Catalpol reduced LPS induced BV2 immunoreactivity through NF-κB/NLRP3 pathways: an in Vitro and in silico study.

Background: Ischemic Stroke (IS) stands as one of the primary cerebrovascular diseases profoundly linked with inflammation. In the context of neuroinflammation, an excessive activation of microglia has been observed. Consequently, regulating microglial activation emerges as a vital target for neuroinflammation treatment. Catalpol (CAT), a natural compound known for its anti-inflammatory properties, holds promise in this regard. However, its potential to modulate neuroinflammatory responses in the brain, especially on microglial cells, requires comprehensive exploration. Methods: In our study, we investigated into the potential anti-inflammatory effects of catalpol using lipopolysaccharide (LPS)-stimulated BV2 microglial cells as an experimental model. The production of nitric oxide (NO) by LPS-activated BV2 cells was quantified using the Griess reaction. Immunofluorescence was employed to measure glial cell activation markers. RT-qPCR was utilized to assess mRNA levels of various inflammatory markers. Western blot analysis examined protein expression in LPS-activated BV2 cells. NF-κB nuclear localization was detected by immunofluorescent staining. Additionally, molecular docking and molecular dynamics simulations (MDs) were conducted to explore the binding affinity of catalpol with key targets. Results: Catalpol effectively suppressed the production of nitric oxide (NO) induced by LPS and reduced the expression of microglial cell activation markers, including Iba-1. Furthermore, we observed that catalpol downregulated the mRNA expression of proinflammatory cytokines such as IL-6, TNF-α, and IL-1ß, as well as key molecules involved in the NLRP3 inflammasome and NF-κB pathway, including NLRP3, NF-κB, caspase-1, and ASC. Our mechanistic investigations shed light on how catalpol operates against neuroinflammation. It was evident that catalpol significantly inhibited the phosphorylation of NF-κB and NLRP3 inflammasome activation, both of which serve as upstream regulators of the inflammatory cascade. Molecular docking and MDs showed strong binding interactions between catalpol and key targets such as NF-κB, NLRP3, and IL-1ß. Conclusion: Our findings support the idea that catalpol holds the potential to alleviate neuroinflammation, and it is achieved by inhibiting the activation of NLRP3 inflammasome and NF-κB, ultimately leading to the downregulation of pro-inflammatory cytokines. Catalpol emerges as a promising candidate for the treatment of neuroinflammatory conditions.

Correction: Liu et al. Endostatin 33 Peptide Is a Deintegrin α6ß1 Agent That Exerts Antitumor Activity by Inhibiting the PI3K-Akt Signaling Pathway in Prostate Cancer. J. Clin. Med. 2023, 12, 1861.

In the original publication [...].

Mechanisms of cuproptosis and its relevance to distinct diseases.

Copper is a trace element required by the organism, but once the level of copper exceeds the threshold, it becomes toxic and even causes death. The underlying mechanisms of copper-induced death are inconclusive, with different studies showing different opinions on the mechanism of copper-induced death. Multiple investigations have shown that copper induces oxidative stress, endoplasmic reticulum stress, nucleolar stress, and proteasome inhibition, all of which can result in cell death. The latest research elucidates a copper-dependent death and denominates it as cuproptosis. Cuproptosis takes place through the combination of copper and lipoylated proteins of the tricarboxylic acid cycle, triggering agglomeration of lipoylated proteins and loss of iron-sulfur cluster proteins, leading to proteotoxic stress and ultimately death. Given the toxicity and necessity of copper, abnormal levels of copper lead to diseases such as neurological diseases and cancer. The development of cancer has a high demand for copper, neurological diseases involve the change of copper contents and the binding of copper to proteins. There is a close relationship between these two kinds of diseases and copper. Here, we summarize the mechanisms of copper-related death, and the association between copper and diseases, to better figure out the influence of copper in cell death and diseases, thus advancing the clinical remedy of these diseases.

An auxiliary strategy of partial least squares regression in pharmacokinetic/pharmacodynamic studies: A case of application of guhong injection in myocardial ischemia/reperfusion rats.

Guhong injection (GHI) has been applied in the therapy of cardio-cerebrovascular disease in clinic, but there is no report about the pharmacokinetic/pharmacodynamic (PK/PD) research on GHI treating myocardial ischemia/reperfusion (MI/R) injury in rats. In this study, eight compounds of GHI in plasma, including N-acetyl-L-glutamine (NAG), chlorogenic acid (CGA), hydroxysafflor yellow A (HSYA), p-coumaric acid ( pCA), rutin, hyperoside, kaempferol-3-O-rutinoside, and kaempferol-3-O-glucoside, were quantified by LC-MS/MS. We discovered that the values of t1/2ß, k12, V2, and CL2 were larger than those of t1/2α, k21, V1, and CL1 for all compounds. The levels of four biomarkers, creatine kinase-MB (CK-MB), cardiac troponin I (cTn I), ischemia-modified albumin (IMA), and alpha-hydroxybutyrate dehydrogenase (α-HBDH) in plasma were determined by ELISA. The elevated level of these biomarkers induced by MI/R was declined to different degrees via administrating GHI and verapamil hydrochloride (positive control). The weighted regression coefficients of NAG, HSYA, CGA, and pCA in PLSR equations generated from The Unscrambler X software (version 11) were mostly minus, suggesting these four ingredients were positively correlated to the diminution of the level of four biomarkers. Emax and ED50, two parameters in PK/PD equations that were obtained by adopting Drug and Statistics software (version 3.2.6), were almost enlarged with the rise of GHI dosage. Obviously, all analytes were dominantly distributed and eliminated in the peripheral compartment with features of rapid distribution and slow elimination. With the enhancement of GHI dosage, the ingredients only filled in the central compartment if the peripheral compartment was replete. Meanwhile, high-dose of GHI generated the optimum intrinsic activity, but the affinity of compounds with receptors was the worst, which may be caused by the saturation of receptors. Among the eight analytes, NAG, HSYA, CGA, and pCA exhibited superior cardioprotection, which probably served as the pharmacodynamic substance basis of GHI in treating MI/R injury.

Clinical Reasoning: A 30-Year-Old Woman Presenting With Rapidly Progressive Dementia and Extreme Hypoglycorrhachia.

A 30-year-old woman presented with rapidly progressive dementia 1 month after the coronavirus disease 2019 infection. Repeated CSF analysis showed extreme hypoglycorrhachia, while cultures, metagenomic next-generation sequencing, and cytopathology testing of CSF were negative. Laboratory investigations for possible etiologies revealed elevated blood ammonia and cancer antigen 125. Brain MRI demonstrated bilateral symmetric diffuse cortical lesions with mild hyperintensity on T1-weighted image and postcontrast enhancement. A more thorough history and specific examinations subsequently indicated an underlying etiology. This case provides an approach for evaluating young patients with rapidly progressive dementia, extreme hypoglycorrhachia, and diffuse CNS lesions, highlighting the importance of considering a broad differential diagnosis.

Current and Potential Roles of Ferroptosis in Bladder Cancer.

Ferroptosis, a type of regulated cell death driven by iron-dependent lipid peroxidation, is mainly initiated by extramitochondrial lipid peroxidation due to the accumulation of iron-dependent reactive oxygen species. Ferroptosis is a prevalent and primitive form of cell death. Numerous cellular metabolic processes regulate ferroptosis, including redox homeostasis, iron regulation, mitochondrial activity, amino acid metabolism, lipid metabolism, and various disease-related signaling pathways. Ferroptosis plays a pivotal role in cancer therapy, particularly in the eradication of aggressive malignancies resistant to conventional treatments. Multiple studies have explored the connection between ferroptosis and bladder cancer, focusing on its incidence and treatment outcomes. Several biomolecules and tumor-associated signaling pathways, such as p53, heat shock protein 1, nuclear receptor coactivator 4, RAS-RAF-MEK, phosphatidylinositol 3-kinase-AKT-mammalian target of rapamycin, and the Hippo-tafazzin signaling system, exert a moderating influence on ferroptosis in bladder cancer. Ferroptosis inducers, including erastin, artemisinin, conjugated polymer nanoparticles, and quinazolinyl-arylurea derivatives, hold promise for enhancing the effectiveness of conventional anticancer medications in bladder cancer treatment. Combining conventional therapeutic drugs and treatment methods related to ferroptosis offers a promising approach for the treatment of bladder cancer. In this review, we analyze the research on ferroptosis to augment the efficacy of bladder cancer treatment.

Kinetic and Thermodynamic Analyses of Co-Pyrolysis of Nylon-Polyethylene Pouch Wastes.

In this study, thermogravimetric measurements of nylon-6/polyethylene double-layer pouch wastes were conducted in N2 under a constant heating-rate mode, and the multiple heating-rate results were analyzed in terms of degradation features and specific temperatures. Experimental results show that the waste pyrolysis involves one reaction stage, and all specific parameters appear to increase with the heating rate. Kinetic analysis of non-isothermal data was thoroughly performed using various isoconversional model-free methods for the calculations of the activation energy, resulting in 143~215 kJ/mol over the whole pyrolysis process. By means of the model-fitting method, the reaction mechanism model g(α) and pre-exponential factor lnk0 are concurrently determined with the aid of the linear compensation effect. With such methodology proposed, the Avrami-Erofeev kinetic model A3/2 of g(α) = [-ln(1 - α)]2/3 is found to be the most appropriate mechanism function for describing the pyrolysis of the nylon-6/polyethylene waste along with lnk0 of 23.14 to 34.26 min-1. With the Arrhenius parameters thus obtained, the predictions were made and performed very satisfactorily to correlate experimental results. Additionally, the service life and thermodynamic parameters over the entire pyrolysis process were also estimated.

An adhesive peptide specifically induces microtubule condensation.

Cell function-associated biomolecular condensation has great potential in modulation of molecular activities. We develop a microtubule-trapping peptide that first self-assembles into nanoparticles and then in situ transforms into nanofibers via ligand-receptor interactions when targeted to tubulin. The nanofibers support the increased exposed targets for further adhering to microtubules and induce the self-assembly of microtubules into networks due to multivalent effects. Microtubule condensation with prolonged retention in cells for up to 24 h, which is 6 times longer than that of the non-transformable nanoparticle group, efficiently induces in vitro cell apoptosis and inhibits in vivo tumour growth. These smart transformable peptide materials for targeted protein condensation have the potential for improving retention and inducing cell apoptosis in tumour therapy.

Mitigating the adverse effects of Aflatoxin B1 in LMH, IPEC-J2 and 3D4/21 cells by a novel integrated agent.

This study was to evaluate the efficacy of TOXO-XL (XL), an integrated mycotoxin-mitigating agent, on aflatoxin B1 (AFB1)-induced damage in Leghorn male hepatoma (LMH), porcine jejunum epithelial cell line (IPEC-J2) and porcine alveolar macrophages (3D4/21) cells, and to explore its potential mechanisms. The results showed that 30% inhibition concentration (IC30) of AFB1 in LMH, IPEC-J2 and 3D4/21 cells was 0.5, 15.0, and 2.5 mg/L, respectively. Notably, cell viability, ROS, apoptosis and DNA lesion induced by AFB1 (IC30) could be ameliorated by the supplementation with XL at the dosage of 0.025, 0.025 and 0.005%, respectively. Additionally, the migration and phagocytosis abilities impaired by AFB1 were also restored by XL in 3D4/21. Further experiments revealed that XL supplementation markedly attenuated AFB1-induced inflammatory response by decreasing IL-1ß, IL-6 and IL-10 in LMH, IL-6 in IPEC-J2 and IL-1ß in 3D4/21 cells. Meanwhile, XL supplementation reversed the alterations of BAX, BCL-2 and caspase-3 induced by AFB1 in the three cells, suggesting that AFB1-induced apoptosis may be suppressed via the mitochondria-dependent pathway. Furthermore, XL may have a protective effect on the intestinal barrier through the restoration of occludin protein. Conclusively, these findings indicated that XL could alleviate AFB1-induced cytotoxicity in the three cells, potentially through the regulation of cytokines, ROS, apoptotic and DNA damage signaling.

Implication of Freeze-Thaw Erosion and Mechanism Analysis of High-Performance Aromatic Liquid Crystal Fibers.

According to the demand for high-performance fibers for high-latitude ocean exploration and development, this paper selects representative products of high-performance liquid crystal fibers: thermotropic liquid crystal polymer fibers (TLCP) and poly p-phenylene terephthalamide (PPTA) fibers. Through a series of freeze-thaw (F-T) experiments for simulating a real, cold marine environment, we then measure the retention of mechanical properties of these two kinds of fibers. Before that, due to the difference in their chemical structures, we tested their Yang-Laplace contact angle (YLCA) and water absorption; the results suggested that PPTA fibers would absorb more moisture. Surprisingly, then, compared with thermotropic liquid crystal polymer (TLCP) fibers, the retention of the mechanical properties of poly p-phenylene terephthalamide (PPTA) fibers decreased by around 25% after the F-T experiments. The Fourier-transformed infrared (FT-IR) analysis, the attenuated total reflection (ATR) accessory analysis and the degree of crystal orientation measured by two-dimensional wide-angle X-ray diffraction (2D-WAXD) confirm that no changes in the chemical and the orientation structure of the crystal region of the fibers occurred after they underwent the F-T cycles. However, as observed by scanning electron microscopy (SEM), there are microcracks of various extents on the surface of the PPTA fibers, but they do not appear on the surface of TLCP fibers. It is obvious that these microcracks will lead to the loss of mechanical properties; we infer that the moisture absorbed by the PPTA fibers freezes below the freezing point, and the volume expansion of the ice causes the collapse of the microfibrillar structure. The two sorts of fibers subjected to the F-T experiments are immersed in a sodium chloride solution, and the amount of water infiltrated into the PPTA microfibrillar structure is evaluated according to the content of sodium ions in the fiber surface and subsurface layers through X-ray spectroscopy (EDS) elemental analysis. From the above analysis, we found that TLCP fibers can more effectively meet the operating standards of the severe and cold marine environment.

Danhong injection improves neurological function in rats with ischemic stroke by enhancing neurogenesis and activating BDNF/AKT/CREB signaling pathway.

Danhong injection (DHI) is a traditional Chinese medicine injection that promotes blood circulation and removes blood stasis and has been widely used in the treatment of stroke. Many studies have focused on the mechanism of DHI in acute ischemic stroke (IS); however, few studies have thoroughly explored its role during recovery. In this study, we aimed to determine the effect of DHI on long-term neurological function recovery after cerebral ischemia and explored the related mechanisms. Middle cerebral artery occlusion (MCAO) was used to establish an IS model in rats. The efficacy of DHI was assessed using neurological severity scores, behaviors, cerebral infarction volume and histopathology. Immunofluorescence staining was performed to assess hippocampal neurogenesis. An in vitro oxygen-glucose deprivation/reoxygenation (OGD/R) cell model was constructed and western-blot analyses were performed to verify the underlying mechanisms. Our results showed that DHI treatment greatly reduced the infarct volume, promoted neurological recovery and reversed brain pathological changes. Furthermore, DHI promoted neurogenesis by increasing the migration and proliferation of neural stem cells, and enhancing synaptic plasticity. Moreover, we found that the pro-neurogenic effects of DHI were related to an increase in brain-derived neurotrophic factor (BDNF) expression and the activation of AKT/CREB, which were attenuated by ANA-12 and LY294002, the inhibitors of the BDNF receptor and PI3K. These results suggest that DHI improves neurological function by enhancing neurogenesis and activating the BDNF/AKT/CREB signaling pathways.

Exploring High-order Spatio-temporal Correlations from Skeleton for Person Re-identification.

Person re-identification (Re-ID) has become a hot research topic due to its widespread applications. Conducting person Re-ID in video sequences is a practical requirement, in which the crucial challenge is how to pursue a robust video representation based on spatial and temporal features. However, most of the previous methods only consider how to integrate part-level features in the spatio-temporal range, while how to model and generate the part-correlations is little exploited. In this paper, we propose a skeleton-based dynamic hypergraph framework, namely Skeletal Temporal Dynamic Hypergraph Neural Network (ST-DHGNN) for person Re-ID, which resorts to modeling the high-order correlations among various body parts based on a time series of skeletal information. Specifically, multi-shape and multi-scale patches are heuristically cropped from feature maps, constituting spatial representations in different frames. A joint-centered hypergraph and a bone-centered hypergraph are constructed in parallel from multiple body parts (i.e., head, trunk, and legs) with spatio-temporal multi-granularity in the entire video sequence, in which the graph vertices representing regional features and hyperedges denoting relationships. Dynamic hypergraph propagation containing the re-planning module and the hyperedge elimination module is proposed to better integrate features among vertices. Feature aggregation and attention mechanisms are also adopted to obtain a better video representation for person Re-ID. Experiments show that the proposed method performs significantly better than the state-of-the-art on three video-based person Re-ID datasets, including iLIDS-VID, PRID-2011, and MARS.

Pyrolysis and Oxidative Thermal Decomposition Investigations of Tennis Ball Rubber Wastes through Kinetic and Thermodynamic Evaluations.

Thermal decomposition of tennis ball rubber (TBR) wastes in nitrogen and air has been studied through thermogravimetric analysis. The samples were thermally decomposed from room temperature to 950 K at heating rates of 3 to 20 K/min with a purging flow of 30 cm3/min. The degradation features and specific temperatures for two purging gases are thus compared according to the nonisothermal results. Kinetic analyses of two thermal decomposition processes have been isoconversionally performed using differential or integral methods. The activation energy as a function of mass conversion has been thus obtained over the entire decomposition range, varying from 116.7 to 723.3 kJ/mol for pyrolysis and 98.2 to 383.6 kJ/mol for oxidative thermal decomposition. The iterative Flynn-Wall-Ozawa method combined with the linear compensation effect relationship has been proposed for determining the pre-exponential factor and reaction mechanism function, resulting in chemical order reaction models of f(α) = (1 - α)5.7 and f(α) = (1 - α)5.8 for describing pyrolysis and the oxidative thermal degradation of TBR wastes, respectively. With these kinetic parameters, very satisfactory matching against experimental data has been obtained for both gases. Additionally, the thermodynamic parameters, such as the changes of entropy, enthalpy and Gibbs free energy, over the whole thermal degradation processes have also been evaluated.

Endostatin 33 Peptide Is a Deintegrin α6ß1 Agent That Exerts Antitumor Activity by Inhibiting the PI3K-Akt Signaling Pathway in Prostate Cancer.

BACKGROUND: Prostate cancer (PCa) is the leading cause of death in men and has poor therapeutic outcomes. METHODS: A novel endostatin 33 peptide was synthesized by adding a specific QRD sequence on the basis of the endostatin 30 peptide (PEP06) with antitumor activity. Then, bioinformatic analysis and subsequent experiments were performed to validate the antitumor function of this endostatin 33 peptide. RESULTS: We found that the 33 polypeptides significantly inhibited growth, invasion and metastasis and promoted the apoptosis of PCa in vivo or vitro, which is more significant than PEP06 under the same conditions. According to 489 cases from the TCGA data portal, the α6ß1 high expression group was closely associated with the poor prognosis (Gleason score, pathological N stage, etc.) of PCa and was mainly enriched in the PI3K-Akt pathway. Subsequently, we demonstrated that endostatin 33 peptide can down-regulate the PI3K-Akt pathway via the targeted inhibition of α6ß1, thereby inhibiting the epithelial-mesenchymal transition and matrix metalloproteinase in C42 cell lines. CONCLUSION: The endostatin 33 peptide can exert antitumor effects by inhibiting the PI3K-Akt pathway, especially in tumors with a high expression of the integrin α6ß1 subtype, such as prostate cancer. Therefore, our study will provide a new method and theoretical basis for the treatment of prostate cancer.

The potential mechanism of the Ruhao Dashi formula in treating acute pneumonia via network pharmacology and molecular docking.

BACKGROUND: Acute pneumonia (AP) has a high seasonal prevalence every year, which seriously threatens the lives and health of patients. Six traditional Chinese medicines in Ruhao Dashi formula (RDF) have excellent antiinflammatory, antibacterial, and antiviral effects. RDF is commonly used in the clinical treatment of AP. However, the mechanism and target of RDF are unclear. Therefore, this study aimed to use network pharmacology and molecular docking to evaluate the target and mechanism of RDF in the treatment of AP. METHODS: The Herbs and Disease Gene databases were searched to identify common targets of AP and RDF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and Protein-Protein Interaction (PPI) network analyses were performed to identify the potential molecular mechanisms behind RDF. Molecular docking was performed to compare the binding activities of the active molecules with that of the target protein. RESULTS: The "drug-component-common target" network contained 64 active compounds and 134 targets. GO and KEGG analyses indicated that RDF could act by regulating cell death, cell proliferation, apoptosis, and hypoxic response. The PPI network and "pathway-target" network identified 31 core targets. Molecular docking revealed that the 14 active ingredients of RDF bind vigorously to the core targets. CONCLUSION: Through network pharmacology and molecular docking, we found that RDF contains 14 active components and 31 core AP targets. These targets were linked to the development of an antiinflammatory response and could be used to develop new drugs to treat AP.

PKM2 allosteric converter: A self-assembly peptide for suppressing renal cell carcinoma and sensitizing chemotherapy.

Stronger intrinsic Warburg effect and resistance to chemotherapy are the responses to high mortality of renal cell carcinoma (RCC). Pyruvate kinase M2 (PKM2) plays an important role in this process. Promoting PKM2 conversion from dimer to tetramer is a critical strategy to inhibit Warburg effect and reverse chemotherapy resistance. Herein, a PKM2 allosteric converter (PAC) is constructed based on the "in vivo self-assembly" strategy, which is able to continuously stimulate PKM2 tetramerization. The PAC contains three motifs, a serine site that is protected by enzyme cleavable ß-N-acetylglucosamine, a self-assembly peptide and a AIE motif. Once PAC nanoparticles reach tumor site via the EPR effect, the protective and hydrophilic ß-N-acetylglucosamine will be removed by over-expressed O-GlcNAcase (OGA), causing self-assembled peptides to transform into nanofibers with large serine (PKM2 tetramer activator) exposure and long-term retention, which promotes PKM2 tetramerization continuously. Our results show that PAC-induced PKM2 tetramerization inhibits aberrant metabolism mediated by Warburg effect in cytoplasm. In this way, tumor proliferation and metastasis behavior could be effectively inhibited. Meanwhile, PAC induced PKM2 tetramerization impedes the nuclear translocation of PKM2 dimer, which restores the sensitivity of cancer cells to first-line anticancer drugs. Collectively, the innovative PAC effectively promotes PKM2 conversion from dimer to tetramer, and it might provide a novel approach for suppressing RCC and enhancing chemotherapy sensitivity.

Classification, risk factors, and outcomes of patients with progressive hemorrhagic injury after traumatic brain injury.

BACKGROUND: According to the pathoanatomic classification system, progressive hemorrhagic injury (PHI) can be categorized into progressive intraparenchymal contusion or hematoma (pIPCH), epidural hematoma (pEDH), subdural hematoma (pSDH), and traumatic subarachnoid hemorrhage (ptSAH). The clinical features of each type differ greatly. The objective of this study was to determine the predictors, clinical management, and outcomes of PHI according to this classification. METHODS: Multivariate logistic regression analysis was used to identify independent risk factors for PHI and each subgroup. Patients with IPCH or EDH were selected for subgroup propensity score matching (PSM) to exclude confounding factors before evaluating the association of hematoma progression with the outcomes by classification. RESULTS: In the present cohort of 419 patients, 123 (29.4%) demonstrated PHI by serial CT scan. Of them, progressive ICPH (58.5%) was the most common type, followed by pEDH (28.5%), pSDH (9.8%), and ptSAH (3.2%). Old age (≥ 60 years), lower motor Glasgow Coma Scale score, larger primary lesion volume, and higher level of D-dimer were independent risk factors related to PHI. These factors were also independent predictors for pIPCH, but not for pEDH. The time to first CT scan and presence of skull linear fracture were robust risk factors for pEDH. After PSM, the 6-month mortality and unfavorable survival rates were significantly higher in the pIPCH group than the non-pIPCH group (24.2% vs. 1.8% and 12.1% vs. 7.3%, respectively, p < 0.001), but not significantly different between the pEDH group and the non-pEDH group. CONCLUSIONS: Understanding the specific patterns of PHI according to its classification can help early recognition and suggest targeted prevention or treatment strategies to improve patients' neurological outcomes.

Structure Evolution on Manifold for Graph Learning.

Graph has been widely used in various applications, while how to optimize the graph is still an open question. In this paper, we propose a framework to optimize the graph structure via structure evolution on graph manifold. We first define the graph manifold and search the best graph structure on this manifold. Concretely, associated with the data features and the prediction results of a given task, we define a graph energy to measure how the graph fits the graph manifold from an initial graph structure. The graph structure then evolves by minimizing the graph energy. In this process, the graph structure can be evolved on the graph manifold corresponding to the update of the prediction results. Alternatively iterating these two processes, both the graph structure and the prediction results can be updated until converge. It achieves the suitable structure for graph learning without searching all hyperparameters. To evaluate the performance of the proposed method, we have conducted experiments on eight datasets and compared with the recent state-of-the-art methods. Experiment results demonstrate that our method outperforms the state-of-the-art methods in both transductive and inductive settings.

KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.

KDM2A is a histone demethylase, which primarily catalyzes the demethylation of H3K36me2. Abnormal expression of KDM2A is observed in many types of cancers; however, the molecular events connected to KDM2A expression remain unclear. We report that KDM2A performs an oncogenic function in esophageal squamous cell carcinoma (ESCC) and is robustly expressed in ESCC cells. ShRNA-mediated knockdown of KDM2A resulted in a significant inhibition of the malignant phenotype of ESCC cell lines, whereas ectopic expression of KDM2A showed the opposite effect. We also analyzed the function of KDM2A using a CRISPR-CAS9 depletion system and subsequent rescue experiment, which also indicated a cancerous role of KDM2A. Interestingly, analysis of the gene expression network controlled by KDM2A using RNA-seq revealed an unexpected feature: KDM2A could induce expression of a set of well-documented oncogenic genes, including IL6 and LAT2, while simultaneously suppressing another set of oncogenes, including MAT2A and HMGCS1. Targeted inhibition of the upregulated oncogene in the KDM2A-depleted cells led to a synergistic suppressive effect on the malignant phenotype of ESCC cells. Our results revealed the dual role of KDM2A in ESCC cells, which may have therapeutic implications.

Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum.

BACKGROUND: Cinnamomum longepaniculatum (Gamble) N. Chao ex H. W. Li, whose leaves produce essential oils, is a traditional Chinese medicine and economically important tree species. In our study, two C. longepaniculatum varieties that have significantly different essential oil contents and leaf phenotypes were selected as the materials to investigate secondary metabolism. RESULT: The essential oil content and leaf phenotypes were different between the two varieties. When the results of both transcriptome and metabolomic analyses were combined, it was found that the differences were related to phenylalanine metabolic pathways, particularly the metabolism of flavonoids and terpenoids. The transcriptome results based on KEGG pathway enrichment analysis showed that pathways involving phenylpropanoids, tryptophan biosynthesis and terpenoids significantly differed between the two varieties; 11 DEGs (2 upregulated and 9 downregulated) were associated with the biosynthesis of other secondary metabolites, and 12 DEGs (2 upregulated and 10 downregulated) were related to the metabolism of terpenoids and polyketides. Through further analysis of the leaves, we detected 196 metabolites in C. longepaniculatum. The abundance of 49 (26 downregulated and 23 upregulated) metabolites differed between the two varieties, which is likely related to the differences in the accumulation of these metabolites. We identified 12 flavonoids, 8 terpenoids and 8 alkaloids and identified 4 kinds of PMFs from the leaves of C. longepaniculatum. CONCLUSIONS: The combined results of transcriptome and metabolomic analyses revealed a strong correlation between metabolite contents and gene expression. We speculate that light leads to differences in the secondary metabolism and phenotypes of leaves of different varieties of C. longepaniculatum. This research provides data for secondary metabolite studies and lays a solid foundation for breeding ideal C. longepaniculatum plants.