Project description:To assess the impact of Arpp21 deficiency on the TCR repertoire, we generated Arpp21-deficient mice from which we isolated CD4 T cells and subjected them to NGS sequencing.
2024-01-17 | GSE226369 | GEO
Project description:TCR repertoire analysis of Tregs
Project description:To assess the impact of Rag1 3'-UTR deficiency on the TCR repertoire, we generated Rag1 3'-UTR -deficient mice from which we isolated CD4 T cells and subjected them to NGS sequencing.
Project description:Primary outcome(s): 1. Evaluation of genome abnormality and gene expression by omics analysis of tumor etc. 2. TCR repertoire analysis and RNA expression analysis etc. of T cells in tumor tissue and peripheral blood. 3. Prediction and identification of tumor neo-antigen and evaluation of immunogenicity etc. 4. Analyze ctDNA(16S rRNA PCR) and feces of patients with advanced solid malignancies over time to profile and monitor cancer-related genomic alterations 5. Assessment of the relationship between the analysis above and clinical pathological features or therapeutic efficacy etc.
Project description:Temporal analysis of T-cell receptor (TCR) repertoire has been used to monitor treatment-induced changes in antigen-specific T cells in patients with cancer. However, lack of experimental model that allows the temporal analysis of TCR repertoire in same individual in homogeneous population limit the understanding of causal relationship between changes in TCR repertoire and antitumor responses. A bilateral tumor model, in which tumor cells were inoculated into the bilateral backs of mice, can be used for temporal analysis in TCR repertoire. In this study, we examined the prerequisite for this strategy: TCR repertoire are conserved between the bilateral tumor with same growth rate. The bilateral tumors with equivalent tumor size and draining lymph nodes (dLN) were collected 13 days after the tumor inoculation to analyze the TCR repertoire of CD4+ and CD8+ T cells. Most of the tumor-infiltrating T-cell clones were highly conserved between the bilateral tumors, and the extent of clonal expansion was equivalent. In addition, the similarity between bilateral tumors were equivalent to the heterogeneity in one side of the tumor. The similarity of TCR repertoire in the bilateral dLN was markedly lower than that of the tumor, suggesting that tumor-reactive T-cell clones induced independently in each dLN were integrated during recirculation and then infiltrated the tumor. These findings suggest that our bilateral tumor model is suitable for temporal monitoring of TCR repertoire to evaluate temporal and treatment-induced changes in tumor-reactive T-cell clones.
Project description:The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identified 642 RBPs in the thymus and focused on Arpp21, which shows selective and dynamic expression in early thymocytes. Arpp21 was downregulated in response to T cell receptor (TCR) and Ca2+ signals. Downregulation required Stim1/Stim2 and CaMK4 expression and involved Arpp21 protein phosphorylation, polyubiquitination and proteasomal degradation. Arpp21 directly bound RNA through its R3H domain, with a preference for uridine-rich motifs, promoting the expression of target mRNAs. Analysis of the Arpp21-bound transcriptome revealed strong interactions with the Rag1 3'-UTR. Arpp21-deficient thymocytes showed reduced Rag1 expression, delayed TCR rearrangement and a less diverse TCR repertoire. This phenotype was recapitulated in Rag1 3'-UTR mutant mice harboring a deletion of the Arpp21 response region. These findings show how thymocyte-specific Arpp21 promotes Rag1 expression to enable TCR repertoire diversity until signals from the TCR terminate Arpp21 and Rag1 activities.
