Project description:Mice were infected with the pancreatic cancer cell line Pan02 (into their pancreas). 30 days later, pancreas was extracted, cells digested and BD Rhapsody RNAseq targeted against the MM immune panel was performed.
Project description:scRNAseq of HPMCs isolated ex vivo from 3 Patients. Targeted scRNASeq was applied using BD onco Panel with a additional genes. Purpose of the experiment was to characterize HPMC phenotype ex vivo and compare with the phenotype observed in RNAseq of HPMCs treated with IL17A and TNF.
Project description:We conducted single-cell gene expression analysis of neutrophils from mouse tumors with and without microbial treatment to investigate neutrophil response in the tumor microenvironment (TME). Briefly, tumor-infiltrating Ly6G+CD11b+ neutrophils were isolated from unmanipulated tumors (resting), tumors treated with a vehicle control (control), and tumors treated with S. aureus bioparticles (stimulated) 24 hours after treatment. To survey the whole spectrum of the TME, we also isolated and sequenced non-neutrophil leukocytes in each sample.
Project description:4 groups of mice : Control, antibiotics, antibiotics + 4days of recolonization, antibiotics + 4days of recolonization + Enterocloster clostridioformis. Tumor draining lymph node were harvested after CFSE injection were harvested and CFSE+ cells were sorted and proccessed in order to generate single cell RNA-sequencing using BD Rhapsody mouse immune response targeted panel. Groups were barcoded using BD Rhapsody Multiplexing Kit.
Project description:scRNA-seq data from human eosinophils purified from blood samples. Samples include three healthy patients and three asthmatic donors.
Project description:SPP1 stimulation of human leukocytes drives proinflammatory monocyte activation and differentiation of dysregulated CD274(PDL-1)pos neutrophil phenotype.
Project description:Immunotherapy using CD19-directed chimeric antigen receptor (CAR)-T cells has shown excellent results for treatment of B-cell leukaemia and lymphoma. To produce CAR-T cells, the patient’s own T cells are isolated from the blood and modified in a laboratory with a genetic vector to express a tumor antigen-directed CAR on its surface. The CAR-T cells are then expanded in numbers and given back to the patient with the aim to eradicate the tumors. However, some patients display primary resistance to CAR-T treatment while others relapse quickly after CAR-T treatment. In this experiment, we seek to understand whether the quality of the individual CAR-T cell product the patients were given can predict outcome to the therapy. We investigate the transcriptional profile of the individual CAR-T infusion products using single-cell RNA sequencing. In this dataset, we identified a T cell subset correlating with response that could be used as an indicator for clinical outcome. Targeted RNA and protein single-cell libraries were obtained using the BD Rhapsody platform (BD Biosciences). In total four separate targeted libraries were produced with 6 patients per library. Sequencing was performed on NovaSeq 6000 S1 sequencer at the SNP&SEQ Technology Platform (Uppsala, Sweden). The raw scRNA-seq data was pre-processed by BD Biosciences using the Rhapsody Analysis pipeline to convert the raw reads into Unique Molecular Identifier (UMI) counts. UMIs are further adjusted within Rhapsody by applying BD’s Recursive Substitution Error Correction (RSEC) and Distribution-Based Error Correction (DBEC) in order to remove false UMIs caused by sequencing or library preparation errors. Pooled samples were deconvoluted using Sample-tag reads. The scRNA-seq and AbSeq counts were loaded, processed and used for clustering and differential gene expression with Seurat v. 4.0.0.
Project description:The immunosuppressive tumour microenvironment constitutes a significant hurdle to immune checkpoint inhibitors response. Both soluble factors and specialised immune cells such as regulatory T cells (TReg) are key components of active intratumoural immunosuppression. Previous studies have shown that Inducible Co-Stimulatory receptor (ICOS) can be highly expressed in the tumour microenvironment, especially on immunosuppressive TReg, suggesting that it represents a relevant target for preferential depletion of these cells. Here, we performed immune profiling of samples from paired tumour and peripheral blood of 5 patients with non-small cell lung cancer (NSCLC). We found Icos mRNA expression in NSCLC samples was higher in TRegs than in other T cell subsets and higher in the TME than in the periphery with the expression pattern in both compartments following the general trend of: TReg > CD4non-TReg > CD8 > Other.
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:To dissect the precise roles of ST-DC2 clusters and ST-iDC3 clusters in T-cell activation, we co-cultured each cluster separately with autologous memory CD4pos T-cells. FACS-sorted ST-DC2 clusters and ST-iDC3 clusters from synovial tissue of active RA or remission RA were co-cultured for 5 days with FACS-sorted autologous blood memory CD4pos T-cells in the presence of anti-CD3 stimulation to mimic TCR activation. We investigated the frequency and phenotype of the resultant co-culture T-cell populations by carrying out single cell sequencing and analysing the output. It was observed that the DC2 and iDC3 group could differentially support distinct T-Cell populations in both frequency, and transcriptional profile.