Single-cell and multi-algorithm profiling identifies SNRPG as a Claudin-1-associated regulator of malignant progression in triple-negative breast cancer.

BACKGROUND: The epithelial-cell states and molecular drivers underlying breast cancer (BC) metastasis remain incompletely defined. This study aimed to identify and validate core molecules associated with metastatic progression. METHODS: Single-cell transcriptomics, high-dimensional weighted gene co-expression network analysis, machine learning, and public cohort analyses were integrated to nominate progression-associated candidate genes. The functional relevance of SNRPG and its association with Claudin-1 expression were evaluated using clinical specimens, in vitro functional assays, dual-luciferase reporter assays, a subcutaneous xenograft model, and a tail-vein experimental lung metastasis model. RESULTS: Single-cell analysis revealed a lymph node-enriched epithelial subpopulation with elevated copy-number variation burden and stemness-related features. Multi-algorithm screening prioritized SNRPG as a recurrent candidate feature associated with adverse tumor progression. SNRPG was upregulated in breast cancer and showed high expression in triple-negative breast cancer. Higher SNRPG expression was associated with poorer outcomes in exploratory microarray-based survival analyses. SNRPG knockdown reduced malignant phenotypes in vitro, restrained subcutaneous tumor growth, and decreased thoracic bioluminescence in a tail-vein experimental lung metastasis model. In TNBC cells, SNRPG knockdown increased Claudin-1 expression and CLDN1 promoter activity, whereas concomitant Claudin-1 knockdown counteracted several phenotypic effects of SNRPG depletion in vitro and in vivo. CONCLUSIONS: SNRPG is associated with lymph node-enriched epithelial-cell states and supports malignant phenotypes in the TNBC models examined. Increased CLDN1 expression contributes to the phenotypic effects of SNRPG depletion, although the mechanism linking SNRPG to CLDN1 remains unresolved.