Search Results (665)

Metabolism is a tightly controlled, but plastic network of pathways that allow cells to grow and maintain homeostasis. As a normal cell transforms into a malignant cancer cell and proliferates to establish a tumor, it utilizes a variety of metabolic pathways that support growth, proliferation, and survival. Cancer cells alter metabolic pathways in different contexts, leading to complex metabolic heterogeneity within a tumor. There is an unmet need to characterize how cancer cells alter how they use resources from the environment to evolve, spread to other sites of the body, and survive current standard-of-care therapies. We review key techniques and methods that are currently used to study cancer metabolism and provide drawbacks and considerations in using one over another. The goal of this review is to provide a methods’ guide to study different aspects of cell and tissue metabolism, how they can be applied to cancer, and discuss future perspectives on advancements in these areas. Full article

Background/Objectives: Gout, a complex metabolic disorder of increasing global incidence, remains incompletely understood in its pathogenesis. Current diagnostic approaches exhibit significant limitations, including insufficient specificity and the requirement for invasive joint aspiration, highlighting the need for non-invasive, sensitive biomarkers for early detection. Methods: Urine metabolites were extracted from 28 healthy controls, 13 asymptomatic hyperuricemia (HUA) patients, and 29 acute gouty arthritis (AGA) patients. The extracted metabolites were analyzed by UHPLC-MS/MS for untargeted metabolomics. Differential metabolites were screened by partial least squares discriminant analysis (PLS-DA) and volcano plot analysis. Pathway analysis determined the core disorder pathway of gout progression. Results: A total of 278 differential metabolites associated with gout progression were identified. The most pronounced metabolic alterations were observed between the AGA and control groups, indicative of substantial metabolic reprogramming during disease transition. Metabolic pathway analysis revealed four significantly dysregulated pathways: histidine metabolism, nicotinate and nicotinamide metabolism, phenylalanine metabolism, and tyrosine metabolism. Receiver operating characteristic (ROC) curve analysis revealed that three urine markers with high diagnostic efficacy—oxoamide, 3-methylindole, and palmitic acid—exhibited progressive alterations across the disease continuum. Conclusions: This metabolomics study identified core regulatory metabolites and newly discovered metabolic pathways underlying gout pathogenesis, along with novel urinary biomarkers capable of predicting HUA-to-AGA progression. The aberrant levels of key metabolites in the disordered pathway implicate neuroimmune dysregulation, energy metabolism disruption, and oxidative stress in gout pathogenesis. These findings provide new foundations and strategies for the daily monitoring and prevention of gout. Full article

Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational metabolomic dataset to identify metabolites and provide insights into gut fungal metabolic capabilities. Methods: Gut fungi were cultured anaerobically in rumen-fluid-based media with a soluble substrate (cellobiose), and metabolites were extracted using the Metabolite, Protein, and Lipid Extraction (MPLEx) method, enabling metabolomic and proteomic analysis from the same cell samples. Samples were derivatized and analyzed via GC-MS, followed by compound identification by spectral matching to reference databases, molecular networking, and statistical analyses. Results: Distinct metabolites were identified between A. robustus and C. churrovis, including 2,3-dihydroxyisovaleric acid produced by A. robustus and maltotriitol, maltotriose, and melibiose produced by C. churrovis. C. churrovis may polymerize maltotriose to form an extracellular polysaccharide, like pullulan. GC-MS profiling potentially captured sufficiently volatile products of proteomically detected, putative non-ribosomal peptide synthetases and polyketide synthases of A. robustus and C. churrovis. The triterpene squalene and triterpenoid tetrahymanol were putatively identified in A. robustus and C. churrovis. Their conserved, predicted biosynthetic genes—squalene synthase and squalene tetrahymanol cyclase—were identified in A. robustus, C. churrovis, and other anaerobic gut fungal genera. Conclusions: This study provides a foundational, untargeted metabolomic dataset to unmask gut fungal metabolic pathways and biosynthetic potential and to prioritize future efforts for compound isolation and identification. Full article

The β-glucosidases (BGLUs) of Glycoside Hydrolase Family 1 (GH1) exhibit essential functions in plant secondary metabolism and stress responses, mediated by their dual catalytic capabilities in hydrolysis and transglycosylation. This study identified 149 BGLU family members within B. napus (Brassica napus L.), which were systematically categorized into 10 distinct subgroups. Subsequent characterization encompassed detailed examination of their motif composition, chromosomal distribution, gene collinearity, selection pressure, and expression profiling. Transient overexpression of BnBGLU77 in N. benthamiana (Nicotiana benthamiana), combined with untargeted metabolomics analysis, revealed pronounced modulatory effects on the degradation and accumulation of β-glucosidic compounds, suggesting potential roles of the protein encoded by BnBGLU77 in metabolic homeostasis and stress response mechanisms. These experimental results first validated the bidirectional catalytic activity of a BGLU enzyme in B. napus, while simultaneously advancing fundamental understanding of BnBGLU gene functions and providing new insights for developing stress-resistant rapeseed cultivars through targeted genetic improvement. Full article

Selenium can be absorbed and utilized by plants, influencing their growth by altering their physiological metabolism. In this study, based on plant physiology methods, compared to the CK treatment, the height and leaf length of oat seedlings under the T0.02 (0.02 g/kg Na₂SeO₃) treatment significantly increased by 18.36% and 15.81%, respectively (p < 0.05). Under the T0.1 (0.1 g/kg Na₂SeO₃) treatment, the levels of malondialdehyde (MDA), proline, soluble sugar content, and peroxidase (POD) activity significantly increased (p < 0.05). However, the seedling height and leaf length under the T0.1 treatment significantly decreased by 33.24% and 23.25%, respectively. Additionally, the contents of chlorophyll a, chlorophyll b, and carotenoids, as well as ascorbate peroxidase (APX) activity and the superoxide anion radical generation rate (O₂⁻) significantly decreased (p < 0.05). The total selenium, organic selenium, and inorganic selenium contents, as measured by the atomic fluorescence spectroscopy method, were also increased in oat seedling roots and leaves under T0.1 treatment (p < 0.05). Selenium had a high coefficient of mobility from root to leaf of 6.01 under T0.02 and 4.65 under T0.1 treatment, and from soil to leaf of 4.98 under T0.02 and 4.55 under T0.1 treatment. Through untargeted metabolomics, six differential phenylpropanoid compounds and 18 differential flavonoid compounds were found in oat seedlings. Based on transcriptomic analysis of oat seedlings, 29 DEGs associated with phenylpropanoid metabolism and 13 DEGs related to flavonoid biosynthesis were identified. Over 60% of the genes (25/42) in the phenylpropanoid and flavonoid biosynthesis pathway were associated with the accumulation of about 74% (20/27) of the compounds in oat leaves. Based on transcriptomic and metabolomics analysis, there were nine major genes (including PAL1, PAL4, CHS2, PAL7, POD3, PAL6, CCR1, CCR4, POD4) modulating the metabolism of phenylpropanoid and flavonoid biosynthesis pathway. This study offers novel insights and genetic resources for exploring the mechanisms underlying plant responses to selenium treatment, thereby further enhancing selenium tolerance in plants. Full article

Background: Type 2 diabetes (T2D), the most common form of diabetes, is associated with a significantly elevated risk of cardiovascular and cerebrovascular complications. However, circulating metabolic signatures that reliably predict the transition to insulin resistance, and are potentially linked to increased vascular risk, remain incompletely characterized. Rodent models, particularly those induced by a high-fat diet (HFD) combined with low-dose streptozotocin (STZ), are widely used to study the progression of T2D. However, the systemic metabolic shifts associated with this model, especially at the plasma level, are poorly defined. Methods: In this study, we performed untargeted liquid chromatography–mass spectrometry (LC-MS)-based metabolomic profiling on plasma samples from control, HFD-only (obese, insulin-sensitive), and HFD + STZ (obese, insulin-resistant) C57BL/6 mice. Results: In the HFD + STZ cohort, plasma profiles showed a global shift toward lipid classes; depletion of aromatic and branched-chain amino acids (BCAAs); accumulation of phenylalanine-derived co-metabolites, consistent with gut–liver axis dysregulation; elevations in glucose, fructose-6-phosphate, and nucleoside catabolites, indicating impaired glucose handling and heightened nucleotide turnover; increased free fatty acids, reflecting membrane remodeling and lipotoxic stress; and higher cAMP, thyroxine, hydrocortisone, and uric acid, consistent with endocrine and redox imbalance. By contrast, HFD-only mice exhibited elevations in aromatic amino acids and BCAAs relative to controls, a pattern compatible with early obesity-associated adaptation while insulin signaling remained partially preserved. KEGG analysis revealed disturbances in carbohydrate metabolism, amino acid degradation, nucleotide turnover, and hormone-related pathways, and HMDB mapping linked these changes to T2D, obesity, heart failure, and renal dysfunction. Conclusion: Collectively, these findings delineate insulin resistance-specific plasma signatures of metabolic inflexibility and inflammatory stress in the HFD + STZ model, distinguishing it from HFD alone and supporting its utility for mechanistic studies and biomarker discovery. Importantly, this plasma metabolomics study shows that insulin-sensitive and insulin-resistant states exhibit distinct variation in circulating metabolites and cardiovascular risk factors, underscoring the translational value of plasma profiling. Full article

Background/Objectives: Cocaine is a widely used illicit stimulant with significant toxicity. Despite its clinical relevance, the broader metabolic alterations associated with cocaine use remain incompletely characterized. This study aims to identify novel biomarkers for cocaine exposure by applying untargeted metabolomics to retrospective urine drug screening data. Methods: We conducted a retrospective analysis of a raw mass spectrometry (MS) dataset from urine comprehensive drug screening (UCDS) from 363 patients at the University of Pittsburgh Medical Center Clinical Toxicology Laboratory. The liquid chromatography–quadrupole time-of-flight mass spectrometry (LC-qToF-MS) data were preprocessed with MS-DIAL and subjected to multiple statistical analyses to identify features significantly associated with cocaine-enzyme immunoassay (EIA) results. Significant features were further evaluated using MS-FINDER for feature annotation. Results: Among 14,883 features, 262 were significantly associated with cocaine-EIA results. A subset of 37 more significant features, including known cocaine metabolites and impurities, nicotine metabolites, norfentanyl, and a tryptophan-related metabolite (3-hydroxy-tryptophan), was annotated. Cluster analysis revealed co-varying features, including parent compounds, metabolites, and related ion species. Conclusions: Features associated with cocaine exposure, including previously underrecognized cocaine metabolites and impurities, co-exposure markers, and alterations in an endogenous metabolic pathway, were identified. Notably, norfentanyl was found to be significantly associated with cocaine -EIA, reflecting current trends in illicit drug use. This study highlights the potential of repurposing real-world clinical toxicology data for biomarker discovery, providing a valuable approach to identifying exposure biomarkers and expanding our understanding of drug-induced metabolic disturbances in clinical toxicology. Further validation and exploration using complementary analytical platforms are warranted. Full article

Tropical forage crops vary widely in biochemical composition, resulting in inconsistent silage quality. Understanding how plant traits shape microbial and metabolic networks during ensiling is crucial for optimizing fermentation outcomes. Eight tropical forages—Sorghum bicolor (sweet sorghum), Sorghum × drummondii (sorghum–Sudangrass hybrid), Sorghum sudanense (Sudangrass), Pennisetum giganteum (giant Napier grass), Pennisetum purpureum cv. Purple (purple elephant grass), Pennisetum sinese (king grass), Leymus chinensis (sheep grass), and Zea mexicana (Mexican teosinte)—were ensiled under uniform conditions. Fermentation quality, bacterial and fungal communities (16S rRNA and ITS sequencing), and metabolite profiles (untargeted liquid chromatography–mass spectrometry, LC-MS) were analyzed after 60 days. Sweet sorghum and giant Napier grass showed optimal fermentation, with high lactic acid levels (111.2 g/kg and 99.4 g/kg, respectively), low NH₄⁺-N (2.4 g/kg and 3.1 g/kg), and dominant Lactiplantibacillus plantarum. In contrast, sheep grass and Mexican teosinte exhibited poor fermentation, with high NH₄⁺-N (6.7 and 6.1 g/kg) and Clostridium dominance. Fungal communities were dominated by Kazachstania humilis (>95%), while spoilage-associated genera such as Cladosporium, Fusarium, and Termitomyces proliferated in poorly fermented silages. Metabolomic analysis identified 15,827 features, with >3000 significantly differential metabolites between silages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed divergence in flavonoid biosynthesis, lipid metabolism, and amino acid pathways. In the sweet sorghum vs. sheep grass comparison, oxidative stress markers ((±) 9-HODE, Agrimonolide) were elevated in sheep grass, while sweet sorghum accumulated antioxidants like Vitamin D3. Giant Napier grass exhibited higher levels of antimicrobial flavonoids (e.g., Apigenin) than king grass, despite both being dominated by lactic acid bacteria. Sorghum–Sudangrass hybrid silage showed enrichment of lignan and flavonoid derivatives, while Mexican teosinte accumulated hormone-like compounds (Gibberellin A53, Pterostilbene), suggesting microbial dysbiosis. These findings indicate that silage fermentation outcomes are primarily driven by forage-intrinsic traits. A “forage–microbiota–metabolite” framework was proposed to explain how plant-specific properties regulate microbial assembly and metabolic output. These insights can guide forage selection and development of precision inoculant for high-quality tropical silage. Full article

C. humilis is a small shrub belonging to the Rosaceae family, and grafting is one of the main ways for propagation. However, the influence of different rootstocks on volatile aroma is still unclear. In this study, an untargeted metabolomics approach based on gas chromatography–mass spectrometry (GC-MS) was utilized to analyze the volatile differential metabolites between the rootstock–scion combinations and self-rooted seedlings. Furthermore, metabolic pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In total, 191,162 and 150 volatile differential metabolites were identified in different rootstock–scion combinations. The rootstock–scion combinations of ZG/MYT and ZG/BT could improve the volatile aroma in the fruit of C. humilis and made significant contributions to the rose and fruity flavors. KEGG pathway analysis indicated that the differential metabolites were mainly enriched in the butanoate metabolism and glycolysis/gluconeogenesis pathways, showing an increasing trend. Prunus tomentosa and Amygdalus communis can serve as preferred rootstocks for enhancing the aroma quality of C. humilis fruits. These results provide new insight into rootstock-based propagation and breeding and also offer some guidance for graft-based fruit production. Full article

Disease caused by Plasmodiophora brassicae severely disrupts cruciferous crops by altering root physiology and rhizosphere ecology. While pathogen-induced shifts in rhizosphere microbiomes are documented, the mechanisms linking root exudate reprogramming to microbial community remodeling remain poorly understood. Here, we integrated untargeted metabolomics and 16S rRNA sequencing to investigate how root exudates reshape the rhizosphere microbiome of tumorous stem mustard (Brassica juncea var. tumida) through P. brassicae infection. Metabolomic profiling identified 1718 root exudate metabolites, with flavones (e.g., apigenin 7-O-β-D-rutinoside, VIP > 1.5) and phenolic derivatives (e.g., gastrodin) being selectively enriched in infected plants. P. brassicae infection significantly increased rhizobacterial richness (ACE index, p < 0.05) and restructured the community composition, marked by enrichment of Paenibacillus (LDA score > 3.0). Procrustes analysis revealed tight coupling between microbial community shifts and metabolic reprogramming (M² = 0.446, p = 0.005), while Spearman correlations implicated pathogen-induced metabolites like geniposidic acid in recruiting beneficial Paenibacillus. Our results reveal that plant hosts dynamically secrete defense-related root metabolites to remodel the rhizosphere microbiome in response to P. brassicae infection. This dual-omics approach elucidates a chemical dialogue mediating plant–microbe–pathogen interactions, offering novel insights for engineering disease-suppressive microbiomes through root exudate manipulation. Full article

Polystyrene nanoplastics (NPs) threaten agricultural ecosystems and the food chain; however, their hepatotoxicity in chickens, a key poultry species, remains unclear. This study investigated the effects of chronic NP exposure on hepatic metabolism to evaluate food safety risks in poultry products. Chickens were orally exposed to 100 nm polystyrene NPs via feed for 120 days. Histopathological evaluation, serum biochemical analysis revealed hepatotoxicity in NP-exposed poultry, characterized by histopathological liver injury, elevated lipid droplet accumulation, significantly increased alanine aminotransferase (ALT) activity, and elevated triglyceride (TG) levels (p < 0.05). Untargeted LC-MS/MS Metabolomics profiling identified 193 differentially abundant metabolites—predominantly organic acids and lipids—with L-leucine and NADH emerging as pivotal metabolic hubs. A KEGG pathway analysis demonstrated significant enrichment in purine metabolism and oxidative phosphorylation, while a gene set enrichment analysis (GSEA) confirmed the suppression of ABC transporters. Notably, the key biomarkers 9-cis-retinal and phenylalanyl phenylalanine were significantly altered, reflecting metabolic disturbances linked to NPs exposure. Overall, this study characterized exposure-associated metabolic signatures and established NP-induced hepatic injury phenotypes in poultry production systems. Full article

Background: Molybdenum (Mo) is an essential trace element for animals, but too much intake can cause adverse effects. Due to the metabolic characteristics of goats and other ruminants, they are more susceptible to the cumulative effects of Mo toxicity. A high Mo intake can cause multi-organ toxicity in ruminants, but the mechanism of damage to the pancreas is still unclear. The aim of this study was to systematically analyze the key regulatory pathways of pancreatic injury induced by Mo in goats using a metabolomics approach. Methods: Twenty male Yudong Black goats (22.34 ± 1.87 kg, six months) were randomly divided into a control group (fed a basal diet) and the Mo group (fed a basal diet supplemented with 50 mg·kg⁻¹ Na₂MoO₄·2H₂O). After 60 days of continuous feeding, their pancreatic tissues were collected and the mineral elements, antioxidant capacity, and inflammatory factors were examined. Untargeted metabolomics based on HILIC UHPLC-Q-EXACTIVE MS was used to analyze changes in metabolites. The core regulatory mechanisms were revealed by KEGG enrichment analysis. Results: The results demonstrated that goats in the Mo group showed obvious clinical signs, such as lethargy, loss of appetite, and unsteady gait. The pancreatic tissue of goats in the Mo group exhibited significantly elevated levels of Mo and copper, accompanied by a marked reduction in antioxidant capacity and concurrent increases in inflammatory cytokine levels. Between the Mo group and control group, 167 differentially expressed metabolites were identified. KEGG enrichment analysis showed that it disrupted multiple metabolic pathways, including glycine, serine, and threonine metabolism, cysteine and methionine metabolism, and butanoate metabolism. Conclusions: This study mainly revealed, at the metabolomics level, that Mo exposure would disrupt the metabolic pathways related to antioxidant capacity in goat pancreata. It provides new insights into the molecular mechanisms of Mo-induced pancreatic injury in goats. Full article

Tacrolimus (TAC)-induced chronic nephrotoxicity (TAC nephrotoxicity) remains a major contributor to late allograft dysfunction in kidney transplant recipients. Although detailed mechanisms remain incompletely understood, our previous metabolomic studies revealed disruptions in carnitine-related and redox pathways, suggesting impaired mitochondrial β-oxidation of fatty acids. To further characterize metabolic alterations associated with this condition, we conducted an untargeted lipidomic analysis of renal tissues using a murine model of TAC nephrotoxicity. TAC (1 mg/kg/day) or saline was subcutaneously administered to male ICR mice for 28 days, and kidney tissues were harvested for comprehensive lipidomic profiling. Lipidomic analysis was performed with liquid chromatography–tandem mass spectrometry (p < 0.05, n = 5/group). Triacylglycerols (TGs) were the predominant lipid class identified. TAC-treated mice exhibited reduced levels of unsaturated TG species with low carbon numbers, whereas TGs with higher carbon numbers and various degrees of unsaturation were increased. All detected TGs containing docosahexaenoic acid (DHA) showed an increasing trend in TAC-treated kidneys. Although accumulation of polyunsaturated TGs has been previously observed in chronic kidney disease, the preferential increase in DHA-containing TGs appears to be a unique feature of TAC-induced nephrotoxicity. These results suggest that DHA-enriched TGs may serve as a metabolic signature of TAC nephrotoxicity and offer new insights into its pathophysiology. Full article

The genus Panax contains traditional herbs that have been widely used in traditional medicine. The active constituents, collectively known as ginsenosides, are well characterized in the most representative species, P. notoginseng. However, the major bioactive chemical constituents of P. stipuleanatus together with P. vietnamensis are relatively less studied. In this study, an untargeted metabolomic analysis was performed in P. notoginseng, P. stipuleanatus, and P. vietnamensis using root and leaf organs. Further metabolomic differences in P. stipuleanatus were compared with those of the two most prevalent species. The analysis results revealed tissue-specific qualitative and quantitative metabolic differences in each species. Several differentially accumulated metabolites were enriched in the biosynthesis of secondary metabolites, including the biosynthesis of ginsenosides I. The ginsenosides Rb1, Rf, Rg1, Rh1, Rh8, and notoginsenosides E, M, and N had a higher abundance level in the roots of both P. notoginseng and P. vietnamensis. In P. stipuleanatus, the accumulation of potentially important ginsenosides is mainly found in the leaf. In particular, the dammarane-type ginsenosides Rb3, Rb1, Mx, and F2 as well as the notoginsenosides A, Fe, Fa, Fd, L, and N were identified to have a higher accumulation in the leaf. The strong positive correlation network of different ginsenosides probably enhanced secondary metabolism in each species. The comparative analysis revealed a significant differential accumulation of metabolites in the leaves of both species. The various compounds of dammarane-type ginsenoside, such as Rb1, Rg1, Rg6, Rh8, Rh10, Rh14, and majoroside F2, had a significantly higher concentration level in the leaves of P. stipuleanatus. In addition, several notoginsenoside compounds such as A, R1, Fe, Fd, and Ft1 showed a higher abundance in the leaf. These results show that the abundance level of major ginsenosides is significant in P. stipuleanatus and provides an important platform to improve the ginsenoside quality of Panax species. Full article

High semen quality is vital for reproductive success in the swine industry; however, seasonal fluctuations often compromise this quality. The molecular mechanism underlying these seasonal effects on semen quality remains largely unclear. This study employed untargeted metabolomic profiling of boar seminal plasma (SP) to identify metabolites and metabolic pathways associated with semen quality during the summer and winter months. Semen samples were collected from mature Duroc boars at a commercial boar stud and classified as Passed or Failed based on motility and morphology. SP from five samples per group was analyzed using ultra-high-performance liquid chromatography–mass spectrometry (UHPLC-MS). In total, 373 metabolites were detected in positive ion mode and 478 in negative ion mode. Several differentially expressed metabolites (DEMs) were identified, including ergothioneine, indole-3-methyl acetate, and avocadyne in the summer, as well as LysoPC, dopamine, and betaine in the winter. These metabolites are associated with key sperm functions, including energy metabolism, antioxidant defense, and capacitation. KEGG pathway analysis indicated enrichment in starch and sucrose metabolism, pyrimidine metabolism, and amino acid metabolism across the seasons. Overall, the results reveal that SP metabolomic profiles vary with the season, thereby influencing semen quality. The identified metabolites may serve as potential biomarkers for assessing semen quality and enhancing reproductive efficiency in swine production. Full article