Analysis of tumor-related features of non-small cell lung cancer based on TCR repertoire workflow

doi:10.3969/j.issn.1674-8115.2023.12.006

Abstract

Abstract:

Objective ·To explore the immune-related characteristics of non-small cell lung cancer (NSCLC), discover potential tumor markers in V-J genes, and lay the foundation for establishing a TCR-antigen recognition prediction model. Methods ·A total of 704 NSCLC samples were collected to establish a comprehensive T-cell receptor (TCR) repertoire analysis workflow. The upstream analysis included steps such as raw data processing, quality control, filtering, TCR sequence identification, and extraction. The downstream analysis included repertoire clone distribution, clone typing, V-J gene sharing, CDR3 distribution characteristics, and clone tracking. The sample clone distribution was analyzed by using indices such as Shannon-Weiner index and Chao1 index. Clone typing was performed based on the number of clone amplifications to explore differences among different types. The degree of V-J gene segment sharing was analyzed, and the sharing of low-frequency clone types was determined through clone amplification weight analysis of V-J genes by using two samples of papillary thyroid carcinoma. Finally, analysis of the distribution characteristics of V genes and high-frequency clone type CDR3, and clone tracking analysis were conducted to monitor changes in tumor immune clone frequencies before and after analysis, aiming to identify potential tumor markers. Results ·① Significant differences were observed in clone distribution and clone typing among different NSCLC tissues, as well as among different ages and genders. ② Specific highly-shared V-J genes were identified in the analysis of V-J gene sharing, and non-normal distribution of high-clone V genes and amino acid high-frequency clone types were found in the CDR3 distribution analysis. ③ In the analysis of high-frequency clone type clone tracking, highly expressed or newly expressed high-frequency clone types were observed in NSCLC, suggesting that these clone types could serve as potential tumor-associated antigens or bind with CDR3 reference sequences of new antigens. ④ It was found that the expression frequency of TRBJ2-5 gene, originally low-expressed, significantly increased, indicating its potential role as a key low-frequency gene in tumor immune response. Conclusion ·The TRAV21 and TRBV6.5 genes show high clone amplification in NSCLC and could serve as potential tumor biomarkers.

Key words: T cell receptor (TCR), TCR repertoire, tumor immunity, non-small cell lung cancer (NSCLC)

CLC Number:

Q939.91

ZHAO Zhuoming, LIU Zhenhao, LU Manman, ZHANG Yu, XU Linfeng, XIE Lu. Analysis of tumor-related features of non-small cell lung cancer based on TCR repertoire workflow[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2023, 43(12): 1520-1528.

Figures/Tables 5

Fig 1 NSCLC clonal distribution and clonal proportion analysis

Fig 2 V-J gene sharing of TRA and TRB

Fig 3 Distribution characteristics of TRA and TRB V gene and high frequency clonotype CDR3 in NSCLC patients

Fig 4 High-frequency clonotype clone tracking in NSCLC patients

Fig 5 Comparison of clonal amplification and clonotype gene sharing in PTC

TrendMD

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