell-associated fibro-inflammatory zonation and fibroblast transformation, suggesting that shared mechanisms can drive fibrosis across stromal compartments of skin. We apply these findings to a large publicly available scleroderma dataset and find that similar processes occur in SSc. Mechanistically, ablation of CD8+ T cells in mice ameliorates bleomycin-driven inflammation and fibrosis, as does fibroblast-intrinsic abrogation of IFN-{gamma} signaling. These data establish CD8+ T cell-driven fibrogenesis as a key feature of fibrosing skin diseases and raise the prospect of targeting CD8+ T cells in autoimmune fibrosis more broadly. One sentence summarySpatial profiling of morphea-spectrum diseases reveals CD8 T cells as key drivers of fibrosis through fibroblast IFN-{gamma} signaling.

immunology↗

Temporal AI model predicts drivers of cell state trajectories across human aging

Foundational AI models have recently shown promise for predicting the impact of perturbations on cell states. However, current models typically consider only one cell state at a time, limiting their ability to learn how cellular responses unfold over time, particularly across long trajectories such as diseases of aging. Here, we develop a temporal AI model, MaxToki, trained on nearly 1 trillion gene tokens including cell state trajectories across the human lifespan to generate cell states across long timelapses of human aging. MaxToki generalized to unseen trajectories through in-context learning and predicted novel age-modulating targets that were experimentally verified to influence age-related gene programs and functional decline in vivo. MaxToki represents a promising strategy for temporal modeling to accelerate the discovery of interventions for programming therapeutic cellular trajectories.

bioinformatics↗

Tumor Heterogeneity Induces Pro- and Anti-metastatic Myeloid Cell Phenotypes in Breast Cancer Lung Metastasis

Metastasis is a major cause of cancer-related mortality, yet targeting metastatic cells directly has been largely unsuccessful due to their plasticity and heterogeneity. Myeloid cells play diverse pro- and anti-metastatic functions and are an attractive alternative target for treating metastasis, but how tumor heterogeneity influences myeloid cell phenotypes during metastasis remains poorly understood. Here, we profiled myeloid cells from primary tumors and matched metastatic lungs of 12 heterogeneous and differentially metastatic patient-derived xenograft models of breast cancer. Comparative analysis of cell type abundances revealed distinct myeloid remodeling specific to primary tumors or metastatic lungs. Beyond compositional differences, we identified gene expression programs that were associated with metastatic burden, such as number or size of metastatic nodules, indicating distinct microenvironmental requirements for metastatic seeding and outgrowth. Examining these metastasis-associated programs using time-course datasets, we discovered an evolution from anti- to pro-metastatic monocyte phenotypes during metastatic progression. We further showed that this phenotypic shift was driven by an increase in two distinct myeloid-derived suppressor cell signatures, and a transcriptionally regulated impairment of monocyte differentiation leading to the depletion of non-classical monocytes. Our results comprehensively dissect the heterogeneity of myeloid cell phenotypes across primary tumor and metastatic sites, opening novel avenues for myeloid-targeting therapies specific to metastasis.

cancer biology↗

Congenital CMV infection drives oligoclonal expansion of cytotoxic γδ T cells from early fetal progenitors

Gamma delta T cells ({gamma}{delta} T cells) emerge early during human gestation and are uniquely equipped to protect the fetus and infant following in utero infection with viruses such as cytomegalovirus (CMV). Previous research showed that fetal {gamma}{delta} T cells in early gestation are transcriptionally pre-programmed for effector functions in the thymus. Infants with congenital CMV infection (cCMV) exhibit expansions of {gamma}{delta} T cells with CMV-reactive TCRs; however, the functional and transcriptional programming of these innate-like effector cells has not been characterized. Here, we analyzed cord blood mononuclear cells from cCMV+ and uninfected neonates in Uganda using flow cytometry and single-cell RNA and TCR sequencing. We find that {gamma}{delta} T cells in cCMV+ neonates are more differentiated, activated, cytotoxic, and proliferative. TCR repertoires of cCMV+ infants exhibit oligoclonal expansions with an enrichment of {gamma}{delta}TCRs that possess shorter CDR3 lengths and fewer N additions, which suggest they arise from early fetal progenitor cells. These expanded {gamma}{delta} T cell clonotypes in cCMV+ infants are more frequently public and exhibit cytotoxic transcriptional programming. These findings demonstrate that cCMV infection drives an oligoclonal expansion of highly cytotoxic effector {gamma}{delta} T cells with fetal-like TCR features, underscoring their specialized roles in early-life immunity.

immunology↗

TriLeukeVax: A CD80/IL-15/IL-15Rα Expressing Autologous AML Cell Vaccine Elicits Robust Anti-Leukemic Cytolytic Activity

Acute myeloid leukemia (AML) is the most common acute leukemia in adults and is associated with poor outcomes due to frequent relapse after remission induction. While hematopoietic stem cell transplantation (HSCT) can improve survival, many individuals, especially older patients, are ineligible. Prior immunotherapies have not reliably induced effective anti-leukemic immunity and have been associated with severe and unpredictable toxicities. Thus, there is a need for safe and effective therapies that reduce relapse and increase overall survival (OS). We have developed a universally applicable, patient-specific, lentivirally engineered autologous AML cell vaccine, TriLeukeVax (TLV), designed to stimulate leukemia-specific cytolytic immune responses in AML patients in remission. To generate TLV, AML cells are engineered to express the highly synergistic combination of the co-stimulatory protein CD80 and the IL-15/IL-15-receptor alpha (IL-15R) heterodimer. Prior proof-of-concept (POC) studies demonstrated eradication of disease in >80% of leukemic mice with serial administration of TLV. In the current studies, TLV was generated from 59/60 cryopreserved, diagnostic bone marrow-derived patient AML samples. Ex vivo priming of post-remission patient T-cells by ex vivo co-culture with autologous TLV stimulated robust proliferative and cytotoxic responses. In secondary co-cultures, T-cells previously primed by initial co-culture with TLV, showed greater clonal expansion and leukemia-specific cytolytic activity towards de novo autologous AML blasts than did control, unprimed T-cells. The enhanced anti-leukemic activity of TLV-primed T-cells against de novo AML confirms the potential for vaccine administration to effectively target minimal residual disease (MRD) persisting after chemotherapy and reduce relapse. Key PointsO_LITriLeukeVax induces proliferation, activation, and effective anti-leukemic cytolytic responses in remission T-cells. C_LIO_LIPrimed T-cells show polyclonal expansion and transcription profiles associated with proliferation, memory, and cytotoxicity. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/687000v2_ufig1.gif" ALT="Figure UFIG"> View larger version (38K): org.highwire.dtl.DTLVardef@5c1827org.highwire.dtl.DTLVardef@35b2e2org.highwire.dtl.DTLVardef@1732914org.highwire.dtl.DTLVardef@18df655_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual Abstract.C_FLOATNO TriLeukeVax (TLV) workflow and mechanism of action. Diagnostic AML patient bone marrow aspirates are collected, purified in Ficoll and cryopreserved. Samples are thawed and lentivirally transduced to produce TLV. Vaccination of AML patients in remission with TLV will stimulate the activation and expansion of leukemia-specific T-cells, effector memory cells, and NK cells by combining the co-stimulatory effects of CD80 with immune stimulation by the IL-15/IL-15R heterodimer expressed by the transduced AML cells, thereby targeting MRD and potentially increasing relapse-free survival in AML patients. C_FIG

cancer biology↗

STING activation reshapes the tumor microenvironment leading to tumor regression in osteosarcoma

Osteosarcomas are characterized by a high degree of aneuploidy, chromothripsis and micronuclei, yet these tumors typically have an immunosuppressive, macrophage-rich, T-cell depleted tumor microenvironment. cGAS-STING dysregulation is a possible mechanism by which immune activation in response to tumor genomic instability could be repressed. We identified almost universal repression of cGAS or STING in human osteosarcomas. However, a STING-activation gene signature was predictive of survival in osteosarcoma patients suggesting potential for activation of this pathway in the osteosarcoma tumor microenvironment. Indeed, in immunocompetent osteosarcoma models, systemic STING agonism led to complete regression and induced lasting immunologic memory. Host STING activation is sufficient to promote this anti-tumor immunity even in the absence of tumor STING. These results nominate the cGAS-STING pathway as an important therapeutic target in osteosarcoma, a disease in which no new curative therapies have been developed in the last 40 years. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/684275v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@15b1e5corg.highwire.dtl.DTLVardef@12650aaorg.highwire.dtl.DTLVardef@79ef71org.highwire.dtl.DTLVardef@15704c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses

Chronic infection with hepatitis B virus (HBV), a major global pathogen, often leads to immune-mediated progressive liver injury and liver cancer. While seroclearance of the surface antigen (HBsAg) defines clinical cure and reduces disease-associated risks, HBsAg clearance is rarely observed and remains therapeutically elusive. Here we overcome some of the challenges to studying immune mechanisms of HBsAg clearance in chronic hepatitis B (CHB) using our mouse model of age-dependent HBsAg clearance and persistence, and samples from our BeNEG-DO clinical trial that provided longitudinal PBMCs from patients who either cleared HBsAg or retained stable HBsAg levels after stopping nucleos(t)ide analog therapy. We show that young mice fail to clear HBsAg and have impaired ability to efficiently initiate and sustain HBV-specific CD4+ T cell responses. We also demonstrate a role for CD4+ T cells in hepatic leukocyte organization and cytotoxicity, and in HBV-specific CD8+ T cell cytotoxicity and HBsAg clearance. Upstream of the CD4+ T cell response, we reveal that hepatic dendritic cells, particularly cDC2s, direct effective CD4+ T cell activation and differentiation. Studies in CHB patients identified immune features of HBsAg clearance that overlap with the mouse model, including TH1 and cytotoxic CD4+ T cell activation and CD8+ T cell cytotoxic effector function. These findings identify an essential role for potent CD4+ T cell activation in the clinical cure of CHB and illuminate potential immunotherapeutic targets for enhancing CD4+ T cell responses to achieve greater HBsAg clearance rates. One Sentence SummaryUsing a mouse model of hepatitis B and longitudinal PBMCs from patients with chronic hepatitis B, we identify shared mechanisms of HBsAg seroclearance.

immunology↗

Differential Assembly of Mouse and Human Tumor Microenvironments

Mouse models are frequently used to develop treatments for human cancer. Yet, we lack a comprehensive understanding of the comparative organization of mouse and human tumor microenvironments (mu/huTMEs). Through immunoprofiling of commonly used mouse models, we found that the immune composition of most muTMEs resemble poorly infiltrated human tumors extensively biased toward high macrophages densities. Relatedly, we discover species-specific biases of chemokine expression networks, factors which drive TMEs assembly. Further, assessing coarse cellular networks, we find conserved correlations between some immune cell frequencies, while other relationships only appear conserved in the huTMEs matching muTME profiles. Despite this variable alignment, we define robust cell type-specific gene expression programs conserved in TMEs across species and cohorts and identify ones that are coordinated between cell populations in both species. Together, we isolate and offer methods to study the multiple areas of hazard and opportunities for using mice to model human cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/661217v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@22bcf7org.highwire.dtl.DTLVardef@a410b7org.highwire.dtl.DTLVardef@1455eb5org.highwire.dtl.DTLVardef@14cc6f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State

Obesity potently alters immune responses across various inflammatory contexts1-7. However, it is unclear whether a transient high-fat diet (HFD) can affect immune function despite minimal effects on body weight. Here, we demonstrate that a short-term HFD regimen significantly exacerbates disease severity in a model of experimental psoriasis, comparable to what is observed in obese mice on long-term HFD. We find that a critical 4-day window of HFD coinciding with disease onset is sufficient to overactivate the immune response, leading to worsened disease outcomes. Mechanistically, we identify the CD4+ T cell compartment as an essential mediator of HFD-induced disease severity. Within the compartment, we functionally validate that disease exacerbation is driven by increased differentiation of a pathogenic population of T helper 17 (TH17) cells8 expressing IL1R1 (interleukin-1 receptor, type I)9, which is triggered by localized activation of the NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome10. This brief window of HFD at disease onset leads to immune-dependent sensitization, as disease severity is increased upon a subsequent flare, despite complete recovery and under a low-fat diet (LFD) regimen. Our data indicate that transient dietary changes during the initial stages of an inflammatory event can rewire the immune milieu, profoundly influencing disease progression and inflammatory memory11. This phenomenon may have broad implications for conditions where obesity, and not diet itself, is considered the primary risk factor.

immunology↗

CD38 expression by neonatal human naïve CD4+ T cells shapes their distinct metabolic state and high regulatory T cell potential

Neonatal life is marked by rapid antigen exposure, necessitating establishment of peripheral immune tolerance via conversion of naive CD4+ T cells into regulatory T cells (Tregs). Here, we demonstrate heighted capacity for FOXP3 expression and tolerogenic function among cord blood versus adult blood naive CD4+ T cells and that this is linked to their unique metabolic profile and elevated expression of the NADase, CD38. Early life naive CD4+ T cells demonstrate a metabolic preference for glycolysis, which directly facilitates their differentiation trajectory. We reveal an age-dependent gradient in CD38 levels on naive CD4+ T cells and show that high CD38 expression contributes to both the glycolytic state and tolerogenic potential of neonatal CD4+ T cells, effects that are mediated at least in part via the NAD-dependent deacetylase SIRT1. Thus, the early life window for peripheral tolerance in humans is critically enabled by the immunometabolic state of the naive CD4+ compartment.

immunology↗

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states

Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains incompletely understood. Therefore, we performed multi-omic profiling of 110 healthy participants through the ImmunoMicrobiome study. A factor-based integrative approach identified coordinated variation, revealing that the tonic interferon response was amongst the most variable immune features in healthy participants. Microbiome composition, pathways, and stool metabolites varied concomitantly with interferon response pathways. Distinct transcriptional programs involving inflammation and TGF-{beta} in SIGLEC-1high monocytes and CD69high activated MAIT and NK cells were representative of these programs. Our study provides extensive data to examine the relationship between the immune states and microbiomes of healthy individuals at steady state, which paves the way for delineating inter-individual differences relevant for disease susceptibility and responses to therapy.

immunology↗

A Multiomics, Spatiotemporal, and Single Cell Atlas for Mapping Cell-Type-Specific Dysregulation at the Maternal-Fetal Interface

The placenta, the first organ to functionally mature, undergoes disordered development in many pregnancy complications. Molecular investigations have been hampered by the extreme cellular heterogeneity of the placenta, and this complexity is further exaggerated at the maternal-fetal interface where maternal and fetal cells co-mingle. We generated the paired single nucleus epigenomes and transcriptome for each of [~]200,000 cells at the human maternal-fetal interface from early pregnancy to term. These data identified cell-type-specific transcriptional regulatory programs and uncovered key transcription factors driving the lineage differentiation of placental cytotrophoblasts. Integrating spatial single cell proteomics profiling, we localized the observed cell types in situ, and characterized the dynamic stages and distinct features of endothelial cells of maternal spiral arteries remodeled by extravillous cytotrophoblasts. Integrative analyses of the single cell data across gestation enabled fine-mapping of the developmental trajectories of cytotrophoblasts and decidual stromal cells, and defining the signature molecular profiles of known and novel cell (sub)types. To demonstrate clinical value, we integrated the reference single cell data with large-scale population genomes from pregnancy complications and identified the most vulnerable maternal and fetal cell types in preeclampsia, preterm birth, and miscarriage. This study presents the most comprehensive placental and decidual single cell resource across gestation to date, reveals new insights into the drivers of normal human placentation, and uncovers the cellular basis of dysfunction associated with common pregnancy complications.

genomics↗

Critical role of CD206+ macrophages in organizing anti-tumor immunity

Tumor-associated macrophages (TAMs) are frequently categorized as being M1 or M2 polarized, even as substantial data challenges this binary modeling of macrophage cell state. One molecule consistently referenced as a delineator of a putative immunosuppressive M2 state is the surface protein CD206. We thus made a novel conditional CD206 (Mrc1) knock-in mouse to specifically visualize and/or deplete CD206+ M2-like TAMs and assess their correspondence with pro-tumoral immunity. Early, but not late depletion of CD206+ macrophages and monocytes (here, Mono/Macs) led to an indirect loss of a key anti-tumor network of NK cells, conventional type I dendritic cells (cDC1) and CD8 T cells. Among myeloid cells, we found that the CD206+ TAMs are the primary producers of CXCL9, and able to differentially attract activated CD8 T cells. In contrast, a population of stress-responsive TAMs ("Hypoxic" or Spp1+) and immature monocytes, which lack CD206 expression and become prominent following early depletion, expressed markedly diminished levels of CXCL9. Those NK and CD8 T cells which enter CD206- depleted tumors express vastly reduced levels of the corresponding receptor Cxcr3, the cDC1- attracting chemokine Xcl1 and cDC1 growth factor Flt3l transcripts. Consistent with the loss of this critical network, early CD206+ TAM depletion decreased tumor control by antigen specific CD8 T cells in mice. Likewise, in humans, the CD206Replete, but not the CD206Depleted Mono/Mac gene signature correlated robustly with CD8 T cell, NK cell and stimulatory cDC1 gene signatures and transcriptomic signatures skewed towards CD206Replete Mono/Macs associated with better survival. Together, these findings negate the unqualified classification of CD206+ M2-like macrophages as immunosuppressive by illuminating contexts for their role in organizing a critical tumor-reactive archetype of immunity.

immunology↗

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data

In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.

immunology↗

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted by metastasis

CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment (TME), recent studies in mice identified responses in lymph nodes (LN) as essential; however, the role of LN in human cancer patients remains unknown. We examined CD8+ T cells in human head and neck squamous cell carcinomas, regional LN, and blood using mass cytometry, single-cell genomics, and multiplexed ion beam imaging. We identified progenitor exhausted CD8+ T cells (Tpex) that were abundant in uninvolved LN and clonally related to terminally exhausted cells in the TME. After anti-PD-L1 immunotherapy, Tpex in uninvolved LN reduced in frequency but localized near dendritic cells and proliferating intermediate-exhausted CD8+ T cells (Tex-int), consistent with activation and differentiation. LN responses coincided with increased circulating Tex-int. In metastatic LN, these response hallmarks were impaired by immunosuppressive cellular niches. Our results identify important roles for LN in anti-tumor immune responses in humans.

immunology↗

Deep Immunophenotyping Reveals Endometriosis is Marked by Dysregulation of the Mononuclear Phagocytic System in Endometrium and Peripheral Blood

BackgroundEndometriosis is a chronic, estrogen-dependent disorder where inflammation contributes to disease-associated symptoms of pelvic pain and infertility. Immune dysfunction includes insufficient immune lesion clearance, a pro-inflammatory endometrial environment, and systemic inflammation. Comprehensive understanding of endometriosis immune pathophysiology in different hormonal milieu and disease severity has been hampered by limited direct characterization of immune populations in endometrium, blood, and lesions. Simultaneous deep phenotyping at single cell resolution of complex tissues has transformed our understanding of the immune system and its role in many diseases. Herein, we report mass cytometry and high dimensional analyses to study immune cell phenotypes, abundance, activation states, and functions in endometrium and blood of women with and without endometriosis in different cycle phases and disease stages. MethodsA case-control study was designed. Endometrial biopsies and blood (n=60 total) were obtained from women with (n=20, n=17, respectively) and without (n=14, n=9) endometriosis in the proliferative and secretory cycle phases of the menstrual cycle. Two mass cytometry panels were designed; one broad panel and one specific for mononuclear phagocytic cells (MPC), and all samples were multiplexed to characterize both endometrium and blood immune composition at unprecedented resolution. We combined supervised and unsupervised analyses to finely define the immune cell subsets with an emphasis on MPC. Then, association between cell types, protein expression, disease status, and cycle phase were performed. ResultsThe broad panel highlighted a significant modification of MPC in endometriosis; thus, they were studied in detail with an MPC-focused panel. Endometrial CD91+ macrophages overexpressed SIRP (phagocytosis inhibitor) and CD64 (associated with inflammation) in endometriosis, and they were more abundant in mild versus severe disease. In blood, classical and intermediate monocytes were less abundant in endometriosis, whereas plasmacytoid dendritic cells and non-classical monocytes were more abundant. Non-classical monocytes were higher in severe versus mild disease. ConclusionsA greater inflammatory phenotype and decreased phagocytic capacity of endometrial macrophages in endometriosis are consistent with defective clearance of endometrial cells shed during menses and in tissue homeostasis, with implications in endometriosis pathogenesis and pathophysiology. Different proportions of monocytes and plasmacytoid dendritic cells in blood from endometriosis suggest systemically aberrant functionality of the myeloid system opening new venues for the study of biomarkers and therapies for endometriosis.

immunology↗

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer

T cell exhaustion is a major impediment to anti-tumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here we show that the biology of tumor-associated macrophages (TAM) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAM reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique long-lasting antigen-specific synaptic interactions that fail to activate T cells, but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/461866v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1fb1c4aorg.highwire.dtl.DTLVardef@fe4571org.highwire.dtl.DTLVardef@1812f76org.highwire.dtl.DTLVardef@5317d5_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

The tumor immune microenvironment (TIME) is commonly infiltrated by diverse collections of myeloid cells. Yet, the complexity of myeloid cell identity and plasticity has challenged efforts to define bona fide populations and determine their connections to T cell function and their relation to patient outcome. Here we leverage single-cell RNA-sequencing (scRNA-seq) analysis of several mouse and human tumors and find that monocyte-macrophage diversity is characterized by a combination of conserved lineage states as well as transcriptional programs accessed along the differentiation trajectory. Using mouse models, we also find that tumor monocyte-to-macrophage progression is profoundly tied to regulatory T cell (Treg) abundance. Importantly, in human kidney cancer, heterogeneity in macrophage accumulation and myeloid composition corresponded to variance in, not only Treg density, but also the quality of infiltrating CD8+ T cells. In this way, holistic analysis of monocyte-to-macrophage differentiation creates a framework for critically different immune states in kidney tumors.

immunology↗