CYLD induces high oxidative stress and DNA damage through class I HDACs to promote radiosensitivity in nasopharyngeal carcinoma.

Abnormal expression of Cylindromatosis (CYLD), a tumor suppressor molecule, plays an important role in tumor development and treatment. In this work, we found that CYLD binds to class I histone deacetylases (HDAC1 and HDAC2) through its N-terminal domain and inhibits HDAC1 activity. RNA sequencing showed that CYLD-HDAC axis regulates cellular antioxidant response via Nrf2 and its target genes. Then we revealed a mechanism that class I HDACs mediate redox abnormalities in CYLD low-expressing tumors. HDACs are central players in the DNA damage signaling. We further confirmed that CYLD regulates radiation-induced DNA damage and repair response through inhibiting class I HDACs. Furthermore, CYLD mediates nasopharyngeal carcinoma cell radiosensitivity through class I HDACs. Thus, we identified the function of the CYLD-HDAC axis in radiotherapy and blocking HDACs by Chidamide can increase the sensitivity of cancer cells and tumors to radiation therapy both in vitro and in vivo. In addition, ChIP and luciferase reporter assays revealed that CYLD could be transcriptionally regulated by zinc finger protein 202 (ZNF202). Our findings offer novel insight into the function of CYLD in tumor and uncover important roles for CYLD-HDAC axis in radiosensitivity, which provide new molecular target and therapeutic strategy for tumor radiotherapy.

ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks.

In recent years, drug design has been revolutionized by the application of deep learning techniques, and molecule generation is a crucial aspect of this transformation. However, most of the current deep learning approaches do not explicitly consider and apply scaffold hopping strategy when performing molecular generation. In this work, we propose ScaffoldGVAE, a variational autoencoder based on multi-view graph neural networks, for scaffold generation and scaffold hopping of drug molecules. The model integrates several important components, such as node-central and edge-central message passing, side-chain embedding, and Gaussian mixture distribution of scaffolds. To assess the efficacy of our model, we conduct a comprehensive evaluation and comparison with baseline models based on seven general generative model evaluation metrics and four scaffold hopping generative model evaluation metrics. The results demonstrate that ScaffoldGVAE can explore the unseen chemical space and generate novel molecules distinct from known compounds. Especially, the scaffold hopped molecules generated by our model are validated by the evaluation of GraphDTA, LeDock, and MM/GBSA. The case study of generating inhibitors of LRRK2 for the treatment of PD further demonstrates the effectiveness of ScaffoldGVAE in generating novel compounds through scaffold hopping. This novel approach can also be applied to other protein targets of various diseases, thereby contributing to the future development of new drugs. Source codes and data are available at https://github.com/ecust-hc/ScaffoldGVAE .

Clinical Evaluation of Cystic Renal Masses With Bosniak Classification by Contrast-Enhanced Ultrasound and Contrast-Enhanced Computer Tomography.

OBJECTIVES: The study aims to compare retrospectively three clinically applied methods for the diagnostic performance of cystic renal masses (CRMs) by contrast-enhanced ultrasound (CEUS) and contrast-enhanced computer tomography (CECT) with Bosniak classification system. METHODS: A total of 52 cases of Bosniak II-IV CRMs in 49 consecutive patients were diagnosed from January 2013 to July 2022 and their data were analyzed. All patients had been subjected to CEUS and CECT simultaneously. Pathological diagnoses and masses stability were used as standard references to determine whether lesions were malignant or benign. Then 49 CRMs only with pathologic results were classified into group 1 and 2. RESULTS: A total of 52 CRMs in 49 enrolled patients were classified into 8 category II, 16 category IIF, 15 category III, and 13 category IV by CEUS (EFSUMB 2020), 10 category II, 13 category IIF, 16 category III, and 13 category IV by CEUS (V2019), while 15 category II, 9 category IIF, 13 category III, and 15 category IV by CECT (V2019). Pathological results and masses stability longer than 5 years follow-up performed substantially for CEUS (EFSUMB 2020), CEUS (V2019), and CECT (V2019) (kappa values were 0.696, 0.735, and 0.696, respectively). Among 49 pathologic approving CRMs, wall/septation thickness ≥4 mm, wall/septation thickness, presence of enhancing nodule and the diameter were found to be statistically significant for malignancy. Twenty-two malignant masses were correctly diagnosed by CEUS (V2019), while 21 malignant masses were both correctly diagnosed by CEUS (EFSUMB 2020) and CECT (V2019), and 1 mass was misdiagnosed. CONCLUSIONS: Bosniak classification of EFSUMB 2020 version might be as accurate as version 2019 CEUS and version 2019 CECT in diagnosing CRMs, and CEUS is found to have an excellent safety profile in dealing with clinical works.

LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty.

Deep learning-based molecular generative models have garnered considerable interest in the field of de novo drug design. However, most extant models focus on either ligand-based or structure-based strategies, thereby failing to effectively harness the combined knowledge derived from both ligands and the structure of the binding target. In this article, we introduce LS-MolGen, a novel ligand and structure-integrated molecular generative model. This model synergistically combines representation learning, transfer learning, and reinforcement learning. The targeted knowledge assimilation from transfer learning, coupled with an advanced exploration strategy in reinforcement learning, empowers LS-MolGen to efficiently generate novel and high-affinity molecules efficiently. The comparable performance of our model is affirmed through multiple evaluations, including EGFR, DRD3, CDK2, AA2AR, ADRB2, and a dedicated case study of inhibitor design for SARS-CoV-2 Mpro. The results indicate that LS-MolGen performs better than other ligand-based or structure-based generative models in de novo designing promising compounds with novel scaffolds and high binding affinity. This proof-of-concept study signifies the potential of our ligand- and structure-based generative model, LS-MolGen, as a promising new tool for target-specific molecular generation and drug design.

Sestrin2 provides cerebral protection through activation of Nrf2 signaling in microglia following subarachnoid hemorrhage.

Subarachnoid hemorrhage (SAH) is a neurological emergency characterized by dysfunctional inflammatory response. However, no effective therapeutic options have been reported so far. Microglia polarization has been proposed to exert an essential role in modulating inflammatory response after SAH. Sestrin2 is a stress response protein. Growing evidence has reported that sestrin2 could inhibit M1 microglia and promote M2 microglia polarization. The current study investigated the effects of sestrin2 on microglia phenotype switching and the subsequent brain injury and sought to elucidate the underlying mechanism. We conducted an endovascular perforation SAH model in mice. It was found that sestrin2 was significantly increased after SAH and was mainly distributed in neurons and microglia. Exogenous recombinant human sestrin2 (rh-sestrin2) evidently alleviated inflammatory insults and oxidative stress, and improved neurofunction after SAH. Moreover, rh-sestrin2 increased M2-like microglia polarization and suppressed the number of M1-like microglia after SAH. The protection by rh-sestrin2 was correlated with the activation of Nrf2 signaling. Nrf2 inhibition by ML385 abated the cerebroprotective effects of rh-sestrin2 against SAH and further manifested M1 microglia polarization. In conclusion, promoting microglia polarization from the M1 to M2 phenotype and inducing Nrf2 signaling might be the major mechanism by which sestrin2 protects against SAH insults. Sestrin2 might be a new molecular target for treating SAH.

Conduction Mechanism in Graphene Oxide Membranes with Varied Water Content: From Proton Hopping Dominant to Ion Diffusion Dominant.

Proton conductors, particularly hydrated solid membranes, have various applications in sensors, fuel cells, and cellular biological systems. Unraveling the intrinsic proton transfer mechanism is critical for establishing the foundation of proton conduction. Two scenarios on electrical conduction, the Grotthuss and the vehicle mechanisms, have been reported by experiments and simulations. But separating and quantifying the contributions of these two components from experiments is difficult. Here, we present the conductive behavior of a two-dimensional layered proton conductor, graphene oxide membrane (GOM), and find that proton hopping is dominant at low water content, while ion diffusion prevails with increasing water content. This change in the conduction mechanism is attributable to the layers of water molecules in GOM nanosheets. The overall conductivity is greatly improved by forming one layer of water molecules. It reaches the maximum with two layers of water molecules, resulting from creating a complete hydrogen-bond network within GOM. When more than two layers of water molecules enter the GOM nanosheets, inducing the breakage of the ordered lamellar structure, protons spread in both in-plane and out-of-plane directions inside the GOM. Our results validate the existence of two conduction mechanisms and show their distinct contributions to the overall conductivity. Furthermore, these findings provide an optimization strategy for the design of realizing the fast proton transfer in materials with water participation.

Exploring the pathological relationships between adamantinomatous craniopharyngioma and contiguous structures with tumor origin.

PURPOSE: Identifying relationships between craniopharyngiomas (CPs) and contiguous structures, and tumor origin are crucial for treatments. This study attempted to explore the relationships and tumor origin. METHODS: CPs that underwent endoscopic surgeries were enrolled. The interfacial specimens of CPs attaching the hypothalamus, pituitary stalk (PS), pituitary grand (PG), optic chiasma (OC) and brain tissue (BT) were pathologically examined. Boundaries between CPs and these structures were observed during operations. Expression of ß-catenin and stem cell markers were analyzed to explore the tumor origin. Outcomes of patients were assessed. RESULTS: A total of 34 CPs were categorized into two groups based on the locations of finger-like protrusions (FP). Group A comprised 18 CPs with FP only present in the specimens attaching to hypothalamus. The surface of these CPs was fused with hypothalamus under endoscopic videos. However, the specimens attaching to the PS, PG, OC, and BT showed no FP. Clear boundaries was observed between these CPs and these structures. Group B comprised 16 CPs with FP only present in the specimens attaching to PS. The tumor surface was fused with PS. Specimens attaching to the hypothalamus, PG, OC and BT showed no FP. Clear boundary was observed among these CPs with these structures. These results implied CPs only invaded a certain part of hypothalamic-pituitary axis. ß-catenin and stem cells markers mainly distributed in the FP tissues of both groups. Patients in group B achieved better outcomes than group A. CONCLUSIONS: CPs only invade the hypothalamic-pituitary axis with FP and the FP would be the tumor origin.

The ω3 scaling of the vibrational density of states in quasi-2D nanoconfined solids.

The vibrational properties of crystalline bulk materials are well described by Debye theory, which successfully predicts the quadratic ω2 low-frequency scaling of the vibrational density of states. However, the analogous framework for nanoconfined materials with fewer degrees of freedom has been far less well explored. Using inelastic neutron scattering, we characterize the vibrational density of states of amorphous ice confined inside graphene oxide membranes and we observe a crossover from the Debye ω2 scaling to an anomalous ω3 behaviour upon reducing the confinement size L. Additionally, using molecular dynamics simulations, we confirm the experimental findings and prove that such a scaling appears in both crystalline and amorphous solids under slab-confinement. We theoretically demonstrate that this low-frequency ω3 law results from the geometric constraints on the momentum phase space induced by confinement along one spatial direction. Finally, we predict that the Debye scaling reappears at a characteristic frequency ω× = vL/2π, with v the speed of sound of the material, and we confirm this quantitative estimate with simulations.

Universal dynamical onset in water at distinct material interfaces.

Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol-1.

MicroRNA-25 promotes cell proliferation, migration and invasion in glioma by directly targeting cell adhesion molecule 2.

Numerous microRNAs (miRNAs/miRs) have been demonstrated to serve oncogenic or suppressive roles in glioma. Exploration of the underlying molecular mechanism of miRNAs in the development and progression of glioma is beneficial for the identification of novel therapeutic targets. In the present study, the function of miR-25 in glioma progression, as well as its underlying mechanism, were investigated. It was determined that miR-25 was significantly upregulated in glioma tissues and cell lines compared with normal brain tissues and cells, respectively. Furthermore, high expression levels of miR-25 were associated with an advanced clinical stage. The knockdown of miR-25 expression significantly reduced glioma cell proliferation, migration and invasion. Cell adhesion molecule 2 (CADM2) was identified as a direct target of miR-25 in glioma cells. Moreover, CADM2 expression level was significantly downregulated and inversely correlated with miR-25 expression level in glioma tissues, indicating that the expression of CADM2 was negatively regulated by miR-25. The inhibition of CADM2 expression counteracted the effects on glioma cell proliferation, migration and invasion caused by miR-25 downregulation. Furthermore, CADM2 knockdown considerably promoted the proliferation and migration of glioma cells. In summary, the present study demonstrated that miR-25 was significantly upregulated in glioma and that it promoted glioma cell proliferation, migration and invasion, at least partially, by directly targeting CADM2. These findings expanded the understanding of the molecular mechanism that underlies glioma progression.

Amorphous Redox-Rich Polysulfides for Mg Cathodes.

The lack of appropriate cathodes is restraining the advances of Mg batteries. Crystalline cathode materials suffer from sluggish reaction kinetics and low-capacity delivery. The finite type of crystalline structure further confines the rational design of cathode materials. Herein, we proposed amorphization and anion enrichment as a brand-new strategy to not only enhance the solid-state ion diffusion and provide more ion-storage sites in amorphous structure but also contribute to the local transfer of multiple electrons through the additional anionic redox centers. Accordingly, a series of amorphous titanium polysulfides (a-TiS x , x = 2, 3, and 4) were designed, which significantly outperformed their crystalline counterparts and achieved a highly competitive energy density of ∼260 Wh/kg. The unique Mg2+ storage mechanism involves the dissociation/formation of S-S bonds and changes in the coordination number of Ti, namely, a mixture of conversion and intercalation reaction, accompanied by the joint cationic (Ti) and anionic (S) redox-rich chemistry. Our proposed amorphous and redox-rich design philosophy might provide an innovative direction for developing high-performance cathode materials for multivalent-ion batteries.

Amorphous anion-rich titanium polysulfides for aluminum-ion batteries.

The strong electrostatic interaction between Al3+ and close-packed crystalline structures, and the single-electron transfer ability of traditional cationic redox cathodes, pose challenged for the development of high-performance rechargeable aluminum batteries. Here, to break the confinement of fixed lattice spacing on the diffusion and storage of Al-ion, we developed a previously unexplored family of amorphous anion-rich titanium polysulfides (a-TiS x , x = 2, 3, and 4) (AATPs) with a high concentration of defects and a large number of anionic redox centers. The AATP cathodes, especially a-TiS4, achieved a high reversible capacity of 206 mAh/g with a long duration of 1000 cycles. Further, the spectroscopy and molecular dynamics simulations revealed that sulfur anions in the AATP cathodes act as the main redox centers to reach local electroneutrality. Simultaneously, titanium cations serve as the supporting frameworks, undergoing the evolution of coordination numbers in the local structure.

MMP12 is a potential therapeutic target for Adamantinomatous craniopharyngioma: Conclusions from bioinformatics analysis and in vitro experiments.

Adamantinomatous craniopharyngioma (ACP) is considered a benign intracranial tumor, but it can also exhibit aggressive characteristics. Due to its unique location in the suprasellar, which brings it close to important nerves and vascular structures, ACP can often lead to significant neuroendocrine diseases. The current treatments primarily include surgical intervention, radiation therapy or a combination of the two, but these can lead to serious complications and adversely affect the quality of life of patients. Thus, it is important to identify effective and safe alternatives. Recently, studies have focused on the tumor genome, transcriptome and proteome in an attempt to identify potential therapeutic targets for clinical use. However, studies on this region of the CP are limited; thus, the present study focused on this region. The GSE94349 and GSE68015 datasets were downloaded from the Gene Expression Omnibus database and analyzed. In the in vitro studies, the effect of the matrix metalloproteinase (MMP)12 inhibitor, MMP408, on cell proliferation and protein expression was assessed. The results demonstrated that MMP408 effectively inhibited cell proliferation and migration of ACP cells, and decreased the expression levels of the related proteins. Thus, MMP12 may be used as a potential therapeutic target for the treatment of ACP.

Involvement of Phosphatase and Tensin Homolog in Cyclin-Dependent Kinase 4/6 Inhibitor-Induced Blockade of Glioblastoma.

Dysregulation of retinoblastoma (Rb) signaling pathway have been established as a requirement for glioblastoma (GBM) initiation and progression, which suggests that blockade of CDK4/6-Rb signaling axis for GBM treatment. Palbociclib, a selective inhibitor of the cyclin-dependent kinases CDK4/6, has been applied for breast cancer treatment. However, its efficacy against glioblastoma has not been well clarified. Here, effects of CDK4/6 inhibitors on various kinds of GBM cell lines are investigated and the functional mechanisms are identified. Data showed that cells with diverse PTEN status respond to palbociclib differently. Gain-of-function and loss-of-function studies indicated that PTEN enhanced the sensitivity of GBM cells to palbociclib in vitro and in vivo, which was associated with suppressions of Akt and ERK signaling and independent of Rb signaling inhibition. Hence, our findings support that palbociclib selectively.

miR-25-3p promotes glioma cell proliferation and migration by targeting FBXW7 and DKK3.

MicroRNAs (miRs) serve important roles in glioma. However, the underlying molecular mechanism of miR-25 in glioma progression remains largely unknown; therefore, it was investigated in the present study. RT-qPCR analysis revealed that miR-25 expression levels were markedly increased in human glioma tissue and glioma cell lines compared with normal brain tissues and normal human astrocytes, respectively. miR-25 upregulation exhibited an association with glioma progression, and the knockdown of miR-25 significantly inhibited glioma cell proliferation and migration. F-box and WD repeat domain containing 7 (FBXW7) and dickkopf WNT signaling pathway inhibitor 3 (DKK3) were identified as target genes of miR-25. FBXW7 and DKK3 expression levels were significantly downregulated in glioma tissue samples compared with normal brain tissue, and their expression levels were negatively regulated by miR-25 expression in glioma cells. Furthermore, inhibition of FBXW7 and DKK3 expression suppressed the miR-25-induced effects on glioma cell proliferation and migration. The findings of the present study suggest that miR-25 may promote glioma cell proliferation and migration by inhibiting the expression of FBXW7 and DKK3. Therefore, miR-25 may serve as a promising molecular target for the treatment of glioma.

Direct Experimental Characterization of Contributions from Self-Motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity.

One fundamental challenge in biophysics is to understand the connection between protein dynamics and its function. Part of the difficulty arises from the fact that proteins often present local atomic motions and collective dynamics on the same time scales, and challenge the experimental identification and quantification of different dynamic modes. Here, by taking lyophilized proteins as the example, we combined deuteration technique and neutron scattering to separate and characterize the self-motion of hydrogen and the collective interatomic motion of heavy atoms (C, O, N) in proteins on the pico-to-nanosecond time scales. We found that hydrogen atoms present an instrument-resolution-dependent onset for anharmonic motions, which can be ascribed to the thermal activation of local side-group motions. However, the protein heavy atoms exhibit an instrument-resolution-independent anharmonicity around 200 K, which results from unfreezing of the relaxation of the protein structures on the laboratory equilibrium time (100-1000 s), softening of the entire bio-macromolecules.