GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE311nnn/GSE311396/primaryOK200TranscriptomicsHomo sapiensExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311396GEOGSEfalseNELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancerOverexpression of YAP is associated with oncogenesis and tumor progression in multiple malignancies. YAP is the key transcriptional effector of a highly conserved Hippo signaling pathway, from Drosophila (Yki) to humans (YAP). In our previous Drosophila screen, we identified NELFA, a core component of the promoter-proximal pausing (PPP) complex, as a suppressor of Yki-driven hyperproliferation. Building on this observation, we investigated whether this PPP–YAP regulatory interaction is conserved in mammalian cells, using breast cancer as a model system. Using HEK293T and MDA-MB-231 cells, we demonstrate that NELFA depletion selectively amplifies YAP-driven transcription, thereby enhancing the expression of canonical YAP target genes. Whole-transcriptome analysis of NELFA-depleted MDA-MB-231 cells revealed widespread reprogramming upon NELFA loss, with strong enrichment of conserved YAP signatures, EMT and TGF-β pathways, and AP-1/TEAD-SMAD3 transcriptional networks—indicating that NELFA regulates a broad YAP-centered oncogenic module. Clinical analysis of an Indian breast cancer cohort and TCGA revealed a striking 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. Collectively, these findings reveal that NELFA’s role in YAP-driven transcription is context-dependent in the breast cancer setting.2026/05/15GSE311396GSM9324449GSM9324445GSM9324456GSM9324446GSM9324447GSM9324448GSM9324452GSM9324453GSM9324454GSM9324455GSM9324450GSM932445134284311396Homo sapiens[42100387]