High-throughput sequencing and analyses of the TCR repertoire
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA688233 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13313409_1.fastq.gz | Fastqsanger.gz | |||
| SRR13313409_2.fastq.gz | Fastqsanger.gz | |||
| SRR13313410_1.fastq.gz | Fastqsanger.gz | |||
| SRR13313410_2.fastq.gz | Fastqsanger.gz | |||
| SRR13313411_1.fastq.gz | Fastqsanger.gz |
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Project description:We co-cultured T cells with Mo-DCs exposed to ConA for 24 h and used multiplex PCR and next-generation sequencing to detect the TCRα repertoire.The length of the amino acids of CDR3 in each group was 4–59 amino acids, and all presented a normal distribution. Moreover, the length of the amino acids of CDR3 was not different between ConA and control groups. The number of clonotypes and unique clonotypes in the ConA group was increased significantly compared with that in control groups. However, the difference of high-frequency CDR3 amino-acid clonotypes between ConA and control groups was not significant (cutoff = 0.2%). Our results for the V and J gene segments of TCR diversity showed a marked increase in the number of clonotypes in the ConA group. The Shannon–Wiener Diversity Index of ConA was lower than that in the control group, and the top-20 V and J gene segments of ConA showed a higher usage frequency than that in the control group, but the difference between ConA and the control group was not significant. Collectively, these data indicated that ConA could reduce CDR3 diversity and augment usage of high-frequency CDR3.
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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.
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