Integrated transcriptome study reveals a stress response state CD4 +T cells related to immune tolerance in breast cancer.

BACKGROUND: Lymph node status is of great clinical importance in tumor staging and prognosis where antitumoral immunity is generated and preserved. However, the immune landscape of lymph nodes before and after metastasis in breast cancer is not clear. METHODS: We analyze a total of 67 samples from breast cancers and lymph nodes to profile immune cells at single-cell resolution. Additionally, 13 patients with breast cancer were enrolled to confirm our findings using flow cytometry and immunofluorescence with primary breast tumors and axillary lymph nodes. RESULTS: The distribution of immune cells is similar in uninvolved lymph nodes, but heterogeneity of immune cells is observed in metastatic lymph nodes (metLNs) across different subtypes of breast cancer. In metLNs, a cluster of CD4 +T cells (CD4 +T(str) cells) is predominantly found in luminal-like breast cancer with a state of anergy, probably due to immunosuppression caused by myeloid and tumor cells. By comparing scRNA and single-cell T cell receptor seq data, these un-expanded CD4+T(str) cells seldom show shared T cell receptor sequence between primary tumors and paired metLNs, therefore do not migrate from paired metLNs. Moreover, CD4+T(str) cells are associated with poor survival and predicted tolerance to immunotherapy in triple-negative breast cancer. CONCLUSIONS: In summary, we identify a specific cluster of CD4 +T cells related to immune tolerance that serves as a new predictor for immunotherapy in breast cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13058-025-02205-4.