Shashidhara, L. S. | bioRxiv Science

bioRxiv2025

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

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-{beta} 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 NELFAs role in YAP-driven transcription is conserved in mammalian system and it manifests in a context-dependent manner in the breast cancer.

cancer biology↗

bioRxiv2024

Differences in Cellular mechanics and ECM dynamics shape differential development of wing and haltere in Drosophila

Diverse organ shapes and sizes arise from the complex interplay between cellular properties, mechanical forces, and gene regulation. Drosophila wing-a flat structure and the globular haltere are two homologous flight appendages emerging from a similar group of progenitor cells. The activity of a single Hox transcription factor, Ultrabithorax (Ubx), governs the development of these two distinct organs-wing and haltere with different cell and organ morphologies. Our work reported here on differential development of wing and haltere suggest that the localisation and abundance of actomyosin complexes, apical cell contractility, properties of extracellular matrix, and cell size and shape, which is a result of various cell intrinsic and extrinsic forces, plausibly influence the flat vs. globular geometry of these two organs. We followed the three-dimensional architecture of developing wing and halteres during early pupal morphogenesis, indicating the role of the above-mentioned factors in force generation and in driving differential morphogenesis, leading to different organ shapes. Loss of Ubx function led to wing cell-like cellular features in haltere discs, and corresponding changes at the level of adult organs. We also observed that RNAi-mediated downregulation of Atrophin or Pten, in the background of downregulated Expanded (or elevated Yki), gave rise to varying degrees of haltere to wing homeotic transformations at the cellular as well as adult organ levels. Finally, we provide simulated scenarios based on computational modelling that propose key ingredients required for producing wing- or haltere-like morphologies in Drosophila.

developmental biology↗