Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB20467 | ENA |
REPOSITORIES: ENA
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Project description:Tumor-infiltrating regulatory T cells contribute to an immunosuppressive tumor microenvironment. We applied single-cell RNA sequencing (scRNA-seq) , TCR sequencing combined with cellular indexing of transcriptomes and epitopes (CITE-seq) on CD4 T cells to decipher the heterogeneity of intratumoral Tregs in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), compared with non-malignant tonsillar tissue.
2023-09-12 | GSE242756 | GEO
Project description:Single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq of human tonsillar CD4+ T cells
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Project description:Single cells from human colorectal cancer and normal adjacent colon of 16 patients were used for single-cell RNA-seq, TCR-seq, CITE-seq and Cell hashing. In brief, single cells were incubated for 3h with or without PMA/Ionomycin, and were treated with Cell hashing and CITE-seq antibodies to distinguish samples, stimulation/non-stimulation, and cell surface proteins. Sorted viable CD3+TCRαβ+ single cells were loaded into 10x genomics ChromiumTM controller to make nanoliter-scale droplets with uniquely barcoded 5’ gel beads called GEMs. After GEM-RT and the following some cDNA amplification steps, cDNAs derived from cellular mRNA were pooled for downstream processing and library preparation according to the manufacturer’s instructions. The 5’ transcript library was sequenced with Illumina Novaseq. The single cell TCR enriched library was sequenced with Illumina Miseq using 150 paired-end reads. HTO/ADTs from Cell hashing or CITE-seq were amplified using specific primers that append P5 and P7 sequences for illumina sequencing (Miseq or Nextseq). All fastq files were demultiplexed. Cell hashing and CITE-seq barcodes are available in attached text files. Fastq files from RNA-seq and TCR-seq can be processed through cellranger and vdjranger by 10xgenomics. The datasets include the data of independent experiments at May 29, June 16, June 23, and Aug 13, 2019. Details are available in Masuda et al., bioRxiv, 2020, The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.
2022-03-02 | E-MTAB-9455 | biostudies-arrayexpress
Project description:The development of CD4+ T cells and CD8+ T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-MHCI or MHCII by the T cell antigen receptor (TCR) determines the CD8+ T cell or CD4+ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell state for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4+ T cell lineage differentiation during an initial wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8+ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR-calcineurin-NFAT-GATA3 axis in driving the CD4+ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate multiple redundant mechanisms in guiding lineage choice.
2023-06-30 | GSE186078 | GEO
Project description:This dataset contains single cell RNAseq and CITE-seq of human hematopoietic progenitors differentiated in vitro from hiPSCs. We provide processed files corresponding to counts and metadata for the RNA-seq and the CITE-seq. For the RNA-seq dataset suspension CD235a-CD43+live cells collected at day 13 of differentiation were analysed. For the CITE-seq dataset, suspension CD235a-live cells and adherent CD31+ and CD31- were analysed. ADT tags for membrane markers are also contained in the dataset. More details are available in Fidanza et al, Blood 2020.
2020-07-06 | E-MTAB-9295 | biostudies-arrayexpress
Project description:In chronic inflammatory diseases with an autoimmune component like atherosclerosis, some regulatory T cells (Tregs) lose their regulatory function and become exTregs. The present study was designed to identify surface markers specific of human exTregs, using an integrated approach from sorted mouse exTregs bulk RNA-Seq to human scRNA-Seq with CITE-Seq, to sort human exTregs and characterize them by transcriptome and function. We crossed inducible Treg lineage tracker mice (FoxP3-eGFP-Cre-ERT2 ROSA26CAG-fl-stop-fl-tdTomato) to atherosclerosis-prone Apoe -/- mice, sorted Tregs and exTregs from lymph nodes and spleens of replicate mice and determined their transcriptomes by bulk RNA sequencing (RNA-Seq). A support vector machine (SVM) approach identified the leading signature genes for exTregs as CST7, NKG7, GZMA, PRF1, TBX21 and CCL4. Projecting these genes onto feature maps of human PBMC single cell (sc)RNA-Seq with CITE-Seq from 61 subjects with and without atherosclerosis showed that CST7, NKG7, GZMA, PRF1, TBX21 and CCL4 mapped to CD4 T cells that expressed CD56 and CD16. This finding was validated in a second, independent scRNA- and CITE-Seq dataset. Even in healthy volunteers, a subpopulation of CD4 T cells expressed both CD56 and CD16. Bulk RNA-Seq identified these cells as cytotoxic CD4 T cells, which was functionally confirmed in a cell killing assay. DNA sequencing for TCRβ showed clonal expansion of Treg CDR3 sequences in CD16 + CD56 + exTregs. Taken together, we identify mouse and human exTregs as cytotoxic CD4 T cells.
2023-07-25 | GSE217010 | GEO
Project description:Severe cutaneous adverse reactions (SCAR) are rare but life-threatening drug reactions mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SCAR cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing (5' scRNA-TCR-CITE-seq, 10x Genomics) on unaffected skin, affected skin, and blister fluid from diverse SCAR patients.
2024-09-18 | GSE275871 | GEO
Project description:In human studies, mononuclear cells from peripheral blood (PBMC) often serve as a source of clinical study markers. Therefore, it is essential to understand to what extent phenotypes of PBMCs reflect their tissue-resident equivalents. In order to determine the heterogeneity of T-follicular helper (TFH) cells in peripheral blood versus tonsils, CD3+CD4+CD45RA–CXCR5+ cells of both origins were sorted and transcriptomes, TCR repertoires and cell-surface protein expression were analysed by single-cell RNA sequencing, flow cytometry and immunohistochemistry. Four subsets of TFH cells with classical T-follicular gene expression patterns were mostly found in tonsils. Interestingly, however, all circulating CD3+CD4+CXCR5+ T-cell subpopulations also appeared in tonsils. Still, when circulating, cells of the same cluster rather displayed markers of proliferation and migration, whereas their tonsillar counterparts exhibited known TFH characteristics resembling bona fide germinal center-typical TFH cell subtypes. Surprisingly, one distinct and oligoclonal CD4+CXCR5+ subpopulation displayed pronounced cytotoxic properties. Those ‘killer TFH (TFK) cells’ were found among PBMCs as well as tonsillar cells but were located outside of germinal centers. Accordingly, they were the only CD4+CXCR5+ T-cell subtype in tonsils featuring transcripts for CXCR3 and PSLG1. They appeared terminally differentiated and could be distinguished from all other TFH subsets by expression of NKG7 (TIA-1), granzymes, perforin, CCL5, CCR5, EOMES, CRTAM and CX3CR1. This hitherto undescribed subpopulation is indicative for chronic infection and inflammation and therefore is a valuable candidate to be included in any CD4+CXCR5+ TFH cell assessment.
2024-06-24 | GSE218131 | GEO
Project description:Purpose: Chronic pancreatitis (CP) is considered an irreversible fibroinflammatory pancreatic disease with no active FDA approved therapy. Due to difficulty in accessing pancreas tissues, little is known about local immune responses in human CP. Here we attempted to uncover the disease-specific immune responses in pancreata from two different etiologies of CP (hereditary and idiopathic CP) compared with those from non-diseased controls by using CITE-seq and scTCR-seq. Methods: We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) and T cell receptor sequencing of pancreatic immune cells isolated from organ donors (n=3) and CP patients (Hereditary CP, n=5; Idiopathic CP, n=4) who underwent total pancreatectomy. Results: Deep single-cell sequencing revealed distinct immune characteristics and a significantly enriched CCR6+ CD4+ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T cell clonality was observed due to the increased CD4+ T (Th) cells that replaced tissue resident CD8+ T cells. Lineage tracing analysis with scRNA/TCR-seq data also unveiled unique interactions between CCR6+ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of the CCR6 expression in CD4+ T cells was confirmed by flow cytometry and migration assay. Conclusions: Our approaches with integrative single-cell analyses unveiled distinct pancreatic immune signatures and pathways between different etiologies of CP. Our study specifically unveiled pancreas-specific immune crosstalks through a CCR6-CCL20 axis that might be leveraged as a potential future target in human hereditary CP
2021-09-01 | GSE165045 | GEO
Project description:T cell development in the human thymus has primarily been studied using antibody-based approaches, such as flow cytometry, which can create difficulties in translating phenotypic findings to scRNA-seq data. In order to bridge this gap and obtain paired surface protein and RNA information for individual cells, we carried out CITE-seq with a 143-plex customised antibody panel on human postnatal thymocytes. This was further combined with TCR-seq for TRA and TRB loci to gain insights into the V(D)J recombination progress in developing cells. Using information from all three modalities, we annotated over 30 different stages of human T cell development, which align with known surface marker profiles. This data was utilised in the context of the human thymus spatial atlas for high-resolution spatial mapping of developing T cells, which revealed differences in the migration and maturation kinetics of CD4 and CD8 lineage single positive thymocytes.
2024-07-08 | GSE271304 | GEO