Biology subjects

Nagarkar, S.

Publications and source records attributed to Nagarkar, S..

5 recordsLinked to original sources

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↗

bioRxiv2025

Elemental Composition and Degradation Rate Impact the Biocompatibility of Copper Chalcogenide Nanocrystals

Copper chalcogenide nanocrystals (NCs) are promising candidates for biophotonic applications due to their tunable optical properties. Concrete methods to examine the relationship between their degradation and toxicity are necessary to enable development of nanoconstructs with reduced toxicity. This study compares the degradation and acute cytotoxicity of three compositions of micelle-coated copper chalcogenide NCs: the fluorescent semiconductor copper indium sulfide (CuInS2), and the plasmonic semiconductors copper sulfide (Cu2-xS) and chalcopyrite copper iron sulfide (CuFeS2). We developed a quantitative degradation assay to assess ion release from these ultra-small nanocrystals, revealing that while all three particles biodegrade, CuInS2 and CuFeS2 undergo rapid degradation in artificial lysosomal fluid, leading to a burst release of indium and iron ions. In cellular toxicity assays, CuInS2 exhibited significantly higher acute cytotoxicity than Cu2-xS and CuFeS2, primarily due to indium-induced necrosis. To mitigate this toxicity, an alternative surface-binding polymer coating was introduced, effectively reducing both the degradation rate and cytotoxicity of CuInS2. These findings highlight the influence of both nanocrystal composition and coating chemistry in moderating the acute cytotoxity of degradable nanocrystals, demonstrating that tuning of composition and degradation rate can be used to moderate nanoparticle toxicity.

pharmacology and toxicology↗

bioRxiv2023

DYRK1A interacts with Tuberous Sclerosis complex and promotes mTORC1 activity

DYRK1A, a ubiquitously expressed kinase, is linked to the dominant intellectual developmental disorder, microcephaly and Down syndrome in humans. It regulates numerous cellular processes such as cell cycle, vesicle trafficking and microtubule assembly. DYRK1A is a critical regulator of organ growth; however, how it regulates organ growth is not fully understood. Here, we show that the knockdown of DYRK1A results in reduced cell size, which depends on mTORC1. Using proteomic approaches, we found that DYRK1A interacts with the Tuberous sclerosis complex (TSC) proteins, namely TSC1 and TSC2, which negatively regulate mTORC1 activation. Further, we show that DYRK1A phosphorylates TSC2 at T1462, a modification known to inhibit TSC activity and promote mTORC1 activity. We also found that the reduced cell growth upon knockdown of DYRK1A can be rescued by overexpression of RHEB, an activator of mTORC1. Our findings suggest that DYRK1A inhibits TSC complex activity through inhibitory phosphorylation on TSC2, thereby promoting mTORC1 activity. Further, using the Drosophila neuromuscular junction as a model, we show that the mnb, the fly homologues of DYRK1A, is rescued by RHEB overexpression, suggesting a conserved role of DYRK1A in TORC1 regulation.

molecular biology↗

bioRxiv2019

Promoter proximal pausing limits Yki-induced tumorous growth in Drosophila

Promoter proximal pausing (PPP) of RNA Polymerase II has emerged as a crucial rate-limiting-step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT) and the Negative Elongation Factor (NELF) which are highly conserved from Drosophila to humans. Here we show that RNAi-mediated depletion of bin3 or Hexim of the 7SK snRNP complex or depletion of individual components of the NELF complex enhance Yki-driven growth leading to neoplastic transformation of Drosophila wing imaginal discs. We also show that increased CDK9 expression cooperates with Yki, in driving neoplastic growth. Interestingly, over-expression of CDK9 on its own or in the background of depletion of one of the components of 7SK snRNP or the NELF complex necessarily and specifically needed Yki over-expression to cause tumorous growth. Genome-wide gene expression analyses suggested that deregulation of protein homeostasis is associated with tumorous growth of wing imaginal discs. As both Fat/Hippo/Yki pathway and PPP are highly conserved, our observations may provide insights into mechanisms of oncogenic function of YAP, the orthologue of Yki in human.

cancer biology↗

bioRxiv2019

Genome-wide RNAi screen for context-dependent tumor suppressors identified using in vivo models for neoplasia in Drosophila

Genetic approaches in Drosophila have successfully identified many genes involved in regulation of growth control as well as genetic interactions relevant to the initiation and progression of cancer in vivo. Here, we report on large-scale RNAi-based screens to identify potential tumor suppressor genes that interact with known cancer-drivers: The Epidermal Growth Factor Receptor and the Hippo pathway transcriptional cofactor Yorkie. These screens were designed to identify genes whose depletion drove tissue expressing EGFR or Yki from a state of benign overgrowth into neoplastic transformation in vivo. We also report on an independent screen aimed to identify genes whose depletion suppressed formation of neoplastic tumors in an existing EGFR-dependent neoplasia model. Many of the positives identified here are known to be functional in growth control pathways. We also find a number of novel connections to Yki and EGFR driven tissue growth, mostly unique to one of the two. Thus, resources provided here would be useful to all researchers who study negative regulators of growth in the context of activated EGFR and/or Yki and positive regulators of growth in the context of activated EGFR.

developmental biology↗