PPI Network Research Articles

Danggui Shaoyao San and disassembled prescription: neuroprotective effects via AMPK/mTOR-mediated autophagy in mice

BackgroundDanggui Shaoyao San (DSS), a frequently prescribed Chinese medicine formula, has demonstrated clinical efficacy in the treatment of Alzheimer’s disease (AD). This study aims to explore the differences in therapeutic effects of DSS and its disassembled prescriptions, Suangan (SG) and Xingan (XG), in treating Alzheimer’s Disease and the mechanism of DSS recovering autophagy in AD.MethodsA network pharmacology strategy was employed to delineate the bioactive constituents, associated targets, and regulatory mechanisms of DSS in AD, encompassing in silico target forecasting, the generation and scrutiny of PPI networks, alongside GO and KEGG-based pathway elucidation. An AD mouse model, induced by intracerebroventricular injection of Aβ1–42, was used to evaluate the therapeutic effects of DSS and its disassembled prescriptions on AD. Cognitive function was evaluated using the Morris water maze. Expression levels of inflammatory cytokines were quantified via RT-qPCR and ELISA. Western blotting was used to detect the expression of proteins related to AD pathological markers and the AMPK/mTOR signaling pathway.Results50 active compounds and 718 HUB genes were screened from relevant databases and literature. KEGG and GO analyses indicated that DSS’s potential mechanisms against AD involved the AMPK/mTOR signaling pathway and mitophagy. In vivo animal model, the results demonstrated that DSS, SG, and XG treatments improved cognitive function and ameliorated neuroinflammation in mice. Additionally, they alleviated the pathological changes of neuronal cells. These treatments also increased the protein level of PSD-95, and decreased levels of APP and p-Tau. Among them, DSS exhibited the best efficacy. Furthermore, DSS, SG, and XG upregulated the expression of LC3, Beclin1, and p-AMPK, while decreasing the expression of P62 and p-mTOR.ConclusionsDSS, SG, and XG were found to ameliorate AD-related pathological symptoms in Aβ1−42-injected mice, likely through the AMPK/mTOR autophagy signaling pathway.

Elucidation of the anti-fibrotic diseases mechanism of chelerythrine by integrative approach of network pharmacology and experimental verification

In the present study, we conducted an integrative approach of network pharmacology and experimental validation study to elucidate the underlying mechanisms of Chelerythrine (CLT), in treating fibrotic diseases (FD), which are disorders characterised by excessive accumulation of extracellular matrix. 27 common targets of CLT against FD were analysed, and these common targets were used to construct the PPI network. The results of GO and KEGG enrichment analyses suggested that CLT exerted pharmacological effects on FD by regulating mTOR signalling pathway, AKT-PI3K pathway and apoptosis signalling pathway. Finally, molecular docking confirmed a strong binding affinity between CLT and the core target proteins. CLT has inhibitory effects on the proliferation and migration of L929 cells, CLT could promote cell apoptosis. CLT decreased levels of the Bcl-2, p-AKT/AKT, p-mTOR/mTOR and p-PI3K/PI3K, meanwhile increased levels of the Bax. Taken together, these results indicate that CLT may be a potential drug for anti-fibrotic diseases therapy.

Active Targets and Potential Mechanisms of Erhuang Quzhi Formula in Treating NAFLD: Network Analysis and Experimental Assessment.

The purpose of this research was to investigate the main active components, potential targets of action, and pharmacological mechanisms of Erhuang Quzhi Formula (EHQZF) against NAFLD using network pharmacology, molecular docking, and experimental validation. The main active chemical components of EHQZF and the potential targets for treating NAFLD were extracted and analyzed. The PPI network diagram of "Traditional Chinese Medicine-Active Ingredients-Core Targets" was constructed and the GO, KEGG, and molecular docking analysis were carried out. Identification of components in traditional Chinese medicine compounds was conducted by LC-MS. NAFLD models were established and relevant pathologic indicators and Western blot were analyzed in vivo and ex vivo. Totally 8 herbs attributed to the liver meridian and 20 corresponding targets of NAFLD were obtained from EHQZF. Flavonoids and phenolic acids as the main components of EHQZF treated NAFLD through the MAPK/AKT signaling pathway. Pathway enrichment analysis focused on the MAPK/AKT signaling pathway and apoptosis signaling pathway. Molecular docking showed that Quercetin and Luteolin had stable binding structures with AKT1, STAT3, and other targets. Experiments showed that EHQZF reduced lipid accumulation, regulated changes in adipose tissue, inhibited the MAPK/AKT signaling pathway and exert multiple components, several targets, and multiple pathway interactions to treat NAFLD.

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology.

A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Two distinct types of computational methodologies have emerged: one focuses on analyzing clustering of mutations within protein sequences and 3D structures, while the other characterizes mutations by leveraging the topology of protein-protein interaction network. Their insights are largely non-overlapping, offering complementary strengths. Here, we established a unified, end-to-end 3D structurally-informed protein interaction network propagation framework, NetFlow3D, that systematically maps the multiscale mechanistic effects of somatic mutations in cancer. The establishment of NetFlow3D hinges upon the Human Protein Structurome, a comprehensive repository we compiled that incorporates the 3D structures of every single protein as well as the binding interfaces of all known protein interactions in humans. NetFlow3D leverages the Structurome to integrate information across atomic, residue, protein and network levels: It conducts 3D clustering of mutations across atomic and residue levels on protein structures to identify potential driver mutations. It then anisotropically propagates their impacts across the protein interaction network, with propagation guided by the specific 3D structural interfaces involved, to identify significantly interconnected network "modules", thereby uncovering key biological processes underlying disease etiology. Applied to 1,038,899 somatic protein-altering mutations in 9,946 TCGA tumors across 33 cancer types, NetFlow3D identified 1,4444 significant 3D clusters throughout the Human Protein Structurome, of which ~55% would not have been found if using only experimentally-determined structures. It then identified 26 significantly interconnected modules that encompass ~8-fold more proteins than applying standard network analyses. NetFlow3D and our pan-cancer results can be accessed from http://netflow3d.yulab.org.

Antitumorigenic potential of Lactobacillus-derived extracellular vesicles: p53 succinylation and glycolytic reprogramming in intestinal epithelial cells via SIRT5 modulation

ObjectiveColorectal cancer progression involves complex cellular mechanisms. This study examines the effects of Lactobacillus plantarum-derived extracellular vesicles (LEVs) on the SIRT5/p53 axis, focusing on glycolytic metabolic reprogramming and abnormal proliferation in intestinal epithelial cells.MethodsLEVs were isolated from Lactobacillus plantarum and incubated with Caco-2 cells. Differential gene expression was analyzed through RNA sequencing and compared with TCGA-COAD data. Key target genes and pathways were identified using PPI network and pathway enrichment analysis. Various assays, including RT-qPCR, EdU staining, colony formation, flow cytometry, and Western blotting, were used to assess gene expression, cell proliferation, and metabolic changes. Co-immunoprecipitation confirmed the interaction between SIRT5 and p53, and animal models were employed to validate in vivo effects.ResultsBioinformatics analysis indicated the SIRT5/p53 axis as a critical pathway in LEVs' modulation of colorectal cancer. LEVs were found to inhibit colorectal cancer cell proliferation and glycolytic metabolism by downregulating SIRT5, influencing p53 desuccinylation. In vivo, LEVs regulated this axis, reducing tumor formation in mice. Clinical sample analysis showed that SIRT5 and p53 succinylation levels correlated with patient prognosis.ConclusionLactobacillus-derived extracellular vesicles play a pivotal role in suppressing colonic tumor formation by modulating the SIRT5/p53 axis. This results in decreased glycolytic metabolic reprogramming and reduced proliferation in intestinal epithelial cells.

Distinct Gene Expression and Immune Features Between Different Neutrophil Extracellular Trap-Related Osteosarcoma Subtypes.

We sought to determine neutrophil extracellular trap (NET)-related genes' potential value in improving the efficacy of diagnosis and identifying novel therapeutic targets for osteosarcoma. Data were obtained from TARGET, GEO, and CCLE database. Differentially expressed genes were identified between the subtypes based on NET-related genes. PPI network was constructed using STRING, following by ClueGO enrichment analysis. Infiltration of immune cells was calculated by ssGSEA. Risk Score model was built by LASSO Cox regression analysis. Western blot and qRT-PCR were applied to validate the expression of genes used in the model. We identified 19 NET-related genes with prognostic potential in osteosarcoma using univariate Cox regression analysis. Patients from TARGET were clustered into two subtypes with distinct prognosis and immune features. 381 DEGs were identified between the two NET subtypes. Risk Score based on BST1, SELPLG, FPR1 and TNFRSF10C was reliable to predict the prognosis of osteosarcoma patients. The four genes expressed significantly lower in osteosarcoma than normal cells. Low Risk Score individuals only existed in C1 subtype with better prognosis. Osteosarcoma were clustered into two subtypes based on NET-related genes. Risk Score model constructed by four NET-related gene was able to independently predict the prognosis of osteosarcoma.

Identifying the keyhub genes linked with lung squamous cell carcinoma by examining the differentially expressed and survival genes.

Lung Squamous Cell Carcinoma is characterised by significant alterations in RNA expression patterns, and a lack of early symptoms and diagnosis results in poor survival rates. Our study aimed to identify the hub genes involved in LUSC by differential expression analysis and their influence on overall survival rates in patients. Thus, identifying genes with the potential to serve as biomarkers and therapeutic targets. RNA sequence data for LUSC was obtained from TCGA and analysed using R Studio. Survival analysis was performed on DE genes. PPI network and hub gene analysis was performed on survival-relevant genes. Enrichment analysis was conducted on the PPI network to elucidate the functional roles of hub genes. Our analysis identified 2774 DEGs in LUSC patient datasets. Survival analysis revealed 511 genes with a significant impact on patient survival. Among these, 20 hub genes-FN1, ACTB, HGF, PDGFRB, PTEN, SNAI1, TGFBR1, ESR1, SERPINE1, THBS1, PDGFRA, VWF, BMP2, LEP, VTN, PXN, ABL1, ITGA3 and ANXA5-were found to have lower expression levels associated with better patient survival, whereas high expression of SOX2 correlated with longer survival. Enrichment analysis indicated that these hub genes are involved in critical cellular and cancer-related pathways. Our study has identified six key hub genes that are differentially expressed and exhibit significant influence over LUSC patient survival outcomes. Further, in vitro and in vivo studies must be conducted on the key genes for their utilisation as therapeutic targets and biomarkers in LUSC.

Transcriptomic analyses provide molecular insight into the cold stress response of cold-tolerant alfalfa

BackgroundDaye No.3 is a novel cultivar of alfalfa (Medicago sativa L.) that is well suited for cultivation in high-altitude regions such as the Qinghai‒Tibet Plateau owing to its high yield and notable cold resistance. However, the limited availability of transcriptomic information has hindered our investigation into the potential mechanisms of cold tolerance in this cultivar. Consequently, we conducted de novo transcriptome assembly to overcome this limitation. Subsequently, we compared the patterns of gene expression in Daye No. 3 during cold acclimatization and exposure to cold stress at various time points.ResultsA total of 15 alfalfa samples were included in the transcriptome assembly, resulting in 141.97 Gb of clean bases. A total of 441 DEGs were induced by cold acclimation, while 4525, 5016, and 8056 DEGs were identified at 12 h, 24 h, and 36 h after prolonged cold stress at 4 °C, respectively. The consistency between the RT‒qPCR and transcriptome data confirmed the accuracy and reliability of the transcriptomic data. KEGG enrichment analysis revealed that many genes related to photosynthesis were enriched under cold stress. STEM analysis demonstrated that genes involved in nitrogen metabolism and the TCA cycle were consistently upregulated under cold stress, while genes associated with photosynthesis, particularly antenna protein genes, were downregulated. PPI network analysis revealed that ubiquitination-related ribosomal proteins act as hub genes in response to cold stress. Additionally, the plant hormone signaling pathway was activated under cold stress, suggesting its vital role in the cold stress response of alfalfa.ConclusionsUbiquitination-related ribosomal proteins induced by cold acclimation play a crucial role in early cold signal transduction. As hub genes, these ubiquitination-related ribosomal proteins regulate a multitude of downstream genes in response to cold stress. The upregulation of genes related to nitrogen metabolism and the TCA cycle and the activation of the plant hormone signaling pathway contribute to the enhanced cold tolerance of alfalfa.

Network Pharmacology-Based and Molecular Docking combined with GEO gene chips to Investigate the Potential Mechanism of Duhuo Jisheng Decoction against Rheumatoid Arthritis.

Background： Rheumatoid Arthritis (RA) is a chronic autoimmune disease with various symptoms in patients. Duhuo Jisheng Decoction (DHJSD) has been used to treat RA in China for a long history as a classic TCM formula. However, the underlying pharmacological mechanism still needs to be elucidated. Purpose： In the current study, we combined network pharmacology with molecular docking to investigate the potential mechanism of DHJSD treating RA. Methods: The active compounds and related targets of DHJSD were obtained from the TCMSP database. The RA targets were retrieved from the GEO database. The PPI network of overlapping targets was constructed, whereas the core genes were selected by CytoNCA for molecular docking. GO and KEGG enrichment analyses were used to further explore the biological process and pathways of overlapping targets. On this basis, molecular docking was carried out to verify the interrelations of the main compounds and core targets. Results： In this study, we found 81 active components corresponding to 225 targets of DHJSD. Moreover, 775 RA-related targets were obtained, of which 12 were shared between DHJSD targets and RA genes. From GO and KEGG analysis, there were 346 GO items and 18 signaling pathways. As the molecular docking showed, the binding of components was stable with the core gene. Conclusion： In conclusion, our works revealed the underlying mechanism of DHJSD for treating RA using network pharmacology and molecular docking, which provided a theoretical basis for further clinical application in the future.

Dendrobium nobile alkaloids modulate calcium dysregulation and neuroinflammation in Alzheimer's disease: A bioinformatic analysis

IntroductionDendrobium nobile Lindl alkaloids, or DNLA for short, are the most active ingredients found in D.nobile, a top grade plant in Shen Nong Ben Cao Jing, with an extensive history of medicinal use in Chinese traditional medicine (TCM) as a multifunctional therapeutic agent. Recent evidence has emerged linking the neuroprotective and anti-aging effects of DNLA to their involvement in promoting autophagy of toxic amyloid-β (Aβ) plaques and modulation of key enzymes involved in the hyperphosphorylation of Tau proteins. Although amyloid buildup and the aggregation of Tau proteins are central to the onset of Alzheimer's disease (AD), evidence on how DNLA relate to other overlooked dysregulated AD-associated pathways is still lacking. MethodsWe intend on deciphering the underlying mechanisms driving the anti-AD effect of DNLA, using a combination of network analysis based on differentially expressed genes found in AD patients, target fishing, centrality analysis, enrichment analysis and hub genes identification. ResultsIn total, 2069 genes were found differentially expressed in SRP181886 and a PPI network constructed with common targets between DNLA and AD. Five hub genes were identified having a discriminatory power greater than 0.7; HTR2A, GRIN2B, GABRA1, HTR2C, GRIN2A, with the former being the top bottleneck node in the network. Enrichment analysis found that DNLA exert an anti-AD effect through the regulation of the calcium signaling pathway and the serotonergic system, by modulating key receptors implicated in excitatory/inhibitory neurotransmission. Additionally, DNLA were found to modulate two subunits of NMDA receptor involved in the release of pro-inflammatory cytokines, underlying the possible involvement of DNLA in neuroinflammation. DiscussionThis further emphasizes the therapeutic value of D.nobile and the multi-target, multi-pathway potential of DNLA to counteract the deleterious effects of calcium dysregulation and excitatory toxicity in AD, while providing evidence-based rationale behind the traditional use of D. nobile in TCM.

A Study Against Colon Cancer Mechanism of Xanthium sibiricum Herba Based on Computer Simulation and Bioinformatics.

Cancer is one of the leading causes of death worldwide, accounting for nearly one in six deaths in 2020. As a folk medicine, Xanthium sibiricum Herba (XSH) has been used many times in clinical practice for the treatment of various diseases. With the increasing number of cancer patients, there is a clinical need to find effective anti-cancer drugs. This study aims to explores the bioactivity and the anti-cancer mechanism of XSH. In this study, bioinformatics, network pharmacology, molecular docking, molecular dynamics simulation techniques, and apoptosis assay were used to explore the bioactivity and the anti- cancer mechanism of XSH. Finally, seven active ingredients in XSH after the screening were obtained, the two most active compounds were β-sitosterol and aloe-emodin, and good anti-cancer activity of XSH was predicted. Four core targets were obtained from the PPI network map, namely Caspase-3 (CASP3), Transcription factor AP-1 (JUN), Myc proto-oncogene protein (MYC), and cellular tumor antigen p53 (TP53). GO and KEGG analyses showed that the mechanism of XSH anti-cancer is mainly related to the apoptosis process, and the main signaling pathways are enriched in the p53 signaling pathway, Apoptosis, and MAPK signaling. The molecular docking and molecular dynamics simulation results showed that CASP3, JUN, MYC, and TP53 had a high affinity with β- sitosterol and aloe-emodin. Bioinformatics analyses demonstrated the importance of core targets. Apoptosis assay showed that XSH could significantly promote the apoptosis of cancer cells, and inhibit their proliferation and migration, especially colon cancer cells. This study uncovered the main active components, bioactivities, and potential targets of XSH, and further revealed the multi-component, multi-target, and multi-pathway mechanism of XSH for cancer treatment and promoting apoptosis.

Based on UPLC-Q-TOF/MS and Network Pharmacology to Explore the Mechanism of Qingre Lishi Decoction in the Treatment of Psoriasis.

Psoriasis is an immune-mediated chronic inflammatory disease. Qingre Lishi Decoction (QRLSD) has achieved great clinical effect in the treatment of psoriasis. However, the potential bioactive components and the mechanisms are yet unclear. To analyze the serum parameters of rats fed with QRLSD, screen out the active components of QRLSD, and explore the potential targets and pathway of QRLSD in the treatment of psoriasis. The active components of serum containing QRLSD were analyzed using ultra-high performance liquid chromatography quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS). The targets of QRLSD in the treatment of psoriasis were predicted by network pharmacology and molecular docking. In vitro experiments verified the underlying mechanism. By UPLC-Q-TOF/MS, 15 prototype components and 22 metabolites were identified in serum containing QRLSD. Subsequently, 260 chemical composition targets and 218 psoriasis targets were overlapped to obtain 23 intersection targets, including LGALS3, TNF, F10, DPP4, EGFR, MAPK14, STAT3 and others. TNF, IL-10, GAPDH, STAT3, EGFR, ITGB1, LGALS3 genes were identified as potential drug targets in the PPI network analyzed by CytoHubba. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that QRLSD may improve psoriasis by regulating immune and inflammatory pathways, the cytokine mediated signal transduction pathways and other signaling pathways. Molecular docking results showed that the main active components of the serum containing QRLSD had higher affinities for TNF and LGALS3. In vitro experiments confirmed that QRLSD may decrease levels of inflammatory cytokines by suppressing the NF-κB signaling pathway activated by TNF-α in human keratinocytes. This study explores the potential compounds, targets and signaling pathways of QRLSD in the treatment of psoriasis, which will help clarify the efficacy and mechanism of QRLSD.

Promotion Effect of Catalpol on Angiogenesis and Potential Mechanisms: A Research Based on Network Pharmacology.

Catalpol, a natural iridoid glycoside, has potential therapeutic benefits, including anti-inflammatory and neuroprotective effects. Investigating catalpol's role in angiogenesis is critical for understanding its potential therapeutic applications, particularly in diseases where modulating angiogenesis is beneficial. This study investigates catalpol's influence on angiogenesis and its mechanisms, combining network pharmacology and invitro experiments. The target genes corresponding to the catalpol were analyzed by SwissTargetPrediction. Then angiogenesis-related targets were acquired from databases like GeneCards. Subsequently, the Database for Annotation, Visualization and Integrated Discovery was employed for Gene Ontology and pathway analysis, while Cytoscape visualized protein interactions. The effect of catalpol on viability and angiogenesis of HUVECs was further examined using Cell Counting Kit-8 and angiogenesis assays. RT-qPCR and western blot were applied to check the expression of angiogenesis-related proteins. Totally, 312 target genes of catalpol and 823 angiogenesis-related targets were obtained with 56 common targets leading to PPI network analysis, highlighting hub genes (AKT1, EGFR, STAT3, MAPK3, and CASP3). These hub genes were mainly enriched in lipid and atherosclerosis pathway and EGFR-related pathway. The invitro experimental results showed that catalpol achieved a concentration-dependent increase in HUVECs viability. Catalpol also promoted the migration and angiogenesis of HUVECs and up-regulated the expression of EGFR. EGFR knockdown inhibited the effect of catalpol on HUVECs. Catalpol promotes angiogenesis in HUVECs by upregulating EGFR and angiogenesis-related proteins, indicating its potential therapeutic application in vascular-related diseases.

Discovering the effect of combination of celecoxib and sorafenib on hepatocellular carcinoma

IntroductionHepatocellular carcinoma (HCC) is a common and fatal cancer, and its molecular mechanisms are still not fully understood. This study aimed to explore the potential molecular mechanisms and immune infiltration characteristics of celecoxib combined with sorafenib in the treatment of HCC by analyzing the differentially expressed genes (DEGs) from the GSE45340 dataset in the GEO database and identifying key genes.MethodsThe GSE45340 dataset was downloaded from the GEO database, and DEGs were screened using GEO2R, and visualization and statistical analysis were performed. Metascape was used to perform functional annotation and protein–protein interaction network analysis of DEGs. The immune infiltration was analyzed using the TIMER database, and the expression of key genes and their relationship with patient survival were analyzed and verified using the UALCAN database.ResultsA total of 2181 DEGs were screened through GEO2R analysis, and heat maps were drawn for the 50 genes with the highest expression. Metascape was used for enrichment analysis, and the enrichment results of KEGG and GO and the PPI network were obtained, and 44 core genes were screened. Analysis of the TIMER database found that 12 genes were closely related to tumor immune infiltration. UALCAN analysis further verified the differential expression of these genes in HCC and was closely related to the overall survival of patients.ConclusionsThrough comprehensive bioinformatics analysis, this study identified a group of key genes related to the treatment of HCC with celecoxib combined with sorafenib. These genes play an important role in tumor immune infiltration and patient survival, providing important clues for further studying the molecular mechanism of HCC and developing potential therapeutic targets.

Comparison of the gene expression profiles of endometrial and trophoblastic cells in women with recurrent miscarriage: A bioinformatics approach.

Recurrent miscarriage (RM) remains unsolved in 50% of patients and causes physical and psychological problems in women without specific risk factors for miscarriage. For a successful pregnancy, acceptance of the endometrium and invasion of trophoblast cells into the endometrium is necessary. This study aimed to use computational analysis to identify key genes and related pathways in endometrial and trophoblast cells derived from RM samples. In this bioinformatics study, we explored the differential expression of genes in endometrial and trophoblast cells by analyzing the GSE165004 and GSE76862 datasets, respectively with the limma package in R software. Subsequently, overlapped genes between 2 datasets were selected, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. The overlapped genes were integrated to construct a protein-protein interaction network and hub genes selection. We observed 41 overlapped genes between endometrial and trophoblast cells, and future analysis was accomplished in overlapped and nonoverlapped genes. Kyoto Encyclopedia of Genes and Genomes analysis indicated that overlapped genes were significantly enriched in the complement and coagulation cascades, pluripotency of stem cells, and synthesis and degradation of ketone bodies. Gene ontology analysis suggested that the genes were enriched in the cell cycle, apoptosis, and cell division. The top 10 genes included: IRS1, FGF2, MAPK6, MAPK1, MAPK3, MAPK8, MAPK9, PLK1, PRKACA, and PRKCA were identified from the PPI network. This study identified the key genes and potential molecular pathways underlying the development of RM. This could provide novel insights to determine the possible mechanisms and interventional strategies associated with miscarriage.

Clinical Significance and Potential Mechanism of Circ_00008842 in Acute Myocardial Infarction.

This study aimed to evaluate the clinical value of circ_0008842 in acute myocardial infarction (AMI) and explore the potential mechanisms.GSE149051 and GSE160717 datasets analyze common differentially expressed circRNAs (coDEcircRNA) in AMI. RT-qPCR analysis of circ_0008842 mRNA levels in patients with AMI. ROC curve assesses the diagnostic value of circ_0008842 in AMI. A cell model of AMI was constructed by hypoxia-reoxygenation (H/R) -induced H9c2. Cell viability and apoptosis were examined by CCK-8 and flow cytometry. Enzyme-linked immunosorbent assay was used to explore myocardial injury markers CK-MB and cTnI secretion. Dual luciferase reporter assays validate circ_0008842 binding to miRNA. PPI network and gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment reveal potential functions and pathways of targets from the miRNA in AMI.circ_0008842 is recognized as coDEcircRNA in AMI-related databases. circ_0008842 was greatly lower and miR-574-5p was significantly higher in patients with AMI than in healthy individuals. miR-574-5p is a target of circ_0008842. The sensitivity and specificity of circ_0008842 for diagnosing patients with AMI were 87.40% and 83.50%, respectively. Overexpression of circ_0008842 inhibited H/R induced apoptosis, increased cell viability, and decreased CK-MB and cTnI levels, which were partially abrogated by overexpression of miR-574-5p. Calmodulin-like protein 4 (CALML4) was the most connected hub gene in the PPI network of miR-574-5p predicted target genes.circ_0008842 is a diagnostic biomarker for AMI and participates in myocardial injury in AMI by regulating miR-574-5p. Our study provides new insights into the diagnosis for AMI.

Anti-inflammatory Properties of Tongfeng Li'an Granules in an Acute Gouty Arthritis Rat Model.

To examine the anti-inflammatory properties and underlying mechanisms of Tongfeng Li'an Granules (TFLA), a traditional medicine, in acute gouty arthritis using a rat model. We identified 55 major compounds in TFLA via ultrahigh-performance liquid chromatography connected to quadrupole time-of-flight mass spectrometry (UPLC-TQF-MS/MS). Databases were employed for the prediction of potential targets, followed by PPI network construction as well as GO and KEGG analyses. After network-pharmacology-based analysis, a rat gouty arthritis model was used to validate the anti-inflammatory mechanism of TFLA. UPLC-TQF-MS/MS and network pharmacology analyses revealed 55 active ingredients and 160 targets of TFLA associated with gouty arthritis, forming an ingredient-target-disease network. The PPI network identified 20 core targets, including TLR2, TLR4, IL6, NFκB, etc. Functional enrichment analyses highlighted the Toll-like receptor signaling pathway as significantly enriched by multiple targets, validated in in vivo experiments. Animal experiments demonstrated that TFLA improved pathological changes in gouty joint synovium, with decreased ankle joint circumference, serum IL6, IL10, and TNFα levels, as well as reduced protein and mRNA expression of NLRP3, TLR2, and TLR4 in ankle joint synovial tissue observed in the middle- and high-dose TFLA and positive control groups compared to the model group (p < 0.05). This research elucidated the pharmacological mechanisms of TFLA against gouty arthritis, implicating various ingredients, targets, and signaling pathways. Animal experiments confirmed TFLA's efficacy in alleviating inflammation in acute gouty arthritis by modulating Toll-like receptor signaling and NLRP3 expression.

Mass Spectrometric and Artificial Intelligence-Based Identification of the Secretome of Plasmodium falciparum Merozoites to Provide Novel Candidates for Vaccine Development Pipeline.

Merozoites are the only extracellular form of blood stage parasites, making it a worthwhile target. Multiple invasins that are stored in the merozoite apical organelles, are secreted just prior to invasion, and mediates its interaction with RBC. A comprehensive identification of all these secreted invasins is lacking and this study addresses that gap. Pf3D7 merozoites were enriched and triggered to discharge apical organelle contents by exposure to ionic conditions mimicking that of blood plasma. The secreted proteins were separated from cellular contents and both the fractions were subjected to proteomic analysis. Also, the identified secreted proteins were subjected to GO, PPI network analysis, and AI-based in silico approach to understand their vaccine candidacy. A total of 63 proteins were identified in the secretory fraction with membrane and apical organellar localization. This includes various MSPs, micronemal EBAs and rhoptry bulb proteins, which play a crucial role in initial and late merozoite attachment, and majority of them qualified as vaccine candidates. We, for the first time, report the secretory repertoire of merozoite and its status for vaccine candidacy. This information can be utilized to develop better invasion blocking multisubunit vaccines, comprising of immunological epitopes from several secreted invasins.

Comprehensive analysis of circRNA-miRNA-mRNA network related to angiogenesis in recurrent implantation failure

BackgroundAbnormal endometrial blood flow causes a decrease in endometrial receptivity and is considered a relatively independent risk factor for recurrent implantation failure (RIF). This study aimed to explore the potentially functional circRNA-miRNA-mRNA network in RIF, and further explore its mechanism.MethodsDatasets were downloaded from the GEO database to identify differentially expressed circRNAs, miRNAs and mRNAs. The circRNA–miRNA–mRNA and PPI networks were constructed using Cytoscape 3.6.0 and the STRING database, the hub genes were identified with the cytoHubba plug-in, and a circRNA–miRNA–hub mRNA regulatory sub-network was constructed. Then, GO and KEGG pathway enrichment analyses of the hub genes were performed to comprehensively analyze the mechanism of hub mRNAs in RIF. Due to the results of circRNAs-miRNAs-hub mRNAs regulatory network, we verified the expression of circRNA_0001721, circRNA_0000714, miR-17-5p, miR-29b-3p, HIF1A and VEGFA in the RIF mouse model by qRT‒PCR and western blotting.ResultsWe initially identified 175 DEmRNAs, 48 DEmiRNAs and 56 DEcircRNAs in RIF associated with angiogenesis and constructed a circRNA-miRNA‒mRNA network and PPI network. We further identified six hub genes in the acquired network. Based on these genes, functional enrichment analysis revealed that the HIF-1 signaling pathway plays a vital role in endometrial angiogenesis in RIF. In addition, the interaction networks of circRNA_0001721/miR-17-5p/HIF1A and the circRNA_0000714/miR-29b-3p/VEGFA axis were predicted. In the RIF mouse model, circRNA_0001721, circRNA_0000714, HIF1A and VEGFA were down-regulated, whereas miR-17-5p and miR-29b-3p were up-regulated according to qRT‒PCR and western blotting.ConclusionThis study revealed that the HIF-1 signaling pathway plays a vital role in endometrial angiogenesis in RIF. The circRNA_0001721/miR-17-5p/HIF1A and circRNA_0000714/miR-29b-3p/VEGFA axes might play a role in the pathogenesis of endometrial angiogenesis in RIF.

Paeoniflorin alleviates high glucose-induced endothelial cell apoptosis in diabetes mellitus by inhibiting HRAS-activated RAS pathway.

Paeoniflorin (Pae) can improve diabetes mellitus (DM), especially endothelial dysfunction induced by high glucose (HG). Molecularly, the mechanism pertinent to Pae and DM lacks further in-depth research. Hence, this study determined the molecular mechanism of Pae in treating DM through network pharmacology. The target of Pae was analyzed by TCMSP database, and DM-related genes were dissected by Genecards database and Omim database. PPI network was constructed for cross targets through Cytoscape 3.9.1 and STRING platform. GO and KEGG analyses were carried out on the cross targets. Protein molecular docking verification was completed by AutoDockTools and Pymol programs. Human umbilical vein endothelial cells (HUVECs) were separately treated with HG, Pae (5, 10, 20 μM) and/or HRAS overexpression plasmids (oe-HRAS). The cell viability, apoptosis and the protein expressions of HRAS and Ras-GTP were evaluated. There were 50 cross targets between Pae and DM, and VEGFA, EGFR, HRAS, SRC and HSP90AA1 were the key genes identified by PPI network analysis. GO and KEGG analyses revealed signal paths such as Rap1 and Ras. Molecular docking results confirmed that Pae had a good binding ability with key genes. In HG-treated HUVECs, Pae dose-dependently facilitated cell viability, attenuated cell apoptosis, and dwindled the expressions of HRAS and Ras-GTP, but these effects of Pae were reversed by oe-HRAS. In conclusion, Pae regulates the viability and apoptosis of HG-treated HUVECs by inhibiting the expression of HRAS.