KEGG Research Articles

Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation.

A network pharmacology study on the biological action of ginseng in the treatment of colorectal cancer (CRC) by regulating the tumor microenvironment (TME). To investigate the potential mechanism of action of ginseng in the treatment of CRC by regulating TME. This research employed network pharmacology, molecular docking techniques, and bioinformatics validation. Firstly, the active ingredients and the corresponding targets of ginseng were retrieved using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), the Traditional Chinese Medicine Integrated Database (TCMID), and the Traditional Chinese Medicine Database@Taiwan (TCM Database@Taiwan). Secondly, the targets related to CRC were retrieved using Genecards, Therapeutic Target Database (TTD), and Online Mendelian Inheritance in Man (OMIM). Tertiary, the targets related to TME were derived from screening the GeneCards and National Center for Biotechnology Information (NCBI)-Gene. Then the common targets of ginseng, CRC, and TME were obtained by Venn diagram. Afterward, the Protein-protein interaction (PPI) network was constructed in the STRING 11.5 database, intersecting targets identified by PPI analysis were introduced into Cytoscape 3.8.2 software cytoHubba plugin, and the final determination of core targets was based on degree value. The OmicShare Tools platform was used to analyze the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the core targets. Autodock and PyMOL were used for molecular docking verification and visual data analysis of docking results. Finally, we verified the core targets by Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases in bioinformatics. A total of 22 active ingredients and 202 targets were identified to be closely related to the TME of CRC. PPI network mapping identified SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 as possible core targets. Go enrichment analysis showed that it was mainly involved in T cell co-stimulation, lymphocyte co-stimulation, growth hormone response, protein input, and other biological processes; KEGG pathway analysis found 123 related signal pathways, including EGFR tyrosine kinase inhibitor resistance, chemokine signaling pathway, VEGF signaling pathway, ErbB signaling pathway, PD-L1 expression and PD-1 checkpoint pathway in cancer, etc. The molecular docking results showed that the main chemical components of ginseng have a stable binding activity to the core targets. The results of the GEPIA database showed that the mRNA levels of PIK3R1 were significantly lowly expressed and HSP90AA1 was significantly highly expressed in CRC tissues. Analysis of the relationship between core target mRNA levels and the pathological stage of CRC showed that the levels of SRC changed significantly with the pathological stage. The HPA database results showed that the expression levels of SRC were increased in CRC tissues, while the expression of STAT3, PIK3R1, HSP90AA1, and AKT1 were decreased in CRC tissues. Ginseng may act on SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 to regulate T cell costimulation, lymphocyte costimulation, growth hormone response, protein input as a molecular mechanism regulating TME for CRC. It reflects the multi-target and multi-pathway role of ginseng in modulating TME for CRC, which provides new ideas to further reveal its pharmacological basis, mechanism of action and new drug design and development.

Improvement effect and mechanism of XuanFuDaiZhe tang on rats with diarrheal irritable bowel syndrome induced by colorectal dilation

Ethnopharmacological relevanceXuanFuDaiZhe Tang (XFDZT) is used in traditional Chinese medicine (TCM) to treat diarrhoea-predominant irritable bowel syndrome (IBS-D). Our laboratory has demonstrated that XFDZT remarkably improves various gastrointestinal motility disorders in animal models. However, previous studies have only focused on one or several protein targets without systematically investigating dynamic changes and protein interrelations. Aim of the studyTo explore the mechanisms underlying the therapeutic action of XFDZT in IBS-D using a network pharmacology approach and in vivo experiments. Materials and methodsThe active compounds of XFDZT were selected from TCM Systems Pharmacology and TCM Integrated databases, and potential targets were identified using the Swiss Target Prediction databases. Targets related to IBS-D were mined from the DisGeNet, Drug Bank, and Therapeutic Target databases. The intersecting protein–protein interactions (PPIs) of the drug–disease crossover genes were analysed, and a central PPI network was constructed using the STRING database and Cytoscape 3.7.2. Following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, a gene pathway network was constructed to identify key target genes and pathways. Using haematoxylin and eosin staining and western blotting, we validated how XFDZT controls water expression in the body to treat IBS-D infection. ResultsFirst, the results showed that XFDZT contained 1037 active ingredients and 1458 corresponding targets. After intersecting the 252 IBS targets, 108 targets were identified. The main targets of XFDZT were albumin, aquaporins such as AQP1 and AQP3, calmodulin, and the cellular enzyme CYP2C9. GO and KEGG enrichment predicted that the action pathways were the neuroactive ligand–receptor interaction, calcium signalling pathway, serotonergic synapse signalling pathway, cGMP–PKG signalling pathway, cAMP signalling pathway, and MLCK–MLC signalling pathway. Second, an IBS-D rat model was constructed using colorectal dilation (CRD). CRD can significantly induce IBS-D symptoms such as diarrhoea, abdominal pain, and anxiety and depression-like behaviour in rats. XFDZT (10, 20, and 40 g/kg) administered for 14, 21, and 28 days significantly reversed these changes in IBS-D rats in a time- and dose-dependent manner, suggesting that XFDZT significantly improved IBS-D. Finally, the mechanism by which XFDZT improves IBS-D was explored from the perspective of AQPs, tight junction proteins, and motility-related proteins in colon tissue. Compared with the control group, the protein expression of AQP1, AQP3, and AQP8 in the colon tissue of IBS-D rats was significantly downregulated, whereas the protein expression of AQP7 was significantly upregulated. The expression of tight junction-related proteins claudin-1, occludin, and ZO-1 in colon tissue was significantly downregulated, whereas the expression of motility-related proteins p-MLC, MLC, MLCK, and CaM in colon tissue was significantly upregulated, suggesting that IBS-D rats had AQP disorders, epithelial intercellular connections, and motility in colon tissue. The above changes were significantly reversed by XFDZT administration (5, 10, and 20 g/kg) for 14 days. ConclusionXFDZT significantly improved diarrhoea, abdominal pain, anxiety, and depression in IBS-D rats, and its mechanism of action may be related to the regulation of AQPs, tight junction proteins, and the MLCK–MLC pathway. This study provided a pharmacological experimental basis for the development of XFDZT as a novel drug for the treatment of IBS-D.

Potential Molecular Mechanisms of Danggui-Shaoyao-San in the Treatment of Melasma Based on Network Pharmacology with Molecular Docking

Although Danggui-Shaoyao-San (DSS) is frequently used in China to treat melasma, its underlying mechanism still needs to be better understood. Our aim is to determine the mechanism behind DSS in treating melasma through network pharmacology (NP). The DSS active compounds alongside corresponding target genes are identified by accessing the TCMSP database and SwissTargetPrediction. Melasma-associated targets are retrieved from the GeneCards, DisGeNet, Durgbanks, OMIM, and TTD databases. Next, we build a component-target association network via Cytoscape software while generating a protein-protein interaction network utilizing the STRING database. Subsequently, both core target genes and active compounds are determined. Through the DAVID database and Bioinformatics tools, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses are conducted. Lastly, the CB-Dock2 server is deployed to conduct molecular docking (MOD). The results manifest that alisol B, cerevisterol, and Wallichilide, among others, are active compounds in DSS, while PTGS2, ESR1, and ESR2 are core target genes. Both GO and KEGG analyses showcase that the potential core drug components modulate pathways in cancer, chemical carcinogenesis-receptor activation, calcium, relaxin, and estrogen signaling by exerting their effects on biological processes. These processes include negative gene expression regulation as well as positive regulation of both cytosolic calcium ion concentration and transcription from the RNA polymerase II promoter, thereby playing an anti-melasma pharmacological role. The MOD displays that core target genes have good binding activity with the active compounds. To conclude, NP demonstrates that DSS can serve as an innovative medication for treating melasma.

Ammopiptanthus nanus (M. Pop. ) Cheng f. stem ethanolic extract ameliorates rheumatoid arthritis by inhibiting PI3K/AKT/NF-κB pathway-mediated macrophage infiltration

Ethnopharmacological RelevanceAmmopiptanthus nanus (M. Pop. ) Cheng f. (A. nanus), a traditional Kirgiz medicinal plant, its stem has shown potential in treating rheumatoid arthritis (RA) in China, either through oral medication or by topical application directly to the affected joints, but its underlying mechanism of action remains unexplored. Aim of the studyThe purpose of this study is to elucidate pharmacological mechanism of A. nanus in ameliorating RA using a comprehensive approach that combines network pharmacology, molecular docking and experimental evaluations. Materials and MethodsFirstly, the major constituents of A. nanus stem ethanolic extract were identified and quantified by High-Performance Liquid Chromatography (HPLC). Disease target data from Gene Cards database was then used to define RA-associated targets. A protein-protein interaction (PPI) network was created via STRING database. The DAVID database powered gene ontology (GO) function and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis to gain functional insights. In vitro, RAW264.7 cells were treated with A. nanus to investigate the roles of target proteins and pathways during lipopolysaccharide (LPS) - induced inflammation. Immunofluorescence assays were performed to assess the effects of A. nanus on macrophage infiltration. The key targets and signalling pathways were validated using enzyme-linked immunosorbent assay (ELISA), real-time quantitative polymerase chain reaction (RT-qPCR), molecular docking, immunohistochemical analysis, western blotting and immunofluorescence. Finally, the therapeutic potential of A. nanus in RA was evaluated in a carrageenan-induced rat model. ResultsNetwork analysis identified 31 potential targets of A. nanus associated with RA, including 10 hub targets. KEGG analysis highlighted the involvement of PI3K/AKT signaling pathway. In vivo experiments demonstrated that A. nanus treatment significantly protected against carrageenan-induced inflammatory paw tissue and attenuated macrophage infiltration. Both in vivo and in vitro experiments confirmed that A. nanus significantly downregulated the protein expression of COX-2, iNOS and IL-1β, and inhibited PI3K/AKT/NFκB pathway, which are closely linked to RA. Furthermore, molecular docking and cellular thermal shift assay revealed that licoflavanone showed a strong binding affinity with key targets. ConclusionIn summary, this study provides the first evidence of the potent anti-inflammatory activity of A. nanus in experimental RA. The mechanism of action appears to involve inactivation of the PI3K/AKT/NF-κB pathway-mediated macrophage infiltration. These findings indicate that A. nanus has significant potential as a therapeutic potential agent for RA treatment and offer novel insights for future research and drug development in this field.

Integrated physiological and transcriptome analyses of the effects of water-soluble amino acid fertilizer on plant growth

Tobacco is a key component of China’s economy, serving as a major cash crop. With traditional fertilizers reaching their maximum potential in promoting tobacco growth, the exploration of new fertilizers has emerged as a viable solution for advancing experimental sustainable development. Spraying foliar fertilizer is a key measure to improve tobacco yield and quality. This study employed a combination of field and pot experiments to investigate the effects of applying water-soluble amino acid fertilizers on the growth, development, and quality of tobacco. The results of transcriptome analysis and physiological index measurements indicate that the application of water-soluble amino acid fertilizer can enhance the area of tobacco leaves, promote photosynthesis, and improve the chemical composition of the leaves. This research determined that the optimal concentration for spraying water-soluble amino acid fertilizer is diluted 500 times. Transcriptome analysis identified a total of 6,489 differentially expressed genes (DEGs), including 3,843 genes that were up-regulated and 2,646 genes that were down-regulated. Gene Ontology (GO)analysis demonstrated that these DEGs were significantlyassociatedwithprocessesincludingcell recognition, photosynthesis,thylakoidcomponents, calcium ion binding, and carbohydrate binding.Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis emphasized that the DEGs were largely found in pathwaysrelated tophotosynthesis-antenna proteins, interactions between plants and pathogens, photosynthesisitself, phenylpropanoid biosynthesis, andplant hormone signaling. Further research revealed that a significant number of genes involved in the auxin, gibberellin, salicylic acid, and jasmonic acid signal transduction pathways exhibited varying expression patterns following the application of water-soluble amino acid fertilizers.Additionally, the expression levels of bZIP, MYB, WRKY, bHLH, and AP2/ERF transcription factors exhibited significant variations following the application of water-soluble amino acid fertilizer. These results analyze the mechanisms of action of water-soluble amino acid fertilizers, offering new effective strategies to enhance both the yield and quality of tobacco.

Association between the levels of toxic heavy metals and schizophrenia in the population of Guangxi, China: A Case-Control Study

The relationship between body levels of heavy metals and the risk of schizophrenia remains unclear. This study investigates the relationship between plasma levels of toxic heavy metals and the risk of schizophrenia among adults in Guangxi, China. Plasma concentrations of lead (Pb), cadmium (Cd), arsenic (As), and chromium (Cr) were measured using inductively coupled plasma mass spectrometry (ICP-MS). To evaluate both the single and combined effects of metal exposure on the risk of schizophrenia, we employed multivariate logistic regression, Bayesian Kernel Machine Regression (BKMR), and generalized Weighted Quantile Sum (gWQS) models. Additionally, we employed the Comparative Toxicogenomics Database (CTD) to analyze the mechanistic pathways through which metal mixtures may induce schizophrenia. Relative mRNA expression levels were measured using Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to predict potential biological functions. In logistic regression models, compared to the lowest exposure group (Q1), the odds ratios (ORs) for Pb in groups Q2, Q3, and Q4 were 2.18 (95% CI: 1.20 - 3.94), 4.74 (95% CI: 2.52 - 8.95), and 3.62 (95% CI: 1.80 - 7.28), respectively. Both BKMR and gWQS models indicated a positive correlation between the combined effects of toxic heavy metal mixtures and the risk of schizophrenia, with Pb demonstrating the most substantial impact, particularly in older adults and females. Elevated levels of tumor necrosis factor (TNF) and interleukin-1 beta (IL-1β) were observed in patients with schizophrenia, while the expression of tumor protein p53 (TP53) was significantly reduced. These findings underscore the critical need to avoid exposure to toxic heavy metals to prevent schizophrenia, highlighting significant public health implications.

Role of Hippocampal Glutamatergic Synaptic Alterations in Sevoflurane-Induced Cognitive Dysfunction in Aged Mice.

Perioperative neurocognitive disorders (PND), including postoperative delirium (POD) and postoperative cognitive dysfunction (POCD), are common following anesthesia and surgery in older patients and significantly increase morbidity and mortality. However, the underlying mechanism of PND is unclear. Our study aims to analyze the differentially expressed genes (DEGs) in excitatory neurons and investigate the role of hippocampal glutamatergic synaptic alterations in sevoflurane-induced cognitive dysfunction in aged mice. We performed single-nucleus RNA sequencing (snRNA-seq) technology to examine the alterations of excitatory neurons in hippocampus induced by sevoflurane in aged mice. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs were performed in excitatory neurons. At last, immunofluorescence staining was used to validate sevoflurane-induced alternation of glutamatergic synapses in the hippocampus of aged mice. This study demonstrates that DEGs in excitatory neurons are associated with reduction of glutamatergic synapses and cognitive dysfunction. After immunofluorescence staining validation, we also confirmed that sevoflurane anesthesia decreased the density of glutamatergic synapses in the hippocampus of aged mice. Our findings demonstrated a key role of hippocampal glutamatergic synaptic alterations in sevoflurane-induced cognitive dysfunction in aged mice.

Retinol metabolism signaling participates in microbiota-regulated fat deposition in obese mice

Obesity is a global pandemic threatening public health, excess fat accumulation and overweight are its characteristics. In this study, the interplay between gut microbiota and retinol metabolism in modulating fat accumulation was verified. We observed gut microbiota depletion reduced the body weight (P<0.05) and the ratios of white adipose tissues (WATs) to body weight (P<0.05) in high-fat diet (HFD) fed-mice. Both the hepatic metabolomics and transcriptomics analyses confirmed that gut microbiota modulated fat accumulation in obese mice. Besides, the kyoto encyclopedia of genes and genomes (KEGG) analysis and protein-protein interaction (PPI) network of RNA-seq results indicated that retinol metabolism signaling may be involved in the microbiota-regulated fat deposition. Furthermore, activated retinol metabolism signaling by all-trans retinoic acid (atRA) supplementation reduced body weight (P<0.05) and WAT accumulation in obese mice. On the other hand, 16S rRNA gene sequencing of the ileal microbiota suggested that atRA supplementation, in turn, increased the microbial diversity and induced the growth of beneficial bacteria including Parabacteroides, Bacteroides, Clostridium_XVIII, Bifidobacterium, Enterococcus, Bacillus, Leuconostoc, and Lactobacillus in obese mice. Spearman correlation showed that atRA decreased the bacteria (Parvibacter, Asaccharobacter, Romboutsia, and Clostridium_IV) that were positively associated with body and WAT weights, whereas increased the bacteria (Lactobacillus) that were negatively associated with body and WAT weights. Together, this study reveals the interaction between the gut microbiota and retinol metabolism signaling in regulating adipose accumulation and obesity. It is expected of this finding to provide new insights to prevent and develop therapeutic measures of obesity-related metabolic syndrome.

Exploring the potential mechanism of Radix Bupleuri in the treatment of sepsis: a study based on network pharmacology and molecular docking

AimTo explore, using network pharmacology and RNA-seq technologies, potential active targets and mechanisms underpinning Radix Bupleuri’s effectiveness during sepsis treatment.MethodsFollowing the Sepsis-3.0 criteria, the research cohort, comprising 23 sepsis patients and 10 healthy participants, was obtained from public databases. Peripheral blood samples were collected and subjected to RNA-seq analysis. Active ingredients and potential targets of Radix Bupleuri were identified using the Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine 2.0 (BATMAN-TCM 2.0) database and TCMSP database. Subsequently, protein-protein interaction (PPI) network construction, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted to explore cross-targets between disease and drugs. Survival analysis of key targets was performed using the GSE65682 dataset, and single-cell RNA-seq was employed for cellular localization analysis of key genes. Finally, molecular docking and Molecular dynamics simulation of the core target was conducted.ResultsDifferential expression analysis revealed 4253 genes associated with sepsis. Seventy-six active components and 1030 potential targets of Radix Bupleuri were identified. PPI, GO, and pathway enrichment analyses indicated involvement in the regulation of transmembrane transport, monatomic ion transport, and MAPK signaling. Survival curve analysis identified PIK3CD, ARRB2, SUCLG1, and SPI1 as key targets associated with lower mortality in the high expression group, while higher mortality was observed in the high PNP and FURIN expression groups. Single-cell RNA sequencing unveiled the cellular localization of PIK3CD, PNP, SPI1, and FURIN within macrophages, while ARRB2 and SUCLG1 exhibited localization in both macrophages and T-cells. Subsequent molecular docking and Molecular dynamics simulation indicated a potential binding interaction for Carvone-PIK3CD, Encecalin-ARRB2, Lauric Acid-SUCLG1, Pulegone-FURIN, Nootkatone-SPI1, and Saikogenin F-PNP.ConclusionRadix Bupleuri could modulate immune function by affecting PIK3CD, ARRB2, SUCLG1, FURIN, SPI1, and PNP, thereby potentially improving the prognosis of sepsis.

The modulation of proteomics and antioxidant stress is involved in the effect of nitazoxanide against Japanese encephalitis virus in vitro

Japanese encephalitis virus (JEV) is a significant circulating arbovirus flavivirus and the primary cause of viral encephalitis in Asia. Previous studies have demonstrated that nitazoxanide (NTZ), an antiparasitic gastroenteritis medication classified as a thiazolide, exhibits efficacy against JEV both in vitro and in vivo. To explore the potential antiviral mechanisms, we employed Tandem Mass Tag (TMT)-based quantitative proteomics to identify differentially expressed proteins (DEPs) among three groups: Blank cell group, JEV-infected cell group, and JEV-infected cells treated with NTZ. Our analysis revealed that NTZ treatment led to the upregulation of 30 DEPs and downregulation of 54 DEPs in JEV-infected cells. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that these DEPs are involved in various biological processes and signaling pathways, including transport, localization, response to wounding, P53 pathway activation, and fatty acid metabolism-related pathways. Moreover, we observed that the expression trend of TMX2, a protein associated with redox homeostasis, was consistent with findings from TMT-based quantitative proteomics. Further investigations into reactive oxygen species (ROS), mitochondrial membrane potential, antioxidant enzyme activity, and the KEAP1-NRF2 pathway demonstrated that NTZ effectively regulates the KEAP1-NRF2 pathway while suppressing oxidative stress induced by JEV infection. In conclusion, the proteomic data along with antioxidant stress results presented herein provide a foundational basis for further research into the molecular mechanisms and potential targets of NTZ against JEV.

Network-based pharmacology and experimental validation to explore the mechanism of action of the Jiawei Pentongling formula for the treatment of endometriosis-related pain.

To investigate the effects and mechanisms of the Jiawei Pentongling formula (, JWPTL) in treating endometriosis-related pain using network pharmacology study and experimental validation. Active ingredients and relevant targets of JWPTL, as well as genes for endometriosis-related pain, were collected from public databases. Prediction of core targets and pathways of JWPTL against pain associated with endometriosis by protein-protein interaction (PPI) network work, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis. The Sprague-Dawley rat endo-metriosis model was constructed using the autologous endosomal transplantation method, and the successfully modeled rats were randomly divided into the model group and the JWPTL group, with 8 rats in each group. Another 8 rats were set up in the sham group. Rats in the JWPTL group used the rectal delivery method with the addition of JWPTL (7.77 g·kg-1·d-1) once a day for 28 d. Rats in the model and sham-operated groups were given equal amounts of saline using the same administration method. The 50% paw withdrawal threshold (PWT) of the rats was measured at different time points. After the intervention, the expression of phosphatidylinositol 3-kinase (PI3K) and protein kinase B (Akt) proteins and mRNA in endometriotic tissues was detected by immune-ohistochemistry and reverse transcription-polymerase chain reaction. From GeneCards, Online Mendelian Inheritance in Man and other databases, a total of 964 endometriosis (EMs) -related pain targets were screened, 142 active ingredients of JWPTL, 605 targets, and 221 potential targets were obtained by intersection of Venn diagram; 44 core targets were identified by constructing PPI network. KEGG enrichment analysis showed that JWPTL mainly involves the PI3K-Akt signaling pathway, estrogen signaling pathway, hypoxia inducible factor-1 signaling pathway, tumour necrotizing factor signaling pathway, and other signaling pathways in the treatment of EMs-related pain. Animal experiments showed that JWPTL could up-regulate the mechanical pain threshold and reduce the expression of PI3K and Akt proteins and mRNA in ectopic endometrial tissues of model rats. The present study preliminarily analyzed the pharmacological mechanism of the formula, and molecular docking and animal experiments showed the feasibility of this study, suggesting that the formula may inhibit the release of inflammatory factors and reverse the pain associated with EMs by downregulating the PI3K/Akt signaling pathway.

Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing.

GULP1 is an engulfment adaptor protein containing a phosphotyrosine-binding (PTB) domain, and existing studies have shown that it can promote glucose uptake in 3T3-L1 adipocytes. To further explore key metabolically related differential genes downstream of GULP1, this study conducted transcriptome analysis on adipocytes and skeletal muscle cells overexpressing GULP1. Subsequently, abnormally expressed genes were subjected to bioinformatic analysis, and real-time fluorescent quantitative PCR (qRT-PCR) was used for mutual validation with transcriptome sequencing. The results indicated that, with a threshold of P < 0.05 and |Log2FoldChange| ≥ 1 for screening differentially expressed genes, compared with control cells, there were 278 upregulated and 263 downregulated genes in adipocytes overexpressing GULP1. Metabolism-related GO (Gene Ontology) terms included cholesterol biosynthetic process, cholesterol metabolic process, response to lipopolysaccharide, lipid metabolic process, etc. A total of 52 metabolically related differentially expressed genes were enriched in 10 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, with lipid metabolism being highly enriched. In skeletal muscle cells overexpressing GULP1, there were 280 upregulated and 302 downregulated genes, with metabolism-related GO terms including hormone metabolic process, response to lipopolysaccharide, one-carbon metabolic process, etc. A total of 86 metabolically related differentially expressed genes were enriched in 10 KEGG pathways, with amino acid metabolism, lipid metabolism, and carbohydrate metabolism being highly enriched. GULP1's biological functions are extensive, including lipid metabolism and oncology. This study, through transcriptomics and bioinformatic analysis, identified key metabolically related differential genes downstream of GULP1, obtained metabolically related differential genes and signaling pathways after GULP1 overexpression, providing important theoretical basis for future research on GULP1 downstream target genes.

Prognostic value of PLEKHA4 and its correlation with tumor-infiltrating immune cells in breast cancer: a comprehensive study based on bioinformatics and clinical analysis validation.

Pleckstrin homology containing family A, number 4 (PLEKHA4) plays a role in a number of biological processes in human cells, including cell polarization, growth, and proliferation. However, the relationship between PLEKHA4 expression and survival in breast cancer (BC) remains unclear. The aim of this study is to investigate the potential of PLEKHA4 as a prognostic indicator in BC. We obtained gene expression profiles of BC and normal tissues from the Tumor Immune Estimation Resource (TIMER), UALCAN web. Immunohistochemistry (IHC) staining was performed to investigate the protein expression and prognostic value of PLEKHA4 in BC patients. The prognostic value was analyzed using Kaplan-Meier curve analysis and Cox regression analysis in R software after downloading The Cancer Genome Atlas (TCGA) databases. The correlations between PLEKHA4 and tumor immune infiltrates were investigated via gene set variation analysis (GSVA). Signaling pathways related to PLEKHA4 expression were identified by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Both bioinformatics and IHC results showed that PLEKHA4 was expressed at low levels in BC tissues compared with the adjacent tissues. Furthermore, the expression of PLEKHA4 was negatively correlated with ages (χ2=6.394, P=0.01), molecular subtype (χ2=15.606, P=0.001), lymph node metastasis (χ2=13.753, P=0.004), tumor-node-metastasis (TNM) stage (χ2=22.616, P<0.001). Kaplan-Meier curves implicated low expression of PLEKHA4 was associated with worse survival of BC patients [hazard ratio (HR) =0.46, P=0.01]. Cox regression models showed that low PLEKHA4 expression could be an independent risk factor for BC (HR =0.911, P=0.006). The results of gene set enrichment analysis (GSEA) showed that cell cycle, Notch signaling pathway, nuclear factor erythroid 2-related factor 2 (NRF2) signaling pathway, and Rho GTPases were highly enriched in the low PLEKHA4 expression group, as identified by GO and KEGG. Additionally, in BC, PLEKHA4 expression displayed a positive correlation with the infiltration of natural killer (NK) cells (P<0.001), CD8+ T cells (P<0.001), B cells (P<0.001), neutrophils (P<0.001), and dendritic cells (DCs) (P<0.001). The findings indicate that PLEKHA4 is an independent prognostic biomarker associated with key signaling pathways and immune infiltration in BC. Targeting PLEKHA4 may contribute to improving immunotherapy for BC.

A pilot study of microRNAs expression profile in plasma of patients with hydatid disease: potential immunomodulation of hydatid disease.

Echinococcosis is a zoonotic disease, which seriously endangers human health. The immune game between parasite and host is not fully understood. Exosomes are thought to be one of the ways of information communication between parasite and host. In this study, we attempted to explore the communication between Echinococcus granulosus and its host through the medium of exosomes. We collected plasma from E. granulosus patients (CE-EXO) and healthy donors (HD-EXO) and extracted exosomes from the plasma. The expression profile of miRNA in plasma was determined by second generation sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to annotate the function of target genes of differential miRNAs. Meanwhile, we co-cultured plasma exosomes from healthy donors and plasma exosomes from E. granulosus patients with Jurkat T cells with or without phytohaemagglutinin (PHA) stimulation. The expression of CD69 on Jurkat T cells was detected by flow cytometry. The results showed that the miRNA of exosomes between healthy donors and E. granulosus patients was significantly different. GO and KEGG were used to annotate the function of target genes of differential miRNAs. The results indicate that many important pathways are involved in inflammation, metabolism, and immune response after parasite infection, such as p53 signaling pathway, PI3K-Akt signaling pathway, and glycolysis/gluconeogenesis. Flow cytometry showed that CE-EXO reduced the expression of CD69 + on Jurkat T cells. Our present results suggest that these differentially expressed miRNAs may be important regulators of parasite-host interactions. Meanwhile, functional prediction of its target genes provides valuable information for understanding the mechanism of host-parasite interactions. These results provide clues for future studies on E. granulosus escape from host immune attack, which could help control E. granulosus infection.

Investigating the MicroRNA 10b Regulatory Network: A Bioinformatic Approach to Transcription Factor Binding and Cancer Implications.

miR-10b, that stands for microRNA 10 in bovine serum protein refers to a subgroup of small molecules belonging to the body especially involved in physiological processes with regard cancers initiation and progression as well cellular differentiation. An understanding of the regulation miR-10b along with identification of its corresponding transcription factors (TFs) that bind to the so-called mirR-10b Regulated-DNA Sequence (MRDS) as well discovering potential targets serves a powerful tool not only in elucidation but also pharmacological arsenal targeting miRNAs. In this work, two bioinformatics databases (JASPAR and PROMO) were used to suggest the putative TFs that can interact with miR-10b MRDS. Most interestingly, among the set of TFs common to both databases were a number have previously associated with histone modification. Since the function of miR-10b is well known, we focused only on TFs with documented associations to regulation by this particular miRNA. These TFs were E2F1, P53, SP1 and NFKB. In an attempt to investigate the regulatory network of TFs involved TFs associated with miR-10b, STRING database was utilized to study the interactions among the identified TFs and their functional enrichments. Through this analysis, we found important Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways linked with different kinds of cancer, the transcriptional regulation, and gene expression. This study aims to provide an inclusive analysis of TFs that control miR-10b by applying bioinformatics predictions and validate these findings over existing literature evidence. This method will deepen our knowledge towards miR-10b regulatory network and its implications in cancer biology and eventually discovering new treatment interventions.

Network pharmacology-based investigation and experimental validation of the mechanism of metformin in the treatment of acute myeloid leukemia

Metformin, a widely used anti-diabetic agent, has shown significant anti-cancer properties as reported in in various cancers, including acute myeloid leukemia. However, the detailed mechanisms by which metformin influences acute myeloid leukemia remain unrevealed. Employing a synergistic approach of network pharmacology and experimental validation, this study systematically identifies and analyzes potential metformin targets and AML-related genes. These findings are then cross-referenced with biomedical databases to construct a target-gene network, providing insights into metformin's pharmacodynamics in AML treatment. Protein–Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses are utilized. Results show metformin's effectiveness in inhibiting AML cell proliferation and inducing apoptosis through the AKT/HIF1A/PDK1 signaling pathway. This research provides insights into metformin's clinical application in AML treatment.

In silico and in vitro evaluation of compounds from Methanol whole extracts of Solanum aculeastrum Dunal berries against benign prostatic hyperplasia and prostate cancer

Background: This study evaluated anti-prostate potentials of compounds from methanol extract of Solanum aculeastrum Dunal berries (MESADB) against benign prostatic hyperplasia (BPH) and prostate cancer (PC). Methods: We used Swiss ADME and pKCSM tools to select drug-like candidates from MESADB. DisGeNET and related databases were used to identify targets for compounds of MESADB, BPH and PC. Molecular roles, biological processes, cellular components involved, and crucial pathways associated with biological processes of gene enrichment were obtained using Gene Ontology (GO) &amp; Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. Docking was achieved using VINA tool. Antiproliferative and gene expression profiling were determined using 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) bioassay, and RT-qPCR respectively, and data analyzed using Graph Pad Prism (version 8.4). Results: Three ideal drug-like candidates [Undecane; D-Arabinitol; and 9-Oxabicyclo [3.3.1] nonan-2-one,6-hydroxy-] were identified. Key targets included TLR4, PTGS2, STAT3, ESR1, MTOR, SRC, MMP9, HDAC1, AKT1 and EGFR. GO analysis revealed key targets were mainly enriched in 601 biological processes (BP), 53 molecular function (MF) and 24 cellular components (CC) terms (p &lt; 0.05). KEGG analysis presented pathways for cancer, pathway of proteoglycans in cancer, amongst others. Docking revealed [D-Arabinitol; and 9-Oxabicyclo [3.3.1] nonan-2-one,6-hydroxy-] demonstrated high binding affinity with PTGS2 and EGFR. MESADB significantly (p &lt; 0.0001) inhibited growth of DU-145 cells with IC50 value and selectivity index of 5.11μg/ml and 14.84, respectively, while sparing Vero CCL-81 cells. There were significant (p &lt; 0.0001) downregulations of EGFR, PTGS2 and BCL-2, in treated DU-145 cells compared to control. Conclusion: MESADB possesses antiprostate potentials.

Transcriptome Responses in Medicago sativa (Alfalfa) Associated with Regrowth Process in Different Grazing Intensities.

Medicago sativa L. (alfalfa), a perennial legume, is generally regarded as a valuable source of protein for livestock and is subjected to long and repeated grazing in natural pastures. Studying the molecular response mechanism of alfalfa under different grazing treatments is crucial for understanding its adaptive traits and is of great significance for cultivating grazing-tolerant grass. Here, we performed a transcriptomic analysis to investigate changes in the gene expression of M. sativa under three grazing intensities. In total, 4184 differentially expressed genes (DEGs) were identified among the tested grazing intensities. The analysis of gene ontology (GO) revealed that genes were primarily enriched in cells, cellular processes, metabolic processes, and binding. In addition, two pathways, the plant-pathogen interaction pathway and the plant hormone signal pathway, showed significant enrichment in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Protein kinases and transcription factors associated with hormones and plant immunity were identified. The plant immunity-related genes were more activated under high grazing treatment, while more genes related to regeneration were expressed under light grazing treatment. These results suggest that M. sativa exhibits different strategies to increase resilience and stress resistance under various grazing intensities. Our findings provide important clues and further research directions for understanding the molecular mechanisms of plant responses to grazing.

Identification of key lncRNAs and mRNAs in muscle development pathways of Tan sheep

The study aimed to identify the long noncoding RNA (lncRNA) responsible for regulating muscle development in Tan sheep. RNA-seq analysis was conducted on longissimus dorsi samples from 1-day-old and 60-day-old Tan sheep to investigate the molecular processes involved in muscle development. A total of 5517 lncRNAs and 2885 mRNAs were found to be differentially expressed in the 60-day-old Tan sheep. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these differentially expressed lncRNAs and mRNAs were linked to pathways crucial for muscle development, such as MAPK, cAMP, and calcium-mediated signaling pathways. Key genes like CDKN1A, MAPK14, TGFB1, MEF2C, MYOD1, and CD53 were identified as significant players in muscle development. The study validated the RNA-seq results through RT-qPCR, confirming the consistency of expression levels of differentially expressed lncRNAs and mRNAs. These findings indicate that lncRNA-mRNA networks produce a remarked effect on modulating muscle development in Tan sheep, such as lncRNAs (MSTRG.12808.1/MSTRG.22662.3/MSTRG.18310.1) and mRNAs (MSTRG.10027/MSTRG.10029/MSTRG.10258/MSTRG.11011/MSTRG.10354), laying the groundwork for future research in this area.

Potential functions and mechanisms of lysine crotonylation modification (Kcr) in tumorigenesis and lymphatic metastasis of papillary thyroid cancer (PTC).

To examine the putative functions and mechanisms of lysine crotonylation (Kcr) during the development and progression of papillary thyroid cancer (PTC). Samples of thyroid cancer tissues were collected and subjected to liquid chromatography-tandem mass spectrometry. Crotonylated differentially expressed proteins (DEPs) and differentially expressed Kcr sites (DEKSs) were analyzed by Motif, dynamic expression model analysis (Mfuzz), subcellular localization, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Go Ontology (GO) annotation, and protein-protein interaction analysis (PPI). Validation was performed by immunohistochemistry (IHC). A total of 262 crotonylated DEPs and 702 DEKSs were quantitated. First, for the tumor/normal comparison, a dynamic expression model analysis (Mfuzz) of the DEKSs revealed that clusters 1, 3, and 4 increased with the progression of thyroid cancer; however, cluster 6 showed a dramatic increase during the transition from N0-tumor to N1-tumor. Furthermore, based on GO annotation, KEGG, and PPI, the crotonylated DEPs were primarily enriched in the PI3K-Akt signaling pathway, Cell cycle, and Hippo signaling pathway. Of note, crosstalk between the proteome and Kcr proteome suggested a differential changing trend, which was enriched in Thyroid hormone synthesis, Pyruvate metabolism, TCA cycle, Cell cycle, and Apoptosis pathways. Similarly, for the LNM comparison group, the DEKSs and related DEPs were primarily enriched in Hydrogen peroxide catabolic process and Tight junction pathway. Finally, according to The Cancer Genome Atlas Program (TCGA) database, the differential expression of Kcr DEPs were associated with the prognosis of thyroid cancer, indicating the prognostic significance of these proteins. Moreover, based on the clinical validation of 47 additional samples, Kcr was highly expressed in thyroid tumor tissues compared with normal tissue (t = 9.792, P < 0.001). In addition, a positive correlation was observed between Kcr and N-cadherin (r = 0.5710, P = 0.0015). Moreover, N-cadherin expression was higher in the relatively high Kcr expression group (χ2 = 18.966, P < 0.001). Higher Kcr expression was correlated with thyroid tumorigenesis and lymphatic metastasis, which may regulate thyroid cancer progression by Pyruvate metabolism, TCA cycle, Cell cycle, and other pathways.