Project description:While immune signaling has emerged as a defining feature of the glioma microenvironment, local selection of responding T cells and their anti-tumor potential as a population are difficult to measure directly in patients. High-throughput sequencing of T cell receptor repertoires (TCRseq) provides a population-wide statistical description of how T cells respond to disease. Here, we define new immunophenotypes in glioma based on TCRseq and RNA-Seq of tumor tissue, non-neoplastic brain tissue, and peripheral blood from patients. Using information theory, we characterize antigen-driven selection in glioma and its relationship with the expression of distinct immune-functional pathways in the tumor microenvironment. Finally, we identify a strong relationship between usage of certain TCR in peripheral blood and the divergence of the infiltrating T cell population from the peripheral repertoire. We anticipate that these immunophenotypes will be foundational to monitoring and predicting response to anti-glioma vaccines and immunotherapy. We characterized the T cell receptor (TCR) repertoires of 11 high-grade glioma patients, three low-grade glioma patients, and thee non-glioma patients by TCRseq of brain-infiltrating T cells and matching peripheral blood. In addition, we obtained gene expression profiles from brain tissue of each patient by RNA-Seq. We additionally measured the TCR repertoires exclusively from peripheral blood of one additional non-glioma patient.
Project description:Thymic education of Tregs is superior to negative selection in the prevention of autoimmunity. To address this hypothesis, TCR repertoires of thymic and peripheral Tcells (including Tregs) from conditional NIK KO and WT mice have been sequenced and compared.
Project description:We performed single-cell RNA-sequencing to create a cell census of the human thymus during development, early childhood and adult life. We sampled 15 embryonic and fetal thymi spanning thymic developmental stages between 7 post-conception weeks (PCW) to 17 PCW, and 9 postnatal thymi from paediatric and adult samples. We compared the cellular composition and T cell differentiation within human and mouse thymus using newly generated and repository mouse datasets. Finally, we investigated the bias in the recombination and selection of human versus mouse TCR repertoires.
Project description:In this work, we studied clonal T-cell repertoires of synovial fluid from a large cohort of SpA patients aiming to characterise the TCR repertoire structure and to identify specific T-cell clonal expansions
Project description:The data corresponds to the analysis of T cell receptor (TCR) repertoires of FACS-purified Tstem, Tpex and TEM cells of six individuals. The analysis of the TCR beta chain (TRB) demonstrated the differences between Tstem and Tpex repertoire properties. In total, 36 samples were analyzed using the Human TCR Profiling Kit (MiLaboratory LLC) for sequencing libraries preparation and Illumina NextSeq 550 sequencing (150+150bp) followed by the demultiplexing procedure using MIGEC software.
Project description:The purpose of this study was to evaluate the influence of ablating PD-1+ cells on alloreactive T cell repertoires. We established the murine skin transplantation model and obtained the draining lymph nodes (dLNs) T cells from recipients for TCR repertoires sequencing.
Project description:Disease relevant B cells during post-rituximab (RTX)relapseemerge from the unsuccessfuldepletion of pre-existing B cell clones; single-celltranscriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cellsubsets.
2020-08-03 | GSE149133 | GEO
Project description:TCR repertoires in murine T cell transfer colitis experiment 20160223
| PRJNA587989 | ENA
Project description:TCR repertoires in murine T cell transfer colitis experiment 20151214
| PRJNA588015 | ENA
Project description:TCR repertoires in murine T cell transfer colitis experiment 20160126
