Multi-omics single-cell dissection of malignant epithelial heterogeneity identifies GJB2 as an EMT-driving biomarker in triple-negative breast cancer

Tumor heterogeneity poses a major challenge to elucidating the mechanisms underlying tumor progression and metastasis. However, the cellular heterogeneity of triple-negative breast cancer (TNBC) remains incompletely understood. We performed an integrated analysis of publicly available single-cell RNA sequencing (scRNA-seq) datasets from TNBC to identify distinct malignant cell subtypes. Multiple analytical approaches were then applied to comprehensively characterize the metastasis-related subtype. Subsequently, we validated GJB2 as a biomarker of this subtype and confirmed its association with epithelial–mesenchymal transition (EMT) in TNBC cell lines. Based on six scRNA-seq datasets from GSE180286 and GSE161529, we constructed a comprehensive landscape of malignant-cell heterogeneity in TNBC and identified three malignant cell subtypes: an EMT-Subtype, a secretory-like subtype (Sec-like Subtype), and a metabolic subtype (Metab-Subtype). We further identified GJB2 as a marker of the EMT-Subtype. Enrichment analyses indicated that GJB2 was closely associated with the TGF-β signaling pathway, and this finding was further supported by in vitro functional assays. By classifying malignant TNBC cells into three subtypes, we identified GJB2 as a marker of the EMT-Subtype. Mechanistically, GJB2 may promote EMT through the TGF-β signaling pathway and therefore represent a potential therapeutic target in TNBC. Targeting the GJB2–TGF-β axis may provide a promising strategy for suppressing the highly metastatic behavior of TNBC.