Biology subjects

Nguyen, K. N.

Publications and source records attributed to Nguyen, K. N..

5 recordsLinked to original sources

bioRxiv2025

Dual RNA Polymerase I Inhibition with CX-5461 and BMH-21 Synergizes in Breast Cancer by Activating p53-Dependent Stress

1Hyperactivated ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is a hallmark of cancer and drives elevated ribosome biogenesis required for rapid tumor growth. Several Pol I inhibitors have been identified that induce potent anti-cancer effects. However, clinical application of the first-in-class Pol I inhibitor, CX-5461, has been limited by patient toxicity, which is comparable to other chemotherapies. Identifying synergistic drug combinations offers a promising strategy to maintain on-target anti-cancer effects while minimizing adverse reactions. Synergistic drug combinations involve drugs that enhance each others effect, enabling dose reduction while preserving efficacy. Synergistic drug combinations of Pol I inhibitors and other anti-cancer agents have been reported; however, it remains unclear whether Pol I inhibitors can synergize with each other. We therefore explored whether two Pol I inhibitors synergize in cancer treatment. We found that CX-5461 and BMH-21 significantly reduced MCF-7 breast cancer cell viability at clinically relevant doses. Combined treatment with these inhibitors led to profound viability defects at sub-micromolar concentrations. Our biochemical analysis showed that CX-5461 and BMH-21 combination therapy enhanced Pol I inhibition and p53 activation compared to monotherapy, promoting growth arrest and apoptosis. Collectively, our findings demonstrate that CX-5461 and BMH-21 are complementary in inhibiting Pol I, activating p53, and suppressing cancer cell growth. Based on these pre-clinical findings, dual Pol I inhibition with CX-5461 and BMH-21 represents a promising therapeutic strategy for treating cancer that is potentially both broadly applicable and tolerable.

cancer biology↗

bioRxiv2025

Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence

The SARS-CoV-2 Spike glycoprotein is central to viral infectivity and immune evasion, making it a key target for vaccine and therapeutic design. This trimeric peplomer undergoes dynamic conformational changes, particularly in its Receptor Binding Domain (RBD), which transitions between closed (down) and ACE2-accessible (up) states relative to the rest of the protein, to facilitate host cell entry. Structural understanding of such critical inter-domain motions, as well as epitope exposure quantification, is essential for obtaining an effective molecular handle over this protein and, in turn, exploiting it towards improved immunogen development. Focusing on the early circulating D614G form and the later emerging Delta (B.1.617.2) variant with higher virulence, we performed large-scale molecular dynamics simulations of the soluble form of the Spike in both down and up conformations of the RBD. Guided by differences in overall fluctuations, we described reaction coordinates based on domain rotations and tilting to extract features that distinguish D614G versus Delta structural behavior of the N-terminal Domain (NTD) and RBD. Using reaction coordinate analysis and Principal Component Analysis (PCA), we identify allosteric coupling between the N-terminal Domain (NTD) and RBD, where NTD tilting influences RBD gating. While some of these motions are conserved across variants, Delta exhibits an optimized RBD-gating mechanism that enhances ACE2 accessibility. Additionally, glycan remodeling in Delta enhances shielding at the NTD supersite, contributing to reduced sensitivity to neutralizing antibodies. Finally, we uncover the impact of the D950N mutation in the HR1 region, which modulates downstream Spike dynamics and immune evasion. Together, our findings reveal variant-specific and conserved structural determinants of SARS-CoV-2 Spike function, providing a mechanistic basis for allosteric modulation, glycan-mediated immune evasion, and viral adaptation. These insights offer valuable guidance for rational vaccine and therapeutic design against SARS-CoV-2 and emerging variants.

biophysics↗

bioRxiv2024

Extracellular vesicles from a novel chordoma cell line, ARF-8, promote tumorigenic microenvironmental changes when incubated with the parental cells and with human osteoblasts.

Chordomas are rare, generally slow-growing spinal tumors that nonetheless exhibit progressive characteristics over time, leading to malignant phenotypes and high recurrence rates, despite maximal therapeutic interventions. The tumors are notoriously resistant to therapies and are often in locations that make gross total resections difficult. Here, we describe a new chordoma cell line (ARF-8) derived from an extensive clival chordoma that extended back to the cervical spine. From the cultured cell line we characterized the ARF-8 cellular and extracellular vesicle (EV) proteomes, as well as the impacts of ARF-8 EVs on proteomes and secretomes of recipient cells (both ARF-8 and human osteoblasts) in autocrine and paracrine settings. All the characteristics associated with chordomas as cancers - migration and invasion, therapeutic resistance, metastatic potential - can be driven by tumor EVs. Our proteomic analyses suggested roles for transforming growth factor beta (TGFB) and cell-matrix interactions involving the epithelial-to-mesenchymal transition (EMT), and cell/extracellular matrix interactions in cell migration, consistent with a metastatic tumor phenotype. Our results demonstrated that ARF-8 tumor cell migration was dependent on general (arginine-glycine-aspartic acid [RGD]-based) integrin activity, and ARF-8 EVs could promote such migration. ARF-8 EVs also prompted proteomic/secretomic changes in human osteoblast cells, again with indications that cell-cell and cell-extracellular matrix interactions would be activated. Overall, the EVs promoted predicted tumorigenic phenotypes in recipient cells.

cancer biology↗

bioRxiv2024

Long G4-rich enhancer physically interacts with EXOC3 promoter via a G4:G4 DNA-based mechanism

Enhancers are genomic sequences that function as regulatory elements capable of increasing the transcription of a given gene often located at a considerable distance. The broadly accepted model of enhancer activation involves bringing an enhancer-bound activator protein complex into close spatial proximity to its target promoter through chromatin looping. Equally relevant to the work described herein, roles for guanine (G) rich sequences in transcriptional regulation are now widely accepted. Non-coding G-rich sequences are commonly found in gene promoters and enhancers, and various studies have described specific instances where G-rich sequences regulate gene expression via their capacity to form G-quadruplex (G4) structures under physiological conditions. In light of this, our group previously performed a search for long human genomic stretches significantly enriched for minimal G4 motifs (referred to as LG4s herein) leading to the identification of 301 LG4 loci with a density of at least 80 GGG repeats / 1,000 basepairs (bp) and averaging 1,843 bp in length. Further, in agreement with previous reports indicating that minimal G4s are highly enriched in promoters and enhancers, we found 217/301 LG4 sequences overlap a GeneHancer annotated enhancer, and the gene promoters regulated by these LG4 enhancers were found to be similarly, markedly enriched with G4-capable sequences. Importantly, while the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study was designed to test an alternative hypothesis: that LG4 enhancers physically interact with their cognate promoters via a direct G4:G4 DNA-based mechanism. As such, this work employs a combination of informatic mining and locus-specific immunoprecipitation strategies to establish the spatial proximity of enhancer:promoter pairs within the nucleus then biochemically confirms the ability of individual LG4 ssDNAs to directly and specifically interact with DNA sequences found in their target promoters. In addition, we also identify four single nucleotide polymorphisms (SNPs), occurring within a LG4 enhancer on human chromosome 5, significantly associated with Cystic Fibrosis (CF) lung disease severity (avg. p value = 2.83E-9), presumably due to their effects on the expressions of CF-relevant genes directly regulated by this LG4 enhancer (e.g., EXOC3 and CEP72). Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/577212v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1fee785org.highwire.dtl.DTLVardef@11f0a9org.highwire.dtl.DTLVardef@1cf198corg.highwire.dtl.DTLVardef@1963a55_HPS_FORMAT_FIGEXP M_FIG C_FIG In brief: LG4 enhancers physically interact with gene promoters by forming composite G4 structures where both the LG4 and cognate promoter contribute half of the necessary sequence for G4 formation.

genetics↗

bioRxiv2023

A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture

Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial inner membrane-localized MICOS complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS complexes to promote normal mitochondrial morphology and respiratory function. Bioinformatic analyses reveal that Mmc1 is a distant relative of the Dynamin-Related Protein (DRP) family of GTPases, which are well established to shape and remodel membranes. We find that, like DRPs, Mmc1 self-associates and forms high molecular weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting it does not dynamically remodel membranes. These data are consistent with a model in which Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.

cell biology↗