Dca23f3c-c32b-4ecd-9def-aef945f90182 - samples
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ABSTRACT:
PROVIDER: EGAD00001006977 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:In order to characterize the T cell receptor (TCR) repertoire of DQ2.5-hor-3-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.5:DQ2.5-hor-3- tetramer binding CD4+ T cells isolated from biopsies of celiac disease patients. We also sequenced the TCR of the T-cell clones (TCCs) that were generated by cloning by limited dilution and antigen-free expansion of HLA-DQ2.5:DQ2.5-hor-3-tetramer binding CD4+ T cells from biopsies of celiac disease patients.
| EGAS00001003674 | EGA
Project description:In order to characterize the T cell receptor (TCR) repertoire of DQ2.5-hor-3-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.5:DQ2.5-hor-3- tetramer binding CD4+ T cells isolated from biopsies of celiac disease patients. We also sequenced the TCR of the T-cell clones (TCCs) that were generated by cloning by limited dilution and antigen-free expansion of HLA-DQ2.5:DQ2.5-hor-3-tetramer binding CD4+ T cells from biopsies of celiac disease patients.
| EGAD00001005048 | EGA
Project description:In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.
| EGAS00001003673 | EGA
Project description:In this study relative quantitative analysis of endogenous peptides by mass spectrometry combined with neural network analysis have been used to address why the alpha- or beta-chain sharing human leukocyte antigen (HLA)-DQ molecules DQ2.5, DQ2.2 and DQ7.5 display different risks for celiac disease. Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. It has recently been shown that T cells of DQ2.5 and DQ2.2 patients recognize different sets of gluten epitopes suggesting that these celiac disease associated DQ molecules select different peptides for display. To explore whether this is the case, we performed a comprehensive, large-scale comparison of the endogenous self-peptides bound to HLA-DQ molecules of B-lymphoblastoid cell lines (B-LCLs). Peptides were eluted from affinity-purified HLA molecules of nine cell lines and subjected to quadrupole orbitrap mass spectrometry and MaxQuant software analysis. Altogether, 12712 endogenous peptides were identified at very different relative abundances. Hierarchical clustering of normalized quantitative data demonstrated significant differences in repertoires of peptides between the three DQ variant molecules. The neural network-based method, NNAlign, was used to identify peptide-binding motifs. The binding motifs of DQ2.5 and DQ7.5 concurred with previously established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine at position P3. The study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease.
2014-12-04 | PXD001205 | Pride
Project description:In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Celiac disease (CeD) is an autoimmune disease where dietary gluten-derived peptides bind the MHC- II molecules HLA-DQ2 or -DQ8 to initiate immune-mediated duodenal mucosal injury. Here, we generated air-liquid interface (ALI) duodenal organoids from endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The ALI organoid immune diversity spanned T, B, plasma, NK and myeloid cells with extensive T and B cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing CeD patient organoids, which was antagonized by MHC-II or NKG2C/D blockade. Gluten epitopes stimulated a CeD organoid network response in lymphoid and myeloid subsets alongside anti-TG2 autoantibody production. Functional studies in CeD organoids revealed IL-7 as a novel gluten-inducible pathogenic modulator which regulated CD8+ T cell-NKG2C/D expression and was necessary and sufficient for epithelial destruction. Further, endogenous IL-7 was markedly induced in patient biopsies from active CeD versus remission disease, predominantly in lamina propria mesenchyme. By preserving epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, facilitates mechanistic investigation, and establishes proof-of-principle for organoid modeling of autoimmunity.
2024-07-12 | GSE200075 | GEO
Project description:In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.
| EGAD00001005047 | EGA
Project description:In this study relative quantitative analysis of endogenous peptides by mass spectrometry combined with neural network analysis have been used to address why the alpha- or beta-chain sharing human leukocyte antigen (HLA)-DQ molecules DQ2.5, DQ2.2 and DQ7.5 display different risks for celiac disease. Celiac disease is caused by intolerance to cereal gluten proteins, and HLA-DQ molecules are involved in the disease pathogenesis by presentation of gluten peptides to CD4+ T cells. It has recently been shown that T cells of DQ2.5 and DQ2.2 patients recognize different sets of gluten epitopes suggesting that these celiac disease associated DQ molecules select different peptides for display. To explore whether this is the case, we performed a comprehensive, large-scale comparison of the endogenous self-peptides bound to HLA-DQ molecules of B-lymphoblastoid cell lines (B-LCLs). Peptides were eluted from affinity-purified HLA molecules of nine cell lines and subjected to quadrupole orbitrap mass spectrometry and MaxQuant software analysis. Altogether, 12712 endogenous peptides were identified at very different relative abundances. Hierarchical clustering of normalized quantitative data demonstrated significant differences in repertoires of peptides between the three DQ variant molecules. The neural network-based method, NNAlign, was used to identify peptide-binding motifs. The binding motifs of DQ2.5 and DQ7.5 concurred with previously established binding motifs. The binding motif of DQ2.2 was strikingly different from that of DQ2.5 with position P3 being a major anchor having a preference for threonine and serine. This is notable as three recently identified epitopes of gluten recognized by T cells of DQ2.2 celiac patients harbor serine at position P3. The study demonstrates that relative quantitative comparison of endogenous peptides sampled from our protein metabolism by HLA molecules provides clues to understand HLA association with disease.
2017-04-01 | MSV000080859 | MassIVE
Project description:Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.
| EGAD00001004081 | EGA
Project description:To examine the T-cell receptors of the gluten-specific T cells in celiac disease, we isolated single CD4+ T cells from blood , gut biopsies or T-cell lines generated from gut biopsies using HLA-DQ2.5 tetramers and determined the sequences of rearranged TCRalpha and TCRbeta gene pairs.
| EGAS00001005047 | EGA
Project description:Single-cell paired TCR sequencing of intraepithelial γδ T-cells in gluten-free diet treated and untreated celiac disease patients and in controls. (Paired end, amplicon sequencing).
| EGAS00001003897 | EGA