PMEPA1 modulates YAP1 nuclear translocation to disrupt EMT subtypes and promote metastasis in Biliary tract cancer

Biliary tract cancer (BTC) is an aggressive tumor with poor prognosis and limited treatment options. Epithelial-mesenchymal transition (EMT) significantly contributes to BTC metastasis, yet the critical regulators and underlying molecular mechanisms of EMT remain poorly unclear. In our study, we conducted an integrative analysis of single-cell RNA sequencing (scRNA-seq) data from 47 BTC samples, identifying two EMT-enriched epithelial subpopulations and a BTC specific EMT gene set. Using the EMT gene set, we classified BTC patients and noticed that those with elevated EMT scores had worse prognoses. Additionally, multi-omics analyses identified PMEPA1 as a pivotal EMT regulator, with its high expression levels correlating with adverse prognosis and distant metastasis. Functional assays revealed that PMEPA1 knockdown inhibits, while its overexpression promotes EMT progression by modulating Hippo-YAP signaling, specifically YAP1 nuclear localization. Moreover, we forecast and validated topoisomerase inhibitor SN-38 as a potential EMT-targeting agent. SN-38 effectively inhibited BTC cell migration and metastasis in vivo, likely by attenuating the transcriptional activity of PMEPA1 and its upstream regulator FOS. Overall, this research elucidates EMT-related molecular features in BTC, reveals PMEPA1 as a critical EMT driver via the Hippo-YAP1 pathway, and proposes SN-38 as a promising therapeutic candidate, offering new insights into BTC metastasis and precision therapy. Our study identifies PMEPA1 as a central regulator of EMT and metastasis in BTC. The PMEPA1-a isoform bypasses the tumor-suppressive Hippo pathway by inhibiting LATS1/2 kinase activity. This liberates YAP1 to translocate into the nucleus and initiate a pro-EMT gene expression program. Finally, we demonstrate that the drug candidate SN-38 suppresses metastasis by interfering with this PMEPA1/YAP1 signaling module.