Gene Ontology Functional Analysis Research Articles

Proteome Profiling of Cucurbita pepo Phyllosphere After Infection by Podosphaera xanthii and Application of Reynoutria sachalinensis Extract

Podosphaera xanthii is the main causal agent of powdery mildew (PM) disease for Cucurbita pepo. Disease control is attained principally by applications of chemical fungicides, along with parallel use of tolerant crop varieties and alternate application of elicitors to control development of disease resistance. To get insight into C. pepo molecular responses to P. xanthii infection and elicitor treatment we studied the proteomic profile differences at the phyllosphere of a zucchini cultivar susceptible to PM, at the onset of P. xanthii (PX) infection and after application of Reynoutria sachalinensis (RS) plant extract, respectively, using a nano-LC-HRMS/MS, Q-Exactive-Orbitrap approach. Analysis of peptide sequences regarding four treatment groups (Control; PX; RS; and RSPX (PX-infected priorly treated with RS)) resulted in 2070 CuGenDB annotations. Three comparisons (treatments vs. Control) encompassed most of the Differentially Expressed Proteins (DEPs). In these three comparisons, KEGG and Gene Ontology functional analyses highlighted unique differentially enriched pathways—some of which included highly expressed proteins—in PX-related (proteasome, pentose phosphate pathway, and carbon fixation), RS-related (biosynthesis of secondary metabolites, flavonoids, and starch and sucrose metabolism), and RSPX-related (pyruvate metabolism and polycomb repressive complex) comparisons, respectively, suggesting distinct mechanisms of early plant responses modulated by PX and RS. Furthermore, in four out of six comparisons the thiamine metabolism pathway was found to be enriched, suggesting a pivotal role in PX-induced responses.

Study on the anti-colon cancer effect of Renshen Yangrong Decoction based on network pharmacology, molecular docking, and in vivo and in vitro experiments

Renshen Yangrong Decoction (RSYRD) is a traditional Chinese medicinal compound widely used as an adjuvant in colon cancer treatment. However, the specific role of RSYRD in anti-colon cancer remains unclear. This study aimed to investigate the anti-colon cancer effects of RSYRD using network pharmacology, molecular docking, and in vitro and in vivo experiments. The active ingredients and targets of RSYRD were identified utilizing databases, and RSYRD-ingredient-target and protein-protein interaction (PPI) networks were constructed. Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the anti-colon cancer targets of RSYRD, followed by molecular docking using AutoDockTools 1.5.6. In vitro and in vivo experiments were conducted to explore the mechanism of RSYRD and evaluate its inhibitory efficacy on colon cancer. A total of 233 active ingredients and 88 colon cancer-related targets were identified, including 9 core targets. GO functional analysis revealed that RSYRD exerts anti-tumor effects through processes such as oxidative reactions, closely associated with intracellular reactive oxygen species (ROS). KEGG enrichment analysis indicated that the anti-tumor effect of RSYRD involved the interaction of cancer-related and viral disease-associated pathways, as well as the IL-17, TNF, and PI3K-AKT signaling pathways. Molecular docking showed stable ligand-receptor binding, with binding energies below −5.0 kcal/mol. In vitro experiments demonstrated that RSYRD increased ROS levels, reduced mitochondrial membrane potential (MMP), and promoted apoptosis in SW620 cells, thereby inhibiting cell proliferation and migration. In vivo experiments showed that RSYRD significantly suppressed colon cancer proliferation. This study identified Quercetin, Kaempferol, 7-Methoxy-2-methyl-isoflavone, Licochalcone-a, and Isorhamnetin as core ingredients in RSYRD, likely exerting anti-colon cancer effects by inhibiting proteins such as ESR1, HSP90AA1, NCOA2, and MAPK14, and suppressing the PI3K-AKT signaling pathway, thereby regulating tumor cell proliferation, migration, and apoptosis.

To Reveal the Potential Mechanism of Quercetin against NSCLC Based on Network Pharmacology and Experimental Validation.

This study aimed to initially clarify the potential mechanism of quercetin in the treatment of non-small cell lung cancer (NSCLC) based on network pharmacology, molecular docking and in vitro experiments. TCMSP, SwissTargetPrediction, TCMIP, STITCH, and ETCM databases were applied to obtain the targets of quercetin. NSCLC-related targets were retrieved from GeneCards, OMIM, PharmGKB, TTD, and NCBI databases. Their intersection targets were imported into the STRING database to construct a protein-protein interaction (PPI) network and core targets were identified through the Cytoscape 3.10.0 soft and the CytoHubba tool. Furthermore, Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the intersection targets. A compound-targetspathways network was subsequently constructed to screen for key targets and pathways. Molecular docking was performed with Discovery Studio software to verify the interactions between quercetin and core targets. In vitro validations were conducted employing CCK-8 assays, flow cytometry, and Western blotting (WB). 193 potential targets of quercetin for treating NSCLC were obtained. The top ten core targets identified within the PPI network included TP53, HSP90AA1, AKT1, JUN, SRC, EGFR, ACTB, TNF, MAPK1, and VEGFA. GO analysis yielded 2319 items, and KEGG analysis resulted in 211 enriched pathways. Molecular docking results demonstrated a high affinity of quercetin towards the core targets. Based on the compound-targets-pathways network and molecular docking, the PI3K/AKT/P53 pathway and its key-related proteins (PIK3R1, AKT1, and TP53) were selected for further validation. Quercetin(20 and 40 μg/mL) significantly decreased the viability of A549 NSCLC cells but not BEAS-2B normal cells via CCK-8 assays. Flow cytometry and WB analyses further corroborated that quercetin could promote apoptosis of A549 cells by downregulating and upregulating the expression of Bcl-2 and Bax (P<0.05), respectively. Notably, quercetin did not significantly alter the total protein levels of PI3K, AKT, and P53 but downregulated the phosphorylation levels of PI3K and AKT (P<0.05) and upregulated the phosphorylation level of P53 (P<0.05). Quercetin exhibits therapeutic potential in NSCLC by regulating the PI3K/AKT/P53 pathway to promote cell apoptosis.

Exploring the therapeutic potential of Xiangsha Liujunzi Wan in Crohn's disease: from network pharmacology approach to experimental validation

Ethnopharmacological relevanceXiangsha Liujunzi Wan (LJZW) is a traditional Chinese medicine (TCM) formula containing a variety of traditional Chinese herb components. Its principal components are often used in the treatment of gastrointestinal diseases and contribute to the treatment of Crohn's disease (CD). Aim of the studyTo explore the therapeutic potential of LJZW in CD through network pharmacology, bioinformatics, molecular docking, and experimental verification. MethodsThe principal bioactive components and corresponding targets of LJZW were ascertained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Potential targets for CD were identified in GeneCards, OMIM, DrugBank, DisGeNET, CTD, and Gene Expression Omnibus (GEO) databases. Intersection targets of LJZW and CD were identified using a Venn diagram and visualized using Cytoscape 3.8.0 to construct a protein-protein interaction (PPI) network. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to assess the function of intersection targets. AutoDockTools and PyMOL were used for molecular docking to recognize the association between the core ingredients of LJZW and the core targets of CD. Subsequently, a series of experiments were conducted for validation. ResultsThe network pharmacology results indicated that there were 156 bioactive components and 268 corresponding targets for LJZW, 3023 primary relevant targets for CD, and 169 intersection targets for LJZW and CD. The PPI network was employed to identify five hub genes and six clusters. The GO functional analysis indicated that intersection targets are primarily correlated with oxidative stress and inflammatory responses. KEGG pathway analysis revealed that these targets were primarily associated with the phosphotylinosital 3 kinase (PI3K)-protein kinase B (AKT) and mitogen-activated protein kinase (MAPK) signaling pathways. The molecular docking results showed that the core ingredients of LJZW had good binding ability with the core targets of CD. A series of experiments demonstrated that LJZW could effectively attenuate TNBS-induced colitis symptoms, inhibit the inflammatory response, and protect intestinal barrier function by inhibiting the PI3K-AKT and MAPK signaling pathways, thus preventing and treating CD. ConclusionLJZW has the characteristics of multi-component, multi-target, and multi-pathway treatment, which helps to improve the treatment of CD, protect the intestinal barrier, and exert the effect of anti-inflammatory therapy by inhibiting PI3K-AKT and MAPK signaling pathways.

Transcriptomic Analysis of the Hepatopancreas in the Sex-Related Size Differences of Macrobrachium nipponense.

Macrobrachium nipponense, a commercially popular crustacean species within the Chinese context, is recognized for its exceptional nutritional composition and palatability. There are significant differences in growth between male and female M. nipponense. Herein, transcriptomics was used to determine the hepatopancreas transcriptome differences between sex-related size differences in M. nipponense. We identified 974 differentially expressed genes (DEGs) between the SHE (female) and BHE (male) groups, which were validated using RT-qPCR. The genes encoding matrix metalloproteinase-9 (MM9), Ribosome-binding protein 1 (RBP1), Aly/REF export factor 2, and hematological and neurological expressed 1 (HN1) may play a role in modulating the sex-related size differences observed in M. nipponense. Clusters of orthologous groups and gene ontology functional analysis demonstrated that the DEGs for sex-related size in M.nipponense were associated with various biological functions. The Kyoto Encyclopedia of Genes and Genomes pathways analysis demonstrated that upregulated DEGs were mainly enriched in lysine biosynthesis, tryptophan metabolism, and lysine degradation pathways, whereas the downregulated DEGs were mainly enriched in ascorbate and aldarate metabolism, retinol metabolism, and drug metabolism-cytochrome P450 pathways. The results indicated the molecular mechanism underlying the sex-related size differences and identified key genes. This data will be invaluable to support explanations of individual differences between male and female prawns.

Sodium Fluoride Exposure Induces Developmental Toxicity and Cardiotoxicity in Zebrafish Embryos.

Fluorosis is a worldwide public health problem, in which the heart is an important target organ. However, studies on its toxicological mechanism in embryonic development are limited. This study assessed the toxicity of sodium fluoride (NaF) toward zebrafish embryos. We determined the mortality, hatching rate, phenotypic malformation, heart function, and morphology of zebrafish embryos after exposure to NaF. Subsequently, the molecular mechanism was revealed using high-throughput RNA sequencing analysis. The expression levels of key genes for heart development were detected using quantitative real-time reverse transcription PCR. The 50% lethal concentration (LC50) value of NaF toward zebrafish embryos at 96h post-fertilization was 335.75mg/L. When the concentration of NaF was higher than 200mg/L, severe deformities, such as pericardial edema, yolk sac edema, spine curvature, shortened body length, reduced head area, and eye area, were observed. The heart rate of the embryos exposed to NaF decreased in a dose-dependent fashion. The distance between the sinus venosus and bulbus arteriosus was significantly increased in the NaF-exposed group compared with that in the control group. The stroke volume and cardiac output decreased significantly in the NaF groups. Compared with the control group, the expression levels of Gata4, Tbx5a, Hand2, Tnnt2c, Nppa, and Myh6 were significantly increased in the NaF-treated group. Through transcriptome sequencing, 1354 differentially expressed genes (DEGs) were detected in the NaF (200mg/L) treated groups, including 1253 upregulated genes and 101 downregulated genes. Gene ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEGs showed that cardiac-related pathways, such as actin cytoskeleton regulation, Jak-Stat, PI3k-Akt, and Ras, were activated in the NaF-exposed group. This study revealed the underlying mechanism of fluoride-induced cardiac morphological and functional abnormalities and provides clues for the clinical prevention and treatment of fluorosis.

A systematic investigation of clear cell renal cell carcinoma using meta-analysis and systems biology approaches.

Renal cell carcinoma with clear cells (ccRCC) is the most frequent kind; it accounts for almost 70% of all kidney cancers. A primary objective of current research was to find genes that may be used in ccRCC gene therapy to understand better the molecular pathways underlying the disease. Based on PubMed microarray searches and meta-analyses, we compared overall survival and recurrence-free survival rates in ccRCC patients with those in healthy samples. The technique was followed by a KEGG pathway and Gene Ontology (GO) function analyses, both performed in conjunction with the approach. Tumor immune estimate and multi-gene biomarkers validation for clinical outcomes were performed at the molecular and clinical cohort levels. Our analysis included fourteen GEO datasets based on inclusion and exclusion criteria. A meta-analysis procedure, network construction using PPIs, and four significant gene identification standard algorithms indicated that 11 genes had the most important differences. Ten genes were upregulated, and one was downregulated in the study. In order to analyze RFS and OS survival rates, 11 genes expressed in the GEPIA2 database were examined. Nearly nine of eleven significant genes have been found to beinvolved in tumor immunity. Furthermore, it was found that mRNA expression levels of these genes were significantly correlated with experimental literature studies on ccRCCs, which explained these findings. This study identified eleven gene panels associated with ccRCC growth and metastasis, as well as their immune system infiltration.

Integrated GC-MS and proteomics reveal the changes and correlations between flavor compounds and the proteome in surimi gels treated with high-temperature sterilization

The impact of high-temperature sterilization on the flavor of surimi gels were examined, alongside the utilization of tandem mass tag labeled quantitative proteomics to explore the correlations between flavor and proteome profiles. Notable increase was observed in lipid oxidation, protein degradation, and the types and total content of volatile organic compounds (VOC), particularly aldehydes. A total of 67 shared differentially expressed proteins (DEP) were identified, confirming the aggregation and degradation of proteins. Gene Ontology functional analysis revealed that proteins possibly linked to flavor were primarily concentrated in the myosin complex, motor activity, and hydrolase activity categories. The Kyoto Encyclopedia of Genes and Genomes pathway analysis highlighted a focus on the motor protein pathway. Correlation analysis between DEP and key VOC revealed that most DEP exhibited significant correlations with aldehydes and ketones such as octanal, pentanal, and (Z)-4-heptenal, with flavor-associated proteins mainly concentrated in structural, antioxidant, and redox proteins.

Proteomic analysis of differentially expressed proteins in gastrointestinal neuroendocrine tumors and their liver metastasis

Objective: To investigate the differences of protein expressions in the primary tumors, adjacent tissues, and metastatic tumors of gastrointestinal neuroendocrine neoplasms. Methods: Nine patients with gastrointestinal neuroendocrine tumors (GI-NENs) with liver metastasis who underwent surgery at the National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences from July 2015 to April 2019 were selected. The protein expressions of the primary tissues, liver metastatic tissues, and adjacent tissues were detected by the data independent acquisition (DIA) technology. P<0.05 and | log2FC|>0.5 (FC as the difference multiple) were used as the criteria to identify the differentially expressed proteins in the primary tissues vs adjacent tissues, primary tissues vs liver metastatic tissues, primary tissues with different degrees of differentiation, and liver metastatic tissues with different degrees of differentiation. The differentially expressed proteins were investigated by volcano map analysis, cluster analysis, Gene Ontology (GO) function analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results: Compared with adjacent tissues, 85 proteins were downregulated and 42 proteins were upregulated in the primary tissues of gastric NENs. The differentially expressed proteins were mainly enriched in the biological processes related to the regulation of guanosidase triphosphate activity and the catabolism of deoxyribonucleoside monophosphate, the glycosaminoglycan biosynthesis chondroitin sulfate/dermatan sulfate, pantothenate, and CoA biosynthesis signaling pathways. 114 proteins were downregulated and 155 proteins were upregulated in the primary tissues of intestinal NENs. The differentially expressed proteins were mainly enriched in the biological processes related to glutathione metabolism and sulfur compound metabolism, collecting duct acid secretion, and taurine and hytaurine metabolism signaling pathways. Compared with the primary tissues of neuroendocrine cancers (NECs), 168 proteins were downregulated and 278 proteins were upregulated in G1-2 differentiation primary tissues. The differentially expressed proteins were significantly enriched in biological processes such as DNA metabolism and DNA replication, as well as replication, mismatch repair, and other pathways. Compared with the metastatic tissues of NECs, 95 proteins were downregulated and 97 proteins were upregulated in G1-2 differentiated metastases. The differentially expressed proteins were significantly enriched in the activity and catalytic activity of transcriptional coactivators, base excision repair, and protein efflux pathways. Compared with G1 differentiated primary tissues, 530 proteins were downregulated and 211 proteins were upregulated in G1 differentiated metastatic tissues. Compared with G2 differentiated primary lesions, 53 proteins were downregulated and 96 proteins were upregulated in G2 differentiated metastatic tissues. Compared with the primary lesions of NECs, 109 proteins were downregulated and 92 proteins were upregulated in the metastatic tissues of NECs. In G1 and G2 differentiated GI-NENs, there are many similar signal pathways enriched in differentially expressed proteins between primary lesions and metastases, while only one signal pathway enriched in differentially expressed proteins between primary and metastatic tissues of NECs is the same as that enriched in differentially expressed proteins between primary and metastatic tissues of GI-NENs, which is the drug metabolism signal pathway. The differentially expressed proteins in G1 differentiated primary and metastatic tissues were mainly expressed in cytoplasm (20.26%), mitochondria (18.67%), and nucleus (15.48%). The differentially expressed proteins in the primary and metastatic tissues of G2 differentiation were mainly expressed in the cytoplasm (20.24%), nucleus (18.25%), and cell membrane (15.08%). The differentially expressed proteins in the primary and metastatic tissues of NECs were mainly expressed in the nucleus (23.78%), cytoplasm (22.7%), and cell membrane (11.35%). Conclusion: The protein expressions of GI-NENs in the primary tissues, adjacent tissues, and metastatic tissues were significantly different in different sites and degrees of differentiation.

Exploring biomarkers for diagnosing and predicting organ dysfunction in patients with perioperative sepsis: a preliminary investigation

ObjectiveEarly diagnosis and prediction of organ dysfunction are critical for intervening and improving the outcomes of septic patients. The study aimed to find novel diagnostic and predictive biomarkers of organ dysfunction for perioperative septic patients.MethodThis is a prospective, controlled, preliminary, and single-center study of emergency surgery patients. Mass spectrometry, Gene Ontology (GO) functional analysis, and the protein-protein interaction (PPI) network were performed to identify the differentially expressed proteins (DEPs) from sepsis patients, which were selected for further verification via enzyme-linked immunosorbent assay (ELISA). Logistic regression analysis was used to estimate the relative correlation of selected serum protein levels and clinical outcomes of septic patients. Calibration curves were plotted to assess the calibration of the models.ResultsFive randomized serum samples per group were analyzed via mass spectrometry, and 146 DEPs were identified. GO functional analysis and the PPI network were performed to evaluate the molecular mechanisms of the DEPs. Six DEPs were selected for further verification via ELISA. Cathepsin B (CatB), vascular cell adhesion protein 1 (VCAM-1), neutrophil gelatinase-associated lipocalin (NGAL), protein S100-A9, prosaposin, and thrombospondin-1 levels were significantly increased in the patients with sepsis compared with those of the controls (p < 0.001). Logistic regression analysis showed that CatB, S100-A9, VCAM-1, prosaposin, and NGAL could be used for preoperative diagnosis and postoperative prediction of organ dysfunction. CatB and S100-A9 were possible predictive factors for preoperative diagnosis of renal failure in septic patients. Internal validation was assessed using the bootstrapping validation. The preoperative diagnosis of renal failure model displayed good discrimination with a C-index of 0.898 (95% confidence interval 0.843–0.954) and good calibration.ConclusionSerum CatB, S100-A9, VCAM-1, prosaposin, and NGAL may be novel markers for preoperative diagnosis and postoperative prediction of organ dysfunction. Specifically, S100-A9 and CatB were indicators of preoperative renal dysfunction in septic patients. Combining these two biomarkers may improve the accuracy of predicting preoperative septic renal dysfunction.Trial registrationThe study was registered at the Chinese Clinical Trials Registry (ChiCTR2200060418) on June 1, 2022.

Cyclophilin A promotes porcine deltacoronavirus replication by regulating autophagy via the Ras/AKT/NF-κB pathway

Porcine deltacoronavirus (PDCoV) is an important enteric coronavirus that has caused major worldwide economic losses in the pig industry. Previous studies have shown that cyclophilin A (CypA), a key player in aetiological agent infection, is involved in regulating viral infection. However, the role of CypA during PDCoV replication remains unknown. Therefore, in this study, the role of CypA in PDCoV replication was determined. The results demonstrated that PDCoV infection increased CypA expression in LLC-PK1 cells. CypA overexpression substantially promoted PDCoV replication. Proteomic analysis was subsequently used to assess changes in total protein expression levels after CypA overexpression. Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to further determine the mechanisms by which CypA affects viral replication. Proteomic analysis revealed that CypA protein overexpression significantly upregulated 75 differentially expressed proteins and significantly downregulated 172 differentially expressed proteins. The differentially expressed proteins were involved mainly in autophagy and activation of the host innate immune pathway. Subsequent experimental results revealed that the CypA protein promoted viral replication by reducing the levels of natural immune cytokines and mitigated the inhibitory effect of chloroquine (CQ) on viral replication. Further investigation revealed that CypA could activate the Ras/AKT/NF-κB pathway, mediate autophagy signalling and promote PDCoV replication. In summary, the findings of this study may help elucidate the role of CypA in PDCoV replication.

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.

Effects and Mechanism of Morinda Officinalis How on Metabolism-Associated Fatty Liver Disease.

This study aims to investigate the effects and mechanism of Morinda Officinalis How (MOH), a lianoid shrub with potential therapeutic properties, on Metabolism- Associated Fatty Liver Disease (MAFLD). bjective: The objective of this study was to construct a MOH-MAFLD network prediction model and explore the effect of MOH on MAFLD and its underlying mechanism in vivo. Screening of MAFLD targets was performed using the DisGeNET database. Venny database was used to establish the MOH-MAFLD interaction network map, while the STRING database was applied to assess the Protein-Protein Interaction (PPI) network. The central target gene was screened using Gene Ontology (GO) function analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. GO function enrichment analysis revealed that MOH affected MAFLD through apoptosis and estrogen-related pathways. KEGG pathway enrichment and PPI network analysis indicated that MOH might mitigate MAFLD by reducing apoptosis and improving lipid metabolism. Additionally, 6 weeks of MOH treatment in rats decreased caspase-3 levels and increased Bcl-2, Estrogen receptor α(Esr1), and JUN proteins, thus ameliorating MAFLD progression. MOH could delay the progression of MAFLD by affecting estrogen-related pathways, reducing cell stress, and inhibiting apoptosis.

Study on the mechanism of inhibition of Escherichia coli by Polygonum capitatum based on network pharmacology and molecular docking technology: A review.

This study aims to analyze the effective components of Polygonum capitatum (PC) inhibiting Escherichia coli based on network pharmacology methods and predict its molecular mechanism of action. PC compounds and targets were collected from the TCMSP database, Swiss Target Prediction, and the literature. E coli targets were searched using the GeneCards database. The targets of E coli and the targets of the active ingredients of PC were taken as intersections to obtain the intersecting targets. The resulting overlapping targets were uploaded to the STRING database to construct the protein interaction network diagram of E coli target inhibition. The key targets for the inhibitory effect of PC on E coli were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed by uploading key targets into the DAVID database. The results showed that there were 50 targets for PC to inhibit E coli. Among them, there are 5 core targets, mainly including AKT1, TNF, EGFR, JUN, and ESR1. A total of 196 gene ontology functional analysis results and 126 Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis results were obtained. These include cellular response to cadmium-ion, cellular response to reactive oxygen species, pathways in cancer, prostate cancer, and PI3K-Akt signaling pathway. Molecular docking results indicate that Lutedin, Hirsutin, Flazin, and Ellagic acid in PC have high affinity for the target genes AKT1, TNF, MAPK3 and EGFR. PC exerts its inhibitory effect on E coli through multi-targets and multi-pathways, which provides a new basis for the new use of PC as an old medicine.

Transcriptome sequencing and bioinformatics analysis of gastrocnemius muscle in type 2 diabetes mellitus rats

ObjectiveType 2 diabetes mellitus (T2DM) is one of the high risk factors for sarcopenia. However, the pathogenesis of diabetic sarcopenia has not been fully elucidated. This study obtained transcriptome profiles of gastrocnemius muscle in normal and T2DM rats based on high-throughput sequencing technology, which may provide new ideas for exploring the pathogenesis of diabetic sarcopenia.MethodsTwelve adult male Sprague-Dawley rats were randomly divided into Control group and T2DM group, and gastrocnemius muscle tissue was retained for transcriptome sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) 6 months later. Screening differentially expressed genes (DEGs), Cluster analysis, gene ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Gnomes (KEGG) functional annotation and enrichment analysis were performed for DEGs. Six DEGs related to apoptosis were selected for qTR-PCR verification.ResultsTranscriptomic analysis showed that there were 1016 DEGs between the gastrocnemius muscle of T2DM and normal rats, among which 665 DEGs were up-regulated and 351 DEGs were down-regulated. GO analysis showed that the extracellular matrix organization was the most enriched in biological processes, with 26 DEGs. The extracellular matrix with 35 DEGs was the most abundant cellular component. The extracellular matrix structural constituent, with 26 DEGs, was the most enriched in molecular functions. The highest number of DEGs enriched in biological processes, cellular components and molecular functions were positive regulation of transcription by RNA polymerase II, nucleus and metal ion binding, respectively. There were 78, 230 and 89 DEGs respectively. KEGG pathway enrichment analysis showed that ECM-receptor interaction, PI3K-Akt signaling pathway and TGF-β signaling pathway(p < 0.001) had higher enrichment degree and number of DEGs. qRT-PCR results showed that the fold change of Map3k14, Atf4, Pik3r1, Il3ra, Gadd45b and Bid were 1.95, 3.25, 2.97, 2.38, 0.43 and 3.6, respectively. The fold change of transcriptome sequencing were 3.45, 2.21, 2.59, 5.39, 0.49 and 2.78, respectively. The transcriptional trends obtained by qRT-PCR were consistent with those obtained by transcriptome sequencing.ConclusionsTranscriptomic analysis was used to obtain the “gene profiles” of gastrocnemius muscle of T2DM and normal rats. qRT-PCR verification showed that the genes related to apoptosis were differentially expressed. These DEGs and enrichment pathways may provide new ideas for exploring the pathogenesis of diabetic sarcopenia.

Exploring the mechanisms of glycolytic genes involvement in pulmonary arterial hypertension through integrative bioinformatics analysis.

The purpose of this study was to identify the mechanisms underlying the involvement of glycolytic genes in pulmonary arterial hypertension (PAH). This study involved downloading 3 datasets from the GEO database at the National Center for Biotechnology Information. The datasets were processed to obtain expression matrices for analysis. Genes involved in glycolysis-related pathways were obtained, and genes related to glycolysis were selected based on significant differences in expression. Gene Ontology functional annotation analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and GSEA enrichment analysis were performed on the DEGs. Combining LASSO regression with SVM-RFE machine learning technology, a PAH risk prediction model based on glycolysis related gene expression was constructed, and CIBERSORTx technology was used to analyse the immune cell composition of PAH patients. Gene enrichment analysis revealed that the DEGs work synergistically across multiple biological pathways. A total of 6 key glycolysis-related genes were selected using LASSO regression and SVM. A bar plot was constructed to evaluate the weights of the key genes and predict the risk of PAH. The clinical application value and predictive accuracy of the model were assessed. Immunological feature analysis revealed significant correlations between key glycolysis-related genes and the abundances of different immune cell types. The glycolysis genes (ACSS2, ALAS2, ALDH3A1, ADOC3, NT5E, and TALDO1) identified in this study play important roles in the development of pulmonary arterial hypertension, providing new evidence for the involvement of glycolysis in PAH.

Integrative Bioinformatics Approaches to Uncover Hub Genes and Pathways Involved in Cardiovascular Diseases.

Cardiovascular diseases (CVD) represent a significant global health challenge resulting from a complex interplay of genetic, environmental, and lifestyle factors. However, the molecular pathways and genetic factors involved in the onset and progression of CVDs remain incompletely understood. Here, we performed an integrative bioinformatic analysis to highlight specific genes and signaling pathways implicated in the pathogenesis of 80 CVDs. Differentially expressed genes (DEGs) were identified through the integrated analysis of microarray and GWAS datasets. Then, hub genes were identified after gene ontology functional annotation analysis and protein-protein internet (PPI) analysis. In addition, pathways were identified through KEGG and gene ontology enrichment analyses. A total of 821 hub genes related to 80 CVDs were identified, including 135 common and frequent CVD-associated genes. TNF, IL6, VEGFA, and TGFB.1 genes were the central core genes expressed in 50% or more of CVDs, confirming that the inflammation is a key pathological feature of CVDs. Analysis of hub genes by KEGG enrichment revealed predominant enrichment in 201 KEGG pathways, of which the AGE-RAGE signaling pathway in diabetic complications was identified as the common key KEGG implicated in 62 CVDs. In addition, the outcomes showed an overrepresentation in pathways categorized under human diseases, particularly in the subcategories of infectious diseases and cancers, which may be common risk factors for CVDs. In conclusion, this powerful approach for in silico fine-mapping of genes and pathways allowed the identification of determinant hubs genes and pathways implicated in the pathogenesis of CVDs which could be employed in developing more targeted and effective interventions for preventing, diagnosing, and treating CVDs. The function of these hub genes in CVDs needs further exploration to elucidate their biological characteristics.

Molecular mechanism of Danxiong Tongmai Granules in treatment of coronary heart disease.

Danxiong Tongmai Granules (DXTMG) are widely utilized in treating coronary heart disease (CHD) in China. This study aims to explore the molecular mechanisms underlying the therapeutic effects of DXTMG on CHD by employing a network pharmacology approach, complemented with experimental validation. Traditional Chinese Medicine (TCM) compounds and targets were identified via searches in the BATMAN-TCM database, and the GeneCards database was used to obtain the main target genes involved in CHD. We combined disease targets with the drug targets to identify common targets. The "TCM-compound-target" network was plotted using Cytoscape 3.7.2 software and a protein-protein interaction (PPI) network was constructed using the STRING database from which core targets were obtained. Gene ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for common drug-disease targets using R Version 4.0.4 (64 bit) software. Molecular docking of core protein-small molecule ligand interaction was modeled using AutoDock software. A molecular dynamics simulation was conducted on the optimal protein-small molecule complex identified through molecular docking, using Amber18 software. The rat model for myocardial ischemia was established through pre-gavage administration of DXTMG, followed by dorsal hypodermic injection of isoprenaline. Myocardial tissues from the rats were analyzed using hematoxylin and eosin (HE) staining and Masson's trichrome staining. Relevant targets were validated by enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry. 162 potential targets of DXTMG involved in CHD were identified. These included INS, ALB, IL-6 and TNF according to PPI network studies. GO enrichment analysis identified a total of 3365 GO pathways, including 3049 biological process pathways (BP) concerned with the heart and circulatory system; 109 cellular component (CC) pathways, including cation channels and membrane rafts and 207 molecular function (MF) pathways related to receptor ligands and activators. KEGG analysis revealed a total of 137 pathways (P < 0.05), including those related to AGE-RAGE signaling associated with diabetic complications, fluid shear stress and atherosclerosis. The results of molecular docking and molecular dynamics simulations demonstrated the robust binding affinity between the compounds and target proteins. Animal experiment findings indicated that, compared with the model group, the DXTMG group effectively ameliorated inflammation and fibrosis in rat myocardial tissues, reduced LDH, cTn-I, and MDA levels (P < 0.05, P < 0.01), elevated SOD and GSH-PX levels (P < 0.05), and reduced the percentage of positive area for IL-6 and TNF-α (P < 0.05). This study preliminarily suggests that DXTMG can modulate oxidative stress, inflammation response, and cardiomyocyte regulation, thereby mitigating the onset and progression of CHD.

Characterization of the transcriptional effects of the plastic additive dibutyl phthalate alone and in combination with microplastic on the green-lipped mussel Perna canaliculus.

The presence and persistence of microplastics (MPs) in diverse aquatic environments are of global concern. Microplastics can impact marine organisms via direct physical interaction and the release of potentially harmful chemical additives incorporated into the plastic. These chemicals are physically bound to the plastic matrix and can leach out. The hazards associated with chemical additives to exposed organisms is not well characterized. We investigated the hazards of plastic additives leaching from plastic. We used the common plasticizer dibutyl phthalate (DBP) as a chemical additive proxy and the New Zealand green-lipped mussel (Perna canaliculus) as a model. We used early-adult P. canaliculus exposed to combinations of virgin and DBP-spiked polyvinyl chloride (PVC), MPs, and DBP alone for 7 days. Whole transcriptome sequencing (RNA-seq) was conducted to assess whether leaching of DBP from MPs poses a hazard. The differences between groups were evaluated using pairwise permutational multivariate analysis of variance (PERMANOVA), and all treatments were significantly different from controls. In addition, a significant difference was seen between DBP and PVC MP treatment. Transcriptome analysis revealed that mussels exposed to DBP alone had the most differentially expressed genes (914), followed by PVC MP + DBP (448), and PVC MP (250). Gene ontology functional analysis revealed that the most enriched pathway types were in cellular metabolism, immune response, and endocrine disruption. Microplastic treatments enriched numerous pathways related to cellular metabolism and immune response. The combined exposure of PVC MP + DBP appears to cause combined effects, suggesting that DBP is bioavailable to the exposed mussels in the PVC MP + DBP treatment. Our results support the hypothesis that chemical additives are potentially an important driver of MP toxicity. Environ Toxicol Chem 2024;43:1604-1614. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Identification of co-expressed central genes and transcription factors in acute myocardial infarction and diabetic nephropathy

BackgroundAcute myocardial infarction (AMI) and diabetic nephropathy (DN) are common clinical co-morbidities, but they are challenging to manage and have poor prognoses. There is no research on the bioinformatics mechanisms of comorbidity, and this study aims to investigate such mechanisms.MethodsWe downloaded the AMI data (GSE66360) and DN datasets (GSE30528 and GSE30529) from the Gene Expression Omnibus (GEO) platform. The GSE66360 dataset was divided into two parts: the training set and the validation set, and GSE30529 was used as the training set and GSE30528 as the validation set. After identifying the common differentially expressed genes (DEGs) in AMI and DN in the training set, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and protein–protein interaction (PPI) network construction were performed. A sub-network graph was constructed by MCODE, and 15 hub genes were screened by the Cytohubba plugin. The screened hub genes were validated, and the 15 screened hub genes were subjected to GO, KEGG, Gene MANIA analysis, and transcription factor (TF) prediction. Finally, we performed TF differential analysis, enrichment analysis, and TF and gene regulatory network construction.ResultsA total of 46 genes (43 up-regulated and 3 down-regulated) were identified for subsequent analysis. GO functional analysis emphasized the presence of genes mainly in the vesicle membrane and secretory granule membrane involved in antigen processing and presentation, lipopeptide binding, NAD + nucleosidase activity, and Toll-like receptor binding. The KEGG pathways analyzed were mainly in the phagosome, neutrophil extracellular trap formation, natural killer cell-mediated cytotoxicity, apoptosis, Fc gamma R-mediated phagocytosis, and Toll-like receptor signaling pathways. Eight co-expressed hub genes were identified and validated, namely TLR2, FCER1G, CD163, CTSS, CLEC4A, IGSF6, NCF2, and MS4A6A. Three transcription factors were identified and validated in AMI, namely NFKB1, HIF1A, and SPI1.ConclusionsOur study reveals the common pathogenesis of AMI and DN. These common pathways and hub genes may provide new ideas for further mechanistic studies.