Synovial sarcoma is an aggressive mesenchymal neoplasm, driven by the SS18-SSX fusion, and characterized by immunogenic antigens expression and exceptionally low T cell infiltration levels.To study the cancer-immune interplay in this disease, we profiled 16,872 cells from 12 human synovial sarcoma tumors using single-cell RNA-sequencing (scRNA-Seq). Synovial sarcoma manifests antitumor immunity, high cellular plasticity and a core oncogenic program, which is predictive of low immune levels and poor clinical outcomes. Using genetic and pharmacological perturbations, we demonstrate that the program is controlled by the SS18-SSX driver and repressed by cytokines secreted by macrophages and T cells in the tumor microenvironment. Network modeling predicted that SS18-SSX promotes the program through HDAC1 and CDK6. Indeed, the combination of HDAC and CDK4/6 inhibitors represses the program, induces immunogenic cell states, and selectively targets synovial sarcoma cells. Our study demonstrates that immune evasion, cellular plasticity, and cell cycle are co-regulated and can be co-targeted in synovial sarcoma and potentially in other malignancies..

Chronic low-grade inflammation is a hallmark of obesity and associated with cardiovascular complications. However, it remains unclear where this inflammation starts. As the gut is constantly exposed to food, gut microbiota, and metabolites, we hypothesized that mucosal immunity triggers an innate inflammatory response in obesity. We characterized five distinct macrophage subpopulations (P1-P5) along the gastrointestinal tract and blood monocyte subpopulations (classical, non-classical, intermediate), which replenish intestinal macrophages, in non-obese (BMI<27kg/m2) and obese individuals (BMI>32kg/m2). To elucidate factors that potentially trigger gut inflammation, we correlated these subpopulations with cardiovascular risk factors and lifestyle behaviors. In obese individuals, we found higher pro-inflammatory macrophages in the stomach, duodenum, and colon. Intermediate blood monocytes were also increased in obesity, suggesting enhanced recruitment to the gut. We identified unhealthy lifestyle habits as potential triggers of gut and systemic inflammation (i.e., low vegetable intake, high processed meat consumption, sedentary lifestyle). Cardiovascular risk factors other than body weight did not affect the innate immune response. Thus, obesity in humans is characterized by gut inflammation as shown by accumulation of pro-inflammatory intestinal macrophages, potentially via recruited blood monocytes. Understanding gut innate immunity in human obesity might open up new targets for immune-modulatory treatments in metabolic disease.

Early malnutrition, the first environmental cause of intra-uterine growth restriction, impairs development of the thymus. Alterations of the thymic structure and function are reported at young ages in murine and ovine models. However, descriptions of thymic consequences of fetal malnutrition at adulthood are scarce. The present study investigates thymic structure, protein expression and cell selection process observed at postnatal day 180 (PND180) in male offspring of rats exposed to maternal low-protein diet (mLPD) compared with control diet during gestation. The thymic index was lower in adult offspring exposed to mLPD (P < 0·05). The thymic cortico-medullar ratio was lower in adult offspring exposed to mLPD (P < 0·05). At PND180, the protein expression of the lymphotoxin β receptor (P < 0·05), the autoimmune regulator (P < 0·05) and Forkhead Box P3 (FoxP3; P < 0·05) was all significantly lower in the mLPD group. The CD4+:CD8+ single-positive thymocyte subpopulation ratio and CD4+:CD8+ lymphocyte subpopulation ratio were increased in the mLPD group (P < 0·05). Among CD3+ lymphocytes, the proportions of CD4+CD8+ double-positive lymphocytes, CD31+ recent thymic emigrants and CD4+FoxP3+ lymphocytes were not significantly different between mLPD and control groups. These findings suggest mLPD during gestation induced long-lasting alterations in the development of thymic structure and thymic cell maturation and selection process in adult male rat offspring.

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The mean CMR was significantly lower in mLPD group relatively to control group (mLPD v. CTRL; mean values with their standard errors; 2•21 v. 2•82; P < 0•05) (Fig. 1). Correction The mean CMR was significantly lower in mLPD group relatively to control group (mLPD vs. CTRL; mean values with their standard errors; 2•21 ± 0•08 v. 3•17 ± 0•68; P < 0•05) (Fig. 1).

Synovial sarcoma is an aggressive mesenchymal neoplasm, driven by the SS18-SSX fusion, and characterized by immunogenic antigens expression and exceptionally low T cell infiltration levels.To study the cancer-immune interplay in this disease, we profiled 16,872 cells from 12 human synovial sarcoma tumors using single-cell RNA-sequencing (scRNA-Seq). Synovial sarcoma manifests antitumor immunity, high cellular plasticity and a core oncogenic program, which is predictive of low immune levels and poor clinical outcomes. Using genetic and pharmacological perturbations, we demonstrate that the program is controlled by the SS18-SSX driver and repressed by cytokines secreted by macrophages and T cells in the tumor microenvironment. Network modeling predicted that SS18-SSX promotes the program through HDAC1 and CDK6. Indeed, the combination of HDAC and CDK4/6 inhibitors represses the program, induces immunogenic cell states, and selectively targets synovial sarcoma cells. Our study demonstrates that immune evasion, cellular plasticity, and cell cycle are co-regulated and can be co-targeted in synovial sarcoma and potentially in other malignancies. epithelial-like malignant cells (in biphasic tumors), suggestive of pluripotential differentiation or mesenchymal to epithelial transitions.Studies of human SyS to date have either relied on bulk tissue (21,22) or on established cellular models (11,18,19), masking important aspects of the tumor ecosystem. Moreover, given this cancer's rarity, even concerted efforts, such as TCGA, profiled only limited numbers of tumors (21-23). Here, we leveraged single-cell RNA-Seq (scRNA-Seq), imaging, functional perturbations, and computational modeling, to study the cancer-immune interplay in SyS. We profiled 16,872 cells from 12 human SyS tumors by scRNA-seq and demonstrate that SyS tumors invariably include a subpopulation of cells expressing a novel core oncogenic program, associated with T cell exclusion. The core oncogenic program is predictive of poor prognosis and is repressed by the genetic inhibition of the SS18-SSX fusion, and by cytokines expressed by T cells and macrophages in the tumor microenvironment. HDAC1 and CDK6 are a key regulator and target of this aggressive cell program, respectively, and their combined inhibition synergistically represses it in SyS cells, triggering antigen presentation and cell autonomous immune responses.Collectively, our findings demonstrate a strong connection between SyS development and immune evasion, and strengthen the notion that de-differentiation, immune evasion, and cell cycle are coregulated, such that cellular immunity can be targeted through modulation of cell cycle and epigenetic processes. RESULTS Cell type inference from expression and genetic features in scRNA-seq of SySTo comprehensively interrogate the SyS ecosystem, we used full-length (24) and droplet-based (25) scRNA-Seq to profile 16,872 high quality malignant, immune, and stromal cells from 12 human SyS tumors ( Fig. 1A,B, Supp. Fig. 1A,B, Supp. Table 1, Methods). We assigned...

Background: Our previous studies in mice showed that high fat diet leads to a pro-inflammatory phenotype of intestinal macrophages. Colon-specific depletion of intestinal macrophages led to improved glycemic control, suggesting a causal link between intestinal macrophages and glycemia. The aim of the current study was to validate our findings in human disease by assessing human gut biopsies and circulating blood monocytes from lean and obese individuals. Research Design and Method: Peripheral blood monocytes were isolated using a Ficoll gradient and characterized by flow cytometry as classical (CD14++CD16-), intermediate (CD14++CD16+) and non-classical (CD14+CD16++) monocytes. Intestinal macrophages of the stomach, duodenum and colon were isolated from biopsies of lean (BMI &lt;27 kg/m2) or obese (BMI &gt;32 kg/m2) individuals undergoing colonoscopy or gastroscopy. Macrophages were characterized as CD14high or CD14low and further subdivided by HLA-DR, CD163 and CD209 into pro-inflammatory P1, P2, intermediate P3 and resident, anti-inflammatory subpopulations P4, P5. Results: Depending on the anatomical location, the composition of intestinal macrophages varied: In the stomach of lean subjects, the ratio of CD14high/CD14low macrophages was 80/20%, while the colon comprised more resident, anti-inflammatory macrophages (CD14high/CD14low: 60/40%). Consistent with our results in mice, we detected an increase in the CD14high pro-inflammatory macrophage subpopulation P2 in obese individuals (Corpus: 1.55±0.61-fold, Duodenum: 1.79±0.45-fold, Colon transversum: 1.71±0.72-fold). Interestingly, also human CD14high intermediate blood monocytes were increased in obese patients. Conclusion: Similar to our mouse data, pro-inflammatory intestinal macrophages are increased in gut biopsies of obese subjects. Higher CD14high blood monocytes suggest enhanced recruitment of monocytes to the gut as the prevailing mechanism. Disclosure T.V. Rohm: None. R. Fuchs: None. Z. Baumann: None. L. Keller: None. R. Schneider: None. D. Labes: None. C. Cavelti-Weder: None. Funding University of Basel

Adoptive cell therapy (ACT) using ex vivo expanded tumor-infiltrating T lymphocytes (TILs) can mediate responses in metastatic melanoma, but long-term efficacy remains limited to a fraction of patients. Here we interrogated tumor-microenvironment (TME) cellular states and interactions of longitudinal samples from 13 metastatic melanoma patients treated with TIL-ACT in our clinical study (NCT03475134). We performed single-cell RNA-seq and spatial proteomic analyses in pre- and post-ACT tumor tissues and showed that responders exhibited higher tumor cell-intrinsic immunogenicity. Also, endogenous CD8+ TILs and myeloid cells of responders were characterized by increased cytotoxicity, exhaustion and costimulation and type-I IFN signaling, respectively. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders have rich baseline intratumoral and stromal tumor-reactive T-cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study reveals CD8+ T-cell network-based biomarkers that could improve patient selection and guide the design of ACT clinical trials.