Deciphering the Effects of the PYCR Family on Cell Function, Prognostic Value, Immune Infiltration in ccRCC and Pan-Cancer.

Pyrroline-5-carboxylate reductase (PYCR) is pivotal in converting pyrroline-5-carboxylate (P5C) to proline, the final step in proline synthesis. Three isoforms, PYCR1, PYCR2, and PYCR3, existed and played significant regulatory roles in tumor initiation and progression. In this study, we first assessed the molecular and immune characteristics of PYCRs by a pan-cancer analysis, especially focusing on their prognostic relevance. Then, a kidney renal clear cell carcinoma (KIRC)-specific prognostic model was established, incorporating pathomics features to enhance predictive capabilities. The biological functions and regulatory mechanisms of PYCR1 and PYCR2 were investigated by in vitro experiments in renal cancer cells. The PYCRs' expressions were elevated in diverse tumors, correlating with unfavorable clinical outcomes. PYCRs were enriched in cancer signaling pathways, significantly correlating with immune cell infiltration, tumor mutation burden (TMB), and microsatellite instability (MSI). In KIRC, a prognostic model based on PYCR1 and PYCR2 was independently validated statistically. Leveraging features from H&E-stained images, a pathomics feature model reliably predicted patient prognosis. In vitro experiments demonstrated that PYCR1 and PYCR2 enhanced the proliferation and migration of renal carcinoma cells by activating the mTOR pathway, at least in part. This study underscores PYCRs' pivotal role in various tumors, positioning them as potential prognostic biomarkers and therapeutic targets, particularly in malignancies like KIRC. The findings emphasize the need for a broader exploration of PYCRs' implications in pan-cancer contexts.

Engineering of Methionine Adenosyltransferase toward Mitigated Product Inhibition for Efficient Production of S-Adenosylmethionine.

S-Adenosylmethionine (SAM) is a crucial metabolic intermediate playing irreplaceable roles in organismal activities. However, the synthesis of SAM by methionine adenosyltransferase (MAT) is hindered by low conversion due to severe product inhibition. Herein structure-guided semirational engineering was conducted on MAT from Escherichia coli (EcMAT) to mitigate the product inhibitory effect. Compared with the wild-type EcMAT, the best variant E56Q/Q105R exhibited an 8.13-fold increase in half maximal inhibitory concentration and a 4.46-fold increase in conversion (150 mM ATP and l-methionine), leading to a SAM titer of 47.02 g/L. Another variant, E56N/Q105R, showed superior thermostability with an impressive 85.30-fold increase in half-life (50 °C) value. Furthermore, molecular dynamics (MD) simulation results demonstrate that the alleviation in product inhibitory effect could be attributed to facilitated product release. This study offers molecular insights into the mitigated product inhibition, and provides valuable guidance for engineering MAT toward enhanced catalytic performance.

Flaring Inflammation and ER Stress by an Organelle-Specific Fluorescent Cage.

The endoplasmic reticulum (ER) plays an important role in protein synthesis and its disruption can cause protein unfolding and misfolding. Accumulation of such proteins leads to ER stress, which ultimately promotes many diseases. Routine screening of ER activity in immune cells can flag serious conditions at early stages, but the current clinically used bio-probes have limitations. Herein, an ER-specific fluorophore based on a biocompatible benzothiadiazole-imine cage (BTD-cage) with excellent photophysical properties is developed. The cage outperforms commercially available ER stains in long-term live cell imaging with no fading or photobleaching over time. The cage is responsive to different levels of ER stress where its fluorescence increases accordingly. Incorporating the bio-probe into an immune disorder model, a 6-, 21-, and 48-fold increase in intensity is shown in THP-1, Raw 246.7, and Jurkat cells, respectively (within 15 min). These results strongly support that this system can be used for rapid visual and selective detection of ER stress. It is envisaged that tailoring molecular interactions and molecular recognition using supramolecular improved fluorophores can expand the library of biological probes for enhanced selectivity and targetability toward cellular organelles.

Abnormal coagulation after hepatectomy in patients with normal preoperative coagulation function.

BACKGROUND: To explore the risk factors for postoperative abnormal coagulation (PAC) and establish a predictive model for patients with normal preoperative coagulation function who underwent hepatectomy. MATERIALS AND METHODS: A total of 661 patients with normal preoperative coagulation function who underwent hepatectomy between January 2015 and December 2021 at the First Affiliated Hospital of Sun Yat-sen University were divided into two groups: the postoperative abnormal coagulation group (PAC group, n = 362) and the normal coagulation group (non-PAC group, n = 299). Univariate and multivariate logistic analyses were used to identify the risk factors for PAC. RESULTS: The incidence of PAC in 661 patients who underwent hepatectomy was 54.8% (362/661). The least absolute shrinkage and selection operator (LASSO) method was used for multivariate logistic regression analysis. The preoperative international normalized ratio (INR), intraoperative succinyl gelatin infusion and major hepatectomy were found to be independent risk factors for PAC. A nomogram for predicting the PAC after hepatectomy was constructed. The model presented a receiver operating characteristic (ROC) curve of 0.742 (95% confidence interval (CI): 0.697-0.786) in the training cohort. The validation set demonstrated a promising ROC of 0.711 (95% CI: 0.639-0.783), and the calibration curve closely approximated the true incidence. Decision curve analysis (DCA) was performed to assess the clinical usefulness of the predictive model. The risk of PAC increased when the preoperative international normalized ratio (INR) was greater than 1.025 and the volume of intraoperative succinyl gelatin infusion was greater than 1500 ml. CONCLUSION: The PAC is closely related to the preoperative INR, intraoperative succinyl gelatin infusion and major hepatectomy. A three-factor prediction model was successfully established for predicting the PAC after hepatectomy.

An Amphiphilic Cell-Penetrating Macrocycle for Efficient Cytosolic Delivery of Proteins, DNA, and CRISPR Cas9.

The discovery of safe platforms that can circumvent the endocytic pathway is of great significance for biological therapeutics that are usually degraded during endocytosis. Here we show that a self-assembled and dynamic macrocycle can passively diffuse through the cell membrane and deliver a broad range of biologics, including proteins, CRISPR Cas9, and ssDNA, directly to the cytosol while retaining their bioactivity. Cell-penetrating macrocycle CPM can be easily prepared from the room temperature condensation of diketopyrrolopyrrole lactams with diamines. We attribute the high cellular permeability of CPM to its amphiphilic nature and chameleonic properties. It adopts conformations that partially bury polar groups and expose hydrophobic side chains, thus self-assembling into micellar-like structures. Its superior fluorescence makes CPM trackable inside cells where it follows the endomembrane system. CPM outperformed commercial reagents for biologics delivery and showed high RNA knockdown efficiency of CRISPR Cas9. We envisage that this macrocycle will be an ideal starting point to design and synthesize biomimetic macrocyclic tags that can readily facilitate the interaction and uptake of biomolecules and overcome endosomal digestion.

Smart touchless human-machine interaction based on crystalline porous cages.

The rise of touchless technology, driven by the recent pandemic, has transformed human-machine interaction (HMI). Projections indicate a substantial growth in the touchless technology market, nearly tripling from $13.6 billion in 2021 to an estimated $37.6 billion by 2026. In response to the pandemic-driven shift towards touchless technology, here we show an organic cage-based humidity sensor with remarkable humidity responsiveness, forming the basis for advanced touchless platforms in potential future HMI systems. This cage sensor boasts an ultrafast response/recovery time (1 s/3 s) and exceptional stability (over 800 cycles) across relative humidity (RH) changes from 11% to 95%. The crystal structure's 3D pore network and luxuriant water-absorbing functional groups both inside and outside of the cage contribute synergistically to superior humidity sensing. Demonstrating versatility, we showcase this cage in smart touchless control screens and touchless password managers, presenting cost-effective and easily processable applications of molecularly porous materials in touchless HMI.

Fluorine-Boosted Kinetic and Selective Molecular Sieving of C6 Derivatives.

Porous molecular sorbents have excellent selectivity towards hydrocarbon separation with energy saving techniques. However, to realize commercialization, molecular sieving processes should be faster and more efficient compared to extended frameworks. In this work, we show that utilizing fluorine to improve the hydrophobic profile of leaning pillararenes affords a substantial kinetic selective adsorption of benzene over cyclohexane (20 : 1 for benzene). The crystal structure shows a porous macrocycle that acts as a perfect match for benzene in both the intrinsic and extrinsic cavities with strong interactions in the solid state. The fluorinated leaning pillararene surpasses all reported organic molecular sieves and is comparable to the extended metal-organic frameworks that were previously employed for this separation such as UIO-66. Most importantly, this sieving system outperformed the well-known zeolitic imidazolate frameworks under low pressure, which opens the door to new generations of molecular sieves that can compete with extended frameworks for more sustainable hydrocarbon separation.

Engineering of Methionine Adenosyltransferase Reveals Key Roles of Electrostatic Interactions in Enhanced Catalytic Activity.

As an important dietary supplement, S-adenosylmethionine (SAM) is currently synthesized by methionine adenosyltransferase (MAT) using ATP and methionine as substrates. However, the activity of MAT is severely inhibited by product inhibition, which limits the industrial production of SAM. Here, MAT from Bacteroides fragilis (BfMAT), exhibiting relatively low product inhibition and moderate specific activity, was identified by gene mining. Based on molecular docking, residues within 5 Å of ATP in BfMAT were subjected to mutagenesis for enhanced catalytic activity. Triple variants M3-1 (E42M/E55L/K290I), M3-2 (E42R/E55L/K290I), and M3-3 (E42C/E55L/K290I) with specific activities of 1.83, 1.81, and 1.94 U/mg were obtained, which were 110.5-125.6% higher than that of the wild type (WT). Furthermore, compared with WT, the Km values of M3-1 and M3-3 were decreased by 31.4% and 60.6%, leading to significant improvement in catalytic efficiency (kcat/Km) by 322.5% and 681.1%. All triple variants showed shifted optimal pH from 8.0 to 7.5. Moreover, interaction analysis suggests that the enhanced catalytic efficiency may be attributed to the decreased electrostatic interactions between ATP and the mutation sites (E42, E55, and K290). Based on MD simulation, coulomb energy and binding free energy analysis further reveal the importance of electrostatic interactions for catalytic activity of BfMAT, which could be an efficient strategy for improving catalytic performance of MATs.

Industrial Separation Challenges: How Does Supramolecular Chemistry Help?

The chemical industry and the chemical processes underscoring it are under intense scrutiny as the demands for the transition to more sustainable and environmentally friendly practices are increasing. Traditional industrial separation systems, such as thermally driven distillation for hydrocarbon purification, are energy intensive. The development of more energy efficient separation technologies is thus emerging as a critical need, as is the creation of new materials that may permit a transition away from classic distillation-based separations. In this Perspective, we focus on porous organic cages and macrocycles that can adsorb guest molecules selectively through various host-guest interactions and permit molecular sieving behavior at the molecular level. Specifically, we summarize the recent advances where receptor-based adsorbent materials have been shown to be effective for industrially relevant hydrocarbon separations, highlighting the underlying host-guest interactions that impart selectivity and permit the observed separations. This approach to sustainable separations is currently in its infancy. Nevertheless, several receptor-based adsorbent materials with extrinsic/intrinsic voids or special functional groups have been reported in recent years that can selectively capture various targeted guest molecules. We believe that the understanding of the interactions that drive selectivity at a molecular level accruing from these initial systems will permit an ever-more-effective "bottom-up" design of tailored molecular sieves that, in due course, will allow adsorbent material-based approaches to separations to transition from the laboratory into an industrial setting.

A nomogram for predicting acute kidney injury following hepatectomy: A propensity score matching analysis.

STUDY OBJECTIVE: The low central venous pressure (LCVP) technique is a key technique in hepatectomy, but its impact on acute kidney injury (AKI) is unclear. The purpose of this study was to explore risk factors (in particular LCVP time) for AKI following hepatectomy. DESIGN: A retrospective case-control study with propensity score matching. SETTING: Operating room. PATIENTS: A total of 1949 patients who underwent hepatectomy were studied. INTERVENTIONS: The patients were grouped with or without AKI within 7 days after surgery. Univariable and multivariable analyses were performed, including recognized intraoperative predictors. The final result is represented as a nomogram. MEASUREMENTS: Preoperative, intraoperative and postoperative data were collected. LCVP is monitored directly through a central venous catheter via the right internal jugular vein. MAIN RESULTS: AKI occurred in 148 patients (7.59%). Surgery time, minimum SBP, furosemide administration and norepinephrine were identified as independent risk factors. The area under the curve for the receiver operating characteristic curves was 0.726 (95% CI 0.668-0.783). CONCLUSION: Intraoperative parameters can be used to predict the probability of postoperative AKI. Although AKI increases the length of stay, it may not increase in-hospital mortality. LCVP time was not confirmed to be a risk factor for AKI.

Caging the Hofmeister Effect by a Biomimetic Supramolecular Receptor.

The effect of anions on the solubility and function of proteins was recognized in 1888 and is now termed the Hofmeister effect. Numerous synthetic receptors are known that overcome the associated anion recognition bias. However, we are unaware of a synthetic host being used to overcome Hofmeister effect perturbations to natural proteins. Here, we report a protonated small molecule cage complex that acts as an exo-receptor and displays non-Hofmeister solubility behavior, with only the chloride complex remaining soluble in aqueous media. This cage allows for the activity of lysozyme to be retained under conditions where anion-induced precipitation would otherwise cause it to be lost. To our knowledge, this is the first time a synthetic anion receptor is used to overcome the Hofmeister effect in a biological system.

Polycage membranes for precise molecular separation and catalysis.

The evolution of the chemical and pharmaceutical industry requires effective and less energy-intensive separation technologies. Engineering smart materials at a large scale with tunable properties for molecular separation is a challenging step to materialize this goal. Herein, we report thin film composite membranes prepared by the interfacial polymerization of porous organic cages (POCs) (RCC3 and tren cages). Ultrathin crosslinked polycage selective layers (thickness as low as 9.5 nm) are obtained with high permeance and strict molecular sieving for nanofiltration. A dual function is achieved by combining molecular separation and catalysis. This is demonstrated by impregnating the cages with highly catalytically active Pd nanoclusters ( ~ 0.7 nm). While the membrane promotes a precise molecular separation, its catalytic activity enables surface self-cleaning, by reacting with any potentially adsorbed dye and recovering the original performance. This strategy opens opportunities for the development of other smart membranes combining different functions and well-tailored abilities.

LDC7559 inhibits microglial activation and GSDMD-dependent pyroptosis after subarachnoid hemorrhage.

Mounting evidence indicates that inhibition of microglial activation and neuronal pyroptosis plays important roles in brain function recovery after subarachnoid hemorrhage (SAH). LDC7559 is a newly discovered gasdermin D (GSDMD) inhibitor. Previous studies have demonstrated that LDC7559 could inhibit microglial proliferation and pyroptosis. However, the beneficial effects of LDC7559 on SAH remain obscure. Based on this background, we investigated the potential role and the mechanism of LDC7559 on SAH-induced brain damage both in vivo and in vitro. The findings revealed that microglial activation and neuronal pyroptosis were evidently increased after SAH, which could be markedly suppressed by LDC7559 both in vivo and in vitro. Meanwhile, LDC7559 treatment reduced neuronal apoptosis and improved behavior function. Mechanistically, LDC7559 decreased the levels of GSDMD and cleaved GSDMD after SAH. In contrast, nod-like receptor pyrin domain-containing 3 (NLRP3) inflammasome activation by nigericin increased GSDMD-mediated pyroptosis and abated the beneficial effects of LDC7559 on SAH-induced brain damage. However, LDC7559 treatment did not significantly affect the expression of NLRP3 after SAH. Taken together, LDC7559 might suppress neuronal pyroptosis and microglial activation after SAH by inhibiting GSDMD, thereby promoting brain functional recovery.

PHLDA1 modulates microglial response and NLRP3 inflammasome signaling following experimental subarachnoid hemorrhage.

Balancing microglia M1/M2 polarization is an effective therapeutic strategy for neuroinflammation after subarachnoid hemorrhage (SAH). Pleckstrin homology-like domain family A member 1 (PHLDA1) has been demonstrated to play a crucial role in immune response. However, the function roles of PHLDA1 in neuroinflammation and microglial polarization after SAH remain unclear. In this study, SAH mouse models were assigned to treat with scramble or PHLDA1 small interfering RNAs (siRNAs). We observed that PHLDA1 was significantly increased and mainly distributed in microglia after SAH. Concomitant with PHLDA1 activation, nod-like receptor pyrin domain-containing protein 3 (NLRP3) inflammasome expression in microglia was also evidently enhanced after SAH. In addition, PHLDA1 siRNA treatment significantly reduced microglia-mediated neuroinflammation by inhibiting M1 microglia and promoting M2 microglia polarization. Meanwhile, PHLDA1 deficiency reduced neuronal apoptosis and improved neurological outcomes after SAH. Further investigation revealed that PHLDA1 blockade suppressed the NLRP3 inflammasome signaling after SAH. In contrast, NLRP3 inflammasome activator nigericin abated the beneficial effects of PHLDA1 deficiency against SAH by promoting microglial polarization to M1 phenotype. In all, we proposed that PHLDA1 blockade might ameliorate SAH-induced brain injury by balancing microglia M1/M2 polarization via suppression of NLRP3 inflammasome signaling. Targeting PHLDA1 might be a feasible strategy for treating SAH.

Discovery of D6808, a Highly Selective and Potent Macrocyclic c-Met Inhibitor for Gastric Cancer Harboring MET Gene Alteration Treatment.

MET alterations have been validated as a driven factor in NSCLC and gastric cancers. The c-Met inhibitors, capmatinib, tepotinib, and savolitinib, are only approved for the treatment of NSCLC harboring exon 14 skipping mutant MET. We used a molecular hybridization in conjunction with macrocyclization strategy for structural optimization to obtain a series of 2-(2-(quinolin-6-yl)ethyl)pyridazin-3(2H)-one derivatives as new c-Met inhibitors. One of the macrocyclic compounds, D6808, potently inhibited c-Met kinase and MET-amplified Hs746T gastric cancer cells with IC50 values of 2.9 and 0.7 nM, respectively. It also strongly suppressed Ba/F3-Tpr-Met cells harboring resistance-relevant mutations (F1200L/M1250T/H1094Y/F1200I/L1195V) with IC50 values of 4.2, 3.2, 1.0, 39.0, and 33.4 nM, respectively. Furthermore, D6808 exhibited extraordinary target specificity in a Kinome profiling against 373 wild-type kinases and served as a promising macrocycle-based compound for further anticancer drug development.

Activation of Sirtuin-1 by Pinocembrin Treatment Contributes to Reduced Early Brain Injury after Subarachnoid Hemorrhage.

Subarachnoid hemorrhage (SAH) as a devastating neurological disorder is closely related to heightened oxidative insults and neuroinflammatory injury. Pinocembrin, a bioflavonoid, exhibits different biological functions, such as immunomodulatory, anti-inflammatory, antioxidative, and cerebroprotective activities. Herein, we examined the protective effects and molecular mechanisms of pinocembrin in a murine model of SAH. Using an endovascular perforation model in rats, pinocembrin significantly mitigated SAH-induced neuronal tissue damage, including inflammatory injury and free-radical insults. Meanwhile, pinocembrin improved behavior function and reduced neuronal apoptosis. We also revealed that sirtuin-1 (SIRT1) activation was significantly enhanced by pinocembrin. In addition, pinocembrin treatment evidently enhanced peroxisome proliferator-activated receptor-γ coactivator expression and suppressed ac-nuclear factor-kappa B levels. In contrast, EX-527, a selective SIRT1 inhibitor, blunted the protective effects of pinocembrin against SAH by suppressing SIRT1-mediated signaling. These results suggested that the cerebroprotective actions of pinocembrin after SAH were through SIRT1-dependent pathway, suggesting the potential application of pinocembrin for the treatment of SAH.

EPAS1 Promoter Hypermethylation is a Diagnostic and Prognostic Biomarker for Non-Small Cell Lung Cancer.

Background: The importance of promoter methylation in non-small cell lung cancers (NSCLC) remains to be understood. Thus, we aimed to determine the diagnostic and prognostic value of the methylation of the endothelial PAS domain containing protein-1 (EPAS1) promoter in NSCLC. Methods: EPAS1 promoter methylation levels were quantitated by methylation-specific PCR. Further, we evaluated the expression, promoter methylation, prognostic value, and impact on immune cell infiltration of EPAS1 by analyzing the TCGA database using web-based bioinformatics tools including GEPIA, UALCAN and MethSurv. Results: Our results demonstrated that promoter methylation of EPAS1 downregulated its expression in NSCLC tissues. Additionally, an AUC value of 0.772 indicated that the methylation of the EPAS1 promoter is a potential diagnostic marker for NSCLC. A Kaplan-Meier analysis demonstrated that high methylation levels of CpG sites in the EPAS1 promoter were indicative of poorer overall survival. Further, EPAS1 expression levels were highly correlated with the infiltration of several types of immune cells, including γδ T cells, T follicular helper cells, CD8+ T cells, and CD4+ T-cells. Conclusion: Collectively, our findings suggest that methylation analyses of the EPAS1 promoter could be used as a prognostic biomarker for NSCLC and that EPAS1 potentially plays an important role in immune cell infiltration in NSCLC.

Institution Publication Feature Analysis Based on Time-Series Clustering.

Based on the time series of articles obtained from the literature, we propose three analysis methods to deeply examine the characteristics of these articles. This method can be used to analyze the construction and development of various disciplines in institutions, and to explore the features of the publications in important periodicals in the disciplines. By defining the concepts and methods relevant to research and discipline innovation, we propose three methods for analyzing the characteristics of agency publications: numerical distribution, trend, and correlation network analyses. The time series of the issuance of articles in 30 important journals in the field of management sciences were taken, and the new analysis methods were used to discover some valuable results. The results showed that by using the proposed methods to analyze the characteristics of institution publications, not only did we find similar levels of discipline development or similar trends in institutions, achieving a more reasonable division of the academic levels, but we also determined the preferences of the journals selected by the institutions, which provides a reference for subject construction and development.

Cycloastragenol Confers Cerebral Protection after Subarachnoid Hemorrhage by Suppressing Oxidative Insults and Neuroinflammation via the SIRT1 Signaling Pathway.

Subarachnoid hemorrhage (SAH) is an acute cerebral vascular disease featured by oxidative insults and neuroinflammation. Cycloastragenol (CAG), the major active component of Astragalus radix, has a wide range of biological functions. However, the potential beneficial effects and the underlying molecular mechanisms of CAG on SAH remain obscure. In the current study, the cerebroprotective effects and mechanism of CAG on SAH were evaluated both in vivo and in vitro. Our results indicated that CAG significantly suppressed SAH-triggered oxidative insults, inflammatory mediators production, microglia activation, and the neutrophil infiltration in the brain. In addition, CAG improved neurological function and ameliorated neuronal apoptosis and degeneration after SAH. In vitro results also revealed the therapeutic effects of CAG on neurons and microglia co-culture system. Mechanistically, CAG treatment upregulated sirtuin 1 (SIRT1) expression, inhibited the levels of FoxO1, nuclear factor-kappa B, and p53 acetylation, and suppressed the subsequent oxidative, inflammatory, and apoptotic pathways. In contrast, inhibiting SIRT1 by pretreatment with Ex527 abrogated the protective actions of CAG both in vivo and in vitro models of SAH. Collectively, our findings indicated that CAG could be a promising and effective drug candidate for SAH.

An immune gene signature to predict prognosis and immunotherapeutic response in lung adenocarcinoma.

Lung adenocarcinoma is one of the most common malignant tumors worldwide. The purpose of this study was to construct a stable immune gene signature for prediction of prognosis (IGSPP) and response to immune checkpoint inhibitors (ICIs) therapy in LUAD patients. Five genes were screened by weighted gene coexpression network analysis, Cox regression and LASSO regression analyses and were used to construct the IGSPP. The survival rate of the IGSPP low-risk group was higher than that of the IGSPP high-risk group. Multivariate Cox regression analysis showed that IGSPP could be used as an independent prognostic factor for the overall survival of LUAD patients. IGSPP genes were enriched in cell cycle pathways. IGSPP gene mutation rates were higher in the high-risk group. CD4 memory-activated T cells, M0 and M1 macrophages had higher infiltration abundance in the high-risk group, which was associated with poor overall survival. In contrast, the abundance of resting CD4 memory T cells, monocytes, resting dendritic cells and resting mast cells associated with a better prognosis was higher in the low-risk group. TIDE scores and the expressions of different immune checkpoints showed that patients in the high-risk IGSPP group benefited more from ICIs treatment. In short, an IGSPP of LUAD was constructed and characterized. It could be used to predict the prognosis and benefits of ICIs treatment in LUAD patients.