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3df1461f-2cfc-439f-8ff3-a746aa33f622 - samples

ABSTRACT: 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.

PROVIDER: EGAD00001005047 | EGA |

REPOSITORIES: EGA

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Single-cell TCR sequencing of DQ2.2-glut-L1-specific T cells

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-ÃŽÂ± and TCR-ÃŽÂ² 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.

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00a21d79-64e3-4f09-a16e-3836d5ab7c74 - samples

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.

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dca23f3c-c32b-4ecd-9def-aef945f90182 - samples

Project description:In order to characterize the T cell receptor (TCR) repertoire of gluten specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-ÃŽÂ± and TCR-ÃŽÂ² genes of the single HLA-DQ2.5:DQ2.5-gluten tetramer binding CD4+ T cells isolated from blood, biopsies and T cell line from celiac disease patients.

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Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

Project description:Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

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Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

Project description:HLA-E molecules can present self and pathogen-derived peptides to both NK-cells and T-cells. T-cells that recognize HLA-E peptides via their T-cell receptor (TCR) are termed donor-unrestricted T-cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T-cells from 21 individuals recognizing HLA-E tetramers (TM) folded with 2 Mtb HLA-E restricted peptides. We sorted HLA-E Mtb TM+ and TMCD8+ T-cells directly ex vivo and performed bulk RNA-sequencing and single cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E Mtb specific T-cells have a highly diverse TCR repertoire.

2024-02-04 | GSE236154 | GEO

Single cell RNA-seq of human CD8+ T cells binding the IAV HLA-A24/PB1 498-505 tetramer

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Project description:<p>High-throughput linking of T cell receptor (TCR) sequences to their binding antigens is vital for immune profiling, yet challenging. We present Tetramer associated TCR Sequencing (TetTCR-Seq) to address this challenge. Binding is determined using a library of DNA-barcoded antigen tetramers that are rapidly and inexpensively generated using an in vitro transcription/translation platform. We included CMV+ donors (CMV seropositive donors who are infected with Cytomegalovirus) to screen for CMV specific TCRs.</p>

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Different Binding Motifs of the Celiac Disease Associated HLA Molecules DQ2.5, DQ2.2 and DQ7.5 Revealed by Relative Quantitative Proteomics of Endogenous Peptide Repertoires

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

Hypocretin-specific CD4+ T cells in narcolepsy patients and controls: in vivo clonal expansion and phenotypes

Project description:Individuals with narcolepsy suffer from abnormal sleep patterns due to loss of neurons that uniquely supply hypocretin (HCRT). Previous studies found the associations of narcolepsy with human leukocyte antigen (HLA)-DQ6 allele and T-cell receptor α (TRA) J24 gene segment and also suggested that in vitro-stimulated T cells can target HCRT. However, DQ6+ individuals generate DQ6-HCRT tetramer+/TRAJ24+ TCRs. Without a proof that an HCRT-reactive cell expressing such TCRs has expanded in vivo, T cell-mediated autoimmunity in narcolepsy remains speculative. Here, we isolated DQ6-HCRT tetramer+/CD4+ T cells (low frequency, <0.04%) from DQ6+ individuals with/without narcolepsy. Within 74 informative TRAJ24+ TCRαβ from 8/12 patients and 11/12 controls, we identified a conserved family of clonotypes shared by 2 patients and 2 controls using identical α/β genes. TRAJ24-G allele+ clonotypes only expanded in the two patients, whereas a TRAJ24-C allele+ clonotype expanded in a control. A representative tetramer+/G-allele+ TCR showed signaling reactivity to the physiologically modified form of the epitope HCRT87-97. Clonally expanded G-allele+ T cells also exhibited an unconventional effector phenotype. In vivo expansion of HCRT-reactive TRAJ24-G allele+ cells provides critical evidence for an autoimmune contribution to narcolepsy development.

2019-10-15 | GSE135852 | GEO

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