Integrated proteomics reveals autophagy landscape and an autophagy receptor controlling PKA-RI complex homeostasis in neurons.

Autophagy is a conserved, catabolic process essential for maintaining cellular homeostasis. Malfunctional autophagy contributes to neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we report a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and brain LC3-interactome reveals roles of neuronal autophagy in targeting proteins of multiple cellular organelles/pathways, including endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) for degradation. By combining phosphoproteomics and functional analysis in human and mouse neurons, we uncovered a function of neuronal autophagy in controlling cAMP-PKA and c-FOS-mediated neuronal activity through selective degradation of the protein kinase A - cAMP-binding regulatory (R)-subunit I (PKA-RI) complex. Lack of AKAP11 causes accumulation of the PKA-RI complex in the soma and neurites, demonstrating a constant clearance of PKA-RI complex through AKAP11-mediated degradation in neurons. Our study thus reveals the landscape of autophagy degradation in human neurons and identifies a physiological function of autophagy in controlling homeostasis of PKA-RI complex and specific PKA activity in neurons.

CYP3A5 unexpectedly regulates glucose metabolism through the AKT-TXNIP-GLUT1 axis in pancreatic cancer.

CYP3A5 is a cytochrome P450 (CYP) enzyme that metabolizes drugs and contributes to drug resistance in cancer. However, it remains unclear whether CYP3A5 directly influences cancer progression. In this report, we demonstrate that CYP3A5 regulates glucose metabolism in pancreatic ductal adenocarcinoma. Multi-omics analysis showed that CYP3A5 knockdown results in a decrease in various glucose-related metabolites through its effect on glucose transport. A mechanistic study revealed that CYP3A5 enriches the glucose transporter GLUT1 at the plasma membrane by restricting the translation of TXNIP, a negative regulator of GLUT1. Notably, CYP3A5-generated reactive oxygen species were proved to be responsible for attenuating the AKT-4EBP1-TXNIP signaling pathway. CYP3A5 contributes to cell migration by maintaining high glucose uptake in pancreatic cancer. Taken together, our results, for the first time, reveal a role of CYP3A5 in glucose metabolism in pancreatic ductal adenocarcinoma and identify a novel mechanism that is a potential therapeutic target.

Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing associated with therapeutic response to splicing inhibitor.

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that jumonji domain containing 6, arginine demethylase, and lysine hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven human neuroblastoma. JMJD6 cooperates with MYC in cellular transformation of murine neural crest cells by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a 'molecular glue' that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

Developing Prussian blue/wood-derived biochar catalyst for persistent organic pollutant degradation: Preparation, characterization, and mechanism.

Biomass-derived biochar shows broad promise for persistent organic pollutants (POPs) degradation and thus establishes a more sustainable homestead. However, effective catalytic performance is still challenging. Herein, an efficient catalyst (Prussian blue decorated wood-derived biochar, PBB) was constructed by introducing Prussian blue (PB) into wood-based biochar to activate peroxymonosulfate (PMS) for removing POPs. After anchoring of PB, the degradation performance of biochar was enhanced (degradation efficiency of methylene blue (MB, 20 mg/L) increased from 52% of biochar to 95% of PBB within 60 min). The PBB presents effective MB degradation performance with a wide pH value (3.0 < pH < 11.0) or co-existing diverse anions (Cl-, NO3-, H2PO4-, and HCO3-). Electron paramagnetic resonance (EPR) analysis as well as electrochemical tests confirmed that the non-radical pathway (1O2) is the key to biochar activation of PMS, but by restricting PB into the biochar, the radical pathway (SO4•- and •OH), the non-radical pathway (1O2), and direct electron transfer can work together to activate PMS. In addition, the degradation efficiency could remain about 80% after five-time cyclic tests. This work elucidates the role of PB nanoparticles in enhancing biochar catalysts, which can inspire the development of a carbon-neutralized, cost-effective, and effective strategy for POPs removal.

Matrin-3 acts as a potential biomarker and promotes hepatocellular carcinoma progression by interacting with cell cycle-regulating genes.

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide. The oncogenic role of Matrin-3 (MATR3), an a nuclear matrix protein, in HCC remains largely unknown. Here, we document the biological function of MATR3 in HCC based on integrated bioinformatics analysis and functional studies. According to the TCGA database, MATR3 expression was found to be positively correlated with clinicopathological characteristics in HCC. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve displayed the diagnostic and prognostic potentials of MATR3 in HCC patients, respectively. Pathway enrichment analysis represented the enrichment of MATR3 in various molecular pathways, including the regulation of the cell cycle. Functional assays in HCC cell lines showed reduced proliferation of cells with stable silencing of MATR3. At the same time, the suppressive effects of MATR3 depletion on HCC development were verified by xenograft tumor experiments. Moreover, MATR3 repression also resulted in cell cycle arrest by modulating the expression of cell cycle-associated genes. In addition, the interaction of MATR3 with cell cycle-regulating factors in HCC cells was further corroborated with co-immunoprecipitation and mass spectrometry (Co-IP/MS). Furthermore, CIBERSORT and TIMER analyses showed an association between MATR3 and immune infiltration in HCC. In general, this study highlights the novel oncogenic function of MATR3 in HCC, which could comprehensively address how aberrant changes in the cell cycle promote HCC development. MATR3 might serve as a prognostic predictor and therapeutic target for HCC patients.

An adaptive stress response that confers cellular resilience to decreased ubiquitination.

Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.

Influence of two kinds of clearance joints on the dynamics of planar mechanical system based on a modified contact force model.

This study takes the slider-crank mechanism with revolute joint and translational joint as the research object and studies the contact force model of the clearance joint and the influence of the hybrid clearance joints on the nonlinear dynamic behavior of the mechanism. A modified contact force model is established based on the simplified elastic oscillator model, which can be used as a normal force in clearance joint. In the new contact force model, the component n of the indentation depth can be arbitrarily selected and it can support the calculation of contact force for both fully elastic recovery, non-elastic recovery and fully inelastic recovery. Based on the LuGre friction model, the tangential friction model of the clearance joint is given. Thus, the normal force and tangential force during the dynamic contact of the clearance joint are formed. Combining Lagrange's equations of the first kind with the modified normal force and tangential friction force, the dynamic equations of the multi-body system with clearance joints are established. The Baumgarte stabilization method is used to improve the numerical stability. The correctness of the dynamic prediction model in the mechanism with clearance joint is verified by experiment. The dynamic analysis of the slider-crank mechanism with mixed clearance joints shows that the revolute clearance joint has a greater influence on the mechanism than the translational clearance, and the revolute clearance joint plays a leading role in the dynamic response.

Modular chimeric cytokine receptors with leucine zippers enhance the antitumour activity of CAR T cells via JAK/STAT signalling.

The limited availability of cytokines in solid tumours hinders maintenance of the antitumour activity of chimeric antigen receptor (CAR) T cells. Cytokine receptor signalling pathways in CAR T cells can be activated by transgenic expression or injection of cytokines in the tumour, or by engineering the activation of cognate cytokine receptors. However, these strategies are constrained by toxicity arising from the activation of bystander cells, by the suboptimal biodistribution of the cytokines and by downregulation of the cognate receptor. Here we show that replacement of the extracellular domains of heterodimeric cytokine receptors in T cells with two leucine zipper motifs provides optimal Janus kinase/signal transducer and activator of transcription signalling. Such chimeric cytokine receptors, which can be generated for common γ-chain receptors, interleukin-10 and -12 receptors, enabled T cells to survive cytokine starvation without induction of autonomous cell growth, and augmented the effector function of CAR T cells in vitro in the setting of chronic antigen exposure and in human tumour xenografts in mice. As a modular design, leucine zippers can be used to generate constitutively active cytokine receptors in effector immune cells.

Preparation of a high-strength, hydrophobic performance starch-based adhesive with oxidative cross-linking via Fenton's reagent.

Starch is a highly attractive carbohydrate in the production for the preparation of adhesives in recent years, due to its widespread availability, renewability, and abundance of reactive hydroxyl groups. However, the mechanical properties, hydrophobicity, self-adhesion, and particularly high energy efficiency are generally unsatisfactory for current starch-based adhesives. On this premise, starch was oxidized using Fenton's reagent in a ""one-pot cooking" process. The prepared oxidized starch was chain expanded by polyvinyl alcohol (PVA) and then cross-linked with a 10 % isocyanate (PM-200) to fabricate a starch-based adhesive (SFA) with a network crosslinked structure. SF12A35%/2.5-55 adhesive shows significantly higher wet shear strength (1.18 MPa), a remarkable 94 % increase compared to SF0A35%/2.5-55. The adhesive film also demonstrates both hydrophobicity (99° contact angle) and exceptional energy efficiency, with a DSC test revealing a notable 10 % elevation in energy efficiency. In addition, the crosslinked structure increases its molecular weight, thereby increasing its self-adhesion (Fig. S1). This study opens up new possibilities for the design and manufacture of multifunctional starch-based adhesives.

Controlling the spacing of the linked graphene oxide system with dithiol linkers under confinement.

2D nanoscale confined systems exhibit behavior that is markedly different from that observed at the macroscale. Confinement can be tuned by controlling the interlayer spacing between confining layers using organic dithiol linkers. Adjusting spacing and selective intercalation have important impacts for catalysis, superconductivity, spin engineering, sodium ion batteries, 2D magnets, optoelectronics, and many other applications. In this study, we report how reaction conditions and organic linkers can be used to create variable, reproducible spacings between graphene oxide to provide confinement systems. We determined the conditions under which the spacing can be variably adjusted by the type of linker used, the concentration of the linker, and the reaction conditions. Employing dithiol linkers of different lengths, such as three (TPDT) and four (QPDT) aromatic rings, we can adjust the spacing between graphene oxide layers under varied reaction conditions. Here, we show that by varying dithiol linker length and using different reaction conditions, we can reproducibly control the spacing between graphene oxide layers from 0.37 nm to over 0.50 nm.

Photocatalytic CO2 Reduction with Dissolved Carbonates and Near-Zero CO2(aq) by Employing Long-Range Proton Transport.

Photocatalytic CO2 reduction (CO2R) in ∼0 mM CO2(aq) concentration is challenging but is relevant for capturing CO2 and achieving a circular carbon economy. Despite recent advances, the interplay between the CO2 catalytic reduction and the oxidative redox processes that are arranged on photocatalyst surfaces with nanometer-scale distances is less studied. Specifically, mechanistic investigation on interdependent processes, including CO2 adsorption, charge separation, long-range chemical transport (∼100 nm distance), and bicarbonate buffer speciation, involved in photocatalysis is urgently needed. Photocatalytic CO2R in ∼0 mM CO2(aq), which has important applications in integrated carbon capture and utilization (CCU), has rarely been studied. Using 0.1 M KHCO3 (aq) of pH 7 but without continuously bubbling CO2, we achieved ∼0.1% solar-to-fuel conversion efficiency for CO production using Ag@CrOx nanoparticles that are supported on a coating-protected GaInP2 photocatalytic panel. CO is produced at ∼100% selectivity with no detectable H2, even with copious protons co-generated nearby. CO2 flux to the Ag@CrOx CO2R sites enhances CO2 adsorption, probed by in situ Raman spectroscopy. CO is produced with local protonation of dissolved inorganic carbon species in a pH as high as 11.5 when using fast electron donors such as ethanol. Isotopic labeling using KH13CO3 was used to confirm the origin of CO from the bicarbonate solution. We then employed COMSOL Multiphysics modeling to simulate the spatial and temporal pH variation and the local concentrations of bicarbonates and CO2(aq). We found that light-driven CO2R and CO2 reactive transport are mutually dependent, which is important for further understanding and manipulating CO2R activity and selectivity. This study enables direct bicarbonate utilization as the source of CO2, thereby achieving CO2 capture and conversion without purifying and feeding gaseous CO2.

Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor.

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

Site-Specific Chemistry on Gold Nanorods: Curvature-Guided Surface Dewetting and Supracolloidal Polymerization.

Control of interparticle interactions in terms of their direction and strength highly relies on the use of anisotropic ligand grafting on nanoparticle (NP) building blocks. We report a ligand deficiency exchange strategy to achieve site-specific polymer grafting of gold nanorods (AuNRs). Patchy AuNRs with controllable surface coverage can be obtained during ligand exchange with a hydrophobic polystyrene ligand and an amphiphilic surfactant while adjusting the ligand concentration (CPS) and solvent condition (Cwater in dimethylformamide). At a low grafting density of ≤0.08 chains/nm2, dumbbell-like AuNRs with two polymer domains capped at the two ends can be synthesized through surface dewetting with a high purity of >94%. These site-specifically-modified AuNRs exhibit great colloidal stability in aqueous solution. Dumbbell-like AuNRs can further undergo supracolloidal polymerization upon thermal annealing to form one-dimensional plasmon chains of AuNRs. Such supracolloidal polymerization follows the temperature-solvent superposition principle as revealed by kinetic studies. Using the copolymerization of two AuNRs with different aspect ratios, we demonstrate the design of chain architectures by varying the reactivity of nanorod building blocks. Our results provide insights into the postsynthetic design of anisotropic NPs that potentially serve as units for polymer-guided supracolloidal self-assembly.

Unraveling Anisotropic and Pulsating Etching of ZnO Nanorods in Hydrochloric Acid via Correlative Electron Microscopy.

Despite much technical progress achieved so far, the exact surface and shape evolution during wet chemical etching is less unraveled, especially in ionically bonded ceramics. Herein, by using in situ liquid cell transmission electron microscopy, a repeated two-stage anisotropic and pulsating periodic etching dynamic is discovered during the pencil shape evolution of a single crystal ZnO nanorod in aqueous hydrochloric acid. Specifically, the nanopencil tip shrinks at a slower rate along [0001̅] than that along the ⟨101̅0⟩ directions, resulting in a sharper ZnO pencil tip. Afterward, rapid tip dissolution happens due to accelerated etching rates along various crystal directions. Concurrently, the vicinal base region of the original nanopencil tip emerges as a new tip followed by the repeated sequence of tip shrinking and removal. The high-index surfaces, such as {101̅m} (m = 0, 1, 2, or 3) and {21̅ 1̅n} (n = 0, 1, 2, or 3), are found to preferentially expose in different ratios. Our 3D electron tomography, convergent beam electron diffraction, middle-angle bright-field STEM, and XPS results indicate the dissociative Cl- species were bound to the Zn-terminated tip surfaces. Furthermore, DFT calculation suggests the preferential Cl- passivation over the {101̅1} and (0001) surfaces of lower energy than others, leading to preferential surface exposures and the oscillatory variation of different facet etching rates. The boosted reactivity due to high-index nanoscale surface exposures is confirmed by comparatively enhanced chemical sensing and CO2 hydrogenation activity. These findings provide an in-depth understanding of anisotropic wet chemical etching of ionic nanocrystals and offer a design strategy for advanced functional materials.

Ribonucleotide reductase subunit switching in hepatoblastoma drug response and relapse.

Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 (RRM2) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B. Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.

Co2Mo6S8 Catalyzes Nearly Exclusive Electrochemical Nitrate Conversion to Ammonia with Enzyme-like Activity.

Electrocatalytic nitrate to ammonia conversion is a key reaction for energy and environmental sustainability. This reaction involves complex multi electron and proton transfer steps, and is impeded by the lack of catalyst for promoting both reactivity and ammonia selectivity. Here, we demonstrate active motifs based on the Chevrel phase Co2Mo6S8 exhibit an enzyme-like high turnover frequency of ∼95.1 s-1 for nitrate electroreduction to ammonia. We reveal strong synergy of multiple binding sites on this catalyst, such that the ligand effect of Co steers Had* toward hydrogenation other than hydrogen evolution, the ensemble effect of Co, and the spatial confinement effect that promote the full hydrogenation of NOx to ammonia without N-N coupling. The catalyst exhibits almost exclusive ammonia conversion with a Faradaic efficiency of 97.1% and ammonia yielding rate of 115.5 mmol·gcat-1·h-1 in neutral electrolytes. The high activity was also confirmed in electrolytes with dilute nitrate and high chloride concentrations.

Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse.

Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 ( RRM2 ) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B . Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.

COVID-19 Detection Using a 3D-Printed Micropipette Tip and a Smartphone.

The COVID-19 pandemic has caused over 7 million deaths worldwide and over 1 million deaths in the US as of October 15, 2022. Virus testing lags behind the level or availability necessary for pandemic events like COVID-19, especially in resource-limited settings. Here, we report a low cost, mix-and-read COVID-19 assay using a synthetic SARS-CoV-2 sensor, imaged and processed using a smartphone. The assay was optimized for saliva and employs 3D-printed micropipette tips with a layer of monoclonal anti-SARS-CoV-2 inside the tip. A polymeric sensor for SARS-CoV-2 spike (S) protein (COVRs) synthesized as a thin film on silica nanoparticles provides 3,3',5-5'-tetramethylbenzidine responsive color detection using streptavidin-poly-horseradish peroxidase (ST-poly-HRP) with 400 HRP labels per molecule. COVRs were engineered with an NHS-PEG4-biotin coating to reduce nonspecific binding and provide affinity for ST-poly-HRP labels. COVRs binds to S-proteins with binding strengths and capacities much larger than salivary proteins in 10% artificial saliva-0.01%-Triton X-100 (as virus deactivator). A limit of detection (LOD) of 200 TCID50/mL (TCID50 = tissue culture infectious dose 50%) in artificial saliva was obtained using the Color Grab smartphone app and verified using ImageJ. Viral load values obtained in 10% pooled human saliva spiked with inactivated SARS-COV-2 virus gave excellent correlation with viral loads obtained from qPCR (p = 0.0003, r = 0.99).