Tumor Necrosis Factor Signaling Pathway Research Articles

Network-Based Method to Investigate the Promoted Cell Apoptosis Mechanisms of Oridonin in OSCC through the RNA-Transcriptome.

The morbidity of oral cancer is high in the world. Oridonin is a traditional Chinese medicine that can effectively inhibit oral squamous cell carcinoma (OSCC) growth, but its mechanism remains unclear. Our previous data showed that oridonin inhibited CAL-27 cell proliferation and promoted apoptosis. Herein, we explored the mechanism and target of oridonin in human OSCC through RNA sequencing and integration of multiple bioinformatics analysis strategies. Differences in gene expression can be analyzed with RNA sequencing. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), gene set enrichment analysis (GSEA), Disease Ontology (DO), and other enrichment analyses were used to evaluate differentially expressed genes (DEGs). Protein-protein interaction (PPI) networks were built via the STRING database. It was found that tumor necrosis factor (TNF) signaling pathway, cytokine-cytokine receptor interaction, and nuclear factor-kappa B (NF-kappaB) signaling pathway were associated with the therapeutic effects of oridonin in OSCC. Three key genes (BIRC3, TNFSF10, and BCL6) were found to associate with cell apoptosis in OSCC cells treated with oridonin. Quantitative PCR assays verified the expression of apoptosis-related DEGs: TNFSF10, BIRC3, AIFM2, BCL6, BCL2L2, and Bax. Western blots were employed for verifying proteins expression associated with DEGs: cleaved caspase 3, Bax, Bcl-w, anti-cIAP2, and anti-TRAIL. In conclusion, our findings reveal the molecular pathways and targets by which oridonin can treat and induce cytotoxic effects in OSCC: by affecting the signaling including TNF, NF-κB, and cytokine-cytokine receptor interaction and by regulating the key gene BIRC3, TNFSF10, and BCL6. It should be noted that further clinical trial validation is very necessary. Combined with current research trends, our existing research may provide innovative research drugs for the treatment of OSCC.

11.4 T ultra-high static magnetic field has no effect on morphology but induces upregulation of TNF signaling pathway based on transcriptome analysis in zebrafish embryos

As magnetic resonance imaging (MRI) scanners with ultra-high field (UHF) have optimal performance, scientists have been working to develop high-performance devices with strong magnetic fields to improve their diagnostic potential. However, whether an MRI scanner with UHF poses a risk to the safety of the organism require further evaluation. This study evaluated the effects of 11.4 Tesla (T) UHF on embryonic development using a zebrafish model. Multiple approaches, including morphological parameters, physiological behaviors, and analyses of the transcriptome at the molecular level, were determined during 5 days after laboratory-controlled exposure from 6 hour post fertilization (hpf) to 24 hpf. No significant effects were observed in embryo mortality, hatching rate, body length, Left-Right patterning, locomotor behavior, etc. RNA-sequencing analysis revealed up-regulated tumor necrosis factor (TNF) inflammatory factors and activated TNF signaling pathways in the 11.4 T exposure group. The results were further validated using qPCR. Our findings indicate that although UHF exposure under 11.4 T has no effect on the development of zebrafish embryos, it has specific effects on the immune response that require further investigation.

Dynamic changes in marker components during the stir-frying of Pharbitidis Semen, and network analysis of its potential effects on nephritis.

Introduction: Pharbitidis Semen (PS) has been widely used in traditional Chinese medicine to treat several diseases such as nephritis. PS is usually stir-fried to enhance its therapeutic efficacy before use in clinical practice. However, the changes in phenolic acids during stir-frying and the mechanisms of their therapeutic effects on nephritis are still unclear. Methods: Here, we studied the processing-induced chemical changes and elucidated the mechanism of PS in the treatment of nephritis. We determined the levels of the 7 phenolic acids in raw PS (RPS) and stir-fried PS (SPS) using high-performance liquid chromatography, analyzed the dynamic compositional changes during stir-frying, and used network analysis and molecular docking to predict and verify compound targets and pathways corresponding to nephritis. Results: The dynamic changes in the 7 phenolic acids in PS during stir-frying are suggestive of a transesterification reaction. Pathway analysis revealed that the targets of nephritis were mainly enriched in the AGE-RAGE, hypoxia-inducible factor-1, interleukin-17, and tumor necrosis factor signaling pathways among others. Molecular docking results showed that the 7 phenolic acids had good binding ability with the key nephritic targets. Discussion: The potential pharmaceutical basis, targets, and mechanisms of PS in treating nephritis were explored. Our findings provide a scientific basis for the clinical use of PS in treating nephritis.

Unravelling the anti-inflammatory mechanism of Allium cepa: an integration of network pharmacology and molecular docking approaches.

Allium cepa, commonly known as onion, is a widely consumed spice that possesses numerous pharmacological properties. A. cepa bioactive components are often explored in the treatment of inflammation-related complications. However, the molecular mechanism via which they exert their anti-inflammatory effects remains unknown. Therefore, this study aimed to elucidate the anti-inflammatory mechanism of A. cepa bioactive components. Consequently, the bioactive compounds of A. cepa were obtained from a database, while the potential targets of the sixty-nine compounds with desirable pharmacokinetic properties were predicted. Subsequently, the targets of inflammation were acquired from the GeneCards database. The protein-protein interaction (PPI) between the sixty-six shared targets of the bioactive compounds and inflammation was retrieved from the String database and visualized using Cytoscape v3.9.1 software. Gene Ontology (GO) analysis of the ten core targets from the PPI network revealed that A. cepa bioactive compounds could be involved in regulating biological processes such as response to oxygen-containing compounds and response to inflammation while Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis revealed that A. cepa compounds might modulate pathways including AGE-RAGE signaling pathway, interleukin (IL)-17 signalling pathway, and tumor necrosis factor signaling pathway. Molecular docking analysis showed that 1-O-(4-Coumaroyl)-beta-D-glucose, stigmasterol, campesterol, and diosgenin have high binding affinities for core targets including EGFR, ALB, MMP9, CASP3, and CCL5. This study successfully elucidated the potential anti-inflammatory mechanism of A. cepa bioactive compounds, hence, providing new insights into the development of alternative anti-inflammatory drugs.

Identification of a Necroptosis-Related Prognostic Signature and Associated Regulatory Axis in Lung Adenocarcinoma.

Lung cancer is considered to be the second most aggressive and rapidly fatal cancer after breast cancer. Necroptosis, a novel discovered pattern of cell death, is mediated by Receptor-interacting serine/threonine-protein kinase 1 (RIPK1), Receptor-interacting serine/threonine-protein kinase 3 (RIPK3), and Mixed Lineage Kinase Domain Like Pseudokinase (MLKL). For the purpose of developing a prognostic model, Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was conducted. Using Pearson's correlation analysis, we evaluated the correlation between necroptosis-related markers and tumor immune infiltration. A bioinformatics analysis was conducted to construct a necroptosis-related regulatory axis. There was a downregulation of most of necroptosis-related genes in lung adenocarcinoma (LUAD) versus lung tissues but an increase in PGAM5, HMGB1, TRAF2, EZH2 levels. We also summarized the Single Nucleotide Variant (SNV) and copy number variation (CNV) of necroptosis-related genes in LUAD. Consensus clustering identified two clusters in LUAD with distinct immune cell infiltration and ESTIMATEScore. Genes related to necroptosis were associated with necroptosis, Tumor necrosis factor (TNF) signaling pathway, and apoptosis according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Four prognostic genes (ALDH2, HMGB1, NDRG2, TLR2) were combined to develop a prognostic gene signature for LUAD patients, which was highly accurate in predicting prognosis. Univariate and multivariate analysis identified HMGB1, pT stage, and pN stage as independent factors impacting on LUAD patients' prognosis. A significant correlation was found between the level of TLR2 and NDRG2 and clinical stage, immunity infiltration, and drug resistance. Additionally, the progression of LUAD might be regulated by lncRNA C5orf64/miR-582-5p/NDRG2/TLR2. The current bioinformatics analysis identified a necroptosis-related prognostic signature for LUAD and their relation to immunity infiltration. This result requires further investigation.

Decoding Hippophae rhamnoides’ action of mechanism in Sjögren’s syndrome: A network pharmacology and molecular docking study

This study aimed to decode the potential bioactive compounds and action mechanism of Hippophae rhamnoides in treating Sjögren’s syndrome using network pharmacology and molecular docking approach. The Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform (TCMSP) and HERB (a High--throughput Experiment- and Reference-guided database of TCM) database were used to identify the active components of -Hippophae rhamnoides and their targets. Databases, including GeneCards, Online Mendelian Inheritance (OMIM), and DisGeNET, were used to acquire the major targets of action in Sjögren’s syndrome. Venn diagrams were constructed to identify the compound gene targets. Then the Search Tool for the Retrieval of Interacting genes/proteins database (STRING) platform was used to build a protein–protein interaction (PPI) network to analyze the potential protein functional modules. Analysis of Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed through the Metascape platform to predict their biological processes and decipher the mechanism of action. The drug component–target–action pathway network was constructed through the Cytoscape 3.8.2 software. Furthermore, the AutoDock Vina software was used to perform molecular docking of core components and key targets, validating binding affinity between potential core components and key targets. Twenty-two Hippophae rhamnoide candidate compounds and 208 potential targets for Sjögren’s syndrome were acquired. The network analysis showed that the core active ingredients of Hippophae rhamnoides in regulating Sjögren’s syndrome were quercetin, kaempferol, and beta-sitosterol (β-sitosterol). Core targets included albumin (ALB), epidermal growth factor receptor (EGFR), Caspase-3 (CASP3), peroxisome proliferator-activated receptor gamma (PPAR-gamma or PPARG), estrogen receptor (ER) ESR1, heat shock protein HSP 90-alpha, EC 3.6.4.10 (HSP90AA1), plasminogen, EC 3.4.21.7 (PLG), MAPK14, MAPK8, and MAPK1. The KEGG analyses demonstrated that Hippophae rhamnoides could exert their functioning against Sjögren’s syndrome by reacting with the lipid and atherosclerosis signaling pathway and tumor necrosis factor (TNF) signaling pathway. Further, molecular docking analysis suggested that 10 compounds of Hippophae rhamnoides could be effective to treat Sjögren’s syndrome by matching five core genes to docking pockets. This study indicated that Hippophae rhamnoides’ functioning effects on Sjögren’s syndrome could be attributed to the regulation of a network comprising multi-targets, multi-compounds, and multi-pathways.

Isorhamnetin inhibits inflammatory response to alleviate DHEA-induced polycystic ovary syndrome in rats

Objective To explore the role of isorhamnetin on polycystic ovary syndrome (PCOS) in rats. Methods Sprague Dawley (SD) rats were subcutaneously injected with dehydroepiandrosteron (DHEA) to establish PCOS model. Hematoxylin and eosin (H&E) staining and TdT-mediated dUTP Nick-End Labeling (TUNEL) were used to measure histological changes and apoptosis of ovary tissues. The levels of serum hormones and inflammatory factors in ovary tissues were measured by enzyme-linked immuno sorbent assay (ELISA). Results In DHEA-induced PCOS rats, the levels of serum glucose, insulin, testosterone and luteinizing hormone (LH) were enhanced, estradiol (E2), sex hormone-binding globulin (SHBG), follicle stimulating hormone (FSH) levels were decreased, inflammatory levels and apoptosis of ovary tissues were increased. Additionally, DHEA increased the body weight, ovary weight, and ovary volume, cystic follicles, and decreased corpus luteum. Moreover, the tumor necrosis factor (TNF) signaling pathway was activated in PCOS rats. The levels of TNF receptor superfamily member 1 A (TNFR1), TNF-α, and fas cell surface death feceptor (FAS) were enhanced in ovary tissues of DHEA induced PCOS rats. Isorhamnetin (ISO) treatment after DHEA modeling markedly reduced serum levels of glucose, insulin, testosterone and LH, increased E2, SHBG, FSH level, decreased inflammatory levels, and inhibited apoptosis and decreased body weight, ovary weight, and ovary volume. The levels of TNFR1, TNF-α, and FAS were markedly decreased after ISO treatment in PCOS rats. Additionally, ISO alone had no significant effect on rats. Conclusion Isorhamnetin inhibits inflammatory response to alleviate DHEA-induced PCOS in rats by inactivating the TNF signaling pathway.

Transcriptome profiling of bovine endometrial epithelial cells induced by lipopolysaccharides in vitro

Endometritis is an inflammation of the surface of the endometrium that does not penetrate the submucosa and can cause infertility and increase the elimination rate in cows. Endometrial epithelial cells are the first barrier of the endometrium against foreign stimuli and bacterial infection. Understanding the genetic changes in stimulated endometrial epithelial cells will help in the efforts to prevent and treat endometritis. This study investigated changes in bovine endometrial epithelial (BEEC) gene expression induced by lipopolysaccharide (LPS)-induced inflammation and compared transcriptome-wide gene changes between LPS- and phosphate-buffered saline (PBS)- treated BEECs by RNA sequencing. Compared with the PBS group, the LPS group showed 60 differentially expressed genes (DEGs) (36 upregulated, 24 downregulated). Gene Ontology enrichment analysis revealed that most enrichment occurred during CXCR chemokine receptor binding, inflammatory response, and neutrophil migration. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed DEGs mainly concentrated in cytokine–cytokine receptor interactions; IL-17, tumor necrosis factor, NOD-like receptor, chemokine, Toll-like receptor, and nuclear factor-κB signaling pathways; and the cytoplasmic DNA sensing pathway. Moreover, results revealed that cytokines SAA3 and HP increased significantly after LPS treatment. These effects of LPS on BEECs transcriptome and the molecular mechanism of endometritis provide a basis for improved clinical treatment and novel drug development.

Material basis and mechanism of Curcuma longa tuberous roots with and without vinegar processing in treating primary dysmenorrhea

Liquid chromatography-mass spectrometry was employed to analyze the chemical components in Curcuma longa tuberous roots(HSYJ), C. longa tuberous roots processed with vinegar(CHSYJ), and rat serum after the administration. The active components of HSYJ and CHSYJ absorbed in serum were identified based on the secondary spectrum of database and literature. The targets of primary dysmenorrhea was screened out from database. The protein-protein interaction network analysis, gene ontology(GO) functional annotation, and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were performed for the common targets shared by the drug active components in serum and primary dysmenorrhea, and the component-target-pathway network was constructed. AutoDock was used to conduct molecular docking between the core components and targets. A total of 44 chemical components were identified from HSYJ and CHSYJ, including 18 absorbed in serum. On the basis of network pharmacology, we identified 8 core components(including procurcumenol, isobutyl p-hydroxybenzoate, ferulic acid, and zedoarondiol) and 10 core targets \[including interleukin-6(IL-6), estrogen receptor 1(ESR1), and prostaglandin-endoperoxide synthase 2(PTGS2)\]. The core targets were mainly distributed in the heart, liver, uterus, and smooth muscle. The molecular docking results showed that the core components were well bound to the core targets, indicating that HSYJ and CHSYJ may exert therapeutic effect on primary dysmenorrhea via estrogen, ovarian steroidogenesis, tumor necrosis factor(TNF), hypoxia-inducible factor-1(HIF-1), IL-17 and other signaling pathways. This study clarifies the HSYJ and CHSYJ components absorbed in serum, as well as the corresponding mechanism, providing a reference for further elucidating the therapeutic material basis and clinical application of HSYJ and CHSYJ.

Serum miR-4488 as a potential biomarker of lean nonalcoholic fatty liver disease.

In lean individuals, nonalcoholic fatty liver disease (NAFLD) is not a benign disease, and these patients have long-term morbidity and mortality similar to those of their nonlean counterparts. Finding biomarkers for noninvasive and early detection is urgent and microRNAs (miRNAs) show potential. The aims of this study were to investigate the potential role of serum miRNAs in the detection of lean NAFLD and to explore the possible pathogenesis of lean NAFLD. A total of 498 patients with NAFLD and 98 healthy controls were included to compare the clinical characteristics of lean NAFLD patients [LNs: body mass index (BMI) <23 kg/m2], nonlean NAFLD patients (NLNs: BMI ≥23 kg/m2) and normal healthy individuals (HIs). A total of 14 serum samples were collected from 4 LNs, 6 NLNs and 4 HIs for high-throughput profiling to identify altered miRNA expression patterns in lean NAFLD. The candidate miRNA, miR-4488, was identified by filtering based on studies in a second independent cohort (31 LNs, 62 NLNs, 72 HIs) that included quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction network analyses were performed to investigate the potential molecular mechanism of miR-4488 in lean NAFLD. LNs were older and had a smaller waist circumference, lower levels of alanine aminotransferase, glutamyl transpeptidase, fasting insulin, and uric acid, lower HOMA-IR score, and higher levels of total cholesterol, high-density lipoprotein cholesterol, and hemoglobin (P<0.05). The serum level of miR-4488 was increased in LNs compared with HIs (P<0.0001) and NLNs (P=0.025). miR-4488 had acceptable performance in predicting [area under the curve (AUC) =0.794, 0.698] lean NAFLD. Moreover, GO and KEGG enrichment analyses revealed that the differentially expressed target genes were mainly involved in choline metabolism in cancer, the tumor-necrosis factor (TNF) signaling pathway and the p53 signaling pathway. PPI analysis identified ARHGAP1, SLC10A1 and SIX5 as the hub genes. Taken together, our findings indicate that serum miR-4488 is a potential biomarker for diagnosing and predicting the pathogenetic mechanisms of lean NAFLD.

Cinnamaldehyde ameliorates dextran sulfate sodium-induced colitis in mice by modulating TLR4/NF-κBsignaling pathway and NLRP3 inflammasome activation.

Ulcerative colitis (UC) is a chronic inflammatory gastrointestinal disease mainly associated with immune dysfunction and microbiota disturbance. Cinnamaldehyde (CIN) is an active ingredient of Cinnamomum cassia with immunomodulatory and anti-inflammatory properties. However, the therapeutic effect and detailed mechanism of CIN on UC remains unclear, and warrant further dissection. In this study, network pharmacology and molecular docking analyses were introduced to predict the potential targets and mechanism of CIN against UC. The therapeutic effect and the predicted targets of CIN on UC were further validated by in vivo and in vitro experiments. Seven intersection targets shared by CIN and UC were obtained, and four hub targets, i.e., toll-like receptor 4 (TLR4), transcription factor p65 (NF-κB), NF-kappa-B inhibitor alpha (IκBα), prostaglandin G/H synthase 2 (COX2) were acquired, which were mainly involved in NF-κB, tumour necrosis factor (TNF), Toll-like receptor and NOD-like receptor signaling pathways. CIN alleviated the symptoms of dextran sulfate sodium (DSS)-induced colitis by decreasing the disease active index (DAI), restoring colon length, and relieving colonic pathology. CIN attenuated systemic inflammation by reducing serum myeloperoxidase (MPO), TNF-α, interleukin-6 (IL-6), and interleukin-1β (IL-1β), down-regulating TLR4, phosphorylated-NF-κB (p-NF-κB), phosphorylated-IκBα (p-IκBα), and COX2 expression in colonic tissues, and decreasing NOD-like receptor protein 3 (NLRP3), Caspase-1, and IL-1β protein expression in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. These results indicate that CIN alleviates DSS-induced colitis inflammattion by modulating TLR4/NF-κB signaling pathway and NLRP3 inflammasome activation.

Temporal transcriptomic changes in microRNAs involved in the host immune response and metabolism during Neospora caninum infection

BackgroundNeospora caninum infection is a major cause of abortion in cattle, which results in serious economic losses to the cattle industry. However, there are no effective drugs or vaccines for the control of N. caninum infections. There is increasing evidence that microRNAs (miRNAs) are involved in many physiological and pathological processes, and dysregulated expression of host miRNAs and the biological implications of this have been reported for infections by various protozoan parasites. However, to our knowledge, there is presently no published information on host miRNA expression during N. caninum infection.MethodsThe expression profiles of miRNAs were investigated by RNA sequencing (RNA-seq) in caprine endometrial epithelial cells (EECs) infected with N. caninum at 24 h post infection (pi) and 48 hpi, and the functions of differentially expressed (DE) miRNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The transcriptome data were validated by using quantitative real-time polymerase chain reaction. One of the upregulated DEmiRNAs, namely chi-miR-146a, was selected to study the effect of DEmiRNAs on the propagation of N. caninum tachyzoites in caprine EECs.ResultsRNA-seq showed 18 (17 up- and one downregulated) and 79 (54 up- and 25 downregulated) DEmiRNAs at 24 hpi and 48 hpi, respectively. Quantitative real-time polymerase chain reaction analysis of 13 randomly selected DEmiRNAs (10 up- and three downregulated miRNAs) confirmed the validity of the RNA-seq data. A total of 7835 messenger RNAs were predicted to be potential targets for 66 DEmiRNAs, and GO and KEGG enrichment analysis of these predicted targets revealed that DEmiRNAs altered by N. caninum infection may be involved in host immune responses (e.g. Fc gamma R-mediated phagocytosis, Toll-like receptor signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, mitogen-activated protein kinase signaling pathway) and metabolic pathways (e.g. lysine degradation, insulin signaling pathway, AMP-activated protein kinase signaling pathway, Rap1 signaling pathway, calcium signaling pathway). Upregulated chi-miR-146a was found to promote N. caninum propagation in caprine EECs.ConclusionsThis is, to our knowledge, the first report on the expression profiles of host miRNAs during infection with N. caninum, and shows that chi-miR-146a may promote N. caninum propagation in host cells. The novel findings of the present study should help to elucidate the interactions between host cells and N. caninum.Graphical

Exploration of Fuzheng Yugan Mixture on COVID-19 based on network pharmacology and molecular docking.

After the World Health Organization declared coronavirus disease 2019 (COVID-19), as a global pandemic, global health workers have been facing an unprecedented and severe challenge. Currently, a mixturetion to inhibit the exacerbation of pulmonary inflammation caused by COVID-19, Fuzheng Yugan Mixture (FZYGM), has been approved for medical institution mixturetion notification. However, the mechanism of FZYGM remains poorly defined. This study aimed to elucidate the molecular and related physiological pathways of FZYGM as a potential therapeutic agent for COVID-19. Active molecules of FZYGM were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), while potential target genes of COVID-19 were identified by DrugBank and GeneCards. Compound-target networks and protein-protein interactions (PPI) were established by Cytoscape_v3.8.2 and String databases, respectively. The gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Finally, a more in-depth study was performed using molecular docking. Our study identified 7 active compounds and 3 corresponding core targets. The main potentially acting signaling pathways include the interleukin (IL)-17 signaling pathway, tumor necrosis factor (TNF) signaling pathway, Toll-like receptor signaling pathway, Th17 cell differentiation, and coronavirus disease-COVID-19. This study shows that FZYGM can exhibit anti-COVID-19 effects through multiple targets and pathways. Therefore, FZYGM can be considered a drug candidate for the treatment of COVID-19, and it provides good theoretical support for subsequent experiments and clinical applications of COVID-19.

ACADL Promotes the Differentiation of Goat Intramuscular Adipocytes.

Intramuscular fat (IMF) deposits help improve meat quality such as marbling, juicy, flavor and tenderness. Long-chain acyl-CoA dehydrogenase (ACADL) is a key enzyme for catalyzing fatty acid oxidation, and studies have shown ACADL is involved in the deposition and differentiation of intramuscular adipocytes. However, the effect of ACADL on intramuscular adipocytes differentiation in goats needs further study. In this study, to explore the mechanism of ACADL on the development of goat intramuscular adipocytes, we constructed an over-expression plasmids and a SI-RNA of ACADL to explore the function of ACADL on the development of goat IMF. It was found that overexpression of ACADL promoted the differentiation of goat intramuscular adipocytes, and promoted the expression of fat cell differentiation marker genes lipoprotein lipase (LPL), peroxisome proliferator activated receptor gamma (PPARγ), APETALA-2-like transcription factor gene (AP2), CCAT enhancer binding protein (CEBPα), preadipocyte Factor 1 (Pref-1) and CCAT enhancer binding protein (CEBPβ), and the opposite trend occurred after interference. In addition, we screened of this related tumor necrosis factor (TNF) signaling pathway by RNA-Seq. So, we validate the signaling pathway with inhibitor of TNF signaling pathway. In summary, these results indicate that ACADL promotes intramuscular adipocytes differentiation through activation TNF signaling pathway. This study provides an important basis for the mechanism of IMF development.

Exploring the mechanism of Xiaoqinglong decoction in the treatment of infantile asthma based on network pharmacology and molecular docking.

To explore the mechanism of Xiaoqinglong decoction (XQLD) in the treatment of infantile asthma (IA) based on network pharmacology and molecular docking. The active ingredients of fdrugs in XQLD were retrieved from Traditional Chinese Medicine Systems Pharmacology database and then the targets of drug ingredients were screened. The disease targets of IA were obtained from OMIM and Gencards databases, and the intersection targets of XQLD in the treatment of IA were obtained by Venny 2.1 mapping of ingredient targets and disease targets. Cytoscape software was used to construct active ingredient-intersection target network. The potential targets of XQLD in the treatment of IA were analyzed by protein-protein interaction network using STRING platform, and the Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were obtained by R Studio software. AutoDock was used to perform molecular docking for verification. In this study, 150 active ingredients of XQLD were obtained, including quercetin, kaempferol, β-sitosterol, luteolin, stigmasterol, and so on. And 92 intersection targets of drugs and diseases were obtained, including interleukin 6 (IL6), cystatin 3, estrogen receptor 1, hypoxia inducible factor 1A, HSP90AA1, epidermal growth factor receptor and so on. There were 127 items of Gene Ontology enrichment analysis and 125 Kyoto Encyclopedia of Genes and Genomes enrichment results, showing that apoptosis, IL-17 signaling pathway, tumor necrosis factor signaling pathway, P13K-Akt signaling pathway and other pathways may play a key role in the treatment of IA by XQLD. The results of molecular docking showed that the key active ingredients including quercetin, kaempferol, β-sitosterol, luteolin, stigmasterol, and the core targets including IL6, cystatin 3, estrogen receptor 1, hypoxia inducible factor 1A, HSP90AA1, and epidermal growth factor receptor had good binding activity. Through network pharmacology and molecular docking, the potential targets and modern biological mechanisms of XQLD in the treatment of IA were preliminarily revealed in the study, which will provide reference for subsequent animal experiments and clinical trials.

Kindlin-2 inhibits TNF/NF-κB-Caspase 8 pathway in hepatocytes to maintain liver development and function.

Inflammatory liver diseases are a major cause of morbidity and mortality worldwide; however, underlying mechanisms are incompletely understood. Here we show that deleting the focal adhesion protein Kindlin-2 expression in hepatocytes using the Alb-Cre transgenic mice causes a severe inflammation, resulting in premature death. Kindlin-2 loss accelerates hepatocyte apoptosis with subsequent compensatory cell proliferation and accumulation of the collagenous extracellular matrix, leading to massive liver fibrosis and dysfunction. Mechanistically, Kindlin-2 loss abnormally activates the tumor necrosis factor (TNF) pathway. Blocking activation of the TNF signaling pathway by deleting TNF receptor or deletion of Caspase 8 expression in hepatocytes essentially restores liver function and prevents premature death caused by Kindlin-2 loss. Finally, of translational significance, adeno-associated virus mediated overexpression of Kindlin-2 in hepatocytes attenuates the D-galactosamine and lipopolysaccharide-induced liver injury and death in mice. Collectively, we establish that Kindlin-2 acts as a novel intrinsic inhibitor of the TNF pathway to maintain liver homeostasis and may define a useful therapeutic target for liver diseases.

The San-Qi-Xue-Shang-Ning formula protects against ulcerative colitis by restoring the homeostasis of gut immunity and microbiota

Ethnopharmacological relevanceUlcerative colitis (UC) is a major cause of morbidity and mortality due to repetitive remissions and relapses, and many severe complications, including colitis-associated cancer (CAC). The San-Qi-Xue-Shang-Ning (SQ) formula has been utilized in clinical practice to treat gut diseases, but its pharmacological evidence is limited and awaits elucidation. Aim of the studyHere, we elucidated the molecular mechanisms of the SQ formula. Materials and methodsIts therapeutic value in combating UC and CAC was predicted from network pharmacology and weighted gene co-expression network analysis (WGCNA). Experimental colitis models were established by feeding dextran sodium sulfate (DSS) to C57BL/6N mice for 7 days, and they were subjected to the SQ formula for 14 days. High-throughput technologies and biochemical investigations were executed to corroborate the anti-colitis effect. ResultsNetwork pharmacology and WGCNA demonstrated that the targets of the SQ formula were associated with interleukin-17 (IL-17), tumor necrosis factor (TNF), IL-1b and peroxisome proliferators-activated receptor (PPAR) signaling pathways, and correlated with the survival in patients with colorectal cancer. In mice with colitis, the SQ treatment hindered colitis progression in a dose-dependent manner, as evidenced by the rescued colon length and weight loss, improved colonic epithelial integrity, and abolished crypt loss. In addition to the suppressed serum IL-17, TNFα, and IL-1b levels, the SQ-treated colitis mice exhibited decreased colonic protein abundance of hypoxia-inducible factor-1α (HIF-1 α), PPARα, and Caspase3 (Casp3) with an increased PPARγ expression. Concurrently, the high dose of SQ promoted the alternative activation of peritoneal macrophages by increasing Arg1 and inhibiting iNOS2, thereby facilitating the migration of NCM460 cells and controlling TNF-induced reactive oxygen species production and apoptosis in intestinal organoids. In colitis-accompanied dysbiosis, the SQ formula reversed the decreased microbiota diversity indexes and restored the microbiome profile in the murine colitis models. ConclusionThe SQ formula is a potent anti-colitis drug that facilitates inflammation resolution and restores gut microbiota homeostasis.

Proteomics comparison between mass-like and non-mass-like breast lesions.

The proteomic differences between mass-like (ML) breast lesions and non-mass-like (NML) breast lesions were compared to explore the formation mechanism of NML ultrasonic morphological characteristics. From January to August 2021, tissue samples were collected from 10 patients with malignant ML (MML), 10 patients with malignant NML (MNML), 10 patients with benign ML (BML), and seven patients with benign NML (BNML). The proteomic differences between the BML and BNML groups and the MML and MNML groups were compared by data-independent acquisition (DIA) quantitative mass spectrometry. The differentially expressed proteins were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) networks analyses. We identified a total of 623 significantly differentially expressed proteins in the MML/MNML group, and 167 significantly differentially expressed proteins in the BML/BNML group, with relative ratios >1.2 or <-0.83. The up-regulated differential proteins were more abundant in the tumor necrosis factor (TNF) signaling pathway in both the MML/MNML and BML/BNML groups, suggesting that the TNF signaling pathway may be related to the ultrasonic morphological characteristics of breast lesions. Dual specificity mitogen-activated protein kinase 3 (MP2K3), a protein factor in the TNF signaling pathway, exhibited significant upregulation in both the malignant and BML groups. The TNF signaling pathway may be associated with the ultrasonic morphological characteristics of breast lesions. MP2K3 is the up-regulated differential expression protein in the MML/MNML and BML/BNML groups, which may be related to the ultrasonic morphological characteristics of breast lesions.

Network Pharmacology Prediction to Explore the Potential Mechanism of Qing'E Pills

Qing’E pills are a classical formula in traditional Chinese medicine that has the effect of tonifying the kidneys and strengthening the bones, first appearing in the tonic formulae in prescriptions of peaceful benevolent dispensary (10th century CE). To preliminarily elucidate the potential mechanisms of Qing’E pills in the treatment of postmenopausal osteoporosis based on network pharmacology. The principal components and corresponding protein targets of Qing’E pills were searched on traditional Chinese medicine systems pharmacology, bioinformatics analysis tool for molecular mechanism-traditional Chinese medicine, SymMap and encyclopedia of traditional Chinese medicine and the compound-target network was constructed by Cytoscape 3.9.1. The targets of postmenopausal osteoporosis were searched on online mendelian inheritance in man, GeneCards, histidine triad nucleotide binding protein and DisGeNET databases. The intersection of compound target and disease target was obtained and the coincidence target was imported into the search tool for retrieval of interacting genes database to construct a protein-protein interaction network. We further performed gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses on the targets. The 33 active compounds in Qing’E pills corresponded to 433 targets. 1647 targets were associated with postmenopausal osteoporosis disease. The active compounds with high degree values were quercetin, stearic acid and marine. The proteins with higher values in the protein-protein interaction network were mitogenactivated protein kinase 1, protein kinase B, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha, phosphoinositide-3-kinase regulatory 1, amyloid beta precursor protein, Src proto-oncogene, nonreceptor tyrosine kinase, mitogen-activated protein kinase 8, heat shock protein 90 alpha family class A member 1, epidermal growth factor receptor, and Janus kinase 2. Gene ontology and Kyoto encyclopedia of genes and genomes analysis showed that Qing’E pills treatment of postmenopausal osteoporosis involves signaling pathways that mainly include the tumor necrosis factor signaling pathway, osteoclast differentiation, Wnt signaling pathway and estrogen signaling pathway. We revealed the active ingredients and potential molecular mechanism of Qing’E pills in the treatment of postmenopausal osteoporosis and provided a reference for subsequent basic research

Exploring the Antibacterial and Antiviral Mechanisms of Baiyaozi Via Network Pharmacology

This paper aims to analyze the antibacterial and antiviral active components of Baiyaozi and predict its molecular mechanisms via network pharmacology. The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and literature were used to screen active components of Baiyaozi (Radix Stephania cepharantha), and Pubchem and Swiss Target Prediction were used to collect the targets of the active components. The GeneCards database was used to search and screen the antibacterial and antiviral targets, intersecting with the practical components' targets to obtain the antibacterial and antiviral core targets of Baiyaozi. Then, the active ingredients and target genes were introduced into Cytoscape to construct the active component-target network regulation map of Baiyaozi. The STRING database was used for protein-protein interaction (PPI) network analysis, and the DAVID platform was used to conduct GO functional and KEGG pathway enrichment analyses of common targets. Eight active ingredients of Baiyaozi acted on 67 antibacterial targets and 130 antiviral targets. Cepharanthine, isocorydine, and berberine might be the main antibacterial and antiviral components of Baiyaozi. The GO function and KEGG pathway enrichment analyses of common targets suggested that the antibacterial and antiviral pathways of Baiyao might focus on apoptosis, autophagy, tumor necrosis factor signaling pathway, HIF-1 signaling pathway, and the PI3K-Akt pathway. Also, the comprehensive PPI, GO, and KEGG analysis indicated that HSP90AA1, SRC, and AKT1 might be the main targets. Conclusion: Baiyaozi has multi-component, multi-target, multi-pathway antibacterial and antiviral molecular mechanisms, providing a theoretical reference for further interpretation.