Tumor Necrosis Factor Signaling Pathway Research Articles

Integration of network pharmacology and transcriptomics to explore the mechanism of isoliquiritigenin in treating heart failure induced by myocardial infarction

BackgroundThe inflammatory response and myocardial remodeling play critical roles in the progression of heart failure (HF) following myocardial infarction (MI). Isoliquiritigenin (ISL) possesses anti-inflammatory properties and has been investigated in cardiovascular diseases such as atherosclerosis. However, the effects and mechanism of ISL on MI-induced HF remain unclear. This research aimed to explore the effects and mechanism of ISL in the treatment of HF on the basis of network pharmacology, transcriptomics, and experimental verification. Methods and resultsWe established an MI-induced HF mouse model in which ISL was administered via gavage for 28 days. Ultrasonic cardiogram data were collected from the mice, and pathological staining was conducted. Then, network pharmacology and molecular docking were performed. Transcriptomic analysis was also conducted on mouse myocardial tissue. Ultimately, we integrated transcriptomic data and network pharmacology to reveal the underlying mechanism, with the results verified through in vivo experiments. Our experiments indicated that ISL improved cardiac function, preserved myocardial structure, inhibited collagen fiber accumulation, reduced inflammatory factor secretion, and mitigated myocardial cell apoptosis in mice with MI-induced HF. A combination of transcriptomics and network pharmacology analysis revealed that core targets of ISL related to HF were significantly enriched in the Tumor Necrosis Factor (TNF) signaling pathway. Molecular docking validation demonstrated that ISL shows strong binding to these core targets. Additionally, in vivo experiments verified that ISL protects against HF post-MI by inhibiting the TNF signaling pathway. ConclusionWe clarified the anti-inflammatory and antimyocardial remodeling mechanisms of ISL in the treatment of HF post-MI, which involves the TNF signaling pathway.

Therapeutic effects of Mudan granules on diabetic retinopathy: Mitigating fibrogenesis caused by FBN2 deficiency and inflammation associated with TNF-α elevation

Ethnopharmacological relevanceMudan granules (MuD), a time-honored traditional Chinese patent medicine (TCPM), are widely utilized in the clinical treatment of diabetic peripheral neuropathy (DPN). In the field of biomedical diagnostics, both diabetic retinopathy (DR) and DPN are recognized as critical microvascular complications associated with diabetes. According to the principles of traditional Chinese medicine (TCM), these conditions are primarily attributed to a deficiency in Qi and the obstruction of collaterals. Despite this, the protective effects of MuD on DR and the underlying mechanisms remain to be comprehensively elucidated. Aims of the studyThe purpose of this study was to investigate the effect of MuD on DR and to further explore the promising therapeutic targets. MethodsA diabetic mouse model was established by administering 60 mg/kg of streptozotocin (STZ) via intraperitoneal injection for five consecutive days. The therapeutic efficacy of MuD was evaluated using a comprehensive approach, which included electroretinogram (ERG) analysis, histopathological examination, and assessment of serum biochemical markers. Then, the pharmacodynamic mechanisms of MuD were systematically analyzed using Tandem Mass Tags-based proteomics. Meanwhile, the candidate compounds of MuD were analyzed by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and molecular docking was applied to estimate the affinity of the active ingredient to their potential key targets. In addition, the functional mechanisms identified through bioinformatics analysis were confirmed by molecular biological methods. ResultsWe demonstrated that MuD provided significant protection to retinal function and effectively mitigated the reduction in retinal thickness observed in the animal model. Through proteomic analysis, we identified a substantial regulation by MuD of 70 biomarkers associated with diabetic retinal damage. These proteins were notably enriched in the tumor necrosis factor (TNF) signaling pathway, a critical mediator in inflammatory processes. A particularly intriguing finding was the significant downregulation of fibrillin-2 (FBN2) in the diabetic retina compared to the control group (0.36 times the level), and its most pronounced upregulation (3.26 times) in the MuD treatment group. This suggests that FBN2 may play a pivotal role in the protective effects of MuD. Molecular docking analyses have unveiled a robust interplay between the components of MuD and TNF-α. Further corroboration was provided by molecular biological methods, which confirmed that MuD could suppress TNF-mediated inflammation and prevent retinal neovascularization and fibrogenesis. ConclusionMuD have the potential to alleviate diabetic retinal dysfunction by effectively curbing the fibrogenesis-associated neoangiogenesis and mitigating the inflammatory response, thereby restoring retinal health and function.

Evaluation and Analysis of Traditional Chinese Medicine Treatment of Bovine Viral Diarrhea/Mucosal Disease Based on Network Pharmacology and In Vitro Studies

Background Bovine viral diarrhea/mucosal disease (BVD-MD) is widely distributed worldwide. The disease causes serious economic losses to animal husbandry every year. Finding targeted antiviral drugs proves to be an effective strategy. Purpose This study was based on network pharmacology and in vitro studies to analyze the potential of traditional Chinese medicine (TCM) in the treatment of BVD-MD. Methods The intersection targets between TCM and the disease were identified. Network topology analysis and protein–protein interaction (PPIs) networks were performed. Intersection targets were analyzed for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment. The molecular docking and molecular dynamics simulation methods were used to reveal the degree of binding of core components to key target genes. Characterization of the anti-Bovine viral diarrhea virus (BVDV) effect of TCM by cytotoxicity and in vitro studies. Results The results revealed the selection of five key Chinese medicines, along with 206 targets associated with BVD-MD. The toll-like receptor, PI3K-AKT, and tumor necrosis factor (TNF) signaling pathways were closely related to the five TCMs. AKT1, EGFR, HSP90AA1, and MAPK1 had good binding with quercetin, the core component of Chinese medicine. Molecular dynamics analysis showed that quercetin exhibited complex stability with AKT1. In vitro studies have demonstrated that the inhibitory effect of quercetin on BVDV is mainly in the initial phase. Quercetin inhibited the expression of AKT1. Conclusion The mechanism of BVDV inhibition by the core Chinese medicines is closely related to MAPK1, AKT1, TNF, and HSP90AA1, with the reduction of AKT1 ultimately affecting viral expression.

Exploring medication rules and mechanism of Chinese medicine for children with cough variant asthma based on data mining, network pharmacology, and molecular docking.

Cough variant asthma (CVA) is a common disease with high incidence among children. Cough is the main clinical symptom and Chinese medicine (CM) has an exact effect on CVA. However, the rules of herb formulation, the pharmacodynamic substances, and the mechanism remained unclear. Therefore, we conducted this article to explore medication rules and molecular mechanism of CM against CVA in children using data mining, network pharmacology, molecular docking, and molecular dynamics simulation. Relevant literatures were collected from China National Knowledge Infrastructure, Chinese Scientific and Technical Journals database, Wanfang database, Pubmed, and Web of science. Excel 2016 was used to extract related data and establish the database for Chinese medical frequency, properties, tastes, and meridian analysis. Association rules were analyzed based on Apriori algorithm using IBM SPSS Modeler 18.0 software and core herb combination was identified. The active ingredients and targets of the core herb combination were acquired form the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. The main targets of CVA were obtained from the GeneCards and Online Mendelian Inheritance in Man database. Core targets were selected by using STRING platform and Cytoscape 3.7.2 software. Metascape platform was utilized to perform gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The results were verified by molecular docking. SwissADME and pkCSM website were used to analyze the pharmacokinetic profiles and toxicity of key components of the core herb combination. Molecular dynamics simulation was utilized to evaluate the stable of protein-ligand complex. Two hundred seventy-five literatures containing 202 herbs were finally collected. Statistics indicated that these herbs possessed bitter, pungent taste, and warm properties, and belonged to lung meridian. Glycyrrhizae radix et rhizome, Ephedrae herba, and Armeniacae semen amarum were the most frequently used herbs. "Glycyrrhizae radix et rhizoma-ephedrae herba-Armeniacae semen amarum" was the core herb combination with highest support and confidence. Network pharmacology predicted that the main active ingredients, like quercetin, kaempferol, luteolin, etc, might target on RAC-alpha serine/threonine-protein kinase, tumor necrosis factor, interleukin-6, vascular endothelial growth factor A, transcription factor AP-1, interleukin-1 beta, matrix metalloproteinase-9, etc. They played a pivotal role in regulating multiple signaling pathways, such as tumor necrosis factor signaling pathway, IL-17 signaling pathway, and PI3K-Akt signaling pathway. Molecular docking revealed that the key active ingredients were well docked with core targets. The absorption, distribution, metabolism, excretion, and toxicity analysis showed that formononetin, luteolin, naringenin, and quercetin have high gastrointestinal absorption, no AMES toxicity, hepatotoxicity, and skin sensitization. Molecular dynamics simulation revealed that the formononetin-matrix metalloproteinase-9 complex was relatively stable. This article revealed that CM against CVA in children focused on dispelling wind and reducing phlegm, warming lung, and relieving cough. The mechanism of the core herb combination of CM for CVA through muti-components, muti-targets, and muti-pathways.

High-dimensional profiling of immune responses to kidney transplant reveals heterogeneous T helper 1 and B cell effectors associated with rejection

Rejection is a primary cause of allograft dysfunction after kidney transplantation. The diversity of immune subpopulations involved in the different endotypes of rejection remains to be delineated at single-cell resolution. In a cohort of 76 kidney transplant recipients, we conducted high-dimensional immune phenotyping of blood CD4 T and B cells, single-cell RNA and T/B cell receptor sequencing, and plasma cytokine profiling. Phenotypic, transcriptional, and clonal states of CD4T and B cells could significantly distinguish stable allograft states from rejection. Patients undergoing T cell-mediated rejection displayed accumulation of clonally expanded cytotoxic T helper (Th)1 cells and Th17-like cells, associated with predominant naive B cell responses. In contrast, antibody-mediated rejection was characterized by clonal expansion of Th1-polarized T follicular helper cells and effector T-bet+ memory B cells, both of which strongly expressed interleukin 12 and tumor necrosis factor-signaling pathways. Plasma cytokine analysis confirmed mixed Th1/Th17 and Th1/T follicular helper cell-driven inflammatory profiles distinguishing T cell-mediated rejection and antibody-mediated rejection, respectively. CD4T and B cell subpopulations and signatures were validated using bulk RNA-seq analysis of matched kidney allografts and using an independent single-cell RNA-seq data set. These data improve mechanistic understanding of the immune pathogenesis of rejection and support the development of more specific immunosuppressive therapies to treat allograft rejection.

Chiral Intranasal Nanovaccines as Antivirals for Respiratory Syncytial Virus.

This study aimed to develop an intranasal nanovaccine by combining chiral nanoparticles with the RSV pre-fusion protein (RSV protein) to create L-nanovaccine (L-Vac). The results showed that L-NPs increased antigen attachment in the nasal cavity by 3.83 times and prolonged its retention time to 72h. In vivo experimental data demonstrated that the intranasal immunization with L-Vac induced a 4.86-fold increase in secretory immunoglobulin A (sIgA) secretion in the upper respiratory tract, a 1.85-fold increase in the lower respiratory tract, and a 20.61-fold increase in RSV-specific immunoglobin G (IgG) titer levels in serum, compared with the commercial Alum Vac, while the neutralizing activity against the RSV authentic virus is 1.66-fold higher. The mechanistic investigation revealed that L-Vac activated the tumor necrosis factor (TNF) signaling pathway in nasal epithelial cells (NECs), in turn increasing the expression levels of interleukin-6 (IL-6) and C-C motif chemokine ligand 20 (CCL20) by 1.67-fold and 3.46-fold, respectively, through the downstream nuclear factor kappa-B (NF-κB) signaling pathway. Meanwhile, CCL20 recruited dendritic cells (DCs) and L-Vac activated the Toll-like receptor signaling pathway in DCs, promoting IL-6 expression and DCs maturation, and boosted sIgA production and T-cell responses. The findings suggested that L- Vac may serve as a candidate for the development of intranasal medicine against various types of respiratory infections.

Mechanism Actions of Coniferyl Alcohol in Improving Cardiac Dysfunction in Renovascular Hypertension Studied by Experimental Verification and Network Pharmacology.

Renovascular hypertension (RH), a secondary hypertension, can significantly impact heart health, resulting in heart damage and dysfunction, thereby elevating the risk of cardiovascular diseases. Coniferol (CA), which has vascular relaxation properties, is expected to be able to treat hypertension-related diseases. However, its potential effects on cardiac function after RH remain unclear. In this study, in combination with network pharmacology, the antihypertensive and cardioprotective effects of CA in a two-kidney, one-clip (2K1C) mice model and its ability to mitigate angiotensin II (Ang II)-induced hypertrophy in H9C2 cells were investigated. The findings revealed that CA effectively reduced blood pressure, myocardial tissue damage, and inflammation after RH. The possible targets of CA for RH treatment were screened by network pharmacology. The interleukin-17 (IL-17) and tumor necrosis factor (TNF) signaling pathways were identified using a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The inflammatory response was identified using a Gene Ontology (GO) enrichment analysis. Western blot analysis confirmed that CA reduced the expression of IL-17, matrix metallopeptidase 9 (MMP9), cyclooxygenase 2 (COX2), and TNF α in heart tissues and the H9C2 cells. In summary, CA inhibited cardiac inflammation and fibrohypertrophy following RH. This effect was closely linked to the expression of MMP9/COX2/TNF α/IL-17. This study sheds light on the therapeutic potential of CA for treating RH-induced myocardial hypertrophy and provides insights into its underlying mechanisms, positioning CA as a promising candidate for future drug development.

Anti-inflammation Mechanisms of Flavones Are Highly Sensitive to the Position Isomers of Flavonoids: Acacetin vs Biochanin A.

Acacetin (ACA) and biochanin A (BCA) are isomeric monomethoxyflavones with different structural positions of the 4'-methoxy-phenyl group. Both of them are present in many commonly consumed foods, such as citrus fruits and vegetables, and have been discovered with anti-inflammatory activities, but their mechanisms of action are not clearly elucidated at the molecular level. Herein, we reported the structure-activity relationship of ACA and BCA regarding their potency in inhibiting nitric oxide (NO) production, proinflammatory enzyme expression, and mRNA expression of proinflammatory cytokines in the lipopolysaccharide (LPS)-induced RAW 264.7 cells. Furthermore, transcriptome analysis was conducted to map out the overall pathways impacted by these two isomers. Our results showed that ACA possessed higher suppressive activity in nitric oxide (NO) production (IC50 = 23.93 ± 1.74 μM for ACA and IC50 = 71.41 ± 8.07 μM for BCA), inducible nitric oxide synthase (iNOS) expression, and proinflammatory interleukin (IL)-1β mRNA expression, but lower inhibitory activity in IL-6 mRNA expression as compared with BCA. Although two compounds were revealed to bind to c-Src protein according to drug affinity responsive target stability (DARTS) and western blotting results, molecular docking and molecular dynamics (MD) simulation showed that they had different binding sites, which subsequently resulted in different signaling transduction. ACA primarily exerted anti-inflammatory activity through the mitogen-activated protein kinase (MAPK) signaling pathway, the tumor necrosis factor (TNF) signaling pathway, and the hypoxia-inducible factor (HIF)-1 signaling pathway, while BCA was particularly involved in the Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway, the nuclear factor kappa B (NF-κB) signaling pathway, the TNF signaling pathway, and the toll-like receptor (TLR) signaling pathway. Moreover, two isomers remained stable in the cell culture medium and did not encounter the biotransformation process in RAW 264.7 cells. However, BCA exhibited insufficient cellular uptake ability and transport efficiency in macrophages compared to ACA. Taken together, ACA is more promising for controlling inflammation and worthy of further study for human use.

Differential expression of plasma cytokines in sepsis patients and their clinical implications.

Sepsis, which is characterized by acute systemic inflammation and is associated with high rates of morbidity and mortality, presents a significant challenge in health care. Some scholars have found that the sequential organ failure assessment (SOFA) and quick SOFA scores are not ideal for predicting severe sepsis and mortality. Microbial culture takes a long time (2-3 d) and provides no information for early diagnosis and treatment. Therefore, new diagnostic methods for sepsis need to be explored. To assess cytokine levels in the plasma of sepsis patients and identify potential biomarkers for diagnosing sepsis. Ten sepsis patients admitted to the emergency department within 24 h of onset were enrolled as the observation group, whereas ten noninfected patients served as the control group. Of the 10 noninfected patients, 9 hypertension combined with cerebral infarction, 1 patients with vertiginous syndrome. Plasma Cytokines were measured using the Bio-Plex Pro™ Human Chemokine Panel 40-plex. Differentially expressed cytokines in plasma of sepsis and nonsepsis patients were analyzed using Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Interleukin (IL)-16, granulocyte-macrophage granulocyte-macrophage colony-stimulating factor (GM-CSF), CX3CL1, CXCL9, CXCL16, CCL25, and CCL23 plasma levels were significantly increased in sepsis patients. GO analysis revealed that these cytokines were mainly associated with cellular structures such as intermediates, nuclear plaques, adhesion plaques, lateral plasma membranes, and cell matrix junctions. These genes were involved in various molecular functions, such as cytokine activity, receptor ligand activity, and signal receptor activator activity, contributing to various biological functions, such as leukocyte chemotaxis, migration, and chemotaxis. KEGG analysis indicated involvement in cytokine cytokine receptor interactions, chemokine signaling pathways, virus-protein interactions with cytokines and cytokine receptors, and the tumor necrosis factor signaling pathway. Elevated serum levels of IL-16, GM-CSF, CX3CL1, CXCL9, CXCL16, CCL25, and CCL23 in sepsis patients suggest their potential as diagnostic biomarkers for sepsis.

Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika's Oncolytic Impact in Glioblastoma Multiforme.

Glioblastoma multiforme (GBM) is an aggressive and lethal form of brain cancer with few effective treatments. In this context, Zika virus has emerged as a promising therapeutic agent due to its ability to selectively infect and kill GBM cells. To elucidate these mechanisms and expand the landscape of oncolytic virotherapy, we pursued a transcriptomic meta-analysis comparing the molecular signatures of Zika infection in GBM and neuroblastoma (NBM). Over-representation analysis of dysregulated coding genes showed significant enrichment of tumor necrosis factor (TNF), NF-κB, and p53 signaling pathways. A refined list of long non-coding RNAs consistently dysregulated in Zika-infected GBMs was also developed. Functional review of these candidates revealed their potential regulatory role in Zika-mediated oncolysis. We performed validation of the less-researched targets in adult and pediatric GBM cell lines and found significant differential regulation, as predicted. Altogether, our results provide novel insights into the molecular mechanisms underlying the effect of Zika on GBM. We highlight potential therapeutic targets that could be further interrogated to improve the efficacy of tumor cell death and the utility of Zika as an adjuvant virotherapy for GBM and other related cancers.

Exploring therapeutic targets and molecular mechanisms for treating diabetes mellitus-associated heart failure with Qishen Yiqi dropping pills: A network pharmacology and bioinformatics approach.

Diabetes mellitus (DM) and heart failure frequently coexist, presenting significant public health challenges. QiShenYiQi Dropping Pills (QSDP) are widely employed in the treatment of diabetes mellitus concomitant with heart failure (DM-HF). Nevertheless, the precise mechanisms underlying their efficacy have yet to be elucidated. Active ingredients and likely targets of QSDP were retrieved from the TCMSP and UniProt databases. Genes associated with DM-HF were pinpointed through searches in the GeneCards, OMIM, DisGeNET, and TTD databases. Differential genes connected to DM-HF were sourced from the GEO database. Enrichment analyses via gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways, as well as immune infiltration assessments, were conducted using R software. Further analysis involved employing molecular docking strategies to explore the interactions between the identified targets and active substances in QSDP that are pertinent to DM-HF treatment. This investigation effectively discerned 108 active compounds and 257 targets relevant to QSDP. A protein-protein interaction network was constructed, highlighting 6 central targets for DM-HF treatment via QSDP. Gene ontology enrichment analysis predominantly linked these targets with responses to hypoxia, metabolism of reactive oxygen species, and cytokine receptor interactions. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways demonstrated that these targets mainly participate in pathways linked to diabetic complications, such as AGE-RAGE signaling, dyslipidemia, arteriosclerosis, the HIF-1 signaling pathway, and the tumor necrosis factor signaling pathway. Further, immune infiltration analysis implied that QSDP's mechanism in treating DM-HF might involve immune-mediated inflammation and crucial signaling pathways. Additionally, molecular docking studies showed that the active substances in QSDP have strong binding affinities with these identified targets. This research presents a new model for addressing DM-HF through the use of QSDP, providing novel insights into incorporating traditional Chinese medicine (TCM) principles in the clinical treatment of DM-HF. The implications of these findings are substantial for both clinical application and further scientific inquiry.

Integrated Network Pharmacology and Molecular Docking to Explore the Mechanisms of Ningshen Wendan Decoction in the Treatment of Schizophrenia.

Schizophrenia (SCZ) is a prevalent chronic mental disorder characterized by a high recurrence rate and significant disability. Currently, no satisfactory pharmacological treatments have been identified. Although Ningshen Wendan decoction (NSWDD) has shown promising results in improving cognitive function in patients with schizophrenia, its underlying mechanism of action remains unclear. This study systematically investigated the mechanisms of NSWDD in SCZ treatment using network pharmacology and molecular docking approaches. Analysis of the interaction genes revealed 307 common targets of NSWDD and SCZ. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated the involvement of multiple signaling pathways including interleukin 17 signaling pathway, multiple virus infections, Advanced glycosylation end products (AGEs) - receptor of AGEs (AGEs-RAGE) signaling pathway, tumor necrosis factor signaling pathway, and Hypoxia-inducible factor-1 (HIF-1) signaling pathway as key pathways influenced by NSWDD in treating SCZ. These pathways are associated with various biological processes such as transcriptional regulation, apoptosis regulation, gene expression regulation, and external stimulus-response. Molecular docking simulations indicated favorable binding interactions between components of NSWDD and target proteins via intermolecular forces. The study provided initial insights into the internal molecular mechanisms underlying the beneficial effect of NSWDD on SCZ through multi-target modulation across multiple pathways.

Mechanism of YJKL Decoction in Treating of PCOS Infertility by Integrative Approach of Network Pharmacology and Experimental Verification.

Currently, there is still no clear treatment for polycystic ovary syndrome (PCOS). YJKL has better therapeutic effects and lower toxic side effects for PCOS type infertility. This study aims to clarify the potential mechanism of YJKL Decoction in the treatment of PCOS based on network pharmacology and experiments verification. Network pharmacology and experimental validation approach were used to investigate the bioactive ingredients, critical targets and potential mechanisms of YJKL Decoction against PCOS. Firstly, we use network pharmacology methods to collect core targets, and then validate their effects on diseases through experiments. Five core targets were screened, Threonine kinase 1 (AKT1), Cellular tumor antigen p53 (TP53), Tumor necrosis factor (TNF), Albumin (ALB) and Vascular endothelial growthfactor A (VEGFA). KEGG analysis showed that YJKL treatment for PCOS mainly include AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway and HIF-1 signaling pathway. The molecular docking results showed that compounds have higher affinity with targets. Finally, experimental results had shown that YJKL Decoction had an better therapeutic effects in the treatment of PCOS. Based on a systematic network pharmacology approach and experimental verification, our results comprehensively illustrated the active ingredients, potential targets, and molecular mechanism of YJKL for application to PCOS and helps to illustrate mechanism of action on a comprehensive level.

Integrated network pharmacology and bioinformatics to identify therapeutic targets and molecular mechanisms of Huangkui Lianchang Decoction for ulcerative colitis treatment

BackgroundHuangkui Lianchang Decoction (HLD) is a traditional Chinese herbal formula for treating ulcerative colitis (UC). However, its mechanism of action remains poorly understood. The Study aims to validate the therapeutic effect of HLD on UC and its mechanism by integrating network pharmacology, bioinformatics, and experimental validation.MethodsUC targets were collected by databases and GSE19101. The active ingredients in HLD were detected by ultra-performance liquid chromatography-tandem mass spectrometry. PubChem collected targets of active ingredients. Protein–protein interaction (PPI) networks were established with UC-related targets. Gene Ontology and Kyoto Encyclopedia (KEGG) of Genes and Genomes enrichment were analyzed for the mechanism of HLD treatment of UC and validated by the signaling pathways of HLD. Effects of HLD on UC were verified using dextran sulfate sodium (DDS)-induced UC mice experiments.ResultsA total of 1883 UC-related targets were obtained from the GSE10191 dataset, 1589 from the database, and 1313 matching HLD-related targets, for a total of 94 key targets. Combined with PPI, GO, and KEGG network analyses, the signaling pathways were enriched to obtain IL-17, Toll-like receptor, NF-κB, and tumor necrosis factor signaling pathways. In animal experiments, HLD improved the inflammatory response of UC and reduced UC-induced pro-inflammatory factors such as Tumor Necrosis Factor Alpha (TNF-α), interleukin 1β (IL-1β), and interleukin 6 (IL-6). HLD suppressed proteins TLR4, MyD88, and NF-κB expression.ConclusionsThis study systematically dissected the molecular mechanism of HLD for the treatment of UC using a network pharmacology approach. Further animal verification experiments revealed that HLD inhibited inflammatory responses and improved intestinal barrier function through the TLR4/MyD88/NF-κB pathway.

The effect of overexpression of CyPA on gene expression in human umbilical vein endothelial cells.

The aim of this study is to screen the differentially expressed genes and genes with alternative splicing in PPIA overexpressing cells by transcriptome sequencing. Transcriptome sequencing was performed to identify differentially expressed genes and genes with altered alternative splicing in PPIA overexpressing cells and results were validated by real-time quantitative polymerase chain reaction. The biological function and pathways of those genes were further explored through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses. A total of 157 significantly upregulated genes and 171 significantly downregulated genes were identified in PPIA overexpressing cells, and the splicing pattern of LHPP, APH1A, BRD1, and ORAI3 was found to be altered. GO analyses showed that the most enriched GO terms of the 157 upregulated genes included extracellular region, protein binding, and metal ion, and the most enriched GO terms of the 171 downregulated genes included binding neuron projection, protein binding, and endoplasmic reticulum unfolded protein response. Kyoto Encyclopedia of Genes and Genomes analyses showed that the 157 upregulated genes were mainly enriched in gastric acid secretion, Mitogen-activated protein kinase signaling pathway, etc, and the 171 downregulated genes were mainly enriched in transcriptional misregulation in cancer, Tumor necrosis factor signaling pathway, etc. The overexpression of PPIA in human umbilical vein endothelial cells causes changes in the expression of downstream genes and induces alternative splicing in multiple genes. PPIA alters the expression or the alternative splicing pattern of downstream genes, leading to pathogenesis of vascular endothelial injury by high glucose mediated through CyPA.

Xiaoke Bitong capsule alleviates inflammatory impairment via inhibition of the TNF signaling pathway to against diabetic peripheral neuropathy

BackgroundXiaoke Bitong capsule (XBC) is a crude herbal compound believed to tonify qi, improve blood circulation, and alleviate blood stasis. It has been used as an herbal formula for the prevention and treatment of diabetic peripheral neuropathy (DPN) under the guidance of traditional Chinese medicine (TCM). However, the pharmacological mechanisms by which XBC ameliorates DPN remain poorly understood. The interaction between pro-inflammatory factors and the activation of tumor necrosis factor (TNF) plays a critical role in the underlying mechanisms of DPN. XBC may protect against DPN through the regulation of the TNF pathway. PurposeMany studies show the association between DPN and nerve dysfunction, however, treatment options are limited. To identify specific therapeutic targets and active components of XBC that contribute to its anti-DPN effects, our study aimed to investigate the potential mechanism of action of XBC during the progression of DPN using a system pharmacology approach. MethodsAn approach involving UPLC-Q-TOF/MS and network pharmacology was used to analyze the compositions, potential targets, and active pathways of XBC. Further, models of streptozocin (STZ) induced mouse and glucose induced RSC96 cells were established to explore the therapeutic effects of XBC. High glucose induced RSC96 cells were pretreated with small interfering RNA (siRNA) to identify potential therapeutic targets of DPN. ResultsSeventy-one active compositions of XBC and five potential targets, including mitogen-activated protein kinase 8 (MAPK), interleukin-6 (IL-6), poly-ADP-ribose polymerase-1 (PARP1), vascular endothelial growth factor A (VEGFA), and transcription factor p65 (NF-κB), were considered as the potential regulators of DPN. In addition, the results revealed that the TNF signaling pathway was closely related to DPN. Moreover, DPN contributed to the decreased expressions of PI3K and AKT, increased TNF-α and IL-1β in RSC96 cells, which were both reversed by XBC or TNF-α siRNA. ConclusionXBC could protect against DPN by inhibiting the release of pro-inflammatory cytokines and regulating the activation of the TNF signaling pathway, further accelerating neurogenesis, and alleviating peripheral nerve lesions. Therefore, this study highlights the therapeutic value of XBC for DPN.

Exploring the effects of matrix metalloproteinase-13 on the malignant biological behavior of tongue squamous cell carcinoma via the TNF signaling pathway based on bioinformatics methods.

Identification of the etiology, molecular mechanisms, and carcinogenic pathways of tongue squamous cell carcinoma (TSCC) is crucial for developing new diagnostic and therapeutic strategies. This study used bioinformatics methods to identify key genes in TSCC and explored the potential functions and pathway mechanisms related to the malignant biological behavior of TSCC. Gene chip data sets (i.e., GSE13601 and GSE34106) containing the data of both TSCC patients and normal control subjects were selected from the Gene Expression Omnibus (GEO) database. Using a gene expression analysis tool (GEO2R) of the GEO database, the differentially expressed genes (DEGs) were identified using the following criteria: |log fold change| >1, and P<0.05. The GEO2R tool was also used to select the upregulated DEGs in the chip candidates based on a P value <0.05. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Ontology (GO) function analysis, and a protein-protein interaction (PPI) network analysis were then conducted. The results were displayed using R language packages, including volcano plots, Venn diagrams, heatmaps, and enriched pathway bubble charts. Genes from the MalaCards database were compared with the candidate genes, and a thorough review of the literature was conducted to determine the clinical significance of these genes. Finally, feature gene-directed chemical drugs or targeted drugs were predicted using the Comparative Toxicogenomics Database (CTD). In total, 767 upregulated DEGs were identified from GSE13601 and 695 from GSE34106. By intersecting the upregulated DEGs from both data sets using a Venn diagram, 100 DEGs related to TSCC were identified. The enrichment analysis of the KEGG signaling pathways identified the majority of the pathways associated with the upregulated DEGs, including the Toll-like receptor signaling pathway, the extracellular matrix-receptor interaction, the tumor necrosis factor (TNF) signaling pathway, cytokine-cytokine receptor interaction, the chemokine signaling pathway, the interlukin-17 signaling pathway, and natural killer cell-mediated cytotoxicity. The PPI network and module analyses of the shared DEGs ultimately resulted in five clusters and 55 candidate genes. A further intersection analysis of the TSCC-related genes in the MalaCards database via a Venn diagram identified three important shared DEGs; that is, matrix metalloproteinase-1 (MMP1), MMP9, and MMP13. In the CTD, seven drugs related to MMP13 were identified for treating tongue tumors. This study identified key genes and signaling pathways involved in TSCC and thus extended understandings of the molecular mechanisms that underlie the development and progression of TSCC. Additionally, this study showed that MMP13 may influence the malignant biological behavior of TSCC through the TNF signaling pathway. This finding could provide a theoretical basis for research into early differential diagnosis and targeted treatment.

The mechanical regulatory role of ATP13a3 in osteogenic differentiation of pre-osteoblasts

PurposeThe process of osteogenic differentiation hinges upon the pivotal role of mechanical signals. Previous studies found that mechanical tensile strain of 2500 microstrain (με) at a frequency of 0.5 ​Hz promoted osteogenesis in vitro. However, the mechanism of the mechanical strain influencing osteogenesis at the cellular and molecular levels are not yet fully understood. This study aimed to explore the mechanism of mechanical strain on osteogenic differentiation of MC3T3-E1 cells. Materials and methodsProteomics analysis was conducted to explore the mechanical strain that significantly impacted the protein expression. Bioinformatics identified important mechanosensitive proteins and the expression of genes was investigated using real-time PCR. The dual-luciferase assay revealed the relationship between the miRNA and its target gene. Overexpression and downexpression of the gene, to explore its role in mechanically induced osteogenic differentiation and transcriptomics, revealed further mechanisms in this process. ResultsProteomics and bioinformatics identified an important mechanosensitive lowexpression protein ATP13A3, and the expression of Atp13a3 gene was also reduced. The dual-luciferase assay revealed that microRNA-3070–3p (miR-3070–3p) targeted the Atp13a3 gene. Furthermore, the downexpression of Atp13a3 promoted the expression levels of osteogenic differentiation-related genes and proteins, and this process was probably mediated by the tumor necrosis factor (TNF) signaling pathway. ConclusionAtp13a3 responded to mechanical tensile strain to regulate osteogenic differentiation, and the TNF signaling pathway regulated by Atp13a3 was probably involved in this process. These novel insights suggested that Atp13a3 was probably a potential osteogenesis and bone formation regulator.

The prognostic value of immune escape-related genes in lung adenocarcinoma.

Lung cancer is one of the most common cancers in humans, and lung adenocarcinoma (LUAD) has become the most common histological type of lung cancer. Immune escape promotes progression of LUAD from the early to metastatic late stages and is one of the main obstacles to improving clinical outcomes for immunotherapy targeting immune detection points. Our study aims to explore the immune escape related genes that are abnormally expressed in lung adenocarcinoma, providing assistance in predicting the prognosis of lung adenocarcinoma and targeted. RNA data and related clinical details of patients with LUAD were obtained from The Cancer Genome Atlas (TCGA) database. Through weighted gene coexpression network analysis (WGCNA), 3112 key genes were screened and intersected with 182 immune escape genes obtained from a previous study to identify the immune escape-related genes (IERGs). The role of IERGs in LUAD was systematically explored through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, which were used to enrich the relevant pathways of IERGs. The least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression analysis were used to identify the key prognostic genes, and a prognostic risk model was constructed. Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data (ESTIMATE) and microenvironment cell populations (MCP) counter methods (which can accurately assess the amount of eight immune cell populations and two stromal cell groups) were used to analyze the tumor immune status of the high and low risk subgroups. The protein expression level of the differentially expressed genes in lung cancer samples was determined by using the Human Protein Atlas (HPA) database. A nomogram was constructed, and the prognostic risk model was verified via the Gene Expression Omnibus (GEO) datasets GSE72094 and GSE30219. Twenty differentially expressed IERGs were obtained. GO analysis of these 20 IERGs revealed that they were mainly associated with the regulation of immune system processes, immune responses, and interferon-γ enrichment in mediating signaling pathways and apoptotic signaling pathways; meanwhile, KEGG analysis revealed that IERGs were associated with necroptosis, antigen processing and presentation, programmed cell death ligand 1 (PD-L1) expression and programmed cell death 1 (PD-1) pathway in tumors, cytokine-cytokine receptor interactions, T helper cell 1 (Th1) and Th2 differentiation, and tumor necrosis factor signaling pathways. Using LASSO and Cox regression analysis, we constructed a four-gene model that could predict the prognosis of patients with LUAD, and the model was validated with a validation cohort. The immunohistochemical results of the HPA database showed that AHSA1 and CEP55 had low expression in normal lung tissue but high expression in lung cancer tissue. We constructed an IERG-based model for predicting the prognosis of LUAD. Among the genes identified, CEP55 and AHSA1 may be potential prognostic and therapeutic targets, and reducing their expression may represent a novel approach in the treatment of LUAD.

A General Strategy toward Self-assembled Nanovaccine Based on Cationic Lentinan to Induce Potent Humoral and Cellular Immune Responses.

Adjuvants play a critical role in the induction of effective immune responses by vaccines. Here, a self-assembling nanovaccine platform that integrates adjuvant functions into the delivery vehicle is prepared. Cationic Lentinan (CLNT) is mixed with ovalbumin (OVA) to obtain a self-assembling nanovaccine (CLNTO nanovaccine), which induces the uptake and maturation of bone marrow dendritic cells (BMDCs) via the toll-like receptors 2/4 (TLR2/4)to produce effective antigen cross-presentation. CLNTO nanovaccines target lymph nodes (LNs) and induce a robust OVA-specific immune response via TLR and tumor necrosis factor (TNF) signaling pathways, retinoic acid-inducible gene I (RIG-I) receptor, and cytokine-cytokine receptor interactions. In addition, CLNTO nanovaccines are found that promote the activation of follicular helper T (Tfh) cells and induce the differentiation of germinal center (GC) B cells into memory B cells and plasma cells, thereby enhancing the immune response. Vaccination with CLNTO nanovaccine significantly inhibits the growth of ovalbumin (OVA)-expressing B16 melanoma cell (B16-OVA) tumors, indicating its great potential for cancer immunotherapy. Therefore, this study presents a simple, safe, and effective self-assembling nanovaccine that induces helper T cell 1 (Th1) and helper T cell (Th2) immune responses, making it an effective vaccine delivery system.