TNF Signaling Pathway Research Articles

Effects of PGK1 on immunoinfiltration by integrated single-cell and bulk RNA-sequencing analysis in sepsis

BackgroundSepsis, a life-threatening organ dysfunction caused by a dysregulated immune response to infection, remains a significant global health challenge. Phosphoglycerate kinase 1 (PGK1) has been implicated in regulating inflammation and immune cell infiltration in inflammatory conditions. However, the role of PGK1 in sepsis remains largely unexplored.MethodsFour microarray datasets and a high throughput sequencing dataset were acquired from GEO database to reveal the PGK1 expression in patients of sepsis. Quantitative real-time PCR and western blotting was then used to validate the PGK1 level. Additionally, microarray and single-cell RNA sequencing data integration, including gene set enrichment analysis (GSEA), KEGG and GO functional enrichment analysis, immune infiltration analysis, and single-cell sequencing analysis, were performed to elucidate the role of PGK1 in sepsis.ResultsOur results revealed a significant upregulation of PGK1 in sepsis patients, with the area under the ROC curve (AUC) exceeding 0.9 across multiple datasets, indicating PGK1’s strong potential as a diagnostic biomarker. Notably, PGK1 was enriched in key immune-related pathways, including the TNF signaling pathways, and leukocyte transendothelial migration, suggesting its involvement in immune regulation. Furthermore, PGK1 expression showed a positive correlation with the levels of inflammatory mediators CXCL1, CXCL16, and the chemokine receptor CCR1. In terms of immune cell infiltration, PGK1 was positively correlated with naive B cells, resting memory CD4 T cell, gamma delta T cells, M0 macrophages, eosinophils and negatively correlated with plasma cells, CD8 T cells, activated memory CD4 T cell, Tregs, activated dendritic cells.ConclusionsThis study concluded that PGK1 served as a novel diagnostic biomarker for sepsis, with potential implications for prognosis and immune regulation. The significant upregulation of PGK1 in sepsis patients and its association with immune-related pathways and cell types highlight its potential role in the pathogenesis of sepsis.

Deciphering the pharmacological mechanism of Radix astragali for allergic rhinitis through network pharmacology and experimental validation

Radix Astragali (RA) has been recognized for its therapeutic potential in allergic rhinitis (AR), yet its potential pharmacological mechanisms remain elusive. This study systematically investigated the physicochemical properties and biological activities of RA’s phytochemicals, aiming to elucidate their targets and mechanisms in AR treatment. We identified 775 potential targets of RA’s key phytochemicals and intersected these with 29,544 AR-related disease targets, pinpointing 747 shared therapeutic targets. A protein-protein interaction network analysis categorized these targets into five subclusters, with TNF, NFKB1, IKBKB, NFKBIA, and CHUK emerging as central nodes. Enrichment analysis revealed their roles in inflammatory and immune responses, particularly through the NF-κB, TNF, IL-17, Toll-like receptor, and NOD-like receptor signaling pathways. Molecular docking and dynamics simulations confirmed the strong binding affinity and stability of RA’s phytochemicals to these targets. In vivo, RA intervention effectively reversed the expression of key inflammatory markers in an IL-13-induced nasal mucosa inflammation model. Our findings suggest that RA’s multitargeted approach involves the modulation of critical inflammatory pathways, highlighting its therapeutic potential.

Exploring Effects and Mechanism of Ingredients of Herba Epimedii on Osteogenesis and Osteoclastogenesis In Vitro.

Herba Epimedii, a commonly used traditional herb, has been proven effective in ameliorating osteoporosis. However, the active ingredients and potential mechanism need further exploration. To screen active ingredients of Herba Epimedii with the effect of ameliorating osteoporosis and to explore their potential mechanisms. TCMSP and Swiss Target Prediction were applied to collect the ingredients of Herba Epimedii and their targets. UniProt, GeneCards, TTD, DisGeNET, and OMIM were adopted to search osteoporosis-related genes. STRING and DAVID were used to perform enrichment analysis. Effects of screened ingredients were evaluated on MC3T3-E1 cells and RAW264.7 cells, respectively. Eleven ingredients were screened by Network Pharmacology. They exerted a promoting effect on MC3T3-E1 cells (10-9-10-5 M). The ingredients didn't significantly affect ALP activity and osteoblastogenesis-related genes. Baohuoside 1, Sagittatoside B, Chlorogenic acid, Cryptochlorogenic acid, and Neochlorogenic acid significantly increased calcium depositions. The ingredients didn't exhibit a dose-dependent inhibition or promotion on RAW264.7 cells. Baohuoside 1, Sagittatoside B, Neochlorogenic acid, Cryptochlorogenic acid, Icariin, Epimedin A, Chlorogenic acid, Sagittatoside A, and Epimedin C suppressed the level of TRACP. Baohuoside 1, Sagittatoside B, Cryptochlorogenic acid, Neochlorogenic acid, Chlorogenic acid, Sagittatoside A, and Icariin decreased the number of multinucleated osteoclastic cells. Baohuoside 1, Sagittatoside B, and Cryptochlorogenic acid could significantly inhibit MMP-9 expression. Neochlorogenic acid, Sagittatoside B, Chlorogenic acid, and Cryptochlorogenic acid promoted MC3T3-E1 differentiation, among which Neochlorogenic acid showed significant promotion in viability, mineralization, and OPN expression. Baohuoside 1, Sagittatoside B, Cryptochlorogenic acid, Neochlorogenic acid, Chlorogenic acid, and Icariin inhibited RAW264.7 differentiation, among which Baohuoside 1 showed significant inhibition on TRACP, multinucleated osteoclastic cells number and MPP-9 expression. The mechanism might relate to the FoxO signaling pathway, MAPK signaling pathway, and TNF signaling pathway.

Network Pharmacology, Molecular Docking and Experimental Verification Revealing the Mechanism of Fule Cream against Childhood Atopic Dermatitis.

The Fule Cream (FLC) is an herbal formula widely used for the treatment of pediatric atopic dermatitis (AD), however, the main active components and functional mechanisms of FLC remain unclear. This study performed an initial exploration of the potential acting mechanisms of FLC in childhood AD treatment through analyses of an AD mouse model using network pharmacology, molecular docking technology, and RNA-seq analysis. The main bioactive ingredients and potential targets of FLC were collected from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and SwissTargetPrediction databases. An herb-compound-target network was built using Cytoscape 3.7.2. The disease targets of pediatric AD were searched in the DisGeNET, Therapeutic Target Database (TTD), OMIM, DrugBank and GeneCards databases. The overlapping targets between the active compounds and the disease were imported into the STRING database for the construction of the protein-protein interaction (PPI) network. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the intersection targets were performed, and molecular docking verification of the core compounds and targets was then performed using AutoDock Vina 1.1.2. The AD mouse model for experimental verification was induced by MC903. The herb-compound-target network included 415 nodes and 1990 edges. Quercetin, luteolin, beta-sitosterol, wogonin, ursolic acid, apigenin, stigmasterol, kaempferol, sitogluside and myricetin were key nodes. The targets with higher degree values were IL-4, IL-10, IL-1α, IL-1β, TNFα, CXCL8, CCL2, CXCL10, CSF2, and IL-6. GO enrichment and KEGG analyses illustrated that important biological functions involved response to extracellular stimulus, regulation of cell adhesion and migration, inflammatory response, cellular response to cytokine stimulus, and cytokine receptor binding. The signaling pathways in the FLC treatment of pediatric AD mainly involve the PI3K-Akt signaling pathway, cytokine‒cytokine receptor interaction, chemokine signaling pathway, TNF signaling pathway, and NF-κB signaling pathway. The binding energy scores of the compounds and targets indicate a good binding activity. Luteolin, quercetin, and kaempferol showed a strong binding activity with TNFα and IL-4. This study illustrates the main bioactive components and potential mechanisms of FLC in the treatment of childhood AD, and provides a basis and reference for subsequent exploration.

Targets and Mechanisms of Xuebijing in the Treatment of Acute Kidney Injury Associated with Sepsis: A Network Pharmacology-based Study.

Sepsis is a state of the systemic inflammatory response of the host induced by infection, frequently affecting numerous organs and producing varied degrees of damage. The most typical consequence of sepsis is sepsis-associated acute kidney injury(SA-AKI). Xuebijing is developed based on XueFuZhuYu Decoction. Five Chinese herbal extracts, including Carthami Flos, Radix Paeoniae Rubra, Chuanxiong Rhizoma, Radix Salviae, and Angelicae Sinensis Radix, make up the majority of the mixture. It has properties that are anti-inflammatory and anti-oxidative stress. Xuebijing is an effective medication for the treatment of SA-AKI, according to clinical research. But its pharmacological mechanism is still not completely understood. First, the composition and target information of Carthami Flos, Radix Paeoniae Rubra, Chuanxiong Rhizoma, Radix Salviae, and Angelicae Sinensis Radix were collected from the TCMSP database, while the therapeutic targets of SA-AKI were exported from the gene card database. To do a GO and KEGG enrichment analysis, we first screened the key targets using a Venn diagram and Cytoscape 3.9.1. To assess the binding activity between the active component and the target, we lastly used molecular docking. For Xuebijing, a total of 59 active components and 267 corresponding targets were discovered, while for SA-AKI, a total of 1,276 targets were connected. There were 117 targets in all that was shared by goals for active ingredients and objectives for diseases. The TNF signaling pathway and the AGE-RAGE pathway were later found to be significant pathways for the therapeutic effects of Xuebijing by GO analysis and KEGG pathway analysis. Quercetin, luteolin, and kaempferol were shown to target and modulate CXCL8, CASP3, and TNF, respectively, according to molecular docking results. This study predicts the mechanism of action of the active ingredients of Xuebijing in the treatment of SA-AKI, which provides a basis for future applications of Xuebijing and studies targeting the mechanism.

Study on the protective mechanism of Xuemaitong Capsule against acute myocardial ischemia rat based on network pharmacology and metabolomics

BackgroundXuemaitong Capsule (XMT) is a widely recognized traditional Miao medicine extensively utilized in Chinese clinical settings. Previous studies have demonstrated XMT protective effects against acute myocardial ischemia (AMI). However, the mechanism by which XMT provides protection to AMI rats is yet to be fully understood. Aim of the studyThe purpose of this study was to investigate the protective mechanism of XMT on AMI rats through network pharmacology, traditional pharmacodynamics and metabolomics. Material and methodsThe components and potential targets of XMT were identified through the application of traditional Chinese medicine system pharmacology and traditional Chinese medicine molecular mechanism bioinformatics analysis tools. We constructed herb-composition-target networks and analyzed protein–protein interaction (PPI) networks. The potential mechanism was explored by pathway enrichment analysis. Subsequently, the AMI model was constructed by ligation of the anterior descending branch of the left coronary artery, and XMT protective effects on AMI rats were evaluated by analyzing the myocardial enzyme profiles, electrocardiograms(ECG), Triphenyltetrazolium chloride(TTC) staining, and Hematoxylin-Eosin (HE) staining in AMI rats. Metabolomics based on UHPLC-Q-Exactive Orbitrap MS was used to observe the protective effect of XMT on the serum metabolic profile of AMI, and multivariate statistical analysis further revealed the differential patterns of metabolites after XMT treatment. Finally, integrated pathway analysis was carried out to reveal the biological metabolic mechanism. ResultsA total of 392 active components of XMT acted with 624 targets for treating AMI. Pathway enrichment analysis revealed that XMT could treat AMI through TNF, MAPK and PI3K-Akt signaling pathways. Further, XMT could effectively prevent ST-segment elevation in the ECG, reduce the size of myocardial infarction, decrease cardiac weight index and cardiac enzyme levels, and mitigate histological damage in the hearts of AMI rats. In addition, XMT callback 117 metabolites and four metabolic pathways, including taurine and hypotaurine metabolism, phenylalanine metabolism, pyrimidine metabolism and retinol metabolism. Through integrating network pharmacology and metabolomics, we explored the biological mechanism by which XMT treats AMI. It was speculated that the mechanism of XMT is to regulate TNF signaling, PI3K-Akt pathway and MAPK signaling pathway, and participate in cell apoptosis, oxidative stress, immune and inflammatory reaction and other biological processes. ConclusionXMT plays a protective role in AMI rats by regulating multiple metabolic biomarkers, multiple targets and pathways. Therefore, XMT may provide a potential strategy for the treatment of AMI.

Unifying Theory and Experiments: Multi-Target Pharmacology of Dajihan Pill Against Hyperlipidemia

Background: The increasing incidence of hyperlipidemia (HLP) is attributed to the imbalance in redox homeostasis, aberrant lipid metabolism, and the excessive intake of empty calories. Dajihan Pill (DJHP) is a Traditional Chinese Medicine (TCM) formula composed of Zingiberis Rhizoma (ZR), Piperis Longi Fructus (PLF), Alpiniae Officinarum Rhizome (AOR), and Cinnamomi Cortex (CC) in a ratio of 3:2:3:2. It exhibits a significant preventive effect on HLP. Certainly, the active components and the precise mechanism of action are not fully understood. Therefore, this study aims to elucidate the preventive and ameliorative mechanisms of DJHP against HLP by integrating network pharmacology, molecular docking, and experimental validation. Methods: Based on the pharmacological method, active ingredients in DJHP and targets were extracted from Traditional Chinese Medicine System Pharmacology (TCMSP) and UniProt. Then core compounds and targets were obtained by constructing “compounds-targets-disease” and proteinprotein interaction (PPI) network. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to elucidate further the associated action mechanism. The molecular binding mechanisms between the core ingredients and targets were elucidated through molecular docking. Additionally, the antioxidant capacities of DJHP extracts were investigated by assessing their DPPH, hydroxyl, and ABTS radical scavenging activities. Results: A total of 45 active compounds and 258 targets were identified in DJHP. Network analysis indicated that quercetin, beta-sitosterol, kaempferol, and oleic acid might serve as core bioactive compounds. Seven core targets, including AKT1, INS, and TNF, were identified as potential preventive targets. GO analysis suggested the improvement of HLP by DJHP may be related to the lipid metabolic process, high-density lipoprotein particle, triglyceride binding, and inflammatory response. The KEGG analysis indicated TNF, HIF-1, and AMPK signaling pathways were involved. The observations of active compounds binding with core targets indicated an excellent combination. Additionally, antioxidant results showed that DJHP exhibited significant DPPH, hydroxyl, and ABTS radical scavenging activities. Conclusion: Theoretical and experimental investigations indicate that DJHP can effectively modulate various signaling pathways and enhance the redox system, thus mitigating HLP. Our work provided a basis for the pharmacological study of DJHP in preventing HLP and further research.

The glycogene alterations and potential effects in esophageal squamous cell carcinoma

BackgroundAberrant glycosylation is one of the hallmarks of cancer. The profile of glycoprotein expression caused by abnormal glycosylation has been revealed, while abnormal glycogenes that may disturb the structure of glycans have not yet been identified in esophageal squamous cell carcinoma (ESCC).MethodsGenomic alterations driven by differentially expressed glycogenes in ESCC were compared with matched normal tissues by multi-omics analysis. Immunohistochemistry, MTT, colony formation, transwell assays, subcutaneous tumor formation experiments and tail vein injection were used to study the expression and the effect on the proliferation and metastasis of the differentially expressed glycogenes POFUT1 and RPN1 in ESCC. In the alkyne fucose labeling experiment, AAL lectin affinity chromatography and immunoprecipitation were used to explore the mechanism of POFUT1 in ESCC.ResultsThe expression of the POFUT1 and RPN1 glycogenes were upregulated, as determined by genomic copy number gain and proteomics analysis. The overexpression of POFUT1 or RPN1 was associated with poor prognosis in ESCC patients and affected the proliferation and metastasis of ESCC in vivo and in vitro. The overexpression of POFUT1 increased the overall fucosylation level and activated the Notch signaling pathway, which partially mediated POFUT1 induced pro-migration in ESCC. The regulation of malignant progression of ESCC by RPN1 may be related to the TNF signaling pathway, p53 signaling pathway, etc.ConclusionsOur study fills a gap in the study of abnormal glycogenes and highlights the potential role of the POFUT1/Notch axis in ESCC. Moreover, our study identifies POFUT1 and RPN1 as promising anticancer targets in ESCC.

Profile of Inflammatory Cytokines in Gingival Crevicular Fluid and Plasma in Patients With Grade C Periodontitis During Orthodontic Treatment: A Longitudinal Case Series Report.

To examine the immune responses in patients diagnosed as grade C periodontitis during orthodontic treatment. Our study included seven orthodontic patients with grade C periodontitis and measured their levels of inflammatory cytokines in gingival crevicular fluid and plasma before orthodontic treatment, during the alignment and levelling phase, and during the detailing and finishing phase. The key signal pathways in the orthodontic process of patients with periodontitis were detected by KEGG analysis. Studies have shown that orthodontic treatment brings great improvement to patients with grade C periodontitis, and most of the local/systemic inflammatory cytokines can be reduced after orthodontic treatment. Simultaneously, orthodontic treatment can reduce the percentage of IFN-γ+ Th1 cells in patients with grade C periodontitis. Through KEGG analysis, the IL-17 signalling pathway and TNF signalling pathway are closely interrelated in the orthodontic treatment of patients diagnosed with grade C periodontitis (p-value < 0.001). Orthodontic treatment can effectively control the local and system levels of inflammation in patients with grade C periodontitis, with IL-17A and TNF-α as potential distinctive inflammatory markers for orthodontic-periodontal combined treatment in individuals with periodontitis.

Comparative mitochondrial proteomic: PGAM5-mediated necroptosis through excessive mitophagy in sheep livers under molybdenum and cadmium co-exposure

Accumulation of excessive molybdenum (Mo) and cadmium (Cd) in the environment poses detrimental effects on organisms. The precise mechanisms of hepatotoxicity that are involved with mitochondria, resulting from the co-exposure to Mo and Cd, remain poorly understood and elusive. To fill the gap, a total of 24 sheep were stratified into two groups: control group and Mo + Cd group (45 mg Mo·kg⁻¹·B.W. and 1 mg Cd·kg⁻¹·B.W.). Results showed that exposure to Mo and Cd adversely co-induced the liver function related biochemical marker alterations in serum, histopathological abnormalities, mitochondrial ultrastructure damage and oxidative stress in the livers of sheep. Sequencing results from isolated mitochondria indicated that a total of approximately 4788 mitochondria-localized proteins were identified, of which 360 exhibited significant differential expression. GO and KEGG database analysis demonstrated excessive Mo and Cd primarily induced hepatotoxicity by affecting mitochondria-mediated oxidation-reduction processes, single-organism metabolic processes, and enhancing the TNF signaling pathway. Mo and Cd co-exposure increased the levels of mitophagy- and necroptosis- related factors regulated by PGAM5 in the livers. Consistently, our findings highlight the co-exposure of Mo and Cd induced necroptosis triggered by PGAM5-mediated mitophagy, which offers valuable insights into the toxicological mechanisms underlying the combined effects of Mo and Cd.

Whole transcriptome sequencing identifies key lncRNAs, circRNAs and miRNAs in sepsis-associated acute lung injury

Purpose: In this study, we identified differentially expressed genes (DEGs) and signaling pathways to gain insight into the pathogenesis of acute lung injury (ALI). Methods: C57BL/6 mice were intravenously injected with lipopolysaccharide (LPS) to establish a sepsis-induced ALI model. Hematoxylin-eosin (H&E) and enzyme-linked immunosorbent assays (ELISAs) were used to evaluate the model. Whole transcriptome sequencing was performed to identify the expression changes in lncRNAs, circRNAs, miRNAs and mRNAs in lung tissues. The crucial RNAs and the biological function of the target genes were confirmed and annotated based on bioinformatics analysis. Real-time quantitative reverse transcription-polymerase chain reaction (qRT–PCR) was employed to verify the expression levels of key lncRNAs, circRNAs, miRNAs and mRNAs in the lung tissues and human bronchoalveolar lavage (BALF). Results: A total of 3304 (1632 upregulated and 1672 downregulated) differentially expressed mRNAs, 794 (397 up and 397 down) differentially expressed lncRNAs, 89 (58 up and 31 down) differentially expressed circRNAs, and 14 (11 up and 3 down) differentially expressed miRNAs were identified between the control and LPS lung tissues. The lncRNA ceRNA subnetwork and circRNA ceRNA subnetwork were constructed based on the observed interaction and co-expression among the differentially expressed RNAs. An analysis of the protein–protein interaction (PPI) network and hub genes revealed crucial mRNAs for circRNA-Tcf20. The lncRNA-Snhg12, Edn1, Stat1, miR-212-3p and miR-223-3p were upregulated in sepsis ARDS patients. CircRNA-Tcf20, Col1a1, Col1a2 and Flt3 were significantly downregulated in sepsis ARDS patients. The biological function analysis indicated that these genes were enriched in the TNF signaling pathway, Necroptosis signaling pathway and the PI3K-Akt signaling pathway. Conclusions: Our findings suggest that circRNA-Tcf20, miR-212-3p, miR-223-3p, Col1a1, Col1a2 and Flt3 may be new regulatory factors that participate in the pathogenesis of sepsis-related acute lung injury. CircRNA-Tcf20, lncRNA-Snhg12 and all the other RNAs may be potential biomarkers for septic ALI/ARDS.

Transcriptome analysis revealed that ischemic post-conditioning suppressed the expression of inflammatory genes in lung ischemia-reperfusion injury.

Ischemic post-conditioning (I-post C) is a recognized therapeutic strategy for lung ischemia/reperfusion injury (LIRI). However, the specific mechanisms underlying the lung protection conferred by I-post C remain unclear. This study aimed to investigate the protective mechanisms and potential molecular regulatory networks of I-post C on lung tissue. Transcriptome analysis was performed on rat lung tissues obtained from Sham, ischemia-reperfusion (IR), and I-post C groups using RNA-seq to identify differentially expressed genes (DEGs). Subsequently, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were conducted to elucidate significantly enriched pathways in the IR and I-post C groups. Additionally, protein-protein interaction (PPI) network analysis was carried out to examine associations among the DEGs. Pathological changes in lung tissues were assessed using hematoxylin-eosin (H&E) staining. The expression levels of CXCL1 and CXCL6 in the IR and I-post C groups were evaluated through immunofluorescence and Western blotting. Our results showed that I-post C significantly attenuated both pulmonary edema and inflammatory cell infiltration. Transcriptome analysis identified 38 DEGs in the I-post C group compared to the IR group, comprising 21 upregulated and 17 downregulated genes. Among these, seven inflammation-related DEGs exhibited co-expression patterns with the Sham and IR groups, with notable downregulation of Cxcl1 and Cxcl6. GO analysis primarily linked these DEGs to neutrophil activation, chemotaxis, cytokine activity, and CCR chemokine receptor binding. KEGG analysis revealed enriched pathways, including the IL-17, TNF, and NF-κB signaling pathways. GSEA indicated downregulation of neutrophil chemotaxis and the IL-17 signaling pathway, correlating with reduced expression of Cxcl1 and Cxcl6. Validation of Cxcl1 and Cxcl6 mRNA expression via immunofluorescence and Western blotting supported the RNA-seq findings. Furthermore, a PPI network was constructed to elucidate interactions among the 29 DEGs. Through RNA-Seq analysis, we concluded that I-post C may reduce inflammation and suppress the IL-17 signaling pathway, thereby protecting against lung damage caused by LIRI, potentially involving neutrophil extracellular traps.

Integrating multi-level interactive network analysis and in vivo studies to explore the protective mechanism of Maillard products of skipjack trypsin hydrolysate in hyperuricemia

This study used skipjack by-products to produce skipjack trypsin hydrolysate (STH), which was then processed through the Maillard reaction to create its Maillard product, STHMS3 (200–1000 Da). We evaluated STHMS3's protective effects against hyperuricemia-induced renal injury in mice. Utilizing in vivo experiments, network pharmacology, and molecular docking, we explored its protective mechanisms. STHMS3 significantly decreased serum uric acid, creatinine, blood urea nitrogen, and xanthine oxidase (XOD) levels, reduced oxidative stress, and enhanced antioxidant protein levels in kidneys. Network pharmacology analysis showed STHMS3's interaction with multiple targets and pathways, including apoptosis, NF-κB, and TNF signaling pathways, suggesting a multi-level interactive network mechanism. Molecular docking confirmed STHMS3's ability to directly inhibit XOD through hydrogen bond formation. This study highlights the therapeutic potential of food-derived peptides in managing hyperuricemia and protecting renal function.

Glycyrrhiza uralensis extract improves dexamethasone-induced sarcopenia via regulating myostatin- and FoxO3a-mediated E3 ubiquitin ligase

Sarcopenia affects the skeletal muscle system and impairs physical activity. This study investigated the effects of Glycyrrhiza uralensis (GU) extract on ameliorating dexamethasone (DEX)-induced sarcopenia in C2C12 myoblasts and C57BL/6J mice. Initially, network pharmacology analysis determined the association between GU and DEX-induced sarcopenia and predicted potentially related signaling pathways. Subsequently, the protective effects of different GU extracts on DEX-induced damage in C2C12 myotubes were evaluated by cell viability assays and Jenner and Giemsa (J&G) staining. Finally, the GU extract screened in vitro was evaluated by body composition analysis, grip strength and endurance tests, serum analysis, histological analysis, and protein expression level analysis in DEX-induced C57BL/6J mice. Network pharmacology confirmed the correlation between GU and DEX-induced sarcopenia involving TNF, MSTN, and FoxO signaling pathways. In DEX-induced damaged myotubes, only GU water extract (GW) dose-dependently increased cell viability. J&G staining of GW-treated myotubes revealed that GW increased the cell fusion index, maturation index and myotube diameter, attenuating DEX-induced cell damage. Oral administration of GW at doses above 300 mg/kg/day restored lean body mass lost due to DEX and subsequently reduced body fat. GW also enhanced grip strength and endurance, reduced muscle tissue injury, and increased the cross-sectional area of muscle fibers in DEX-induced mice. GW reduced the inflammatory response by alleviating serum TNF-α levels and ultimately decreased E3 ubiquitin ligase (MAFbx and MuRF-1) by downregulating myostatin and promoting FoxO3a phosphorylation. These results suggest that GU inhibits muscle protein degradation and is a potential food and medicinal homolog for preventing or treating sarcopenia.

Characterising the transcriptomic response of bovine peripheral blood mononuclear cells to a mycobacterial cell wall fraction

BackgroundInnate immune stimulants, including mycobacterium cell wall fractions (MCWF), offer an alternative control option to prevent and treat disease in livestock, by appropriately augmenting the innate immune response. However, the functional response to mycobacterium cell wall fractions in cattle is not well defined. In this study we report the transcriptomic response of bovine peripheral blood mononuclear cells to MCWF in the product Amplimune®. MethodsAmplimune-induced transcriptomic changes in bovine peripheral blood mononuclear cells were determined following an initial pilot study and a later time course experiment. These cells were cultured in vitro for 24 h. In the pilot experiment, cells were stimulated with 0, 2, 5, 12.5 or 31.25 µg/mL Amplimune. In the time course experiment, cells were stimulated with 0 or 31.25 µg/mL Amplimune. In both experiments the total RNA was extracted at 0 h, 6 h and 24 h following stimulation. Ribosomal RNA depleted samples were sequenced, and data analysed to determine differential gene expression profiles. Differential gene expression was further analysed to determine enriched biological processes and pathways and a co-expression network. Results and conclusionAmplimune induced dose- and time-dependent gene expression profile changes in bovine peripheral blood mononuclear cells, which were enriched into GO-BP regulation of signalling receptor activity, response to cytokine and inflammatory response. Enriched pathways from KEGG analysis were cytokine-cytokine receptor interaction, IL17 signalling and TNF signalling pathways. Selected genes involved in these processes and pathways included IFNG, IL17A, TNF, IL22 and IL23A. PDE1B, CSF2 and IL36G were identified as the most connected genes in a co-expression network, while the connection between SAA2 and SIGLEC5 was the most important for flow of information within the network. Genes encoding for pro-inflammatory cytokines TNF, IL1B, IL6, IL2, and IL12B, and chemokines CCL3, CCL4 and CCL20 were also upregulated at 6 and 24 h post stimulation, as was the β-defensin gene TAP. These results assist in understanding how mycobacterial cell wall fractions alter immune function and may contribute to our understanding of the immune stimulant response attributed to Amplimune.

Transcriptomic response of overexpression ZNF32 in breast cancer cells

Breast cancer is one of the deadliest malignancies in women worldwide. Zinc finger protein 32 (ZNF32) has been reported to be involved in autophagy and stem cell like properties of breast cancer cells. However, the effects, mechanisms, target genes and pathways of ZNF32 in breast cancer development have not been fully explored. In this study, stable ZNF32 overexpression breast cancer cell line was generated, and we used RNA-seq and RT-qPCR to quantify and verify the changes in transcription levels in breast cancer cells under ZNF32 overexpression. Transcriptome analysis showed that high expression of ZNF32 is accompanied by changes in downstream focal adhesion, ECM-receptor interaction, PI3K-AKT, HIPPO and TNF signaling pathways, which are critical for the occurrence and development of cancer. Multiple differentially expressed genes (DEGs) were significantly involved in cell proliferation, adhesion and migration, including 11 DEGs such as CA9, CRLF1 and ENPP2P with fundamental change of regulation modes. All the 11 DEGs were validated by RT-qPCR, and 9 of them contained potential transcriptional binding sequences of ZNF32 in their promoter region. This study provides a holistic perspective on the role and molecular mechanism of ZNF32 in breast cancer progression.

Chinese herbal medicine, Tongxieyaofang, alleviates diarrhea via gut microbiota remodeling: evidence from network pharmacology and full-length 16S rRNA gene sequencing.

Tongxieyaofang (TXYF) was a traditional Chinese medicine (TCM) formula for the treatment of diarrhea with liver stagnation and spleen deficiency syndrome, but the potential targets and mechanisms have not been fully clarified. This study aims to explore the potential mechanisms of TXYF in alleviating diarrhea using network pharmacology and full-length 16S rRNA gene sequencing. Network pharmacology was applied to identify bioactive compounds and potential targets involved in the role of TXYF in alleviating diarrhea. Meanwhile, a model of diarrhea with liver stagnation and spleen deficiency syndrome was constructed by intragastric administration of Folium senna extract combined with restraint and tail pinch stress. The effect of TXYF on intestinal mucosal microbiota of diarrhea mice was analyzed by full-length 16S rRNA gene sequencing. Network pharmacology analysis showed that kaempferol, wogonin, naringenin, and nobiletin were compounds associated with the efficacy of TXYF. TXYF may alleviate diarrhea via multiple BPs and pathways, including TNF signaling pathway, IL-17 signaling pathway, and Toll-like receptor signaling pathway, which are involved in TCM-gut microbiota-host interactions. Then, we found that TXYF administration reshaped the diversity and composition of the intestinal mucosal microbial community of diarrhea mice. Lactobacillus, primarily Lactobacillus johnsonii, was enriched by the administration of TXYF. After TXYF administration, the abundance of Lactobacillus, particularly Lactobacillus johnsonii, was enriched. Oral administration of TXYF may alleviate diarrhea through remodeling intestinal mucosal microbiota. Promoting the colonization of beneficial commensal bacteria in the intestinal mucosa through gut microbiota-host interactions may be a potential mechanism of TXYF in the treatment of diarrhea.

Integrative network pharmacology and multi-omics to study the potential mechanism of Niuhuang Shangqing Pill on acute pharyngitis

Ethnopharmacological relevanceNiuhuang Shangqing Pill (NSP) is a renowned Chinese medicine prescription listed in the Chinese Pharmacopoeia (Edition, 2020; volume 1) and is utilized in clinical practice for treating headaches and acute pharyngitis (AP) associated with “Shanghuo". Despite its widespread use, the pharmacological mechanism and bioactive components underlying NSP in treating AP remain unclear. Aim of the studyThis study delved into evaluate the alleviation effect of NSP on AP and explore the mechanisms by analyzing multi-omics. Materials and methodsUHPLC-Q Exactive Orbitrap HRMS was employed for the chemical ingredients of NSP. Multiple compositions, targets and pathways involved in the treatment of AP with NSP were predicted by network pharmacology. Additionally, wistar rat model of AP induced by capsaicin was established to evaluate the anti-AP activity of NSP in vivo. The potential mechanism of NSP to improve AP was investigated by real-time PCR, pharyngeal transcriptome analysis, non-targeted metabolomics, immunofluorescence and Western blot. Results119 compounds were identified by UHPLC-Q Exactive Orbitrap HRMS. Both clinical data of Gene Expression Omnibus (GEO) and network pharmacology demonstrated that MAPK signaling pathway and TNF signaling pathway were the critical pathway for AP treatment. In rat model of AP induced by capsaicin, NSP demonstrated the ability to reduce the levels of IL-1β, TNF-α, IL-6, CGRP, SP, PGE2, COX-2 in serum. Moreover, Transcriptomics analysis comprehensively indicated that NSP regulated the MAPK signaling pathway, TNF signaling pathway, biosynthesis of phenylalanine, tyrosine and tryptophan, arachidonic acid metabolism in AP rats. Metabolomics analysis verified that NSP could rebalance arachidonic acid metabolism, biosynthesis of phenylalanine, tyrosine and tryptophan and regulate metabolic profiles. Multi-omics Correlation analysis exhibited that the relative expression of Tnfrsf1b was significantly negatively correlated with 12(S)-HPETE. Immunofluorescence, real-time PCR and Western blot of pharyngeal tissue revealed that NSP inhibited the TNF/p38-MAPK/NF-κB signaling pathway. Additionally, in vitro study on RAW264.7 cells confirmed that NSP counteract LPS-induced inflammatory by inhibiting the TNF/p38-MAPK/NF-κB signaling pathway. Overall, NSP effectively ameliorated capsaicin-induced AP by modulating the arachidonic acid metabolism and TNF/p38-MAPK/NF-κB signaling pathway. ConclusionNSP effectively ameliorated capsaicin-induced AP by modulating the arachidonic acid metabolism, biosynthesis of phenylalanine, tyrosine and tryptophan, as well as the TNF/p38-MAPK/NF-κB signaling pathway.

R-Spondin 1 Suppresses Inflammatory Cytokine Production in Human Cortical Astrocytes

Background/Objectives: Wnt signaling pathways are essential in various biological processes, including embryonic development and tissue homeostasis, and are implicated in many diseases. The R-Spondin (RSpo) family, particularly RSpo1, plays a significant role in modulating Wnt signaling. This study aims to explore how RSpo1 binding to astrocytic LGR6 receptors influences central nervous system (CNS) homeostasis, particularly in the context of inflammation. Methods: Human-induced pluripotent stem cell-derived astrocytes were treated with RSpo1 to assess its impact on inflammatory cytokine release. A proteomic analysis was conducted using a Human Cytokine Array Kit to measure differential protein expression. Pathway enrichment analysis was performed to identify affected signaling pathways. Results: RSpo1 treatment led to a suppression of inflammatory cytokines such as IL-10, IFN-γ, and IL-23 in astrocytes, while TNF-α and CXCL12 levels were increased. Pathway analysis revealed significant alterations in key signaling pathways, including cytokine–cytokine receptor interaction, chemokine signaling, and TNF signaling pathways, suggesting RSpo1’s role in modulating immune responses within the CNS. Conclusions: RSpo1 significantly influences inflammatory responses in astrocytes by modulating cytokine release and altering key signaling pathways. These findings enhance our understanding of the interaction between cell-specific Wnt signaling and CNS inflammation, suggesting potential therapeutic applications of RSpo1 in neuroinflammatory and neurodegenerative diseases.

Crystallinity of covalent organic frameworks controls immune responses

Biomaterials can act as pro- or anti-inflammatory agents. However, effects of biomaterials crystallinity on immune responses are poorly understood. We demonstrate that the adjuvant-like behaviour of covalent organic framework (COF) biomaterial is dependent on its crystallinity. COF crystallinity is inversely correlated with the activation of mouse and human dendritic cells (DC), but with antigen presentation by mouse DCs only. Amorphous COFs upregulates NFkB, TNF, and RIG-I signalling pathways, as well as the chemotaxis-associated gene Unc5c, when compared to crystalline COFs. Meanwhile, Unc5c inhibition disrupts the correlation between crystallinity and DC activation. Furthermore, COFs with the lowest crystallinity admixed with chicken ovalbumin (OVA) antigen prevent OVA-expressing B16F10 tumour growth in 60% of mice, with this protection associated with the induction of antigen-specific, pro-inflammatory T cell. The lowest crystalline COFs admixed with TRP2 antigen can also prevent non-immunogenic YUMM1.1 tumour growth in 50% of mice. These findings demonstrate that the crystallinity of biomaterials is an important aspect to consider when designing immunotherapy for pro- or anti-inflammatory applications.