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Molecular Therapy. Oncology Jun 2024The presence of a poly(A) tail is indispensable for the post-transcriptional regulation of gene expression in cancer. This dynamic and modifiable feature of transcripts...
The presence of a poly(A) tail is indispensable for the post-transcriptional regulation of gene expression in cancer. This dynamic and modifiable feature of transcripts is under the control of various nuclear and cytoplasmic proteins. This study aimed to develop a novel cytoplasmic poly(A)-related signature for predicting prognosis, clinical attributes, tumor immune microenvironment (TIME), and treatment response in hepatocellular carcinoma (HCC). Utilizing RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA), non-negative matrix factorization (NMF), and principal-component analysis (PCA) were employed to categorize HCC patients into three clusters, thus demonstrating the pivotal prognostic role of cytoplasmic poly(A) tail regulators. Furthermore, machine learning algorithms such as least absolute shrinkage and selection operator (LASSO), survival analysis, and Cox proportional hazards modeling were able to distinguish distinct cytoplasmic poly(A) subtypes. As a result, a 5-gene signature derived from TCGA was developed and validated using International Cancer Genome Consortium (ICGC) HCC datasets. This novel classification based on cytoplasmic poly(A) regulators has the potential to improve prognostic predictions and provide guidance for chemotherapy, immunotherapy, and transarterial chemoembolization (TACE) in HCC.
PubMed: 38948919
DOI: 10.1016/j.omton.2024.200816 -
BioRxiv : the Preprint Server For... Jun 2024Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative...
Under stress conditions, cells reprogram their molecular machineries to mitigate damage and promote survival. Ubiquitin signaling is globally increased during oxidative stress, controlling protein fate and supporting stress defenses at several subcellular compartments. However, the rules driving subcellular ubiquitin localization to promote these concerted response mechanisms remain understudied. Here, we show that K63-linked ubiquitin chains, known to promote proteasome-independent pathways, accumulate primarily in non-cytosolic compartments during oxidative stress induced by sodium arsenite in mammalian cells. Our subcellular ubiquitin proteomic analyses of non-cytosolic compartments expanded 10-fold the pool of proteins known to be ubiquitinated during arsenite stress (2,046) and revealed their involvement in pathways related to immune signaling and translation control. Moreover, subcellular proteome analyses revealed proteins that are recruited to non-cytosolic compartments under stress, including a significant enrichment of helper ubiquitin-binding adaptors of the ATPase VCP that processes ubiquitinated substrates for downstream signaling. We further show that VCP recruitment to non-cytosolic compartments under arsenite stress occurs in a ubiquitin-dependent manner mediated by its adaptor NPLOC4. Additionally, we show that VCP and NPLOC4 activities are critical to sustain low levels of non-cytosolic K63-linked ubiquitin chains, supporting a cyclical model of ubiquitin conjugation and removal that is disrupted by cellular exposure to reactive oxygen species. This work deepens our understanding of the role of localized ubiquitin and VCP signaling in the basic mechanisms of stress response and highlights new pathways and molecular players that are essential to reshape the composition and function of the human subcellular proteome under dynamic environments.
PubMed: 38948861
DOI: 10.1101/2024.06.20.598218 -
BioRxiv : the Preprint Server For... Jun 2024Gas vesicles (GVs) based on acoustic reporter genes have emerged as potent contrast agents for cellular and molecular ultrasound imaging. These air-filled, genetically...
Gas vesicles (GVs) based on acoustic reporter genes have emerged as potent contrast agents for cellular and molecular ultrasound imaging. These air-filled, genetically encoded protein nanostructures can be expressed in a variety of cell types to visualize cell location and activity or injected systemically to label and monitor tissue function. Distinguishing GVs from tissue signal deep inside intact organisms requires imaging approaches such as amplitude modulation (AM) or collapse-based pulse sequences, however they have limitations in sensitivity or require irreversible collapse of the GVs that restricts its scope for imaging dynamic cellular processes. To address these limitations, this study explores the utility of harmonic imaging to enhance the sensitivity of non-destructive imaging of GVs and cellular processes. Traditional fundamental-frequency imaging utilizing cross-wave AM (xAM) sequences has been deemed optimal for GV imaging. Contrary to this, we hypothesize that harmonic imaging, integrated with xAM could significantly elevate GV detection sensitivity. To verify our hypothesis, we conducted imaging on tissue-mimicking phantoms embedded with purified GVs, mammalian cells genetically modified to express GVs, and live mice after systemic GV infusion. Our findings reveal that harmonic xAM (HxAM) imaging markedly surpasses traditional xAM in isolating GVs' nonlinear acoustic signature, showcasing significant enhancements in signal-to-background and contrast-to-background ratios across all tested samples. Further investigation into the backscattered spectra elucidates the efficacy of harmonic imaging in conjunction with xAM. HxAM imaging enables the detection of lower concentrations of GVs and cells with ultrasound and extends the imaging depth by up to 20% and imaging performance metrics by up to 10dB. These advancements bolster the capabilities of ultrasound for molecular and cellular imaging, underscoring the potential of using harmonic signals to amplify GV detection.
PubMed: 38948831
DOI: 10.1101/2024.06.18.599141 -
BioRxiv : the Preprint Server For... Jun 2024Cascade is a class 1, type 1 CRISPR-Cas system with a variety of roles in prokaryote defense, specifically against DNA-based viruses. The transposon, Tn6677, encodes a...
Cascade is a class 1, type 1 CRISPR-Cas system with a variety of roles in prokaryote defense, specifically against DNA-based viruses. The transposon, Tn6677, encodes a variant of the type 1F Cascade known as type 1F-3. This Cascade variant complexes with a homodimer of the transposition protein TniQ and leverages the sequence specificity of Cascade to direct the integration activity of the heteromeric transposase tnsA/B, resulting in site-specific transposition of Tn6677. We desire to uncover the molecular details behind R Loop formation of 'Cascade-TniQ.' Due to the lack of a complete model of Cascade-TniQ available at atom-level resolution, we first build a complete model using AlphaFold V2.1. We then simulate this model via classical molecular dynamics and umbrella sampling to study an important regulatory component within Cascade-TniQ, known as the Cas8 'bundle.' Particularly, we show that this alpha helical bundle experiences a free energy barrier to its large-scale translatory motions and relative free energies of its states primarily dependent on a loop within a Cas7 subunit in Cascade-TniQ. Further, we comment on additional structural and dynamical regulatory points of Cascade-TniQ during R Loop formation, such as Cascade-TniQ backbone rigidity, and the potential role TniQ plays in regulating bundle dynamics. In summary, our outcomes provide the first all-atom dynamic representation of one of the largest CRISPR systems, with information that can contribute to understanding the mechanism of nucleic acid binding and, eventually, to transposase recruitment itself. Such information may prove informative to advance genome engineering efforts.
PubMed: 38948825
DOI: 10.1101/2024.06.21.600075 -
BioRxiv : the Preprint Server For... Jun 2024The role of dynamics in enzymatic function is a highly debated topic. Dihydrofolate reductase (DHFR), due to its universality and the depth with which it has been...
The role of dynamics in enzymatic function is a highly debated topic. Dihydrofolate reductase (DHFR), due to its universality and the depth with which it has been studied, is a model system in this debate. Myriad previous works have identified networks of residues in positions near to and remote from the active site that are involved in dynamics and others that are important for catalysis. For example, specific mutations on the Met20 loop in DHFR (N23PP/S148A) are known to disrupt millisecond-timescale motions and reduce catalytic activity. However, how and if networks of dynamically coupled residues influence the evolution of DHFR is still an unanswered question. In this study, we first identify, by statistical coupling analysis and molecular dynamic simulations, a network of coevolving residues, which possess increased correlated motions. We then go on to show that allosteric communication in this network is selectively knocked down in N23PP/S148A mutant DHFR. Finally, we identify two sites in the human DHFR sector which may accommodate the Met20 loop double proline mutation while preserving dynamics. These findings strongly implicate protein dynamics as a driving force for evolution.
PubMed: 38948820
DOI: 10.1101/2024.06.18.599103 -
BioRxiv : the Preprint Server For... Jun 2024Trinucleotide repeat expansions fold into long, stable hairpins and cause a variety of incurable RNA gain-of-function diseases such as Huntington's disease, the myotonic...
Trinucleotide repeat expansions fold into long, stable hairpins and cause a variety of incurable RNA gain-of-function diseases such as Huntington's disease, the myotonic dystrophies, and spinocerebellar ataxias. One approach for treating these diseases is to bind small molecules to the structured RNAs. Both Huntington's disease-like 2 (HDL2) and myotonic dystrophy type 1 (DM1) are caused by a r(CUG) repeat expansion, or r(CUG) . The RNA folds into a hairpin structure with a periodic array of 1×1 nucleotide UU loops (5'C U G/3'G U C; where the underlined nucleotides indicate the Us in the internal loop) that sequester various RNA-binding proteins (RBP) and hence the source of its gain-of-function. Here, we report NMR-refined structures of single 5'C U G/3'G U C motifs in complex with three different small molecules, a diguandinobenzoate ( ), a derivative of where the guanidino groups have been exchanged for imidazole ( ), and a quinoline with improved drug-like properties ( ). These structures were determined using nuclear magnetic resonance (NMR) spectroscopy and simulated annealing with restrained molecular dynamics (MD). Compounds , , and formed stacking and hydrogen bonding interactions with the 5'C U G/3'G U C motif. Compound also formed van der Waals interactions with the internal loop. The global structure of each RNA-small molecule complexes retains an A-form conformation, while the internal loops are still dynamic but to a lesser extent compared to the unbound form. These results aid our understanding of ligand-RNA interactions and enable structure-based design of small molecules with improved binding affinity for and biological activity against r(CUG) . As the first ever reported structures of RNA r(CUG) repeats bound to ligands, these structures can enable virtual screening campaigns combined with machine learning assisted design.
PubMed: 38948793
DOI: 10.1101/2024.06.21.600119 -
ArXiv Jun 2024Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs,...
Markov state models (MSMs) are valuable for studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational states, with the dynamics modeled by a series of Markovian transitions among these states at discrete lag times. Constructing the Markovian model at a specific lag time requires state defined without significant internal energy barriers, enabling internal dynamics relaxation within the lag time. This process coarse grains time and space, integrating out rapid motions within metastable states. This work introduces a continuous embedding approach for molecular conformations using the state predictive information bottleneck (SPIB), which unifies dimensionality reduction and state space partitioning via a continuous, machine learned basis set. Without explicit optimization of VAMP-based scores, SPIB demonstrates state-of-the-art performance in identifying slow dynamical processes and constructing predictive multi-resolution Markovian models. When applied to mini-proteins trajectories, SPIB showcases unique advantages compared to competing methods. It automatically adjusts the number of metastable states based on a specified minimal time resolution, eliminating the need for manual tuning. While maintaining efficacy in dynamical properties, SPIB excels in accurately distinguishing metastable states and capturing numerous well-populated macrostates. Furthermore, SPIB's ability to learn a low-dimensional continuous embedding of the underlying MSMs enhances the interpretation of dynamic pathways. Accordingly, we propose SPIB as an easy-to-implement methodology for end-to-end MSM construction.
PubMed: 38947932
DOI: No ID Found -
ACS Omega Jun 2024Green surfactant (GS) flooding, an environmentally friendly chemical Enhanced Oil Recovery (cEOR) method, is explored in this molecular dynamics (MD) simulation study....
Green surfactant (GS) flooding, an environmentally friendly chemical Enhanced Oil Recovery (cEOR) method, is explored in this molecular dynamics (MD) simulation study. This study evaluates the ability of ()-2-dodecanamido-aminobutanedioic as a GS for cEOR, assessing its performance with hexane (C6), dodecane (C12), and eicosane (C20) as representative oils. In the case of the bulk system, a comprehensive molecular-level investigation provides structural details such as the radial distribution function, solvent-accessible surface area, GS adsorption dynamics, diffusivity, and emulsion stability of the GS, oil, and water systems. Also the impact of the three distinct oils on interfacial tension was examined in the existence of GS molecules. The findings reveal rapid GS molecule aggregation and adsorption on oil droplets, with various impacts on emulsion stability depending on the oil type. Additionally, GS enhances the aggregation of heavy C20 oil molecules in a water medium. The study demonstrates GS's role as an effective emulsifier, facilitating oil droplet recovery, with electrostatic interactions governing micelle formation and van der Waals interactions influencing oil droplet emulsification. These results align with prior experimental data, affirming GS's promising application potential in cEOR while prioritizing environmental sustainability.
PubMed: 38947786
DOI: 10.1021/acsomega.4c01332 -
Cureus May 2024Recurrent breast cancer presents clinical challenges due to its dynamic nature. Turning human epidermal growth factor receptor 2 (HER2) status from negative to positive...
Recurrent breast cancer presents clinical challenges due to its dynamic nature. Turning human epidermal growth factor receptor 2 (HER2) status from negative to positive upon recurrence is a rare but clinically significant phenomenon that can impact treatment decisions. We present the case of a 63-year-old female initially diagnosed with stage IIIA breast cancer, characterized as HER2-negative. However, upon recurrence eight years later, the patient exhibited HER2 conversion, indicating a positive status. Subsequent treatment adjustments were made based on this new HER2-positive status, leading to complete remission. HER2 conversion underscores the dynamic nature of tumor biology in recurrent breast cancer. This case highlights the importance of re-biopsy for accurate biomarker assessment and the necessity of personalized treatment strategies based on current molecular profiles. Understanding and recognizing HER2 conversion in recurrent breast cancer is crucial for optimizing patient outcomes and guiding clinical management decisions. Further research is warranted to elucidate the frequency and clinical implications of HER2 conversion in recurrent breast cancer.
PubMed: 38947649
DOI: 10.7759/cureus.61305 -
IScience Jun 2024The intracellular loops of G protein-coupled receptors (GPCRs) have been shown to play a key role in G protein coupling and selectivity. We recently showed that the...
The intracellular loops of G protein-coupled receptors (GPCRs) have been shown to play a key role in G protein coupling and selectivity. We recently showed that the intrinsically disordered third intracellular loop (ICL3) of β2-adrenergic receptor is dynamic and equilibrates between open and closed conformations to regulate the G protein coupling. In this study, using the extensive molecular dynamics simulations in multi-lipid bilayer models, we show that the lipid phosphatidylinositol 4,5-bisphosphate (PIP2) stabilizes the active state of β2-adrenergic receptor by keeping ICL3 in an open conformation. This stabilization results in a tilt of the receptor within the membrane. Additionally, the ganglioside lipid, GM3 interacts with extracellular loops, impacting the ligand binding site allosterically. This demonstrates the active role of the chemistry of lipids in stabilizing specific GPCR conformations.
PubMed: 38947516
DOI: 10.1016/j.isci.2024.110086