Urinary metabolomic profiles uncover metabolic pathways in children with asthma.

OBJECTIVE: The prevalence of asthma has gradually increased worldwide in recent years, which has made asthma a global public health problem. However, due to its complexity and heterogeneity, there are a few academic debates on the pathogenic mechanism of asthma. The study of the pathogenesis of asthma through metabolomics has become a new research direction. We aim to uncover the metabolic pathway of children with asthma. METHODS: Liquid chromatography (LC)-mass spectrometry (MS)-based metabolomic analysis was conducted to compare urine metabolic profiles between asthmatic children (n = 30) and healthy controls (n = 10). RESULTS: Orthogonal projections to latent structures-discrimination analysis (OPLS-DA) showed that there were significant differences in metabolism between the asthma group and the control group with three different metabolites screened out, including traumatic acid, dodecanedioic acid, and glucobrassicin, and the levels of traumatic acid and dodecanedioic acid in the urine samples of asthmatic children were lower than those of healthy controls therein. Pathway enrichment analysis of differentially abundant metabolites suggested that α-linolenic acid metabolism was an asthma-related pathway. CONCLUSIONS: This study suggests that there are significant metabolic differences in the urine of asthmatic children and healthy controls, and α-linolenic acid metabolic pathways may be involved in the pathogenesis of asthma.

Ganfule capsule alleviates bile duct ligation-induced liver fibrosis in mice by inhibiting glutamine metabolism.

Background: Liver fibrosis is a pathological outcome of a variety of liver diseases, and it can also progress into liver cirrhosis and liver cancer. Specific liver antifibrotic drugs have not been clinically approved yet. Studies have demonstrated the protective effects of Ganfule capsule (GFL) on the liver and its therapeutic potential in hepatic cancer. However, the mechanism of GFL is not clear in the treatment of liver fibrosis. Objective: This article aims to study the protective effect of GFL on liver fibrosis and its possible mechanism. Methods: The cholestatic liver fibrosis model was prepared by subjecting C57BL/6 mice to bile duct ligation (BDL). The GFL groups were treated with different concentrations of GFL for 14 days. Pathological analysis, serum biochemical index detection, metabonomic analysis, immunohistochemistry, Western blot, and real-time PCR were carried out. Results: GFL could alleviate liver injury and liver fibrosis caused by BDL in mice. Metabonomic analysis of mice serum showed postoperative metabolic disorder, which could be alleviated by GFL through glutamine metabolism; valine, leucine, and isoleucine biosynthesis; aminoacyl-tRNA biosynthesis; and other metabolic pathways. GFL affected glutamine metabolism by inhibiting the activity of glutaminase 1 (GLS1). The activation of GLS1 is regulated by the NF-κB pathway, and experiments showed that GFL could inhibit IκB-α and NF-κB p65 phosphorylation. Conclusion: This study confirms the protective effect of GFL on liver injury and shows that GFL inhibits glutamine metabolism, which was correlated with the NF-κB pathway, and eventually alleviates liver fibrosis. These results are conducive to the development of new therapeutic drugs for liver fibrosis.

Genome sequence assembly algorithms and misassembly identification methods.

The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.

Reduced miR-519d-3p levels in the synovium and synovial fluid facilitate the progression of post-traumatic osteoarthritis by targeting VEGF.

The present study aimed to investigate the expression and clinical significance of miR-519d-3p in patients with post-traumatic osteoarthritis (PTOA). The levels of miR-519d-3p in the synovium and synovial fluid (SF) of all subjects were detected by reverse transcription-quantitative polymerase chain reaction. The results of the present study demonstrated that the levels of miR-519d-3p in the synovium and SF of patients with PTOA were significantly lower, but that the VEGF content was significantly higher, compared with that of control group. Dual-luciferase reporter and Western blot assays demonstrated that VEGF was a target gene of miR-519d-3p. Furthermore, miR-519d-3p inhibitor-induced cell apoptosis, and cell cycle arrest could be partially reversed by silencing VEGF. Additionally, the level of miR-519d-3p in the synovium and SF of patients with PTOA was negatively correlated with the level of VEGF. ROC analysis demonstrated that miR-519d-3p levels in the synovium and SF could effectively differentiate patients with PTOA from healthy controls, with areas under the ROC curve of 0.928 and 0.896, respectively. In conclusion, reduction of miR-519d-3p in the synovium and SF resulted in the upregulation of VEGF in patients with PTOA, and miR-519d-3p may be a potential therapeutic target of PTOA.

In Vitro-In Vivo Correlation for Solid Dispersion of a Poorly Water-Soluble Drug Efonidipine Hydrochloride.

The aim of this present study was to investigate the ability of different dissolution methods to predict the in vivo performance of efonidipine hydrochloride (EFH). The solid dispersions of EFH were prepared by solvent evaporation method with HPMC-AS as matrix and urea as a pH adjusting agent. The paddle method, the open-loop, and the closed-loop flow-through cell methods were studied. In the study, Weibull's model was the best fit to explain release profiles. The pharmacokinetics behaviors of two kinds of solid dispersions with different release rate were investigated in comparison to the EFH after oral administration in rats. In vivo absorption was calculated by a numerical deconvolution method. In the study, the level A in vivo and in vitro correlation (IVIVC) was utilized. The correlation coefficient was calculated and interpreted by means of linear regression analysis (Origin.Pro.8.5 software). As a result, excellent IVIVC for solid dispersions and crude drug (r2 = 0.9352-0.9916) was obtained for the dissolution rate determined with flow-through cell open-loop system in phosphate buffer solution with 0.1% (w/v) polysorbate 80 at pH 6.5, the flow-rate of 4 mL/min. In addition, the self-assembled flow cell system had good repeatability and accuracy. The dissolution rate of the solid dispersion could be slowed down by the flow-through method, and the difference caused by preparation was significantly distinguished. The study demonstrated that flow-through cell method of the open-loop, compared with paddle method, was suitable for predicting in vivo performance of EFH solid dispersions.

HOXD9 Activates the TGF-ß/Smad Signaling Pathway to Promote Gastric Cancer.

BACKGROUND: Gastric cancer (GC) is the most common malignant tumor of the digestive tract and its molecular mechanism is not clear. HOXD9 plays an important role in tumor progression as transcription factor. In the current study, we explored the role of HOXD9 in GC. METHODS: We predicted the expression and potential mechanism of HOXD9 in GC through an online database. The expression of HOXD9 was detected in GC and adjacent tissues, and then we analyzed the relationship between HOXD9 and the prognosis of patients with GC. In vitro, we investigated the effects of HOXD9 on malignant biological behaviors such as proliferation, migration, and invasion of the GC cell line MCG-803. In addition, we have initially studied the underlying mechanism by Western blot. RESULTS: High expression of HOXD9 in GC was predicted by online database prediction and implied poor prognosis. In the clinical sample, we confirmed the above predictions. In vitro, we found that knockdown of HOXD9 could effectively inhibit the proliferation, migration, and invasion of GC cells. In terms of mechanism, HOXD9 may activate the TGF-ß/Smad signaling pathway. CONCLUSION: HOXD9 promotes the malignant biological process of GC, which may be a potential therapeutic target for GC.

G3BP1 activates the TGF-ß/Smad signaling pathway to promote gastric cancer.

BACKGROUND: GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) is involved in various biological functions, including cell growth, metastasis, differentiation, apoptosis, and RNA metabolism. In current study, we aimed to investigate the effect of G3BP1 on gastric cancer (GC). METHODS: The expression of G3BP1 in GC tissues and cell lines was assessed by immunohistochemistry and Western blotting. Correlations of G3BP1 expression with clinicopathological and prognosis of GC patients were evaluated. The functions of G3BP1 in regulating proliferation, migration and invasion of GC cell were investigated using small interfering RNA (siRNA) strategies. Preliminary exploration of its underlying mechanism using Western blotting. RESULTS: G3BP1 expression was upregulated in GC tissues compared with adjacent tissues, and the higher G3BP1 expression was correlated with poor prognosis. G3BP1 knockdown decreased GC cell proliferation, migration and invasion. Mechanistically, silencing of G3BP1 inhibits the activation of the transforming growth factor (TGF)-ß/Smad signaling pathway in GC cells. CONCLUSION: G3BP1 plays an important role in the progression of GC as an oncogene and may become a new therapeutic target.

The Adenosine Monophosphate (AMP) Analog, 5-Aminoimidazole-4-Carboxamide Ribonucleotide (AICAR) Inhibits Hepatosteatosis and Liver Tumorigenesis in a High-Fat Diet Murine Model Treated with Diethylnitrosamine (DEN).

BACKGROUND The development and progression of hepatocellular carcinoma (HCC) are associated with obesity and hepatosteatosis. AMP-activated protein kinase (AMPK) regulates metabolic homeostasis. This study aimed to investigate the effects of treatment with the adenosine monophosphate (AMP) analog, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) on hepatosteatosis in a mouse model fed a high-fat diet (HFD), and on hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DEN) in the HFD mouse model. MATERIAL AND METHODS Male C57BL/6 male mice from two weeks of age were fed a high-fat diet, resulting in hepatosteatosis. HFD mice (15-20 per group) were treated with AICAR and without AICAR. HFD mice were treated with DEN, with and without AICAR. Mouse liver tissues were examined histologically using lipid histochemical stains, immunohistochemistry, and immunofluorescence. Levels of cytokines, alanine transaminase (ALT), triacylglyceride (TAG), and apoptosis were determined. Western blot was used to detect AMPK, pAMPK, STAT3, and pSTAT3. Real-time polymerase chain reaction (RT-PCR) detected expression of the ACL, FAS, CD36, ATGL, CPT1, and IL6 genes. RESULTS In the HFD mouse model, AICAR treatment inhibited hepatic lipid synthesis and IL-6 expression. In the DEN-treated mice, AICAR treatment reduced tumorigenesis, IL-6 signaling, and STAT3 activation. Short-term AICAR treatment had no significant effect in advanced HCC. CONCLUSIONS In an HFD mouse model, treatment with AICAR reduced the development of hepatosteatosis, and following treatment with the liver carcinogen, DEN, AICAR reduced the development of HCC. These preliminary findings support further studies on the role of AICAR in fatty liver disease and HCC.

Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like family genes activation and regulation during tumorigenesis.

Cancer is currently viewed as a disease of evolving genomic instability and abnormal epigenomic modifications. Most solid cancers harbor oncogenic gene mutations driven by both extrinsic and intrinsic factors. Apolipoprotein B mRNA editing catalytic polypeptide-like family (APOBEC) enzymes have an intrinsic deamination activity to convert cytosine to uracil during RNA editing and retrovirus or retrotransposon restriction. Beyond their natural defense in innate immunity, compelling evidence showed that a subclass of APOBEC3 can cause high mutation burden in various types of cancer genomes, and high expression subtypes of APOBEC3 may contribute to drug resistance and associate with clinical outcomes. The underlying molecular mechanisms of APOBEC-mediated hypermutation phenotype are poorly understood. In this review, we discuss the linkage of activation-induced deaminase (AID)/APOBEC3 enzymes to tumorigenesis, highlight the dysregulatory mechanisms of APOBEC3 activities during cancer development, and propose potential approaches to targeting APOBEC3-mediated mutagenesis for cancer interventions.

Towards a dynamic clamp for neurochemical modalities.

The classic dynamic clamp technique uses a real-time electrical interface between living cells and neural simulations in order to investigate hypotheses about neural function and structure. One of the acknowledged drawbacks of that technique is the limited control of the cells' chemical microenvironment. In this manuscript, we use a novel combination of nanosensor and microfluidic technology and microfluidic and neural simulations to add sensing and control of chemical concentrations to the dynamic clamp technique. Specifically, we use a microfluidic lab-on-a-chip to generate distinct chemical concentration gradients (ions or neuromodulators), to register the concentrations with embedded nanosensors and use the processed signals as an input to simulations of a neural cell. The ultimate goal of this project is to close the loop and provide sensor signals to the microfluidic lab-on-a-chip to mimic the interaction of the simulated cell with other cells in its chemical environment.