NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

Abstract Overexpression of YAP is associated with tumor progression in multiple malignancies. YAP is the key transcriptional effector of Hippo signaling: a conserved pathway from Drosophila (Yki) to humans (YAP). In a Drosophila screen, we identified NELFA, a core component of the promoter-proximal pausing (PPP) complex, as a suppressor of Yki-driven hyperproliferation. We investigated whether PPP–YAP regulatory interaction is conserved in mammalian system. In HEK293T and MDA-MB-231 cells, we demonstrate that NELFA depletion amplifies YAP-driven transcription. Whole-transcriptome analysis of MDA-MB-231 cells revealed widespread reprogramming upon NELFA loss, with strong enrichment of YAP signatures, EMT and TGF-β transcriptional networks—indicating that NELFA regulates a broad YAP-centered gene regulatory module. Clinical analysis of two independent breast cancer cohorts revealed a context-dependent role for NELFA. Low NELFA expression predicted poor disease-free survival in YAP-high tumors—particularly in triple-negative breast cancer (TNBC)—suggesting a tumor-suppressive role. While High NELFA expression correlated with poorer overall survival in all the subtypes. These findings confirm that NELFA’s role in YAP-driven transcription is conserved in mammalian system and it manifests in a context-dependent manner in the breast cancer.