Characteristics and transcriptional regulators of spontaneous epithelial-mesenchymal transition in genetically unperturbed patient-derived non-spindled breast carcinoma

• Published in: Breast cancer research : BCR 2024-09, Vol.26 (1), p.130-19, Article 130
• Main Authors: Lien, Huang-Chun, Yu, Hui-Chieh, Yu, Wen-Hsuan, Lin, Su-Fang, Chen, Tom Wei-Wu, Chen, I-Chun, Hsiao, Li-Ping, Yeh, Ling-Chun, Li, Yu-Chia, Lo, Chiao, Lu, Yen-Shen
• Format: Article
• Language: English
• Subjects: Animals; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Breast cancer; Breast carcinoma; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Breast Neoplasms - pathology; Cancer; Carcinoma; Cell culture; Cell Line, Tumor; Cell morphology; Cells; DNA binding proteins; Down-regulation; EMT gene; Epithelial-Mesenchymal Transition - genetics; Epithelial–mesenchymal transition; Female; Flow cytometry; Gene Expression Regulation, Neoplastic; Genes; Genetic transcription; Genomics; Humans; Immunohistochemistry; Mesenchymal–epithelial transition; Metaplastic breast carcinoma; Mice; Morphology; Phenotypes; Physical characteristics; Polymerase chain reaction; Primary cell culture; Quality control; Ribonucleic acid; RNA; RNA sequencing; Single-cell RNA sequencing; Snail protein; Stem cells; Survival analysis; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Tumor cells; Tumors; Up-regulation; Vimentin; Vimentin - genetics; Vimentin - metabolism; Wound healing; Zinc Finger E-box Binding Homeobox 2 - genetics; Zinc Finger E-box Binding Homeobox 2 - metabolism; Zinc Finger E-box-Binding Homeobox 1 - genetics; Zinc Finger E-box-Binding Homeobox 1 - metabolism
• ISSN: 1465-542X; 1465-5411; 1465-542X
• DOI: 10.1186/s13058-024-01888-5

Although tumor cells undergoing epithelial-mesenchymal transition (EMT) typically exhibit spindle morphology in experimental models, such histomorphological evidence of EMT has predominantly been observed in rare primary spindle carcinomas. The characteristics and transcriptional regulators of spontaneous EMT in genetically unperturbed non-spindled carcinomas remain underexplored. We used primary culture combined with RNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), and in situ RNA-seq to explore the characteristics and transcription factors (TFs) associated with potential spontaneous EMT in non-spindled breast carcinoma. Our primary culture revealed carcinoma cells expressing diverse epithelial-mesenchymal traits, consistent with epithelial-mesenchymal plasticity. Importantly, carcinoma cells undergoing spontaneous EMT did not necessarily exhibit spindle morphology, even when undergoing complete EMT. EMT was a favored process, whereas mesenchymal-epithelial transition appeared to be crucial for secondary tumor growth. Through scRNA-seq, we identified TFs that were sequentially and significantly upregulated as carcinoma cells progressed through the EMT process, which correlated with increasing VIM expression. Once upregulated, the TFs remained active throughout the EMT process. ZEB1 was a key initiator and sustainer of EMT, as indicated by its earliest significant upregulation in the EMT process, its exact correlation with VIM expression, and the reversal of EMT and downregulation of EMT-upregulated TFs upon ZEB1 knockdown. The correlation between ZEB1 and vimentin expression in triple-negative breast cancer and metaplastic breast carcinoma tumor cohorts further highlighted its role. The immediate upregulation of ZEB2 following that of ZEB1, along with the observation that the knockdown of ZEB1 or ZEB2 downregulates both ZEB1 and ZEB2 concomitant with the reversal of EMT, suggests their functional cooperation in EMT. This finding, together with that of a lack of correlation of SNAI1, SNAI2, and TWIST1 expression with the mesenchymal phenotype, indicated EMT-TFs have a context-dependent role in EMT. Upregulation of EMT-related gene signatures during EMT correlated with poor patient outcomes, highlighting the biological importance of the model. Elevated EMT gene signatures and increased ZEB1 and ZEB2 expression in vimentin-positive compared to vimentin-negative carcinoma cells within the corresponding primary tumor tissue confirmed ZEB1 and ZEB2 as