Single cell RNA sequencing of three IDHwt glioblastoma patient tumors
Ontology highlight
ABSTRACT: Single cell RNA sequencing was performed to allow expression-based identification of tumor versus normal cells from glioblastoma patient specimens. Identified tumor cells were then analyzed to assess the expression tumor-cell specific expression of TRIM26, WWP2, and SOX2.
Project description:In this study, human ovarian cortex was characterised on a transcriptional level. Major questions concerned the differences of cortical cell type composition in ovaries donated by Cesarian section and gender reassignment patients, respectively, as well as the presence of putative oogonial stem cells or germline-like cells. Furthermore, comparison to and integration of the scRNA-Seq dataset of human ovarian inner tissue (as compared to the outer cortex) published in 2019 was performed in order to obtain a complete picture of the adult human ovary on a cellular level.
Project description:Toal 13 patient samples (Iliac or pyramidal cancellous) were collected with lung cancer who were pathologically diagnosed in Dazhou Central Hospital from June 2020 to January 2021. Patients were monitored by a professional orthopaedic surgeon in the interventional room prior to collecting the samples. This study was approved by the ethics committee and informed consent of patients (IRB2020023). The obtained samples are quickly placed into an Eppendorf tube with PBS buffer for flushing the blood. Then, the samples were cleaned in a cell preservation solution. Finally, the cleaned samples were placed into a sterile EP tube with 2 mL cell preservation solution before being stored in a refrigerator at 4 ° C. Further, the samples with two replicates were sequenced in a 10x genomic chromium platform with a chemistry library (Single Cell 3; v3). The samples were sequenced at BGI (https://www.bgi.com).
Project description:In this study, we investigated somatic mutations of CD4+ and CD8+ T cells in patients with immune-mediated aplastic anemia (AA). To understand the role of mutations, we performed single-cell level analysis of 6 longitudinal samples of 2 AA patients carrying STAT3 or KRAS and other mutations in CD8+ T cells. The analysis was performed using V(D)J and 5' gene expression platform (10X Genomics). STAT3 mutated clone was clearly distinguishable from other CD8+ T cells and showed a cytotoxic phenotype, attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells can alter T cell phenotype warranting further investigation of their role in the pathogenesis of immune-mediated AA.
Project description:Aberrant activation of the canonical Wnt pathway underlines the development and growth of intestinal tumors. The Apc-min (multiple intestinal neoplasia) mouse strain carries a single nucleotide mutation in one allele of the Apc tumor suppressor gene. Random deactivation of the second allele occurs during the life and results in the formation of multiple adenomas in the small intestine with occasional colonic occurence. The Defa6 promoter is active in adult small intestinal Paneth cells and its activation has been observed also in human colonic adenomas. To investigate the nature of Defa6+ colon adenoma cells, we used the Apc-min Rosa26-tdTomato Defa6-iCre mouse strain. In this strain, cells with an active Defa6 promoter are marked by expression of a red fluorescent protein (tdTomato). We performed gene expression profiling of Defa6-tdTomato+ cells isolated from mouse colon tumors.
Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.
Project description:To comprehensively characterize the changes within the TME during TREM1 deficiency and anti-PD-1 immune checkpoint blockade therapy, we performed scRNA-seq analysis of the CD45+ TICs in melanoma-bearing C57BL/6 mice receiving the various treatments. We analyzed approximately 8,249 CD45+ cells from the treatment groups with t-SNE analysis, identifying 10 distinct clusters of tumor-infiltrating immune cells
Project description:Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk-factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data, and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific autoantibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ T cells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time leading to distinct convalescent immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies.
Project description:This study utilizes multi-omic biological data to perform deep immunophenotyping on the major immune cell classes in COVID-19 patients. 10X Genomics Chromium Single Cell Kits were used with Biolegend TotalSeq-C human antibodies to gather single-cell transcriptomic, surface protein, and TCR/BCR sequence information from 254 COVID-19 blood draws (a draw near diagnosis (-BL) and a draw a few days later (-AC)) and 16 healthy donors.
Project description:To gain a global understanding of the impact of TREM1 silencing, we analyzed the CD45+ tumor infiltrating cells (TICs) of B16F10 tumor-bearing Trem1+/+ and Trem1-/- mice. Utilizing the 10x Genomics Chromium Platform, we analyzed approximately 5390 cells per sample with a coverage rate of 15493 genes per cell.