Biology subjects

Nehri, L. N.

Publications and source records attributed to Nehri, L. N..

3 recordsLinked to original sources

bioRxiv2026

Actinomycin D Drives RNA-Binding Proteins into Dynamic Cytoplasmic Granules

Actinomycin D (Act D) is a global transcriptional inhibitor widely used in research and clinical practice; however, its effects on RNA-binding protein (RBP) dynamics remain poorly understood. Analysis of an RNA-seq dataset from Act D-treated HeLa cells revealed a compensatory stress response enriched in RNA metabolism, processing, and translation. Here, we investigated the effects of Act D on the subcellular localization of RBPs using HuR as a model mRNA stabilizing RBP. Short-term Act D treatment markedly increased cytoplasmic HuR localization in HCT116 and HeLa cells where the protein is known to be active. Analysis of known pathways regulating HuR nucleocytoplasmic translocation did not fully explain this redistribution, suggesting alternative mechanisms. To identify proteins proximal to HuR following Act D treatment, we performed TurboID labeling followed by LC-MS/MS in HCT116 cells. Several proteins involved in RNA regulation were identified. Probabilistic modeling highlighted FUS, an RBP with established roles in phase-separated granule dynamics, as a candidate proximal protein. The Act D-dependent interaction between HuR and FUS was interrogated using molecular dynamics simulations and validated with proximity ligation assays. Furthermore, increased cytoplasmic localization of RBPs following Act D treatment was accompanied by formation of granular structures that were relatively fluid and could be disrupted by hypotonic shock. Collectively, our findings demonstrate that Act D induces cytoplasmic redistribution of multiple RBPs and their sequestration into dynamic granular structures, revealing a previously unrecognized cellular response to transcriptional inhibition. Graphical AbstractAct D induced cytoplasmic re-localization of HuR along with FUS and other RBPs in dynamic, hypotonic shock-sensitive granular structures. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/745449v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@f04186org.highwire.dtl.DTLVardef@15dcb0corg.highwire.dtl.DTLVardef@bdbaf9org.highwire.dtl.DTLVardef@3e54b1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Lysosomal Alkalinization Selects for Metabolically Plastic, Motile Cancer Cells under Nutrient Stress.

Cancer cells exposed to nutrient deprivation activate adaptive programs to survive metabolic stress, often acquiring enhanced plasticity and motility. We have previously reported that colon cancer cell lines that survived nutrient depletion underwent partial epithelial-mesenchymal transition (pEMT), which was further exacerbated when these cells also underwent lysosomal alkalinization. Here, we have attempted to dissect the molecular mechanisms that drive the motility and shape change from cobblestone to elongated in subpopulations of cells. Using RNA-seq-based bioinformatic analyses integrated with pathway scoring, protein-protein interaction networks, probabilistic modeling and confirmatory experimental data, we have identified the coordinated activation of sublethal apoptotic signaling, fatty acid oxidation, mitochondrial ROS generation, and Ca{superscript 2}-dependent lysosomal exocytosis in the nutrient-depleted cells. Among these phenotypes, the cells undergoing starvation and lysosomal alkalinization exclusively mediated lysosomal exocytosis and cell motility. Probabilistic modeling further revealed non-linear relationships between metabolic stress signals and cell fate transitions, highlighting heterogeneous lysosomal functions as a key determinant of the altered phenotype of cells under nutrient depletion. Overall, our study has identified that aberrant lysosomal functioning in cells under nutrient depletion can specifically select for a subpopulation of cells that are highly viable, metabolically plastic and capable of motility.

cell biology↗

bioRxiv2025

Development of an EMT-related exosomal miRNA signature that can predict prognosis in hepatocellular carcinoma

Chemoresistance and epithelial-mesenchymal transition (EMT) are associated with failure of cancer chemotherapy and poor survival of patients. We have previously shown that chemoresistance and stemness in hepatocellular carcinoma (HCC) cells was accompanied by the development of partial EMT (p-EMT) and identified a number of EMT-associated proteins that are released from exosomes. In this study, we aimed to identify and classify the differentially expressed (DE) exosomal miRNAs from chemoresistant HuH7 cells undergoing p-EMT. Out of the fifty-four miRNAs that were enriched in the exosomes from these cells compared to controls, thirteen were identified in the exosomes isolated from the serum of HCC patients. These miRNAs targeted genes that were associated with cell-cell junctions, extracellular matrix, cytoskeleton, transcription and signal transduction. Univariate Cox regression analysis indicated that 11/13 miRNAs were associated with either favorable (n=4) or worse (n=7) prognosis. A machine learning algorithm indicated that seven miRNAs (miR 215-5p, miR 340-5p, miR 210-3p, miR 19a-3p, miR19b-3p, miR 1266-5p and miR 25-3p) could predict worse prognosis in multiple datasets with 64-68% accuracy. A Bayesian Inference network analysis with the thirteen miRNAs and their key target proteins, along with EMT and survival as the nodes indicated that the common denominator was transcription, suggesting that the exosomal miRNAs released from cells undergoing p-EMT can mediate phenotypic changes in cells through transcriptional regulation.

cancer biology↗