Analysis of cancer stem cell mechanism and immune profiling in breast cancer of unknown primary.

[UNLABELLED] Cancer of unknown primary (CUP) encompasses a highly heterogeneous group of cancers with limited therapeutic options and a dismal prognosis. To date, the pathogenesis and immune profiling of CUP have not been fully characterized which could provide more therapeutic targets.Samples of thirteen breast CUPs and five known metastatic breast cancers were subjected to gene expression analysis. The identified cancer stem cell (CSC) phenotype induced by the overexpression of T-cell leukemia/lymphoma-1 A (TCL1A) was validated via cytological experiments.Compared with known metastatic breast cancers, breast CUPs presented various genetic abnormalities mainly involving pluripotency in stem cells and upregulation of immune-related signaling pathways. CUPs also had significantly greater immune cell infiltration and tumor inflammation signature scores, accompanied by a higher trend of PD-L1 expression and tumor-infiltrating lymphocytes. TCL1A, a gene associated with stem cell-like features, was more highly expressed in various types of CUP than in metastases with known primary sites. In triple-negative breast cancer cell lines, overexpression of TCL1A promoted cell proliferation, invasion, and sphere formation and inhibited apoptosis; it also markedly upregulated CSC and epithelial-mesenchymal transition marker expression. Analysis of the downstream signaling pathways affected by TCL1A revealed notable enrichment of the AKT pathway.Breast CUP is characterized by complex genomic alterations and an inflamed immune microenvironment. The significant overexpression of TCL1A and the enrichment of CSC signatures suggest that the TCL1A-AKT axis may serve as a potential therapeutic target, highlighting the CSC phenotype as a critical biological mechanism in the tumorigenesis and progression of CUP.

[SUPPLEMENTARY INFORMATION] The online version contains supplementary material available at 10.1007/s10238-026-02086-7.