Project description:To characterize the consequences of systemic IL-27R agonism via IL-27 overexpression or IL-27 blockade (αIL-27) on anti-tumor CTL, we performed scRNA-seq of M86 neoantigen-specific CD8+ T cells from MC38 tumors and dLN.
Project description:We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of antigen receptors in immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted.
Project description:Oncolytic adenovirus Ad5/3-E2F-d24-hTNFa-IRES-hIL2 (TILT-123, igrelimogene litadenorepvec) shows promise as a therapeutic agent capable of causing tumor regression and activating host immunity. A phase 1 clinical study TUNIMO (NCT04695327) assessed its safety as monotherapy in patients with various solid tumors. Through single-cell profiling of peripheral blood, we identified distinct immunological features distinguishing responders from non-responders. Specifically, at baseline, responders demonstrated enhanced cytotoxic markers and stronger immune cell communication networks. Moreover, higher baseline CD16+ monocytes correlated with improved survival, while elevated regulatory T cells predicted poor response. T and B cell evaluation revealed contrasting patterns: higher specific T cells in responders, while elevated memory B cells predicted poor survival. Both cell types showed receptor segments previously associated with other viral responses. These findings emphasize that comprehensive biomarker analysis of peripheral blood should include not only cell frequencies but also transcriptional changes and distinct patterns of cellular and humoral immunity.
Project description:We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted. This submission augments E-MTAB-11343.
Project description:We hypothesized that treating heart failure mitigates its impact on cancer progression and that different treatments (carvedilol, enalapril, empagliflozin) may have distinct effects. For this reason we have created an mouse model combining both heart failure (LAD ligation) and 4T1 metastatic breast cancer to study the effects of these treatments on breast cancer development at different levels: primary tumor growth in vivo, metastasis development and RNA-sequencing of the primary tumor. Twenty samples divided in five different groups were analyzed with RNA sequencing: group 1= Ctrl; group 2= HF/veh; group 3= HF/car; group 4= HF/emp group 5 HF/ena. HF medications with different mechanisms of action had distinct effects on 4T1 progression when the two diseases coexisted. These effects varied from isolated effects on the tumor transcriptome, to effects on the expansion of the primary tumor and on metastatic spread in the lungs.
Project description:We investigated neural populations mediating the effects of cagrilintide on energy balance in the dorsal vagal complex (DVC). Single-nucleus RNA sequencing and spatial transcriptomics were performed across mouse, rat, and macaque brainstem tissue. Treatment groups include diet-induced obese animals treated acutely or subchronically with cagrilintide or vehicle. The overarching aim was to identify and characterize the neuronal population showing the strongest and most sustained transcriptional response to treatment. Included in this ArrayExpress ID is the bulk-seq data for mouse and rat
Project description:This experiment aims to define DGE when hiPSC derived brain organoids are exposed for long (chronic) or short (pulse) time to T3. Additionally, a comparison regarding T3 responsive genes can be assessed for two different brain organoids systems: cerebral organoids (CO) and Neural Stem Cell derived Organoids (NSCO). CO correspond to unguided differentiation following Lancaster et al. 2013. NSCO are neurospheres derived as desribed in https://dx.doi.org/10.17504/protocols.io.3byl4j6kzlo5/v1
Project description:Tumor-associated macrophages (TAMs) play important roles in cancer progression and resistance to therapy. Recent studies have shown that TAMs include both long-lived resident tissue macrophages (RTMs) and short-lived monocyte-derived macrophages (MDMs) with limited proliferative potential. RTMs and MDMs have been suggested to play divergent roles in tumorigenesis; RTMs are aligned with trophic functions, whereas MDMs are enriched for immune-regulatory pathways. Here we established a specific role for the AP-1 factor JUN in the differentiation and maintenance of MDMs and the specification of pro-tumoral trophic functions during tumor development. Alternatively, the immune-regulatory functions of TAMs remained JUN-independent. JUN was required for the specification and maintenance of pro-tumoral TAMs that support blood vessel maturation and tumor growth. Single-cell transcriptomics analysis uncovered the alternative fates for tumor-infiltrating monocytes and the development of distinct TAM states associated with trophic functions and immune-regulation. These studies demonstrate an important role for JUN in the specification of pro-tumoral monocyte-derived TAMs that could offer opportunities for selective TAM-targeted therapies for cancer.
Project description:The aim of this study was to characterize different adipose tissue depots in rainbow trout (Oncorhynchus mykiss) through the analysis of mRNA and miRNA expression profiles. Mature adipocytes were isolated from visceral (VAT), subcutaneous (SAT), and intramuscular (IMAT) adipose tissues, and RNA sequencing (RNA-seq) was performed. Data were curated, quality-checked, and filtered prior to downstream analyses. This dataset contains the FASTQ files generated in the study. The results will contribute to a better understanding of the molecular differences and similarities among adipose depots in fish reared under standard aquaculture conditions, providing a foundation for improving adiposity control, animal health, fillet yield, and overall product quality.