Search Results (327)

Bovine Mycoplasma bovis pneumonia (MBP) is an important component of bovine respiratory disease, and its management is complicated by persistent infection and antimicrobial stewardship concerns. Houttuynia cordata Thunb. has reported anti-inflammatory and immunomodulatory activities, but its potential host-directed mechanisms in MBP remain unclear. This in silico study used network pharmacology and molecular docking to identify candidate compounds, common drug–disease targets, enriched biological functions, and predicted ligand–target interactions. A total of 145 putative targets of H. cordata and 474 MBP-associated disease targets were obtained from TCMSP, GeneCards, OMIM, and CTD, yielding 43 common drug–disease targets. Dual-confidence STRING analysis, cytoHubba ranking, and MCODE module analysis prioritized TNF, IL6, IL1B, PTGS2, PPARG, IFNG, CASP3, and MMP9 as candidate core targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated convergence on cytokine-mediated signaling, inflammatory response, immune regulation, oxidative stress, IL-17 signaling, and TNF signaling. Molecular docking suggested favorable predicted interactions for quercitrin–PTGS2, quercetin–TNF, quercetin–IL6, and quercitrin–CASP3. These computational findings suggest that H. cordata may be associated with host inflammatory and immune-response modulation in MBP, mainly through flavonoid-related interactions with inflammation- and apoptosis-related targets. Further bovine-specific experimental validation is required before biological activity or practical application can be inferred. Full article

Dysregulated lipid metabolism is a core pathogenic driver of type 2 diabetes. Honokiol (HKL), the major bioactive constituent of Magnolia officinalis, possesses anti-diabetic and lipid-regulatory properties. However, the underlying molecular mechanism remains elusive. This study investigates how HKL ameliorates high-glucose/high-fat (HGHF)-induced hepatic lipid accumulation, with a focus on the role of SIRT3-mediated deacetylation of peroxisome proliferator-activated receptor γ (PPARG). The core targets of HKL were identified through network pharmacology and molecular docking. Human hepatic MIHA cells were treated with glucose (Glu, 40 mM) and palmitic acid (0.2~0.3 mM PA) to establish a lipid accumulation model, followed by treatment with HKL (5–10 μM) with or without a confirmed selective SIRT3 inhibitor 3-(1H-1,2,3-triazol-4-yl) pyridine (3-TYP). Lipid accumulation was assessed by Oil Red O staining and by measuring triglyceride (TG) and total cholesterol (TC) levels. Protein expression and the SIRT3-PPARG interaction were analyzed by Western blot and co-immunoprecipitation (Co-IP). SIRT3 and PPARG were identified as core targets of HKL, exhibiting strong binding with calculated energies of −6.834 and −6.579 kcal/mol, respectively. In MIHA cells, HGHF (40 mM Glu + 0.2–0.3 mM PA) induced lipid accumulation, including increased lipid droplets, and elevated TG (2.5–3.2-fold) and TC (2.2–2.8-fold) contents in a dose-dependent manner, accompanied by downregulated SIRT3/PPARG expression and heightened global protein acetylation. The non-cytotoxic HGHF-M condition (40 mM Glu + 0.2 mM PA) was selected for further experiments. HKL (5–10 μM) dose-dependently reduced lipid accumulation by ~38–60%, decreased TG and TC levels by up to ~13% and ~30%, and restored SIRT3/PPARG expression. The protective effects of HKL were reversed by inhibition of SIRT3 with 3-TYP. Co-IP confirmed the interaction between SIRT3 and PPARG, and SIRT3 overexpression significantly decreased the acetylation level of PPARG. This study suggests that HKL ameliorates hepatic lipid accumulation via SIRT3-mediated deacetylation of PPARG, providing an experimental basis for considering HKL as a potential therapeutic agent against metabolic disorders. Full article

The present study evaluated the stability of candidate reference genes during adipogenic differentiation of 3T3-L1 cells cultured on different extracellular matrices. The aim was to investigate the effects of matrix composition and differentiation stage on the expression of candidate housekeeping genes and to compare validation strategies in dynamic in vitro models. Eleven candidate reference genes (18S, Actb, B2m, Gapdh, Hmbs, Hprt, Nono, Ppia, Rplp0, Tbp, and Ywhaz) were analyzed by RT-qPCR in 3T3-L1 cells cultured on TC, collagen, gelatin, and Matrigel at Days 7 and 14 of differentiation. Gene stability was assessed using geNorm, NormFinder, RefFinder, comparative ΔCt, BestKeeper, generalized linear model (GLM), linear mixed model (LMM), and correlation analyses with the adipogenic markers Pparg and Fasn. The results demonstrated that the expression of most housekeeping genes was influenced by matrix composition, differentiation stage, or their interaction. Actb and 18S exhibited the strongest condition-dependent variability and pronounced matrix sensitivity. Gapdh and Hprt showed significant correlations with both Pparg and Fasn, while Hmbs correlated with Fasn, suggesting that these reference genes may not be fully independent of adipogenic status. Ppia demonstrated markedly contrasting rankings across analytical approaches, highlighting limitations of single-method stability assessment. The findings confirm that universal housekeeping genes are unlikely to exist across different matrix conditions and differentiation stages. The results highlight the need for multi-level validation strategies and experimentally validated normalization panels to minimize normalization bias and avoid misleading RT-qPCR expression profiles. Functional validation identified B2m and Rplp0 as the most suitable two-gene normalization panel for the experimental model evaluated, whereas Tbp remained a strong complementary reference gene candidate. Full article

Background: Plasticizers, including phthalate esters and phthalate-free alternatives, are widely detected environmental chemicals. Although increasing evidence suggests that plasticizers may disrupt gastrointestinal homeostasis, their potential molecular links with inflammatory gastrointestinal disorders (IGDs) remain unclear. Methods: This study aimed to systematically identify potential molecular targets and pathways linking representative plasticizers with IGDs. An integrative network toxicology framework was applied to investigate four plasticizers, including dimethyl phthalate (DMP), diethyl phthalate (DEP), dioctyl phthalate/di(2-ethylhexyl) phthalate (DOP/DEHP), and acetyl tributyl citrate (ATBC), in relation to Crohn’s disease (CD), ulcerative colitis (UC), esophagitis, and gastritis. Plasticizer- and disease-related targets were collected from public databases, followed by overlapping target screening, protein–protein interaction network analysis, functional enrichment analysis, GEO-based transcriptomic validation, molecular docking, molecular dynamics simulation, and single-cell RNA-seq analysis. Results: Disease-specific candidate targets were identified, including CXCL8 and FN1 for CD, IL1B for UC, MAPK3, FASN, FN1, PPARG, CXCL8, FOS, and HIF1A for esophagitis, and MMP9, TNF, TLR4, IL6, CCR2, IFNG, and PTGS2 for gastritis. Cross-disease analysis further identified plasticizer-associated signature targets, including MMP7 for DMP, HMOX1 and NOS2 for DEP, and LTF and CCL11 for ATBC. Enrichment analysis indicated that these targets were mainly involved in inflammatory, chemokine, MAPK-related, and xenobiotic response pathways. Molecular docking and dynamics simulations suggested stable interactions between selected plasticizers and candidate targets, while single-cell analysis revealed their cell-type-specific expression patterns in epithelial, immune, and stromal compartments. Conclusions: This study provides an exploratory network toxicology framework for identifying potential molecular associations between plasticizer exposure and IGDs. The findings highlight disease-specific and plasticizer-associated candidate targets that may guide future experimental validation and environmental risk assessment. Full article

Ovarian cancer (OC) comprises multiple histotypes with distinct mechanisms, molecular features, and clinical behavior. We used Mendelian randomization (MR) to map histotype-stratified metabolic pathways and connect them to drug targets, establishing a translatable target–metabolic node–histotype risk chain. We built a multi-stage MR framework using Integrative Epidemiology Unit (IEU) OpenGWAS summary statistics. After screening 1400 plasma metabolites against overall ovarian cancer in UK Biobank and Ovarian Cancer Association Consortium (OCAC) with KEGG enrichment, we traced a prespecified amino acid/energy–nitrogen axis using histotype-stratified univariable MR and pathway-restricted multivariable MR. We then performed cis drug-target MR for PPARG, DPP4, ABCC8/KCNJ11, and SLC5A2, integrated triangulation, colocalization, and mediation analyses, and experimentally interrogated the prioritized PPARG/ABCC8-KCNJ11–lactate–invasive mucinous ovarian cancer (IMOC) triangle. Screening nominated 55 and 72 metabolites in UK Biobank and OCAC, respectively (IVW p < 0.05), highlighting amino-acid nitrogen and central-carbon metabolism. Univariable Mendelian randomization (UVMR) showed marked heterogeneity: alanine increased low-grade serous ovarian cancer (LGSOC) risk, glutamate was protective for endometrioid OC, and lactate-related traits most consistently implicated the low-grade/borderline serous lineage. In multivariable Mendelian randomization (MVMR), tryptophan and lactate levels emerged as independent risk nodes for serous low-grade plus low malignant potential (LG + LMP). Drug-target MR prioritized PPARG as protective (OR = 0.18) and ABCC8/KCNJ11 as risk-increasing (OR = 7.50) for IMOC, with opposite target → lactate effects supporting a directionally symmetric target–lactate–IMOC triangle. Experimental perturbation in mucinous ovarian cancer models produced concordant reciprocal changes in lactate and malignant phenotypes, extending this triangle biologically. This integrative MR framework delineates histotype-specific metabolic drivers and links them to actionable targets, providing a roadmap from genetic prioritization to mechanistic and translational validation. Full article

Gatifloxacin (GTFX), a fourth-generation fluoroquinolone, causes metabolic disturbances in mammals, but its hepatotoxic mechanisms in aquatic vertebrates remain unclear. This study investigated whether GTFX induces liver injury in zebrafish larvae through oxidative stress or alternative pathways. Larvae at 3 days post-fertilization were exposed to 0.2–2.3 mg/mL GTFX for 48 h. Liver morphology, histopathology, intracellular reactive oxygen species (ROS), and expression of lipid metabolism (pparg) and xenobiotic biotransformation genes (cyp1a, cyp1b1) were assessed. GTFX exposure caused concentration-dependent reductions in liver area, increased hepatic opacity, delayed yolk sac absorption, and hepatocyte swelling with cytoplasmic vacuolization. Despite these structural changes, ROS levels did not differ significantly from those of controls. In contrast, transcriptional analysis revealed significant upregulation of pparg, cyp1a, and cyp1b1, indicating disrupted lipid homeostasis and enhanced detoxification responses. Acute high-dose GTFX exposure induced a metabolism-associated hepatotoxic response in zebrafish larvae, which occurred without a statistically significant change in bulk ROS levels. Together, these findings offer mechanistic insight into fluoroquinolone-associated liver injury. Full article

Primula nutans Georgi, a medicinal herb used in Mongolian and Tibetan medicine for treating respiratory ailments, is a natural agent with antiobesity potential. We investigated the antiobesity and insulin-sensitizing effects of P. nutans Georgi extract (PGE) using in vitro and in vivo models. In 3T3-L1 preadipocytes, PGE inhibited adipocyte differentiation and lipid accumulation without cytotoxicity, accompanied by the reduced expression of adipogenic transcription factors (PPARG, C/EBPA, and adiponectin) and lipogenic genes (FASN, SCD1, and ACC), particularly during the early stages of adipogenesis. Similar effects were observed in primary stromal vascular cells derived from mouse inguinal white adipose tissue. PGE upregulated C/EBP homologous protein and C/EBPB and was associated with altered cell cycle progression, increased G2/M phase distribution, and the potential disruption of mitotic clonal expansion during early adipogenesis. In HFD-induced obese mice, intraperitoneal administration of PGE (10 or 30 mg/kg) significantly reduced body weight gain, white adipose tissue mass, and hepatic steatosis, independent of food intake. PGE downregulated lipogenic and proinflammatory gene expression in adipose and hepatic tissues and increased AMPK phosphorylation in white adipose tissue. PGE improved glucose tolerance and was associated with enhanced insulin sensitivity, as evidenced by reduced areas under the curve in the glucose tolerance and insulin tolerance tests and increased circulating adiponectin levels. Feature-based molecular networking identified 61 compounds from PGE. Network pharmacology analysis revealed several antiobesity targets, including PPARG and AKT1. Molecular docking analyses suggested favorable binding affinities between major compounds and metabolic regulators. Collectively, these findings suggest that PGE may suppress adipogenesis and improve metabolic parameters in obese mice, supporting its potential as a natural candidate for obesity and related metabolic disorders. Full article

Objective: This study investigated the effects of ginsenoside F1 on lipid metabolism using cell-based assays combined with lipidomics. Methods: The optimal non-cytotoxic concentration of ginsenoside F1 was determined by the CCK-8 assay. A hyperlipidemic cell model was established by inducing HepG2 cells with free fatty acids (FFAs). Model cells were treated with ginsenoside F1 (0.2 µM, 0.8 µM, and 3.2 µM) or simvastatin (3.2 µM, positive control) for 24 h. Intracellular lipid accumulation was determined by measuring absorbance at 510 nm, together with quantification of total cholesterol (TC) and triglyceride (TG) contents. Untargeted lipidomics was employed to explore alterations in the lipid profile and identify relevant metabolic pathways. Results: Compared with the model group, lipid deposition, total cholesterol, and triglycerides were significantly reduced by ginsenoside F1 (p < 0.05). A total of 110 differential metabolites, mainly phosphatidylinositol and phosphatidylcholines, were identified by lipidomics, with glycerophospholipid and ether lipid metabolism highlighted as the key regulated pathways. Potential roles of targets including Akt1, PPARG, and EGFR, as well as pathways related to cancer and lipid metabolism, were further indicated by network pharmacology and molecular docking. Conclusions: FFA-induced lipid disorders in HepG2 cells were alleviated by ginsenoside F1, potentially through the regulation of glycerophospholipid metabolism. Full article

Background: Bitong Mixture (BTM) is used clinically for rheumatoid arthritis (RA), but its active components and mechanisms remain unclear. Methods: WGCNA, network pharmacology, machine learning, and ROC analysis were integrated to identify candidate targets. We used molecular docking and molecular dynamics simulations for prioritization. In vitro validation was performed in TNF-α-stimulated MH7A cells. Results: Multiple analytical approaches consistently identified JUN and PPARG. Formononetin and Rhein showed favorable binding and stable interactions. Both compounds significantly reduced IL6 and MMP9 expression and suppressed fibroblast activation. Conclusions: BTM may exert anti-inflammatory effects through a JUN- and PPARG-related regulatory framework, supported by integrated computational and experimental evidence, providing a foundation for further in vivo investigation. Full article

Mice lacking epidermal Pparg (Pparg-/-^epi) exhibit increased cutaneous carcinogenesis, while PPARγ signaling is reduced in actinic keratoses (AKs) and cutaneous squamous cell carcinomas (cSCCs). Using transcriptomic analysis, we now show that the top upregulated genes in Pparg-/-^epi mouse skin, human AKs and cSCCs encode multiple damage-associated molecular patterns (DAMPs) that are TLR4 ligands, while the TLR4 agonist lipopolysaccharide (LPS) is also predicted to be the top common activated upstream regulator in both Pparg-/-^epi mouse skin and in tumor datasets. By single-cell sequencing, DAMP expression was particularly elevated in myeloid cells and myofibroblasts of Pparg-/-^epi mice, and these cell types exhibit transcriptional changes consistent with TLR4 signaling. Myeloid cells also exhibited a loss of Pparg expression and activity. Transcriptional analysis of published LPS-treated macrophages also reveals a decrease in PPARγ activity. Fibroblasts from Pparg-/-^epi mice included cells with a gene expression profile resembling myofibroblasts found in cancer and fibrotic diseases. This was accompanied by increased dermal fibrosis in aged mice and a transcriptomic profile that indicates a key role for both TLR4 and TGFβ signaling. These data suggest that loss of epidermal PPARγ may disrupt counterbalancing PPARγ–TLR4 signals, leading to chronic inflammation and fibrosis, hallmarks of cutaneous neoplasia. Full article

Background/Objectives: Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by severe hepatic steatosis, lobular inflammation, and fibrosis. Although hesperidin, a citrus-derived flavanone, has been reported to exert metabolic and anti-inflammatory effects, its role in severe inflammatory and fibrotic conditions such as MASH remains incompletely understood. This study aimed to evaluate the effects of hesperidin in MASH using integrated in silico and in vivo approaches. Methods: Potential targets of hesperidin were identified using network pharmacology and molecular docking. For in vivo validation, C57BL/6 mice were fed a methionine- and choline-deficient (MCD) diet for five weeks, with oral administration of hesperidin (150 or 300 mg/kg/day) starting from week two. The MCD model induces severe hepatic inflammation and fibrosis but does not fully reflect metabolic features such as obesity and insulin resistance. Hepatic histology, serum transaminases, immune cell populations, and hypothalamic neuroinflammatory markers were assessed. Results: In silico analyses suggested that hesperidin interacts with key regulators associated with MASH, including PPARG, TGFB1, and TNF. In the in vivo MCD-induced model, hesperidin treatment reduced hepatic lipid accumulation and collagen deposition, accompanied by significant decreases in serum ALT and AST levels (by approximately 30–34% and 42–53%, respectively, depending on dose). These effects were associated with downregulation of pro-inflammatory and pro-fibrogenic gene expression and increased expression of antioxidant markers. In addition, hesperidin decreased circulating Ly6C^high monocytes and hepatic Kupffer cells, along with reduced hypothalamic microglial and astrocyte activation. Conclusions: Hesperidin attenuated key pathological features of MASH, including steatosis, inflammation, and fibrosis, and was associated with modulation of peripheral immune responses and central neuroinflammatory markers. These findings suggest that hesperidin may influence the liver–immune–brain axis and warrant further investigation in models that more closely reflect human metabolic conditions. Full article

Background: Adipogenesis is governed by a complex interplay between transcriptional regulation and epigenetic remodeling. While many transcriptional pathways have been well characterized, less is known about how chromatin-level regulation shapes the timing of gene expression, particularly in large animal models such as pigs. In this study, we investigated histone modification patterns associated with four key adipogenic transcription factor genes—PPARG, GATA2, CEBPA, and CEBPB—in porcine mesenchymal stem cells (MSCs) undergoing adipogenic differentiation. Methods: Using RT-qPCR and ChIP-qPCR, we profiled gene transcription levels and epigenetic marks, including promoter- and exon-specific enrichment of the activating histone marks H3K9ac and H4K8ac, as well as the repressive mark H4K20me3, across six time points (day 0, 2, 4, 6, 8, and 10). Results: Although PPARG and GATA2 are located in close proximity on porcine chromosome 13, they exhibited distinct histone modification profiles. PPARG showed progressive promoter acetylation (H4K8ac) accompanied by transcriptional activation, whereas GATA2 displayed decreased exon acetylation (H3K9ac) associated with declining expression. In contrast, the H4K20me3 profile was similar for both genes, suggesting no direct association with their transcriptional activity. Interestingly, CEBPA (chromosome 6) and CEBPB (chromosome 17) exhibited temporally distinct histone modification patterns consistent with their roles in intermediate and early stages of adipogenic differentiation, respectively. Increased enrichment of the H3K9ac mark preceded the rise in transcript levels of the analyzed genes. Promoter regions showed higher enrichment of H4K8ac compared with exonic regions. A higher level of H4K20me3 was also observed for CEBPA and CEBPB than for PPARG and GATA2, which appeared to be more related to chromosomal localization than to direct transcriptional regulation. Conclusions: Together, these results reveal complex interactions between transcriptional dynamics and selected histone modifications that depend on both the gene analyzed and the stage of adipocyte differentiation. This study provides new insights into the epigenetic regulation of porcine adipogenesis and highlights chromatin context as an additional layer influencing transcriptional control. Full article

The aim of this study was to evaluate the nephrotoxicity and molecular mechanism of Evodiamine (EVO). We combined RNA sequencing (RNA-seq) and network toxicology (NT) screening of potential target genes and signaling pathways, used molecular docking to validate core targets, and detected the mRNA expression of the key genes through quantitative real-time polymerase chain reaction (qRT-PCR). After exposure to EVO, body weight of mice decreased significantly, and the levels of renal index, Blood Urea Nitrogen (BUN) and Creatinine (Cr) were significantly increased, with varying degrees of pathological damage to the kidneys. NT identified 125 intersecting targets of EVO exposure related to kidney injury, including AKT1, TNF, TP53, etc. Among the 2888 differentially expressed genes obtained from RNA-seq, 504 genes were up-regulated and 2384 genes were down-regulated. By integrating NT and RNA-seq, 24 intersecting targets were identified. Among them, TRPV1, NOS3, HSP90AA1, and PPARG were selected for molecular docking validation. The results indicated that EVO had the highest affinity for PPARG (−8.07 kcal/mol). The qRT-PCR results indicated that the expression of the Pparg and Hsp90aa1 genes was significantly down-regulated, and the expression of the Nos3 and Trpv1 genes was significantly up-regulated. Immunohistochemistry further confirmed that EVO inhibited the expression of HSP90AA1 and PPARG, while enhancing that of TRPV1 and NOS3. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that EVO-induced nephrotoxicity is related to signaling pathways such as inflammatory mediator regulation of TRP channels, the PPAR signaling pathway, and the Apelin signaling pathway. In summary, the nephrotoxic effect of EVO may be related to the inhibition of the PPARG signaling pathway, the activation of the TRPV1 channel, the reduction in HSP90AA1 expression, and the imbalance of the Apelin-NOS3 pathway. This study provides a theoretical reference for clarifying the potential mechanism of renal injury caused by EVO and guiding its safe use. Full article

Background/Objectives: Natural compounds occupy a pharmacologically rich chemical space, characterized by abundant scaffolds, extensive functional group elaboration, and defined stereochemistry. In this context, Helichrysum italicum, a Mediterranean medicinal plant, represents a valuable source of polyphenols with multiple biological and pharmacological activities. Methods: Here, we introduce an inverse molecular docking fingerprint approach to systematically investigate eight major Helichrysum italicum polyphenols, including $\alpha$-pyrones (arzanol, ethylpyrone), flavonols (gnaphaliin, kaempferol, quercetin), and flavanones (naringenin, pinocembrin, hesperetin). More than 40,000 human protein structures from the Protein Data Bank were screened to generate target-based inverse docking score fingerprints for each compound. Results: Hierarchical clustering of these fingerprints revealed shared binding patterns among structurally related polyphenols and enabled hypothesis generation regarding potential synergistic effects. Notably, favorable interactions were identified with PPARG and CARM1, supporting therapeutic relevance in inflammation and cancer, alongside additional targets associated with neurodegeneration and bone metabolism. Conclusions: This study establishes inverse docking fingerprints as a robust, mechanism-oriented method for natural product research and highlights Helichrysum italicum polyphenols as starting points for medicinal chemistry and drug discovery. Full article

This study reviews the main candidate genes involved in the pathophysiology of Polycystic Ovary Syndrome (PCOS). PCOS is a common endocrine–metabolic disorder in women of reproductive age, characterized by menstrual irregularity, hyperandrogenism, and polycystic ovarian morphology. It is associated with increased metabolic and cardiovascular risk and is a leading cause of infertility. Although its pathophysiology is not fully understood, alterations in the hypothalamic–pituitary–ovarian axis, insulin metabolism, and steroidogenesis have been described. Polymorphisms in genes encoding hormones, enzymes, and receptors in these pathways contribute to clinical variability and ethnic differences, offering potential for early diagnosis and personalized medicine. This review summarizes key candidate genes related to insulin metabolism (INS, INSR, IRS-1), the hypothalamic–pituitary–ovarian axis (LHβ, LHCGR, FSHR, GnRHR, AMH, AMHR2, KISS1, CAPN10), steroidogenesis (CYP11A, CYP17A1, CYP19A1, CYP21, 17β-HSD, SHBG, AR, STAR), and other clinically relevant mechanisms such as obesity, lipid metabolism (PPARG, VDR, FTO), and follicular development (ACE). Full article