Project description:As pancreatic ductal adenocarcinoma (PDAC) is the deadliest solid cancer, and new immunological therapies have only marginally improved patient survival, we aimed at better understainding the immunological fingerprint of this disease. PDAC development involves inflammatory reprogramming and bacterial colonization, conditions that influence the adaptation of mucosa-associated invariant T cells (MAIT). We investigated MAIT signatures in patients with PDAC, chronic pancreatitis (CP), a risk factor for PDAC, and healthy donors (HD) using high-dimensional single-cell techniques, complemented by serum proteomics and multicolor histology. In our manuscript, we identify for the first-time human effector MAIT1 cells likely involved in protecting against PDAC. We characterize the transcriptional, phenotypic, and metabolic signatures of human MAIT1 compared to MAIT17-like cells, their adaptation to the PDAC inflammatory microenvironment, and provide insights into mechanisms underlying MAIT1-mediated protection against PDAC.
Project description:Comparing human T cell repertoire development in humanized mice using CD34+ cell transplantation in NSG strain versus NSG without murine MHC (DKO). Additionally, comparing two preconditioning protocols: busulfan (BU) versus irradiation (IR). In total 4 groups compared: DKO-BU, DKO-IR, NSG-BU and NSG-IR. 3 CB donors were used to humanize these mice.
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:This experiment used single-cell RNA sequencing to characterize transcriptional heterogeneity and tumor-cell state dynamics in primary and metastatic lesions from a mouse B16 melanoma model. For each experimental group, small pieces of tumor tissues were collected from five mice and pooled to generate one sequencing sample. The pooled tumor tissues were dissociated into single-cell suspensions. Single-cell cDNA libraries were generated using the BD Rhapsody single-cell 3' whole transcriptome amplification (WTA) protocol. Briefly, single cells were washed, counted, loaded onto a cartridge, and lysed inside the wells, followed by mRNA capture on cell capture beads, reverse transcription, cDNA extension, amplification, and library construction according to the manufacturer's instructions. Libraries were sequenced on the Illumina NovaSeq X Plus system using 150 nt paired-end sequencing. Raw sequencing reads were processed to generate gene-barcode expression matrices. The resulting matrices were analyzed using Seurat v4.4.0 for quality control, normalization, dimensionality reduction, clustering, cell-type annotation, tumor-cell state annotation, SCENIC/AUCell regulon analysis, and pseudotime analysis.
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:This study investigates the role of dendritic cells (DCs) in anti-tumor immunity, focusing on the phosphatase SHP-1 and its regulation of signaling pathways and interactions with CD8+ T cells. Using conditional knockout mouse models and single-cell transcriptomics, we show that SHP-1 loss in conventional type 1 dendritic cells (cDC1s) and macrophages disrupts interferon responses, antigen presentation, and migratory programs, leading to impaired tumor rejection and reduced efficacy of PD-1 blockade. These findings provide mechanistic insights into dendritic cell biology within the tumor microenvironment (TME) and identify SHP-1 as a key regulator with implications for the design of DC-based cancer immunotherapies.
Project description:Microglia are brain-resident macrophages critical for cerebral development, function and homeostasis. During development, yolk-sac-derived microglial progenitors colonize and populate the brain following a well-defined spatiotemporal pattern. However, the mechanisms driving microglial colonization and proliferation are largely unknown. Herein, using scRNA-seq of conditional inactivation of Colony Stimulating Factor 1 (Csf1), we revealed that embryonic cortical microglia critically rely on neural Csf1, mainly produced by cortical progenitors but also by post-mitotic neurons, and that the action of Csf1 is local, dose-dependent and transient. Alongside, intrinsic Csf1 expressed by ATM contributed to their sustained proliferation at developmental hotspots.
Project description:scRNA-seq data from human eosinophils purified from blood samples. Samples include three healthy patients and three asthmatic donors.
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.