Project description:We performed a study investigating donors previously infected with SARS-CoV-2 during the first wave of the COVID-19 pandemic to understand how vaccination may reshape T cell populations formed after infection. 10 donors were investigated using single-cell RNA-sequencing consisting of a) 3 mild non-hospitalised donors, b) 3 severe hospitalised donors, c) 1 mild recently vaccinated donor and d) 3 recently convalescent donors. For each of these groups we sampled at the following timepoints a) 6-9 months and 18 months after infection, b) 6-9 months and 18 months after infection, c) 13 months and 15 months after infection and d) 35 days after infection. All donors were unvaccinated at the first time point and vaccinated at the second time point. We stimulated PBMC with an overlapping peptide pool derived from the spike glycoprotein of the SARS-CoV-2 virus and sorted spike-specific CD4+ T cells (CD4+CD69+CD40L+) and spike-specific CD8+ T cells (CD8+CD69+4-1BB+) from every donor and time point using flow cytometry for 10X single-cell sequencing (5' protocol). Each time point from Dnr4868 was sequenced across two 10X reactions/libraries performed on the same day. Multiple samples were hashed and pooled together for sequencing using TotalSeq-C anti-human hashing antibodies from BioLegend. Individual library expression matrix files were generated using the CellRanger pipeline from 10X Genomics. The processed data file named immune.combined220929.rds is a Seurat Object containing all samples and generated using the Seurat package in R.
Project description:Assessment of the gene expression differences between HHV-6B-specific and HCMV-specific CD4 T cells at single-cell level. The peripheral blood mononuclear cells samples were collected from normal subjects expressing HLA-DRB1*03:01. The HHV-6B-specific or HCMV-specific T cells were expanded in vitro using known HLA-DRB1*03:01 epitopes derived from HHV-6B (6 epitopes) or HCMV (1 epitope) and isolated after 12-15 days of culture using the corresponding HLA-DRB1*03:01 tetramers.
Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from two healthy donors with an interval of 10 or 6 years.
Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from a single healthy donor with an interval of 4 years.
Project description:The study investigates the interaction between rAAV and the innate immune system. We conducted single cell RNA-sequencing (scRNA-seq) of PBMCs from six healthy human donors, comparing samples taken either before or after 1, 4 or 24 hrs of incubation with rAAV8. As a control, scRNA-seq was performed on untreated whole blood incubated under the same culture conditions to consider the potential impact of the ex vivo culture on the blood cells.
Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.
Project description:Single cell ATAC-seq of PBMC - resting and stimulated. Used for comparison to asses the capabilies of the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication).
Project description:Single cell five-prime end sequencing of PBMC - resting and stimulated. Used to asses the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication)
Project description:Glioblastoma (GBM) is an immunologically cold brain tumor with poor outcome. We report an interim analysis of a first-in-human dose escalation study investigating Temferon, an advanced therapy medicinal product composed of autologous hematopoietic stem/progenitor cells engineered to express alpha-2 interferon selectively in the myeloid progeny recruited into the GBM tumor microenvironment (TME). Twenty-four newly diagnosed GBM patients were treated following conformal focal radiotherapy and non myeloablative conditioning chemotherapy. The primary objective was to assess safety and tolerability over the first 90 days, secondary objectives were long-term safety, definition of dose and conditioning regimen, and signs of activity. Temferon met the primary outcome of safety, with a toxicity profile consistent with autologous stem cell transplantation. No dose limiting toxicities were recorded up to 4x10^6 Temferon cells/kg, and conditioning with busulfan was selected for further development. Median overall- and progression-free survival from infusion (diagnosis) was 13.2 (16.7) and 6.2 (8.1) months, respectively. Most patients maintained good performance status and quality of life. Genetically engineered cells were detected long-term in the bone marrow and the blood, where minimal amounts of IFN-a were measured. Exploratory analyses on post-treatment brain tissue samples showed the presence of transgenic progeny and immune reprogramming of the TME towards enrichment for inflammatory macrophages and CD8 effector T-cells (EudraCT 2018-001404-11).