Abstract
T-cell receptor (TCR) repertoires are central to antitumor immunity, yet their dynamics in digestive system cancers remain poorly defined. We profiled TCR repertoires from 415 tumors in 145 patients with colorectal cancer (CRC, n = 96), gastric cancer (GC, n = 47), and hepatocellular carcinoma (LIHC, n = 2), integrating clinical and pathological features. Distinct repertoire architectures emerged: CRC was characterized by abundant TRB V–J combinations (e.g., TRBV10-2*00–TRBJ2-4*00), whereas GC showed higher abundance of TRG/TRD pairings (e.g., TRGV5P*00–TRGJP1*00, TRDV3*00–TRDJ1*00), reflecting tumor-specific immune surveillance. Conserved motifs (“CATWD,” “YKKLF”) across cancers indicate shared selective pressures, while antigen mapping revealed both common (KRAS, SF3B1, and BST2) and tumor-specific targets (MAGEA10, WT1 in CRC; PABPC1 in GC). In CRC, repertoire dynamics were tightly coupled to disease stage. Metastatic tumors (MT) displayed larger size, vascular invasion, and elevated serum markers, whereas primary tumors (PT) exhibited stronger immune infiltration with lymphocyte- and myeloid-driven responses. Tumor size was significantly and positively correlated with the number of TRD/TRG clonotypes shared between PT and MT. Shared clones were further classified into three categories, including stable, contracted, and expanded. Among these, expanded MT clones were dominated by the “NYGYTF” motif within the TRB chain (e.g., TRBV7-9*00–TRBJ1-2*00). The most abundant “NYGYTF”-containing clones recognized MLANA, a tumor-associated antigen linked to prognosis and therapeutic responsiveness, underscoring its potential role in CRC progression. Collectively, these findings delineate cancer- and stage-specific TCR repertoire alterations and antigen specificities, highlighting novel biomarkers and therapeutic targets to inform TCR-based diagnostics and personalized immunotherapies in CRC and GC.
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Data availability
The raw data generated in this study has been deposited at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1205408. Publicly available data utilized in this research were obtained from the TCGA-COAD transcriptomic expression dataset and associated clinical data. In addition, the GSE110224 dataset36 was obtained from the GEO database and comprises 17 normal tissue samples and 17 colorectal cancer (CRC) tumor samples.
Code availability
All the code used for the analysis can be accessed by the corresponding author on reasonable request.
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Acknowledgements
This work was supported by Shandong Provincial Natural Science Foundation (No. ZR2025MS1517).
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Y.n.Z conceived the study, applied for ethical approval, provided administrative support, and finalized the revised manuscript. L.L. conducted data analysis and drafted the manuscript, while J.L. organized clinical data, performed statistical analyses, and prepared the figures. F.W. collected and processed specimens and contributed to manuscript drafting, and R.J. carried out data analysis and figure preparation. H.W. was responsible for specimen processing, quality control, and guiding the writing and revision of the manuscript. X.L. performed data analysis and contributed to revising the manuscript.
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Li, L., Li, J., Wang, F. et al. T-cell receptor clonotypic diversity and specialization in digestive system cancers. npj Precis. Onc. (2026). https://doi.org/10.1038/s41698-026-01294-4
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DOI: https://doi.org/10.1038/s41698-026-01294-4
