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Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR

ABSTRACT: We report the discovery of T cell receptors that are present and shared in multiple HLA-matched breast cancer patient tumors using a single cell emulsion based RT-PCR technique that pairs the alpha and beta TCR chains for high throughput analysis

ORGANISM(S): Homo sapiens

PROVIDER: GSE81313 | GEO | 2016/05/11

SECONDARY ACCESSION(S): PRJNA321261

REPOSITORIES: GEO

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Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR.

Project description: Not available

| S-EPMC4961128 | biostudies-literature

The Position Beta57 of IAg7 Controls the Early Anti-Insulin Response and Onset of Diabetes in NOD mice to Link MHC and Disease [RT-PCR]

Project description:Abstract- The class II region of the Major Histocompatibility locus is the main contributor to the genetic susceptibility to type 1 diabetes (T1D). The loss of an aspartic acid at position 57 of diabetogenic HLA-DQ8 chains supports this association; it influences the recognition of peptides in the context of HLA-DQ8, and I-Ag7 using a mechanism termed the P9 switch. Here, we built register-specific insulin MHC tetramers, Ins12-20 and Ins13-21, to examine anti-insulin CD4 T cell responses during the early pre-diabetic phase of disease in mice. A single cell gene expression analysis and single cell T cell receptor (TCR) sequencing of anti-insulin CD4 T cells performed in 6 and 12-week-old NOD mice, revealed tissue-specific gene expression signatures. TCR signaling and clonal expansion were found only in the islets of Langerhans. and produced either classical Th1 differentiation or an unusual Treg phenotype, independent of TCR usage. The early phase of the anti-insulin response was dominated by cells specific for Ins12-20, the register that supports a P9 switch mode of recognition. The presence of the switch was demonstrated by TCR sequencing, re-expression, mutagenesis, and functional testing of alpha/beta TCR pairs in vitro. The genetic correction of the beta57 mutation resulted in the disappearance of D/E residues in the CDR3beta of anti-Ins12-20 T cells, and inability of cells normally activated by a switch to recognize the Ins9-23 peptide. These results provide the first molecular mechanistic explanation that links the unique MHC class II polymorphism of T1D with the recognition of islet antigens and disease onset.

2019-07-18 | GSE134440 | GEO

Germline-like TCR alpha chains dominate shared self-reactive T cell receptors in type 1 diabetes

Project description:Human islet antigen reactive CD4+ memory T cells (IAR T cells) play a key role in the pathogenesis of autoimmune type 1 diabetes (T1D). Using single cell RNA-sequencing (scRNA-seq) to identify T cell receptors (TCRs) in IAR T cells, we have identified a class of TCRs that share TCR alpha chains between individuals (“public”).

2021-12-15 | GSE182870 | GEO

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

Characterization of tumor-infiltrating T cells by TCR-β repertoire analyses

Project description:Local administration of IFN-α-producing proliferating myeloid cells (IFN-α-iPSC-pMCs) inhibited the tumor growth not only at the treatment site but also at the distant site (left). T cell receptor (TCR)-β chain repertoire and complementarity determining region 3 (CDR3) gene sequence analyses of tumor-infiltrating lymphocytes (TILs) showed marked enrichment of T cells with identical TCR-β chains in bilateral tumor tissues.

2019-02-13 | GSE126278 | GEO

Germline-like TCR alpha chains dominate shared self-reactive T cell receptors in type 1 diabetes

Project description:Germline-like TCR alpha chains dominate shared self-reactive T cell receptors in type 1 diabetes

| PRJNA758093 | ENA

Characterization of peripheral blood TCR in patients with Type 1 Diabetes Mellitus by BD Rhapsody™ VDJ CDR3 Assay

Project description:We used the latest technology, BD Rhapsody, to analyze the pairing of α and β chains that constitute the TCR of PBMCs from patients with type 1 diabetes at the single-cell level.

2022-02-28 | GSE197456 | GEO

Enrichment of mutations in multiple DNA sequences using COLD-PCR in emulsion.

Project description: Not available

| S-EPMC3516544 | biostudies-literature

Gene expression profiles of rat liver tissues after high-fat emulsion feeding

Project description:Nonalcoholic fatty liver disease (NAFLD) is a common disorder characterized by excessive hepatic fat accumulation, and potentially resulting in non-alcoholic steatohepatitis (NASH), liver cirrhosis (LC) and end-stage liver disease We used Rat Genome 230 2.0 microarray to further highlight the rat liver tissues after high-fat emulsion feeding.

2015-09-29 | GSE73500 | GEO

Single cell RNA-seq and TCR-seq of T cell responses against DNAJB1-PRKACA

Project description:The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma (FL-HCC), a lethal disease lacking specific therapies. Here, we report on the identification, characterization and first immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in FL-HCC. To characterize the T cell response against DNAJB1-PRKACA-derived HLA class I and HLA class II ligands, single cell RNA sequencing (scRNA-seq) and single cell TCR profiling from CD4+ and CD8+ T cells were performed using 10x Genomics single cell immune profiling.

2022-09-12 | GSE210337 | GEO

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